Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction ScaffoldsClick to copy article linkArticle link copied!
- Olga A. MassOlga A. MassMicron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United StatesMore by Olga A. Mass
- Christopher K. WilsonChristopher K. WilsonMicron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United StatesMore by Christopher K. Wilson
- Simon K. RoySimon K. RoyMicron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United StatesMore by Simon K. Roy
- Matthew S. BarclayMatthew S. BarclayMicron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United StatesMore by Matthew S. Barclay
- Lance K. PattenLance K. PattenMicron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United StatesMore by Lance K. Patten
- Ewald A. TerpetschnigEwald A. TerpetschnigSETA BioMedicals, LLC, 2014 Silver Court East, Urbana, Illinois 61801, United StatesMore by Ewald A. Terpetschnig
- Jeunghoon Lee*Jeunghoon Lee*Email: [email protected]Micron School of Materials Science & Engineering and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United StatesMore by Jeunghoon Lee
- Ryan D. Pensack*Ryan D. Pensack*Email: [email protected]Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United StatesMore by Ryan D. Pensack
- Bernard Yurke*Bernard Yurke*Email: [email protected]Micron School of Materials Science & Engineering and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United StatesMore by Bernard Yurke
- William B. Knowlton*William B. Knowlton*Email: [email protected]Micron School of Materials Science & Engineering and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United StatesMore by William B. Knowlton
Abstract
Exciton delocalization plays a prominent role in the photophysics of molecular aggregates, ultimately governing their particular function or application. Deoxyribonucleic acid (DNA) is a compelling scaffold in which to template molecular aggregates and promote exciton delocalization. As individual dye molecules are the basis of exciton delocalization in molecular aggregates, their judicious selection is important. Motivated by their excellent photostability and spectral properties, here, we examine the ability of squaraine dyes to undergo exciton delocalization when aggregated via a DNA Holliday junction (HJ) template. A commercially available indolenine squaraine dye was chosen for the study given its strong structural resemblance to Cy5, a commercially available cyanine dye previously shown to undergo exciton delocalization in DNA HJs. Three types of DNA–dye aggregate configurations—transverse dimer, adjacent dimer, and tetramer—were investigated. Signatures of exciton delocalization were observed in all squaraine–DNA aggregates. Specifically, strong blue shift and Davydov splitting were observed in steady-state absorption spectroscopy and exciton-induced features were evident in circular dichroism (CD) spectroscopy. Strongly suppressed fluorescence emission provided additional, indirect evidence for exciton delocalization in the DNA-templated squaraine dye aggregates. To quantitatively evaluate and directly compare the excitonic Coulombic coupling responsible for exciton delocalization, the strength of excitonic hopping interactions between the dyes was obtained by simultaneously fitting the experimental steady-state absorption and CD spectra via a Holstein-like Hamiltonian, in which, following the theoretical approach of Kühn, Renger, and May, the dominant vibrational mode is explicitly considered. The excitonic hopping strength within indolenine squaraines was found to be comparable to that of the analogous Cy5 DNA-templated aggregate. The squaraine aggregates adopted primarily an H-type (dyes oriented parallel to each other) spatial arrangement. Extracted geometric details of the dye mutual orientation in the aggregates enabled a close comparison of aggregate configurations and the elucidation of the influence of dye angular relationship on excitonic hopping interactions in squaraine aggregates. These results encourage the application of squaraine-based aggregates in next-generation systems driven by molecular excitons.
Introduction
Figure 1
Figure 1. (a) Representative example of the chemical structure of cyanine dye Cy5, where R and R′ are sites of attachment to DNA through phosphoramidite linkers. (b) Representative example of the chemical structure of core-substituted indolenine squaraine dye, where X = O, S, NR1, C(CN)2; R is a site of attachment to DNA through a serinol linker; and R1 is an alkyl (also see Figure S1). (c) Asymmetric DNA sequences to assemble immobile Holliday junctions; complementary regions of ssDNA are color-coded: for example, the purple region of strand A is complementary to the purple region of strand D, and the green region of strand A is complementary to the green region of strand B, and so on. (d) Schematic representation of dye monomer, dimers, and a tetramer in four-armed duplex DNA junctions (Holliday junctions) where squaraine dyes are depicted as blue dots. As discussed in Sections S3 and S10, the DNA HJ may exist primarily in a stacked conformation. ssDNA strands used to assemble DNA HJ are labeled as A, B, C, and D.
Methods
Sample Preparation
Optical Characterization
Results and Discussion
Construct Design and Synthesis
Steady-State Optical Characterization
Figure 2
Figure 2. (a, c, e, g) Acquired steady-state absorption spectra of the DNA–Square 660 dye constructs in 1× TBE, 15 mM MgCl2 at room temperature (dotted lines) and theoretical absorption spectra derived from KRM modeling (solid lines). The DNA–dye construct concentration was 1.5 μM. The insets show a schematic representation of dye monomer, dimers, and tetramer constructs in DNA HJs. (b, d, f, h) Acquired CD spectra of the DNA–Square 660 dye constructs in 1× TBE, 15 mM MgCl2 at room temperature (dotted lines) and theoretical CD spectra derived from KRM modeling (solid lines). The DNA–dye construct concentration was 1.5 μM.
construct | observed Abs maximaa (nm) | calculated Abs maximab (nm) | observed FL maximac (nm) | FL suppressiond (%) | ΦFe |
---|---|---|---|---|---|
monomer | 630; 672 | 630; 672 | 687 | n/a | 0.37 |
trans dimer | 625; 661 | 599; 624; 660; 690 | 688 | 80 | 0.038 |
adj dimer | 630; 662 | 603; 629; 663; 700 | 690 | 92 | 0.023 |
tetramer | 618; 662 | 578; 618; 663; 694 | 689 | 98 | 0.006 |
Measurements were carried out in 1× TBE, 15 mM MgCl2 containing 1.5 μM DNA construct at room temperature.
Values for the monomer are obtained from fitting the data with two Gaussians, and the values for the aggregates are obtained from fitting the data with four Gaussians.
Measurements were carried out in 1× TBE, 15 mM MgCl2 containing 0.5 μM DNA construct at room temperature. Samples were excited at λexc = 650 nm.
Fluorescence suppression relative to the monomer was calculated for 665–740 nm range as described in the Supporting Information.
Fluorescence quantum yield measured in 1× TBE, 15 mM MgCl2.
Theoretical Spectral Modeling
Figure 3
Figure 3. Molecular models of the Square 660 core region adjacent dimer SQ-BC and transverse dimer SQ-AC. The side view shows a J1,2 parameter, in meV, a center-to-center distance R, in Å, and a slip angle θs, in degree. The oblique view shows oblique angle α, in degree, as an angle between vectors 1 and 2 if their centers are superimposed. Note that the fitting procedure determines the position and orientation of the long axes of the Square 660 dyes but not the rotation of the dye core around its long axis. As such, the dye core rotations were arbitrarily chosen.
Figure 4
Figure 4. Molecular model of the Square 660 core region tetramer SQ-ABCD. The side view shows Jm,n parameter between each pair of dyes, in meV, and slip angles θs, in degree. The oblique view shows a center-to-center distance R, in Å, and oblique angle α, in degree.
Conclusions
Supporting Information
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jpcb.0c06480.
Gel electrophoresis, spectral measurements, thermal denaturation, fitting procedures, and KRM modeling (PDF)
Terms & Conditions
Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.
Acknowledgments
This research was supported wholly by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Materials Sciences and Engineering Division, and DOE’s Established Program to Stimulate Competitive Research (EPSCoR) (Award DE-SC0020089), except the following: initial work on squaraine transverse dimer modeling was sponsored by the National Science Foundation INSPIRE (Award no. 1648655). The circular dichroism spectrometer was made available by the Biomolecular Research Center (BRC) at Boise State, which is supported in part by the Institutional Development Awards (IDeA) from the National Institute of General Medical Sciences (Award no. P20GM103408) and the National Institutes of Health (Award no. P20GM109095), the National Science Foundation (Award nos. 0619793 and 0923535), the MJ Murdock Charitable Trust, and the Idaho State Board of Education. We acknowledge Natalie Magnus and Taylor Farmer and Professor Amit Jain for their assistance in KRM Model Simulation Tool software development.
References
This article references 124 other publications.
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- 6Vaitekonis, S.; Trinkunas, G.; Valkunas, L. Red Chlorophylls in the Exciton Model of Photosystem I. Photosynth. Res. 2005, 86, 185– 201, DOI: 10.1007/s11120-005-2747-xGoogle Scholar6https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXhtVWls73I&md5=4bd6b5640f8c4828743db6dfd4a7103fRed Chlorophylls in the Exciton Model of Photosystem IVaitekonis, Sarunas; Trinkunas, Gediminas; Valkunas, LeonasPhotosynthesis Research (2005), 86 (1-2), 185-201CODEN: PHRSDI; ISSN:0166-8595. (Springer)Structural arrangement of pigment mols. of Photosystem I of photosynthetic cyanobacterium Synechococcus elongatus is used for theor. modeling of the excitation energy spectrum. It is demonstrated that a straightforward application of the exciton theory with the assumption of the same mol. transition energy does not describe the red side of the absorption spectrum. Since the inhomogeneity in the mol. transition energies caused by a dispersive interaction with the mol. surrounding cannot be identified directly from the structural model, the evolutionary search procedure is used for fitting the low temp. absorption and CD spectra. As a result, one dimer, three trimers and one tetramer of chlorophyll mols. responsible for the red side of the absorption spectrum with their assignment to the spectroscopically established three bands at 708, 714 and 719 nm are detd. All of them are found to be situated not in the very close vicinity of the reaction center but are encircling it almost at the same distance. In order to explain the unusual broadening on the red side of the spectrum the exciton state mixing with the charge transfer (CT) states is considered. It is shown that two effects can be distinguished as caused by mixing of those states: (i) the oscillator strength borrowing by the CT state from the exciton transition and (ii) the borrowing of the high d. of the CT state by the exciton state. The intermol. vibrations between two counter-charged mols. det. the high d. in the CT state. From the broad red absorption wing it is concluded that the CT state should be the lowest state in the complexes under consideration. Such mixing effect enables resolving the diversity in the mol. transition energies as detd. by different theor. approaches.
- 7Abramavicius, D.; Mukamel, S. Exciton Delocalization and Transport in Photosystem I of Cyanobacteria Synechococcus Elongates: Simulation Study of Coherent Two-Dimensional Optical Signals. J. Phys. Chem. B 2009, 113, 6097– 6108, DOI: 10.1021/jp811339pGoogle Scholar7https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXktFWltb0%253D&md5=fe2ceed4b62c141ca2ed541f52494f74Exciton delocalization and transport in Photosystem I of cyanobacterium Synechococcus elongatus: Simulation study of coherent two-dimensional optical signalsAbramavicius, Darius; Mukamel, ShaulJournal of Physical Chemistry B (2009), 113 (17), 6097-6108CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)Electronic excitations and the optical properties of the photosynthetic complex PSI are analyzed using an effective exciton model developed by Vaitekonis et al. [Photosynth. Res.2005, 86, 185]. States of the reaction center, the linker states, the highly delocalized antenna states and the red states are identified and assigned in absorption and CD spectra by taking into account the spectral distribution of d. of exciton states, exciton delocalization length, and participation ratio in the reaction center. Signatures of exciton cooperative dynamics in nonchiral and chirality-induced two-dimensional (2D) photon-echo signals are identified. Nonchiral signals show resonances assocd. with the red, the reaction center, and the bulk antenna states as well as transport between them. Spectrally overlapping contributions of the linker and the delocalized antenna states are clearly resolved in the chirality-induced signals. Strong correlations are obsd. between the delocalized antenna states, the linker states, and the RC states. The active space of the complex covering the RC, the linker, and the delocalized antenna states is common to PSI complexes in bacteria and plants.
- 8Abramavicius, D.; Palmieri, B.; Mukamel, S. Extracting Single and Two-Exciton Couplings in Photosynthetic Complexes by Coherent Two-Dimensional Electronic Spectra. Chem. Phys. 2009, 357, 79– 84, DOI: 10.1016/j.chemphys.2008.10.010Google Scholar8https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXitVSisLg%253D&md5=be185e45c2c041c6b8c28ea0375ff417Extracting single and two-exciton couplings in photosynthetic complexes by coherent two-dimensional electronic spectraAbramavicius, Darius; Palmieri, Benoit; Mukamel, ShaulChemical Physics (2009), 357 (1-3), 79-84CODEN: CMPHC2; ISSN:0301-0104. (Elsevier B.V.)Signatures of "strong" J and "weak" K exciton couplings in the nonlinear femtosecond optical response of the FMO photosynthetic complex are identified. The two types of couplings originate from interactions of mol. transition charge dipoles and change of mol. permanent dipoles in their ground and excited states, resp. We demonstrate that by combining various two-dimensional optical signals it should be possible to invert spectroscopic data to reconstruct the full exciton Hamiltonian (energies and couplings).
- 9Abramavicius, D.; Palmieri, B.; Voronine, D. V.; Šanda, F.; Mukamel, S. Coherent Multidimensional Optical Spectroscopy of Excitons in Molecular Aggregates; Quasiparticle Versus Supermolecule Perspectives. Chem. Rev. 2009, 109, 2350– 2408, DOI: 10.1021/cr800268nGoogle Scholar9https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXls1GltLw%253D&md5=19f94fb7600ed1c26eeb196b5e2705a5Coherent Multidimensional Optical Spectroscopy of Excitons in Molecular Aggregates; Quasiparticle versus Supermolecule PerspectivesAbramavicius, Darius; Palmieri, Benoit; Voronine, Dmitri V.; Sanda, Frantisek; Mukamel, ShaulChemical Reviews (Washington, DC, United States) (2009), 109 (6), 2350-2408CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review.
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- 11Hestand, N. J.; Spano, F. C. Determining the Spatial Coherence of Excitons from the Photoluminescence Spectrum in Charge-Transfer J-Aggregates. Chem. Phys. 2016, 481, 262– 271, DOI: 10.1016/j.chemphys.2016.06.005Google Scholar11https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtV2nu7jK&md5=8e9c69e654a4e6b8c411c12e52f245e1Determining the spatial coherence of excitons from the photoluminescence spectrum in charge-transfer J-aggregatesHestand, Nicholas J.; Spano, Frank C.Chemical Physics (2016), 481 (), 262-271CODEN: CMPHC2; ISSN:0301-0104. (Elsevier B.V.)The importance of spatial coherence in energy and charge transfer processes in biol. systems and photovoltaic devices has been hotly debated over the past several years. While larger spatial coherences are thought to benefit transport, a clear correlation has yet to be established, partly because a simple and accurate measure of the coherence length has remained elusive. Previously, it was shown that the no. of coherently connected chromophores, NCoh, can be detd. directly from the ratio (SR) of the 0-0 and 0-1 vibronic line strengths in the photoluminescence (PL) spectrum. The relation NCoh = λ20SR, where λ20 is the assocd. monomeric Huang-Rhys parameter, was derived in the Frenkel exciton limit. Here, it is shown that SR remains a highly accurate measure of coherence for systems characterized by significant charge transfer interactions (e.g. conjugated π-stacked systems). The only requirement is that the exciton band curvature must be pos., as in a J-aggregate.
- 12Hestand, N. J.; Spano, F. C. Molecular Aggregate Photophysics Beyond the Kasha Model: Novel Design Principles for Organic Materials. Acc. Chem. Res. 2017, 50, 341– 350, DOI: 10.1021/acs.accounts.6b00576Google Scholar12https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhvVSms7s%253D&md5=ae2fb7f835d1839ea6375df6dcd917d5Molecular Aggregate Photophysics beyond the Kasha Model: Novel Design Principles for Organic MaterialsHestand, Nicholas J.; Spano, Frank C.Accounts of Chemical Research (2017), 50 (2), 341-350CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)A review. The transport and photophys. properties of org. mol. aggregates, films, and crystals continue to receive widespread attention, driven mainly by expanding com. applications involving display and wearable technols. as well as the promise of efficient, large-area solar cells. The main blueprint for understanding how mol. packing impacts photophys. properties was drafted over 5 decades ago by Michael Kasha. K. showed that the Coulombic coupling between 2 mols., as detd. by the alignment of their transition dipoles, induces energetic shifts in the main absorption spectral peak and changes in the radiative decay rate when compared to uncoupled mols. In H-aggregates, the transition dipole moments align side-by-side leading to a spectral blue-shift and suppressed radiative decay rate, while in J-aggregates, the transition dipole moments align head-to-tail leading to a spectral red shift and an enhanced radiative decay rate. Although many examples of H- and J-aggregates were discovered, there are also many unconventional aggregates, which are not understood within the confines of Kasha's theory. Examples include nanopillars of 7,8,15,16-tetraazaterrylene, as well as several perylene-based dyes, which exhibit so-called H- to J-aggregate transformations. Such aggregates are typically characterized by significant wave function overlap between neighboring MOs of small (∼4 Å) intermol. distances, such as those found in rylene π-stacks and oligoacene herringbone lattices. Wave function overlap facilitates charge-transfer which creates an effective short-range exciton coupling that can also induce J- or H-aggregate behavior, depending on the sign. Unlike Coulomb coupling, short-range coupling is extremely sensitive to small (sub-Å) transverse displacements between neighboring chromophores. For perylene chromophores, the sign of the short-range coupling changes several times as 2 mols. are slipped from a side-by-side to head-to-tail configuration, in marked contrast to the sign of the Coulomb coupling, which changes only once. Such sensitivity allows J- to H-aggregate interconversions over distances several times smaller than those predicted by Kasha's theory. Since the total coupling drives exciton transport and photophys. properties, interference between the short- and long-range (Coulomb) couplings, as manifest by their relative signs and magnitudes, gives rise to a host of new aggregate types, referred to as HH, HJ, JH, and JJ aggregates, with distinct photophys. properties. An extreme example is the null HJ-aggregate in which total destructive interference leads to absorption line shapes practically identical to uncoupled mols. The severely compromised exciton bandwidth effectively shuts down energy transport. The new aggregates types described herein can be exploited for electronic materials design. The enhanced exciton bandwidth and weakly emissive properties of HH-aggregates make them ideal candidates for solar cell absorbers, while the enhanced charge mobility and strong emissive behavior of JJ-aggregates makes them excellent candidates for light-emitting diodes.
- 13Hestand, N. J.; Spano, F. C. Expanded Theory of H- and J-Molecular Aggregates: The Effects of Vibronic Coupling and Intermolecular Charge Transfer. Chem. Rev. 2018, 118, 7069– 7163, DOI: 10.1021/acs.chemrev.7b00581Google Scholar13https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXns1Cjurc%253D&md5=eb65f01278db2b376e55512f42ee286fExpanded Theory of H- and J-Molecular Aggregates: Effects of Vibronic Coupling and Intermolecular Charge TransferHestand, Nicholas J.; Spano, Frank C.Chemical Reviews (Washington, DC, United States) (2018), 118 (15), 7069-7163CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. The electronic excited states of mol. aggregates and their photophys. signatures have long fascinated spectroscopists and theoreticians alike since the advent of Frenkel exciton theory almost 90 years ago. The influence of mol. packing on basic optical probes like absorption and photoluminescence was originally worked out by Kasha for aggregates dominated by Coulombic intermol. interactions, eventually leading to the classification of J- and H-aggregates. This review outlines advances made in understanding the relationship between aggregate structure and photophysics when vibronic coupling and intermol. charge transfer are incorporated. An assortment of packing geometries is considered from the humble mol. dimer to more exotic structures including linear and bent aggregates, two-dimensional herringbone and "HJ" aggregates, and chiral aggregates. The interplay between long-range Coulomb coupling and short-range charge-transfer-mediated coupling strongly depends on the aggregate architecture leading to a wide array of photophys. behaviors.
- 14Zhong, C.; Bialas, D.; Collison, C. J.; Spano, F. C. Davydov Splitting in Squaraine Dimers. J. Phys. Chem. C 2019, 123, 18734– 18745, DOI: 10.1021/acs.jpcc.9b05297Google Scholar14https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhsVWjurzO&md5=937cb0798772723adb4a00bbb161da44Davydov Splitting in Squaraine DimersZhong, Chuwei; Bialas, David; Collison, Christopher J.; Spano, Frank C.Journal of Physical Chemistry C (2019), 123 (30), 18734-18745CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)The essential states model (ESM) for donor-acceptor-donor (D-A-D) chromophores is used to explore absorption and photoluminescence (PL) in mol. dimers composed of centrosym. and non-centrosym. squaraine mols. The spectral line shapes and shifts relative to the monomer spectrum are due to an interesting interplay between three-center charge distributions responsible for ground- and excited-state (permanent) dipole and quadrupole moments and two-center charge distributions responsible for transition dipole moments. The Davydov splitting is sensitive only to the interactions between the (extended) transition dipoles , whereas the permanent dipole-dipole and quadruple-quadrupole interactions impact the midpoint frequency of the two Davydov components, leading to a generally asym. splitting relative to the peak monomer transition frequency. The theory accurately reproduces the steady-state absorption and PL line shapes recently obtained for covalently bound squaraine dimers. The ESM also predicts an extreme type of non-Kasha behavior, where both Davydov components are blue-shifted above the monomer transition frequency.
- 15Abramavicius, D.; Mukamel, S. Exciton Dynamics in Chromophore Aggregates with Correlated Environment Fluctuations. J. Chem. Phys. 2011, 134, 174504– 174510, DOI: 10.1063/1.3579455Google Scholar15https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXlslCmu7o%253D&md5=8b093609c81cd3cd62cf54f3deb09816Exciton dynamics in chromophore aggregates with correlated environment fluctuationsAbramavicius, Darius; Mukamel, ShaulJournal of Chemical Physics (2011), 134 (17), 174504/1-174504/10CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)The effects of correlated mol. transition energy fluctuations in mol. aggregates on the d. matrix dynamics, and their signatures in the optical response are studied. Correlated fluctuations do not affect single-exciton dynamics and can be described as a nonlocal contribution to the spectral broadening, which appears as a multiplicative factor in the time-domain response function. Intraband coherences are damped only by uncorrelated transition energy fluctuations. The signal can then be expressed as a spectral convolution of a local contribution of the uncorrelated fluctuations and the nonlocal contribution of the correlated fluctuations. (c) 2011 American Institute of Physics.
- 16Mirkovic, T.; Ostroumov, E. E.; Anna, J. M.; van Grondelle, R.; Govindjee; Scholes, G. D. Light Absorption and Energy Transfer in the Antenna Complexes of Photosynthetic Organisms. Chem. Rev. 2017, 117, 249– 293, DOI: 10.1021/acs.chemrev.6b00002Google Scholar16https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtFyit7vI&md5=7201884bb63ab70347f79f951ff3369aLight absorption and energy transfer in the antenna complexes of photosynthetic organismsMirkovic, Tihana; Ostroumov, Evgeny E.; Anna, Jessica M.; van Grondelle, Rienk; Govindjee; Scholes, Gregory D.Chemical Reviews (Washington, DC, United States) (2017), 117 (2), 249-293CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. The process of photosynthesis is initiated by the capture of sunlight by a network of light-absorbing mols. (chromophores), which are also responsible for the subsequent funneling of the excitation energy to the reaction centers. Through evolution, genetic drift, and speciation, photosynthetic organisms have discovered many solns. for light harvesting. In this review, we describe the underlying photophys. principles by which this energy is absorbed, as well as the mechanisms of electronic excitation energy transfer (EET). First, optical properties of the individual pigment chromophores present in light-harvesting antenna complexes are introduced, and then we examine the collective behavior of pigment-pigment and pigment-protein interactions. The description of energy transfer, in particular multichromophoric antenna structures, is shown to vary depending on the spatial and energetic landscape, which dictates the relative coupling strength between constituent pigment mols. In the latter half of the article, we focus on the light-harvesting complexes of purple bacteria as a model to illustrate the present understanding of the synergetic effects leading to EET optimization of light-harvesting antenna systems while exploring the structure and function of the integral chromophores. We end this review with a brief overview of the energy-transfer dynamics and pathways in the light-harvesting antennas of various photosynthetic organisms.
- 17Spano, F. C. The Spectral Signatures of Frenkel Polarons in H- and J-Aggregates. Acc. Chem. Res. 2010, 43, 429– 439, DOI: 10.1021/ar900233vGoogle Scholar17https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhsFKgurzL&md5=a66d2effbaf73a403bf00e6e198efe0aThe Spectral Signatures of Frenkel Polarons in H- and J-AggregatesSpano, Frank C.Accounts of Chemical Research (2010), 43 (3), 429-439CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)A review. Electronic excitations in small aggregates, thin films, and crystals of conjugated org. mols. play a fundamental role in the operation of a wide array of org.-based devices including solar cells, transistors, and light-emitting diodes. Such excitations, or excitons, are generally spread out over several mols.: a balance between the delocalizing influence of resonant intermol. coupling and the localizing influence of static and dynamic disorder dets. the coherence range of the exciton. Because of the soft nature of org. materials, significant nuclear relaxation in the participating mols. also accompanies the electronic excitations. To properly understand energy or charge transport, 1 must treat intermol. (excitonic) coupling, electron-vibrational coupling, and disorder on equal footing. In this Account, the authors review the key elements of a theor. approach based on a multiparticle representation that describes electronic excitations in org. materials as vibronic excitations surrounded by a field of vibrational excitations. Such composite excitations are appropriately called Frenkel excitonic polarons. For many conjugated mols., the bulk of the nuclear reorganization energy following electronic excitation arises from the elongation of a sym. vinyl stretching mode with energy ∼1400 cm-1. To appreciate the impact of aggregation, the authors study how the vibronic progression of this mode, which dominates the isolated (solvated) mol. absorption and emission spectra, is distorted when mols. are close enough to interact with each other. As the authors demonstrate in this Account, the nature of the distortion provides a wealth of information about how the mols. are packed, the strength of the excitonic interactions between mols., the no. of mols. that are coherently coupled, and the nature of the disorder. The aggregation-induced deviations from the Poissonian distribution of vibronic peak intensities take on 2 extremes identified with ideal H- and J-aggregates. The sign of the nearest neighbor electronic coupling, pos. for H and neg. for J, distinguishes the 2 basic aggregate forms. For several decades, researchers have known that H-aggregates exhibit blue-shifted absorption spectra and are subradiant while J-aggregates exhibit the opposite behavior (red shifted absorption and superradiance). However, the exact inclusion of exciton-vibrational coupling reveals several more distinguishing traits between the 2 aggregate types: in H(J)-aggregates the ratio of the 1st 2 vibronic peak intensities in the absorption spectrum decreases (increases) with increasing excitonic coupling, while the ratio of the 0-0 to 0-1 emission intensities increases (decreases) with disorder and increases (decreases) with increasing temp. These 2 extreme behaviors provide the framework for understanding absorption and emission in more complex morphologies, such as herringbone packing in oligo(phenylene vinylene)s, oligothiophenes and polyacene crystals, as well as the polymorphic packing arrangements obsd. in carotenoids.
- 18Renger, T.; May, V.; Kühn, O. Ultrafast Excitation Energy Transfer Dynamics in Photosynthetic Pigment–Protein Complexes. Phys. Rep. 2001, 343, 137– 254, DOI: 10.1016/S0370-1573(00)00078-8Google Scholar18https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3MXhsVemsrs%253D&md5=50ce79c52301b5d9908904b28e57471aUltrafast excitation energy transfer dynamics in photosynthetic pigment-protein complexesRenger, T.; May, V.; Kuhn, O.Physics Reports (2001), 343 (3), 137-254CODEN: PRPLCM; ISSN:0370-1573. (Elsevier Science B.V.)A review contg. 239 refs. Photosynthetically active membranes of certain bacteria and higher plants contain antenna systems which surround the reaction center to increase its absorption cross section for the incoming sun light. The excitation energy created in the antenna pigments is transferred via an exciton mechanism to the reaction center where charge sepn. takes place. Sub-picosecond laser spectroscopy makes it possible to follow the initial dynamic events of excitation energy (exciton) motion and exciton relaxation in real time. On the other hand, the success of structure resoln. opened the door to the microscopic understanding of spectroscopic data and to an appreciation of the structure-function relationship realized in different systems. Here, it will be demonstrated how the combination of microscopically based theor. models and numerical simulations pave the road from spectroscopic data to a deeper understanding of the functionality of photosynthetic antenna systems. The d. matrix technique is introduced as the theor. tool providing a unified description of the processes which follow ultrafast laser excitation. This includes in particular coherent exciton motion, vibrational coherences, exciton relaxation, and exciton localization. It can be considered as a major result of recent investigations that a theor. model of intermediate complexity was shown to be suitable to explain a variety of expts. on different photosynthetic antenna systems. We start with introducing the structural components of antenna systems and discuss their general function. In the second part the formulation of the appropriate theor. model as well as the simulation of optical spectra is reviewed in detail. Emphasis is put on the mapping of the complex protein structure and its hierarchy of dynamic phenomena onto models of static and dynamic disorder. In particular, it is shown that the protein spectral d. plays a key role in characterizing excitation energy dissipation. The theor. concepts are illustrated in the third part by results of numerical simulations of linear and nonlinear optical expts. for three types of antennae: the peripheral light-harvesting complex 2 of purple bacteria, the Fenna-Mathew-Olson complex of green bacteria, and the light-harvesting complex of photosystem II of green plants.
- 19Schulze, J.; Kühn, O. Explicit Correlated Exciton-Vibrational Dynamics of the FMO Complex. J. Phys. Chem. B 2015, 119, 6211– 6216, DOI: 10.1021/acs.jpcb.5b03928Google Scholar19https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXnsVeisL0%253D&md5=da605f66b2c7c7f4bee69f2068dcaa36Explicit Correlated Exciton-Vibrational Dynamics of the FMO ComplexSchulze, J.; Kuehn, O.Journal of Physical Chemistry B (2015), 119 (20), 6211-6216CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)The coupled exciton-vibrational dynamics of a three-site model of the Fenna-Matthews-Olson complex is investigated using the numerically exact multilayer multiconfiguration time-dependent Hartree approach. Thereby the specific coupling of the vibrational modes to local electronic transitions is adapted from a discretized exptl. spectral d. The soln. of the resulting time-dependent Schr.ovrddot.odinger equation including three electronic and 450 vibrational degrees of freedom is analyzed in terms of excitonic populations and coherences. Emphasis is put onto the role of specific ranges of vibrational frequencies. It is obsd. that modes between 160 and 300 cm-1 are responsible for the sub-picosecond population and coherence decay. Further, it is found that a mean-field approach with respect to the vibrational degrees of freedom is not applicable.
- 20Tretiak, S.; Mukamel, S. Density Matrix Analysis and Simulation of Electronic Excitations in Conjugated and Aggregated Molecules. Chem. Rev. 2002, 102, 3171– 3212, DOI: 10.1021/cr0101252Google Scholar20https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XmsFSqtbY%253D&md5=e786f9963e003aaac58850d89142c063Density Matrix Analysis and Simulation of Electronic Excitations in Conjugated and Aggregated MoleculesTretiak, Sergei; Mukamel, ShaulChemical Reviews (Washington, DC, United States) (2002), 102 (9), 3171-3212CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. A discussion is presented on the collective electronic oscillator (CEO) formalism, electronic coherence sizes underlying the optical response of conjugated mols., optical response in chromophore aggregates.
- 21Richter, M.; Ahn, K. J.; Knorr, A.; Schliwa, A.; Bimberg, D.; Madjet, M. E.-A.; Renger, T. Theory of Excitation Transfer in Coupled Nanostructures – from Quantum Dots to Light Harvesting Complexes. Phys. Status Solidi B 2006, 243, 2302– 2310, DOI: 10.1002/pssb.200668053Google Scholar21https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XovFOisLs%253D&md5=b56c66a0de8f80a2b37e4f4eb677b832Theory of excitation transfer in coupled nanostructures. From quantum dots to light harvesting complexesRichter, Marten; Ahn, Kwang Jun; Knorr, Andreas; Schliwa, Andrei; Bimberg, Dieter; El-Amine Madjet, Mohamed; Renger, ThomasPhysica Status Solidi B: Basic Solid State Physics (2006), 243 (10), 2302-2310CODEN: PSSBBD; ISSN:0370-1972. (Wiley-VCH Verlag GmbH)Spatially localized but electromagnetically coupled electrons are model systems for excitation transfer on nanoscales. A unified description of coupled semiconductor quantum dots and coupled chlorophylls in light harvesting complexes is presented, considering Coulomb interaction including excitonic Foerster-coupling and (bi-) excitonic shifts as well as electron-phonon interaction. Linear absorption spectra are calcd. and principles for the description of third order optical nonlinearities are outlined.
- 22Asanuma, H.; Fujii, T.; Kato, T.; Kashida, H. Coherent Interactions of Dyes Assembled on DNA. J. Photochem. Photobiol., C 2012, 13, 124– 135, DOI: 10.1016/j.jphotochemrev.2012.04.002Google Scholar22https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XntVWhtbk%253D&md5=a6cea5584e14c9a209e452cc91db26a2Coherent interactions of dyes assembled on DNAAsanuma, Hiroyuki; Fujii, Taiga; Kato, Tomohiro; Kashida, HiromuJournal of Photochemistry and Photobiology, C: Photochemistry Reviews (2012), 13 (2), 124-135CODEN: JPPCAF; ISSN:1389-5567. (Elsevier B.V.)A review. The optical behavior of an organized dye assembly is different from that of the isolated dye; this difference is explained using mol. exciton theory. The theory predicts that mutual orientation, the no. of dyes in the cluster, and combinations of different dyes should display given characteristic spectroscopic behaviors due to coherent interactions. Comparison of theor. predictions with exptl. results has been limited so far. One of the reasons is the absence of a rigid and well-organized system that can control the orientation and size of the dye assembly. Recently, the DNA duplex has been used to assemble chromophores in a programmed manner. Use of DNA allows organized dye assembly with a given size and particular orientation. In this review, we evaluate the spectroscopic behavior of the H-type aggregate based on mol. exciton theory and compare it with actual dye assembly with DNA duplex. Furthermore, we demonstrate the importance of coherent interactions on the obsd. optical properties of dyes assembled in a DNA duplex.
- 23Czikklely, V.; Forsterling, H. D.; Kuhn, H. Extended Dipole Model for Aggregates of Dye Molecules. Chem. Phys. Lett. 1970, 6, 207– 210, DOI: 10.1016/0009-2614(70)80220-2Google ScholarThere is no corresponding record for this reference.
- 24Jelley, E. E. Spectral Absorption and Fluorescence of Dyes in the Molecular State. Nature 1936, 138, 1009– 1010, DOI: 10.1038/1381009a0Google Scholar24https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaA2sXht1Gmtg%253D%253D&md5=cc8df78b75b185f7d9581cdddde20711Spectral absorption and fluorescence of dyes in the molecular stateJelley, Edwin E.Nature (London, United Kingdom) (1936), 138 (), 1009-10CODEN: NATUAS; ISSN:0028-0836.Resonance radiation was observed in suspensions of several dyes. Three general methods of prepn. each cause the dye to pass from the dissocd. state in true soln., through a transitory mol. state which exhibits a characteristic absorption and fluorescence, to the cryst. state. The effect is shown strikingly by 1,1'-diethyl-ψ-cyanine chloride. The methods: (1) A concd. soln. in a strongly polar solvent (PhNO2, pyridine) is rapidly dild. with a nonpolar or feebly polar liquid (ligroin, CCl4, C6H6, PhMe, xylene). (2) The dye is dissolved in a strongly polar substance (such as benzophenone) which is crystd. by a sudden chilling, some of the dye remaining molecularly dispersed in the solid. The position of the band depends on the salt of the dye, but not on the dispersing solid. The sharp absorption band is not dichroic (not a function of the vibrational direction); absorption bands of the cryst. dye are strongly dichroic. The method is general for salts of basic dyes. (3) A soln. in MeOH or EtOH is added to 5 M NaCl. A strong fluorescence at 577 mμ and an absorption band at 574 mμ develop. The absorption and fluorescence disappear reversibly at 60°; a similar reversibility occurs on varying the alc. concn. In each of the 3 methods a transient mol. absorption occurs, with a duration from less than a sec. to a few weeks. The fluorescence is unpolarized. In adsorbed dyes (walls of the containing vessel, filter paper, cotton wool, kaolin) the effect sometimes lasts a min. or so, and then disappears rapidly. A similar type of narrow absorption band assocd. with fluorescence of about the same wave length occurs in the ruby: synthetic rubies are made by a process which corresponds to method (2).
- 25Jelley, E. E. Molecular, Nematic and Crystal States of I: I-Diethyl--Cyanine Chloride. Nature 1937, 139, 631, DOI: 10.1038/139631b0Google Scholar25https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaA2sXjt1Cmsw%253D%253D&md5=9c7189699c679fb051e243c2b5f8ed8fMolecular, nematic and crystal states of 1,1'-diethyl-ψ-cyanine chlorideJelley, Edwin E.Nature (London, United Kingdom) (1937), 139 (), 631-2CODEN: NATUAS; ISSN:0028-0836.cf. C. A. 31, 1703.6. By use of spectrographic, ultramicroscopic and streaming birefringence methods in the study of dispersions of 1,1'-diethyl-ψ-cyanine chloride in NaCl solns., it is shown that the dye passes from the dissocd. state through a mol. phase of very brief duration to form very thin threads. These threads are cryst. in the direction of their length only, and correspond to the nematic type of liquid crystal. The abnormal viscosity noted by Scheibe, Kandler and Ecker (C. A. 31, 3785.6) is due, not to a reversible polymerization of the dye ions, but to nematic aggregates of dye mols.
- 26Scheibe, G. ÜBer Die VeräNderlichkeit Der Absorptionsspektren in LöSungen Und Die Nebenvalenzen Als Ihre Ursache. Angew. Chem. 1937, 50, 212– 219, DOI: 10.1002/ange.19370501103Google Scholar26https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaA2sXislegsg%253D%253D&md5=f3123e579aa0f24544a5c349698a3dbdThe variation of absorption spectra in solutions and the side valences as its causeScheibe, G.Angewandte Chemie (1937), 50 (), 212-19CODEN: ANCEAD; ISSN:0044-8249.A comprehensive treatise with forty-five references.
- 27Koepke, J.; Hu, X.; Muenke, C.; Schulten, K.; Michel, H. The Crystal Structure of the Light-Harvesting Complex II (B800-850) from Rhodospirillum Molischianum. Structure 1996, 4, 581– 597, DOI: 10.1016/S0969-2126(96)00063-9Google Scholar27https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XjsVKlsb4%253D&md5=35997bc28f1daaaa4db29192b3131ca0The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianumKoepke, Juergen; Hu, Xiche; Muenke, Cornelia; Schulten, Klaus; Michel, HartmutStructure (London) (1996), 4 (5), 581-597CODEN: STRUE6; ISSN:0969-2126. (Current Biology)The light-harvesting complexes II (LH-2s) are integral membrane proteins that form ring-like structures, oligomers of αβ-heterodimers, in the photosynthetic membranes of purple bacteria. They contain a large no. of chromophores organized optimally for light absorption and rapid light energy migration. Recently, the structure of the nonameric LH-2 of Rhodopseudomonas acidophila has been detd.; we report here the crystal structure of the octameric LH-2 from Rhodospirillum molischianum. The unveiling of similarities and differences in the architecture of these proteins may provide valuable insight into the efficient energy transfer mechanisms of bacterial photosynthesis. The crystal structure of LH-2 from Rs. molischianum has been detd. by mol. replacement at 2.4 Å resoln. using X-ray diffraction. The crystal structure displays two concentric cylinders of sixteen membrane-spanning helical subunits, contg. two rings of bacteriochlorophyll-a (BChl-a) mols. One ring comprises sixteen B850 BChl-as perpendicular to the membrane plane and the other eight B800 BChl-as that are nearly parallel to the membrane plane; eight membrane-spanning lycopenes (the major carotenoid in this complex) stretch out between the B800 and B850 BCHl-as. The B800 BChl-as exhibit a different ligation from that of Rps. acidophila (aspartate is the Mg ligand as opposed to formyl-methionine in Rps. acidophila). The light-harvesting complexes from different bacteria assume various ring sizes. In LH-2 of Rs. molischianum, the Qy transition dipole moments of neighboring B850 and B800 BChl-as are nearly parallel to each other, i.e., they are optimally aligned for Foerster exciton transfer. Dexter energy transfer between these chlorophylls is also possible through interactions mediated by lycopenes and B850 BChl-a phytyl tails; the B800 BChl-a and one of the two B850 BChl-as assocd. with each heterodimeric unit are in van der Waals distance to a lycopene, such that singlet and triplet energy transfer between lycopene and the BChl-as can occur by the Dexter mechanism. The ring structure of the B850 BChl-as is optimal for light energy transfer in that it samples all spatial absorption and emission characteristics and places all oscillator strength into energetically low lying, thermally accessible exciton states.
- 28Chachisvilis, M.; Kuhn, O.; Pullerits, T.; Sundstrom, V. Excitons in Photosynthetic Purple Bacteria: Wavelike Motion or Incoherent Hopping?. J. Phys. Chem. B 1997, 101, 7275– 7283, DOI: 10.1021/jp963360aGoogle Scholar28https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXlsVSns70%253D&md5=ced8c8f2acdfa49361576a1a2e327445Excitons in photosynthetic purple bacteria: Wavelike motion or incoherent hopping?Chachisvilis, Mirianas; Kuehn, Oliver; Pullerits, Tonu; Sundstroem, VillyJournal of Physical Chemistry B (1997), 101 (37), 7275-7283CODEN: JPCBFK; ISSN:1089-5647. (American Chemical Society)The authors have studied excitation energy transfer in the photosynthetic antenna systems LH1 and LH2 of purple bacteria. Femtosecond pump-probe expts. are combined with computer simulations using the recently established crystal structure of these systems to assess the nature of excitation motion. The authors have measured the transient absorption kinetics and spectra of the LH1 and LH2 complexes in the temp. range from 4.2 to 296 K with femtosecond time resoln. The calcns. based on the Pauli master equation disagreed with exptl. measured population and anisotropy kinetics, suggesting that the simple model of excitation hopping between bacteriochlorophyll a mols. is not a proper description for energy transport in LH1 and LH2. As a next step, the authors have used the exciton theory to reproduce the transient absorption spectra of LH2, and we found that the coherence length of the exciton in B850 of LH2 1.5 ps after excitation of B800 is 4 ± 1.
- 29Hu, X.; Damjanovic, A.; Ritz, T.; Schulten, K. Architecture and Mechanism of the Light-Harvesting Apparatus of Purple Bacteria. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 5935– 5941, DOI: 10.1073/pnas.95.11.5935Google Scholar29https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1cXjtlKgs74%253D&md5=725f4350878a0c1db38538e554361c6cArchitecture and mechanism of the light-harvesting apparatus of purple bacteriaHu, Xiche; Damjanovic, Ana; Ritz, Thorsten; Schulten, KlausProceedings of the National Academy of Sciences of the United States of America (1998), 95 (11), 5935-5941CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Photosynthetic organisms fuel their metab. with light energy and have developed for this purpose an efficient app. for harvesting sunlight. The at. structure of the app., as it evolved in purple bacteria, has been constructed through a combination of x-ray crystallog., electron microscopy, and modeling. The detailed structure and overall architecture reveals a hierarchical aggregate of pigments that utilizes, as shown through femtosecond spectroscopy and quantum physics, elegant and efficient mechanisms for primary light absorption and transfer of electronic excitation toward the photosynthetic reaction center.
- 30Jonas, D. M.; Lang, M. J.; Nagasawa, Y.; Joo, T.; Fleming, G. R. Pump-Probe Polarization Anisotropy Study of Femtosecond Energy Transfer within the Photosynthetic Reaction Center of Rhodobacter Sphaeroides R26. J. Phys. Chem. A 1996, 100, 12660– 12673, DOI: 10.1021/jp960708tGoogle Scholar30https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XjvFCit7w%253D&md5=54891085ed6983477104cdca1c659002Pump-Probe Polarization Anisotropy Study of Femtosecond Energy Transfer within the Photosynthetic Reaction Center of Rhodobacter sphaeroides R26Jonas, David M.; Lang, Matthew J.; Nagasawa, Yutaka; Joo, Taiha; Fleming, Graham R.Journal of Physical Chemistry (1996), 100 (30), 12660-12673CODEN: JPCHAX; ISSN:0022-3654. (American Chemical Society)The energy transfer from the accessory bacteriochlorophylls (B) to the special pair (P) in the photosynthetic reaction center has been time resolved with pump-probe polarization anisotropy measurements using 20-25 fs duration pulses near 800 nm. The expts. were carried out at low pulse energies (500 pJ in a 34 μm spot), low repetition rates (5 kHz), and high sample flow velocities (100 cm/s) to avoid artifacts from satn. and photoexcitation of incompletely relaxed reaction centers. The pump excitation corresponds to 1.4 × 106 photons/μm2: the "satn. intensity" for the charge sepn. quantum yield is 3 × 107 photons/μm2. Magic angle pump-probe transients can be satisfactorily fit as biexponential, with an ∼120 fs bleach decay followed by a 2.8 ps bleach rise. (An ∼400 fs bleach decay seen in several previous expts. arises from unrelaxed reaction centers.) The initial pump-probe anisotropy is 0.4 and decays with an ∼80 fs time const., which we attribute to dipole reorientation by electronic energy transfer. Simultaneous kinetic modeling of the parallel, perpendicular, and magic angle pump-probe transients using the reaction center structure and dipole orientations is consistent with energy transfer proceeding in two steps: ∼80 fs electronic energy transfer from the accessory bacteriochlorophylls to the upper exciton component of the special pair (B → P+) followed by an ∼150 fs internal conversion from the upper exciton component to the lower exciton component of the special pair (P+ → P-). Finally, charge sepn. after electron transfer from P- to H causes an electrochromic (Stark) shift of B and produces the 2.8 ps bleach rise. The two-step energy transfer model is supported by the observation of weak quantum beat oscillations (125 cm-1 and 227 cm-1) with near-zero anisotropy in the pump-probe signals. The near-zero anisotropy is only consistent with pump-probe signals from P+ species created by energy transfer from B. The ∼80 fs B → P+ energy transfer is so rapid that it sets vibrational wave packets in motion on the special pair. Because B → P energy transfer is more rapid than conventional energy transfer rates, it may be more appropriate to think of energy transfer between pigments in the reaction center as an intermediate case between energy transfer among sep. pigments and internal conversion within a single supermol.
- 31Arpin, P. C.; Turner, D. B.; McClure, S. D.; Jumper, C. C.; Mirkovic, T.; Challa, J. R.; Lee, J.; Teng, C. Y.; Green, B. R.; Wilk, K. E. Spectroscopic Studies of Cryptophyte Light Harvesting Proteins: Vibrations and Coherent Oscillations. J. Phys. Chem. B 2015, 119, 10025– 10034, DOI: 10.1021/acs.jpcb.5b04704Google Scholar31https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtFyru7nO&md5=2b38e1b9a1e52da45733ea0c3e743352Spectroscopic Studies of Cryptophyte Light Harvesting Proteins: Vibrations and Coherent OscillationsArpin, Paul C.; Turner, Daniel B.; McClure, Scott D.; Jumper, Chanelle C.; Mirkovic, Tihana; Challa, J. Reddy; Lee, Joohyun; Teng, Chang Ying; Green, Beverley R.; Wilk, Krystyna E.; Curmi, Paul M. G.; Hoef-Emden, Kerstin; McCamant, David W.; Scholes, Gregory D.Journal of Physical Chemistry B (2015), 119 (31), 10025-10034CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)The first step of photosynthesis is the absorption of light by antenna complexes. Recent studies of light-harvesting complexes using two-dimensional electronic spectroscopy have revealed interesting coherent oscillations. Some contributions to those coherences are assigned to electronic coherence and therefore have implications for theories of energy transfer. To assign these femtosecond data and to gain insight into the interplay among electronic and vibrational resonances, we need detailed information on vibrations and coherences in the excited electronic state compared to the ground electronic state. Here, we used broad-band transient absorption and femtosecond stimulated Raman spectroscopies to record ground- and excited-state coherences in four related photosynthetic proteins: PC577 from Hemiselmis pacifica CCMP706, PC612 from Hemiselmis virescens CCAC 1635 B, PC630 from Chroomonas CCAC 1627 B (marine), and PC645 from Chroomonas mesostigmatica CCMP269. Two of those proteins (PC630 and PC645) have strong electronic coupling while the other two proteins (PC577 and PC612) have weak electronic coupling between the chromophores. We report vibrational spectra for the ground and excited electronic states of these complexes as well as an anal. of coherent oscillations obsd. in the broad-band transient absorption data.
- 32Brixner, T.; Hildner, R.; Kohler, J.; Lambert, C.; Wurthner, F. Exciton Transport in Molecular Aggregates - from Natural Antennas to Synthetic Chromophore Systems. Adv. Energy Mater. 2017, 7, 1700236 DOI: 10.1002/aenm.201700236Google ScholarThere is no corresponding record for this reference.
- 33Graugnard, E.; Kellis, D. L.; Bui, H.; Barnes, S.; Kuang, W.; Lee, J.; Hughes, W. L.; Knowlton, W. B.; Yurke, B. DNA-Controlled Excitonic Switches. Nano Lett. 2012, 12, 2117– 2122, DOI: 10.1021/nl3004336Google Scholar33https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XjsVSrt7o%253D&md5=b1d332b925c3578e90db2a452b15ef7aDNA-Controlled Excitonic SwitchesGraugnard, Elton; Kellis, Donald L.; Bui, Hieu; Barnes, Stephanie; Kuang, Wan; Lee, Jeunghoon; Hughes, William L.; Knowlton, William B.; Yurke, BernardNano Letters (2012), 12 (4), 2117-2122CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)Fluorescence resonance energy transfer (FRET) is a promising means of enabling information processing in nanoscale devices, but dynamic control over exciton pathways is required. Here, we demonstrate the operation of two complementary switches consisting of diffusive FRET transmission lines in which exciton flow is controlled by DNA. Repeatable switching is accomplished by the removal or addn. of fluorophores through toehold-mediated strand invasion. In principle, these switches can be networked to implement any Boolean function.
- 34Cannon, B. L.; Kellis, D. L.; Davis, P. H.; Lee, J.; Kuang, W.; Hughes, W. L.; Graugnard, E.; Yurke, B.; Knowlton, W. B. Excitonic and Logic Gates on DNA Brick Nanobreadboards. ACS Photonics 2015, 2, 398– 404, DOI: 10.1021/ph500444dGoogle Scholar34https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXivFSrtrc%253D&md5=508e9646c05bd709bf29547e2a71f2d7Excitonic AND Logic Gates on DNA Brick NanobreadboardsCannon, Brittany L.; Kellis, Donald L.; Davis, Paul H.; Lee, Jeunghoon; Kuang, Wan; Hughes, William L.; Graugnard, Elton; Yurke, Bernard; Knowlton, William B.ACS Photonics (2015), 2 (3), 398-404CODEN: APCHD5; ISSN:2330-4022. (American Chemical Society)A promising application of DNA self-assembly is the fabrication of chromophore-based excitonic devices. DNA brick assembly is a compelling method for creating programmable nanobreadboards on which chromophores may be rapidly and easily repositioned to prototype new excitonic devices, optimize device operation, and induce reversible switching. Using DNA nanobreadboards, the authors demonstrated each of these functions through the construction and operation of two different excitonic AND logic gates. The modularity and high chromophore d. achievable via this brick-based approach provide a viable path toward developing information processing and storage systems.
- 35Kellis, D. L.; Rehn, S. M.; Cannon, B. L.; Davis, P. H.; Graugnard, E.; Lee, J.; Yurke, B.; Knowlton, W. B. DNA-Mediated Excitonic Upconversion FRET Switching. New J. Phys. 2015, 17, 115007 DOI: 10.1088/1367-2630/17/11/115007Google Scholar35https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XpsFyksr4%253D&md5=34809198b6a387fbe13f5ccdffe14daeDNA-mediated excitonic upconversion FRET switchingKellis, Donald L.; Rehn, Sarah M.; Cannon, Brittany L.; Davis, Paul H.; Graugnard, Elton; Lee, Jeunghoon; Yurke, Bernard; Knowlton, William B.New Journal of Physics (2015), 17 (Nov.), 115007/1-115007/11CODEN: NJOPFM; ISSN:1367-2630. (IOP Publishing Ltd.)Excitonics is a rapidly expanding field of nanophotonics in which the harvesting of photons, ensuing creation and transport of excitons via F.ovrddot.orster resonant energy transfer (FRET), and subsequent charge sepn. or photon emission has led to the demonstration of excitonic wires, switches, Boolean logic and light harvesting antennas for many applications. FRET funnels excitons down an energy gradient resulting in energy loss with each step along the pathway. Conversely, excitonic energy upconversion via upconversion nanoparticles (UCNPs), although currently inefficient, serves as an energy ratchet to boost the exciton energy. Although FRET-based upconversion has been demonstrated, it suffers from low FRET efficiency and lacks the ability to modulate the FRET.Wehave engineered an upconversion FRET-based switch by combining lanthanide-doped UCNPs and fluorophores that demonstrates excitonic energy upconversion by nearly a factor of 2, an excited state donor to acceptor FRET efficiency of nearly 25%, and an acceptor fluorophore quantum efficiency that is close to unity. These findings offer a promising path for energy upconversion in nanophotonic applications including artificial light harvesting, excitonic circuits, photovoltaics, nanomedicine, and optoelectronics.
- 36Wang, S. Y.; Lebeck, A. R.; Dwyer, C. Nanoscale Resonance Energy Transfer-Based Devices for Probabilistic Computing. IEEE Micro 2015, 35, 72– 84, DOI: 10.1109/MM.2015.124Google ScholarThere is no corresponding record for this reference.
- 37Sawaya, N. P. D.; Rappoport, D.; Tabor, D. P.; Aspuru-Guzik, A. Excitonics: A Set of Gates for Molecular Exciton Processing and Signaling. ACS Nano 2018, 12, 6410– 6420, DOI: 10.1021/acsnano.8b00584Google Scholar37https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhtFKlsrbI&md5=78778908f0ed9dd660e61c3fde263f5bExcitonics: A Set of Gates for Molecular Exciton Processing and SignalingSawaya, Nicolas P. D.; Rappoport, Dmitrij; Tabor, Daniel P.; Aspuru-Guzik, AlanACS Nano (2018), 12 (7), 6410-6420CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)Regulating energy transfer pathways through materials is a central goal of nanotechnol., as a greater degree of control is crucial for developing sensing, spectroscopy, microscopy, and computing applications. Such control necessitates a toolbox of actuation methods that can direct energy transfer based on user input. A proposal is introduced for a mol. exciton gate, analogous to a traditional transistor, for regulating exciton flow in chromophoric systems. The gate may be activated with an input of light or an input flow of excitons. The proposal relies on excitation migration via the 2nd excited singlet (S2) state of the gate mol. It exhibits the following features, only a subset of which are present in previous exciton switching schemes: ps time scale actuation, amplification/gain behavior, and a lack of mol. rearrangement. The device can be used to produce universal binary logic or amplification of an exciton current, providing an excitonic platform with several potential uses, including signal processing for microscopy and spectroscopy methods that implement tunable exciton flux.
- 38Ostroverkhova, O. Organic Optoelectronic Materials: Mechanisms and Applications. Chem. Rev. 2016, 116, 13279– 13412, DOI: 10.1021/acs.chemrev.6b00127Google Scholar38https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xhs1egsLnM&md5=4ab815e1951d3749bf2a5bbd93106a9bOrganic Optoelectronic Materials: Mechanisms and ApplicationsOstroverkhova, OksanaChemical Reviews (Washington, DC, United States) (2016), 116 (22), 13279-13412CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. Org. (opto)electronic materials have received considerable attention due to their applications in thin-film-transistors, light-emitting diodes, solar cells, sensors, photorefractive devices, and many others. The technol. promises include low cost of these materials and the possibility of their room-temp. deposition from soln. on large-area and/or flexible substrates. The article reviews the current understanding of the phys. mechanisms that det. the (opto)electronic properties of high-performance org. materials. The focus of the review is on photoinduced processes and on electronic properties important for optoelectronic applications relying on charge carrier photogeneration. Addnl., it highlights the capabilities of various exptl. techniques for characterization of these materials, summarizes top-of-the-line device performance, and outlines recent trends in the further development of the field. The properties of materials based both on small mols. and on conjugated polymers are considered, and their applications in org. solar cells, photodetectors, and photorefractive devices are discussed.
- 39Bardeen, C. J. The Structure and Dynamics of Molecular Excitons. Annu. Rev. Phys. Chem. 2014, 65, 127– 148, DOI: 10.1146/annurev-physchem-040513-103654Google Scholar39https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtVKjtLvM&md5=476fafa72e54b9775dd1be2c85d785d1The structure and dynamics of molecular excitonsBardeen, Christopher J.Annual Review of Physical Chemistry (2014), 65 (), 127-148CODEN: ARPLAP; ISSN:0066-426X. (Annual Reviews)A review. The photophys. behavior of org. semiconductors is governed by their excitonic states. In this review, I classify the three different exciton types (Frenkel singlet, Frenkel triplet, and charge transfer) typically encountered in org. semiconductors. Exptl. challenges that arise in the study of solid-state org. systems are discussed. The steady-state spectroscopy of intermol. delocalized Frenkel excitons is described, using cryst. tetracene as an example. I consider the problem of a localized exciton diffusing in a disordered matrix in detail, and exptl. results on conjugated polymers and model systems suggest that energetic disorder leads to subdiffusive motion. Multiexciton processes such as singlet fission and triplet fusion are described, emphasizing the role of spin state coherence and magnetic fields in studying singlet ↔ triplet pair interconversion. Singlet fission provides an example of how all three types of excitons (triplet, singlet, and charge transfer) may interact to produce useful phenomena for applications such as solar energy conversion.
- 40Eisfeld, A.; Briggs, J. S. The J-Band of Organic Dyes: Lineshape and Coherence Length. Chem. Phys. 2002, 281, 61– 70, DOI: 10.1016/S0301-0104(02)00594-3Google Scholar40https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XkvFChtLs%253D&md5=4ec746cf9b355203250cab9a08377c2eThe J-band of organic dyes: lineshape and coherence lengthEisfeld, Alexander; Briggs, John S.Chemical Physics (2002), 281 (1), 61-70CODEN: CMPHC2; ISSN:0301-0104. (Elsevier Science B.V.)Self-organized J-aggregates of dye mols., known for >60 yr, are emerging as remarkably versatile quantum systems with applications in photog., opto-electronics, solar cells, photobiol. and as supra-mol. fibers. Recently there was much effort to achieve quantum entanglement and coherence on the nanoscale in atom traps and quantum dot aggregates (for use in quantum computing). The excitonic state of the J-aggregate is a textbook case of mesoscopic quantum coherence and entanglement. The establishment of coherence can literally be seen since the dye changes color dramatically on aggregation due to strong shifts in the absorption spectrum. In a simple theory the shifts and shapes of optical absorption spectra upon aggregation to a polymer are reproduced, and the coherence length of quantum entanglement of monomer wavefunctions are calcd.
- 41Thilagam, A. Entanglement Dynamics of J-Aggregate Systems. J. Phys. A: Math. Theor. 2011, 44, 135306 DOI: 10.1088/1751-8113/44/13/135306Google ScholarThere is no corresponding record for this reference.
- 42Sarovar, M.; Ishizaki, A.; Fleming, G. R.; Whaley, K. B. Quantum Entanglement in Photosynthetic Light-Harvesting Complexes. Nat. Phys. 2010, 6, 462– 467, DOI: 10.1038/nphys1652Google Scholar42https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXmslChsbw%253D&md5=31b0159b3b3e627fc121cb1ecc45cc2dQuantum entanglement in photosynthetic light-harvesting complexesSarovar, Mohan; Ishizaki, Akihito; Fleming, Graham R.; Whaley, K. BirgittaNature Physics (2010), 6 (6), 462-467CODEN: NPAHAX; ISSN:1745-2473. (Nature Publishing Group)Light-harvesting components of photosynthetic organisms are complex, coupled, many-body quantum systems, in which electronic coherence has recently been shown to survive for relatively long timescales, despite the decohering effects of their environments. Here, we analyze entanglement in multichromophoric light-harvesting complexes, and establish methods for quantification of entanglement by describing necessary and sufficient conditions for entanglement and by deriving a measure of global entanglement. These methods are then applied to the Fenna-Matthews-Olson protein to ext. the initial state and temp. dependencies of entanglement. We show that, although the Fenna-Matthews-Olson protein in natural conditions largely contains bipartite entanglement between dimerized chromophores, a small amt. of long-range and multipartite entanglement should exist even at physiol. temps. This constitutes the first rigorous quantification of entanglement in a biol. system. Finally, we discuss the practical use of entanglement in densely packed mol. aggregates such as light-harvesting complexes.
- 43Thilagam, A. Quantum Information Processing Attributes of J-Aggregates; World Scientific Publishing Company: Singapore, 2012; Vol. 2.Google ScholarThere is no corresponding record for this reference.
- 44Ball, P. Physics of Life: The Dawn of Quantum Biology. Nature 2011, 474, 272– 274, DOI: 10.1038/474272aGoogle Scholar44https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXnsFOqsLc%253D&md5=5bc81aac8b360e7b6a9c4c7d062b94c5Physics of life: The dawn of quantum biologyBall, PhilipNature (London, United Kingdom) (2011), 474 (7351), 272-274CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)The key to practical quantum computing and high-efficiency solar cells may lie in the messy green world outside the physics lab.
- 45Lloyd, S. Quantum Coherence in Biological Systems. J. Phys.: Conf. Ser. 2011, 302, 012037 DOI: 10.1088/1742-6596/302/1/012037Google Scholar45https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtFSku7bP&md5=bc97885fd5a4bd840afc0289bd52da4cQuantum coherence in biological systemsLloyd, SethJournal of Physics: Conference Series (2011), 302 (), 012037/1-012037/5CODEN: JPCSDZ; ISSN:1742-6588. (Institute of Physics Publishing)A review. This paper reviews the role of quantum mechanics in biol. systems, and shows how the interplay between coherence and decoherence can strongly enhance quantum transport in photosynthesis.
- 46Vickerstaff, T.; Lemin, D. R. Aggregation of Dyes in Aqueous Solution. Nature 1946, 157, 373, DOI: 10.1038/157373a0Google Scholar46https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaH28XhvV2jtw%253D%253D&md5=ba143cf6c2223197f59b645708c653aeAggregation of dyes in aqueous solutionVickerstaff, T.; Lemin, D. R.Nature (London, United Kingdom) (1946), 157 (), 373CODEN: NATUAS; ISSN:0028-0836.The work of Rabinovitch and Epstein (C.A. 35, 1294.7) on the absorption spectrum of methylene blue 0.002-0.000,002 M was repeated. They reported an absorption band at 6560 A., which decreases in intensity, and one at 6000 A., which increases in intensity, both with increasing concn. Higher extinction coeffs. than those of Rabinovitch and Epstein were found. The second absorption band not only increases in intensity with concn., but also shifts continuously toward shorter wave lengths; at 0.0025 M, the peak is at 6050 A.; at 0.0313 M, it is at 5850 A. This shows that a soln. of methylene blue is not a simple mixt. of monomer and dimer, but contains higher polymers, particularly at higher concns. This is supported by the data of Lange and Herre (C.A. 32, 4051.1) and Sheppard and Geddes (C.A. 39, 866.9).
- 47Dickinson, H. O. The Aggregation of Cyanine Dyes in Aqueous Solution. Trans. Faraday Soc. 1947, 43, 486– 491, DOI: 10.1039/tf9474300486Google Scholar47https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaH1cXht1ygtw%253D%253D&md5=4ccf8fb32ca5788cfb3bfb2cc3f105b8Aggregation of cyanine dyes in aqueous solutionDickinson, H. O.Transactions of the Faraday Society (1947), 43 (), 486-91CODEN: TFSOA4; ISSN:0014-7672.The absorption and photographic sensitizing properties of 2-ethyl-2'-methylpseudocyanine chloride and Isoquinoline Red have been examd. The degree of aggregation of both dyes in aq. soln. has been detd. by osmotic pressure and elec. conductance measurements. The degree of aggregation appears to be fairly const. over the range of concn. studied. The absorption and sensitizing properties of the two dyes have been related to their degree of aggregation.
- 48Heyne, B. Self-Assembly of Organic Dyes in Supramolecular Aggregates. Photochem. Photobiol. Sci. 2016, 15, 1103– 1114, DOI: 10.1039/C6PP00221HGoogle Scholar48https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xhtleit7vP&md5=b61bbc375d19b8a6ff20e8f02a4b9396Self-assembly of organic dyes in supramolecular aggregatesHeyne, BelindaPhotochemical & Photobiological Sciences (2016), 15 (9), 1103-1114CODEN: PPSHCB; ISSN:1474-905X. (Royal Society of Chemistry)Many scientists probably consider dye aggregation in soln. a curse. Here, the adjective "many" should be stressed, as some other researchers thrive on forcing dyes to aggregate in soln. This perspective paper is certainly not meant to be a comprehensive review on the topic. However, for people intrigued by this pervasive phenomenon, I will try to offer a general picture on the self-assembly of dyes into supramol. aggregates by presenting and discussing key information on their thermodn., kinetics, and optical changes. More recent topics will be introduced, such as the impact of external stimuli on dye aggregation, with a particular focus on ion specific effects. Finally, aggregation-induced emission will also be examd.
- 49Engel, G. S.; Calhoun, T. R.; Read, E. L.; Ahn, T. K.; Mancal, T.; Cheng, Y. C.; Blankenship, R. E.; Fleming, G. R. Evidence for Wavelike Energy Transfer through Quantum Coherence in Photosynthetic Systems. Nature 2007, 446, 782– 786, DOI: 10.1038/nature05678Google Scholar49https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXktVeqt78%253D&md5=7b4589af9ac8747b5412060efac43428Evidence for wavelike energy transfer through quantum coherence in photosynthetic systemsEngel, Gregory S.; Calhoun, Tessa R.; Read, Elizabeth L.; Ahn, Tae-Kyu; Mancal, Tomas; Cheng, Yuan-Chung; Blankenship, Robert E.; Fleming, Graham R.Nature (London, United Kingdom) (2007), 446 (7137), 782-786CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centers, where long term energy storage is initiated. The energy transfer mechanism is often described by semiclassical models that invoke 'hopping' of excited-state populations along discrete energy levels. Two-dimensional Fourier transform electronic spectroscopy has mapped these energy levels and their coupling in the Fenna-Matthews-Olson (FMO) bacteriochlorophyll complex, which is found in green S bacteria and acts as an energy 'wire' connecting a large peripheral light-harvesting antenna, the chlorosome, to the reaction center. The spectroscopic data clearly document the dependence of the dominant energy transport pathways on the spatial properties of the excited-state wavefunctions of the whole bacteriochlorophyll complex. But the intricate dynamics of quantum coherence, which has no classical analog, was largely neglected in the analyses-even though electronic energy transfer involving oscillatory populations of donors and acceptors was 1st discussed >70 years ago, and electronic quantum beats arising from quantum coherence in photosynthetic complexes were predicted and indirectly obsd. Here the authors extend previous two-dimensional electronic spectroscopy studies of the FMO bacteriochlorophyll complex, and obtain direct evidence for remarkably long-lived electronic quantum coherence playing an important part in energy transfer processes within this system. The quantum coherence manifests itself in characteristic, directly observable quantum beating signals among the excitons within the Chlorobium tepidum FMO complex at 77 K. This wavelike characteristic of the energy transfer within the photosynthetic complex can explain its extreme efficiency, in that it allows the complexes to sample vast areas of phase space to find the most efficient path.
- 50Lee, H.; Cheng, Y. C.; Fleming, G. R. Coherence Dynamics in Photosynthesis: Protein Protection of Excitonic Coherence. Science 2007, 316, 1462– 1465, DOI: 10.1126/science.1142188Google Scholar50https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXmtFSjsbs%253D&md5=ad1e8c76789a04846ce844220a8e5c3dCoherence Dynamics in Photosynthesis: Protein Protection of Excitonic CoherenceLee, Hohjai; Cheng, Yuan-Chung; Fleming, Graham R.Science (Washington, DC, United States) (2007), 316 (5830), 1462-1465CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)The role of quantum coherence in promoting the efficiency of the initial stages of photosynthesis is an open and intriguing question. We performed a two-color photon echo expt. on a bacterial reaction center that enabled direct visualization of the coherence dynamics in the reaction center. The data revealed long-lasting coherence between two electronic states that are formed by mixing of the bacteriopheophytin and accessory bacteriochlorophyll excited states. This coherence can only be explained by strong correlation between the protein-induced fluctuations in the transition energy of neighboring chromophores. Our results suggest that correlated protein environments preserve electronic coherence in photosynthetic complexes and allow the excitation to move coherently in space, enabling highly efficient energy harvesting and trapping in photosynthesis.
- 51Scholes, G. D.; Fleming, G. R.; Olaya-Castro, A.; van Grondelle, R. Lessons from Nature About Solar Light Harvesting. Nat. Chem. 2011, 3, 763– 774, DOI: 10.1038/nchem.1145Google Scholar51https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXht1ajurzF&md5=356439ff0cf14151e1c943af885f5cddLessons from nature about solar light harvestingScholes, Gregory D.; Fleming, Graham R.; Olaya-Castro, Alexandra; van Grondelle, RienkNature Chemistry (2011), 3 (10), 763-774CODEN: NCAHBB; ISSN:1755-4330. (Nature Publishing Group)A review. Solar fuel prodn. often starts with the energy from light being absorbed by an assembly of mols.; this electronic excitation is subsequently transferred to a suitable acceptor. For example, in photosynthesis, antenna complexes capture sunlight and direct the energy to reaction centers that then carry out the assocd. chem. In this Review, we describe the principles learned from studies of various natural antenna complexes and suggest how to elucidate strategies for designing light-harvesting systems. We envisage that such systems will be used for solar fuel prodn., to direct and regulate excitation energy flow using mol. organizations that facilitate feedback and control, or to transfer excitons over long distances. Also described are the notable properties of light-harvesting chromophores, spatial-energetic landscapes, the roles of excitonic states and quantum coherence, as well as how antennas are regulated and photoprotected.
- 52Scholes, G. D. Quantum Biology Coherence in Photosynthesis. Nat. Phys. 2011, 7, 448– 449, DOI: 10.1038/nphys2013Google Scholar52https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXmvVarsLc%253D&md5=96fd2be3e321c27b173bb704888e912fCoherence in photosynthesisScholes, Gregory D.Nature Physics (2011), 7 (6), 448-449CODEN: NPAHAX; ISSN:1745-2473. (Nature Publishing Group)A review. Evidence has accumulated that quantum coherence plays a role in photosynthesis. A better understanding of this process might help us design more efficient solar cells to harness the Sun's energy.
- 53Fassioli, F.; Dinshaw, R.; Arpin, P. C.; Scholes, G. D. Photosynthetic Light Harvesting: Excitons and Coherence. J. R. Soc., Interface 2014, 11, 20130901 DOI: 10.1098/rsif.2013.0901Google Scholar53https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXmtV2rsrY%253D&md5=1ccc7148540392efb762f7496411895bPhotosynthetic light harvesting: excitons and coherenceFassioli, Francesca; Dinshaw, Rayomond; Arpin, Paul C.; Scholes, Gregory D.Journal of the Royal Society, Interface (2014), 11 (92), 20130901/1-20130901/22CODEN: JRSICU; ISSN:1742-5689. (Royal Society)A review. Photosynthesis begins with light harvesting, where specialized pigment-protein complexes transform sunlight into electronic excitations delivered to reaction centers to initiate charge sepn. There is evidence that quantum coherence between electronic excited states plays a role in energy transfer. In this review, we discuss how quantum coherence manifests in photosynthetic light harvesting and its implications. We begin by examg. the concept of an exciton, an excited electronic state delocalized over several spatially sepd. mols., which is the most widely available signature of quantum coherence in light harvesting. We then discuss recent results concerning the possibility that quantum coherence between electronically excited states of donors and acceptors may give rise to a quantum coherent evolution of excitations, modifying the traditional incoherent picture of energy transfer. Key to this (partially) coherent energy transfer appears to be the structure of the environment, in particular the participation of non-equil. vibrational modes. We discuss the open questions and controversies regarding quantum coherent energy transfer and how these can be addressed using new exptl. techniques.
- 54Dill, K. A.; MacCallum, J. L. The Protein-Folding Problem, 50 Years On. Science 2012, 338, 1042– 1046, DOI: 10.1126/science.1219021Google Scholar54https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xhs12itrnF&md5=bd73e6103d437b24594ce4cd86ad25dcThe protein-folding problem, 50 years onDill, Ken A.; MacCallum, Justin L.Science (Washington, DC, United States) (2012), 338 (6110), 1042-1046CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)A review. The protein-folding problem was 1st posed about one half-century ago. The term refers to 3 broad questions: (1) What is the phys. code by which an amino acid sequence dictates a protein's native structure (2) How can proteins fold so fast and (3) Can one devise a computer algorithm to predict protein structures from their sequences. Here, the authors review progress on these problems. In a few cases, computer simulations of the phys. forces in chem. detailed models have now achieved the accurate folding of small proteins. It has been learned that proteins fold rapidly because random thermal motions cause conformational changes leading energetically downhill toward the native structure, a principle that is captured in funnel-shaped energy landscapes. And thanks in part to the large Protein Data Bank of known structures, predicting protein structures is now far more successful than was thought possible in earlier days. What began as 3 questions of basic science one half-century ago has now grown into the full-fledged research field of protein phys. science.
- 55Yeates, T. O. Geometric Principles for Designing Highly Symmetric Self-Assembling Protein Nanomaterials. Annu. Rev. Biophys. 2017, 46, 23– 42, DOI: 10.1146/annurev-biophys-070816-033928Google Scholar55https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXksVCqsLw%253D&md5=733660019538f9c9ecaf9c0bcb217702Geometric Principles for Designing Highly Symmetric Self-Assembling Protein NanomaterialsYeates, Todd O.Annual Review of Biophysics (2017), 46 (), 23-42CODEN: ARBNCV; ISSN:1936-122X. (Annual Reviews)A review. Emerging protein design strategies are enabling the creation of diverse, self-assembling supramol. structures with precision on the at. scale. The design possibilities include various types of architectures: finite cages or shells, essentially unbounded two-dimensional and three-dimensional arrays (i.e., crystals), and linear or tubular filaments. In nature, structures of those types are generally sym., and, accordingly, symmetry provides a powerful guide for developing new design approaches. Recent design studies have produced numerous protein assemblies in close agreement with geometric specifications. For certain design approaches, a complete list of allowable symmetry combinations that can be used for construction has been articulated, opening a path to a rich diversity of geometrically defined protein materials. Future challenges include improving and elaborating on current strategies and endowing designed protein nanomaterials with properties useful in nanomedicine and material science applications.
- 56Huang, P. S.; Boyken, S. E.; Baker, D. The Coming of Age of De Novo Protein Design. Nature 2016, 537, 320– 327, DOI: 10.1038/nature19946Google Scholar56https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhsFajsrzL&md5=4627161c32d649123f680281b78adbe4The coming of age of de novo protein designHuang, Po-Ssu; Boyken, Scott E.; Baker, DavidNature (London, United Kingdom) (2016), 537 (7620), 320-327CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)A review. There are 20200 possible amino acid sequences for a 200-residue protein, of which the natural evolutionary process has sampled only an infinitesimal subset. De novo protein design explores the full sequence space, guided by the phys. principles that underlie protein folding. Computational methodol. has advanced to the point that a wide range of structures can be designed from scratch with at.-level accuracy. Almost all protein engineering so far has involved the modification of naturally occurring proteins; it should now be possible to design new functional proteins from the ground up to tackle current challenges in biomedicine and nanotechnol.
- 57Bale, J. B.; Gonen, S.; Liu, Y.; Sheffler, W.; Ellis, D.; Thomas, C.; Cascio, D.; Yeates, T. O.; Gonen, T.; King, N. P. Accurate Design of Megadalton-Scale Two-Component Icosahedral Protein Complexes. Science 2016, 353, 389– 394, DOI: 10.1126/science.aaf8818Google Scholar57https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtFyit7bI&md5=830c50306546812190a79aa995396a76Accurate design of megadalton-scale two-component icosahedral protein complexesBale, Jacob B.; Gonen, Shane; Liu, Yuxi; Sheffler, William; Ellis, Daniel; Thomas, Chantz; Cascio, Duilio; Yeates, Todd O.; Gonen, Tamir; King, Neil P.; Baker, DavidScience (Washington, DC, United States) (2016), 353 (6297), 389-394CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)Nature provides many examples of self- and co-assembling protein-based mol. machines, including icosahedral protein cages that serve as scaffolds, enzymes, and compartments for essential biochem. reactions and icosahedral virus capsids, which encapsidate and protect viral genomes and mediate entry into host cells. Inspired by these natural materials, the authors report the computational design and exptl. characterization of co-assembling, two-component, 120-subunit icosahedral protein nanostructures with mol. wts. (1.8 to 2.8 megadaltons) and dimensions (24 to 40 nm in diam.) comparable to those of small viral capsids. Electron microscopy, small-angle x-ray scattering, and x-ray crystallog. show that 10 designs spanning three distinct icosahedral architectures form materials closely matching the design models. In vitro assembly of icosahedral complexes from independently purified components occurs rapidly, at rates comparable to those of viral capsids, and enables controlled packaging of mol. cargo through charge complementarity. The ability to design megadalton-scale materials with at.-level accuracy and controllable assembly opens the door to a new generation of genetically programmable protein-based mol. machines.
- 58Wei, B.; Dai, M.; Yin, P. Complex Shapes Self-Assembled from Single-Stranded DNA Tiles. Nature 2012, 485, 623– 626, DOI: 10.1038/nature11075Google Scholar58https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XnvVyltb4%253D&md5=9c59d1bb62366c9cbbced30e889ed821Complex shapes self-assembled from single-stranded DNA tilesWei, Bryan; Dai, Mingjie; Yin, PengNature (London, United Kingdom) (2012), 485 (7400), 623-626CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)Programmed self-assembly of strands of nucleic acid has proved highly effective for creating a wide range of structures with desired shapes. A particularly successful implementation is DNA origami, in which a long scaffold strand is folded by hundreds of short auxiliary strands into a complex shape. Modular strategies are in principle simpler and more versatile and have been used to assemble DNA or RNA tiles into periodic and algorithmic two-dimensional lattices, extended ribbons and tubes, three-dimensional crystals, polyhedra and simple finite two-dimensional shapes. But creating finite yet complex shapes from a large no. of uniquely addressable tiles remains challenging. Here we solve this problem with the simplest tile form, a single-stranded tile (SST) that consists of a 42-base strand of DNA composed entirely of concatenated sticky ends and that binds to four local neighbors during self-assembly. Although ribbons and tubes with controlled circumferences have been created using the SST approach, we extend it to assemble complex two-dimensional shapes and tubes from hundreds (in some cases more than one thousand) distinct tiles. Our main design feature is a self-assembled rectangle that serves as a mol. canvas, with each of its constituent SST strands-folded into a 3 nm-by-7 nm tile and attached to four neighboring tiles-acting as a pixel. A desired shape, drawn on the canvas, is then produced by one-pot annealing of all those strands that correspond to pixels covered by the target shape; the remaining strands are excluded. We implement the strategy with a master strand collection that corresponds to a 310-pixel canvas, and then use appropriate strand subsets to construct 107 distinct and complex two-dimensional shapes, thereby establishing SST assembly as a simple, modular and robust framework for constructing nanostructures with prescribed shapes from short synthetic DNA strands.
- 59Ke, Y.; Ong, L. L.; Shih, W. M.; Yin, P. Three-Dimensional Structures Self-Assembled from DNA Bricks. Science 2012, 338, 1177– 1183, DOI: 10.1126/science.1227268Google Scholar59https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xhslans7bP&md5=bb760600ffabe6af4759019dbd22226fThree-Dimensional Structures Self-Assembled from DNA BricksKe, Yonggang; Ong, Luvena L.; Shih, William M.; Yin, PengScience (Washington, DC, United States) (2012), 338 (6111), 1177-1183CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)We describe a simple and robust method to construct complex three-dimensional (3D) structures by using short synthetic DNA strands that we call "DNA bricks". In one-step annealing reactions, bricks with hundreds of distinct sequences self-assemble into prescribed 3D shapes. Each 32-nucleotide brick is a modular component; it binds to four local neighbors and can be removed or added independently. Each 8-base pair interaction between bricks defines a voxel with dimensions of 2.5 by 2.5 by 2.7 nm, and a master brick collection defines a "mol. canvas" with dimensions of 10 by 10 by 10 voxels. By selecting subsets of bricks from this canvas, we constructed a panel of 102 distinct shapes exhibiting sophisticated surface features, as well as intricate interior cavities and tunnels.
- 60Rothemund, P. W. K. Folding DNA to Create Nanoscale Shapes and Patterns. Nature 2006, 440, 297– 302, DOI: 10.1038/nature04586Google Scholar60https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XitlKgu7g%253D&md5=583caefdda9b1deb5d3f2ef78d9e6ecbFolding DNA to create nanoscale shapes and patternsRothemund, Paul W. K.Nature (London, United Kingdom) (2006), 440 (7082), 297-302CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)'Bottom-up fabrication', which exploits the intrinsic properties of atoms and mols. to direct their self-organization, is widely used to make relatively simple nanostructures. A key goal for this approach is to create nanostructures of high complexity, matching that routinely achieved by 'top-down' methods. The self-assembly of DNA mols. provides an attractive route towards this goal. Here the author describe a simple method for folding long, single-stranded DNA mols. into arbitrary two-dimensional shapes. The design for a desired shape is made by raster-filling the shape with a 7-kilobase single-stranded scaffold and by choosing over 200 short oligonucleotide 'staple strands' to hold the scaffold in place. Once synthesized and mixed, the staple and scaffold strands self-assemble in a single step. The resulting DNA structures are roughly 100 nm in diam. and approx. desired shapes such as squares, disks and five-pointed stars with a spatial resoln. of 6 nm. Because each oligonucleotide can serve as a 6-nm pixel, the structures can be programmed to bear complex patterns such as words and images on their surfaces. Finally, individual DNA structures can be programmed to form larger assemblies, including extended periodic lattices and a hexamer of triangles (which constitutes a 30-megadalton mol. complex).
- 61Seeman, N. C. DNA in a Material World. Nature 2003, 421, 427– 431, DOI: 10.1038/nature01406Google Scholar61https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXisFGqtLk%253D&md5=a8e40994e5ea08a665aab18697196e62DNA in a material worldSeeman, Nadrian C.Nature (London, United Kingdom) (2003), 421 (6921, Suppl.), 427-431CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)The specific bonding of DNA base pairs provides the chem. foundation for genetics. This powerful mol. recognition system can be used in nanotechnol. to direct the assembly of highly structured materials with specific nanoscale features, as well as in DNA computation to process complex information. The exploitation of DNA for material purposes presents a new chapter in the history of the mol.
- 62Seifert, J. L.; Connor, R. E.; Kushon, S. A.; Wang, M.; Armitage, B. A. Spontaneous Assembly of Helical Cyanine Dye Aggregates on DNA Nanotemplates. J. Am. Chem. Soc. 1999, 121, 2987– 2995, DOI: 10.1021/ja984279jGoogle Scholar62https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1MXhvV2qtbc%253D&md5=ac33b8b50aa9ce58894e6f3f96db44e7Spontaneous Assembly of Helical Cyanine Dye Aggregates on DNA NanotemplatesSeifert, Jennifer L.; Connor, Rebecca E.; Kushon, Stuart A.; Wang, Miaomiao; Armitage, Bruce A.Journal of the American Chemical Society (1999), 121 (13), 2987-2995CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)3,3'-Diethylthiadicarbocyanine (DiSC2(5)) is a sym. cationic cyanine dye consisting of two N-ethylated benzothiazole groups linked by a pentamethine bridge. Spectroscopic anal. indicates dimerization of the dye in the presence of duplex DNA sequences consisting of alternating adenine/thymine (A/T) or inosine/cytosine (I/C) residues, based on the following observations: (i) the absorption max. shifts from 647 to 590 nm, (ii) exciton splitting is obsd. in the induced CD spectrum, and (iii) fluorescence from the dye is strongly quenched. Dimerization on I/C, but not G/C sequences indicates that the cyanine dimers insert into the minor groove, a conclusion that is supported by viscometric anal. Spectroscopic studies with short synthetic oligonucleotide duplexes demonstrate that dimerization is highly cooperative: binding of one dimer greatly facilitates binding of a second dimer. For longer binding sites, this cooperativity leads to the formation of extended helical cyanine dye aggregates consisting of dimers aligned in an end-to-end fashion within the minor groove of the DNA. The DNA structure strictly controls the dimensions of the aggregate, permitting distinction between inter- and intradimer interactions.
- 63Smith, J. O.; Olson, D. A.; Armitage, B. A. Molecular Recognition of PNA-Containing Hybrids: Spontaneous Assembly of Helical Cyanine Dye Aggregates on PNA Templates. J. Am. Chem. Soc. 1999, 121, 2686– 2695, DOI: 10.1021/ja9837553Google Scholar63https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1MXhslektrc%253D&md5=9d19337b31d6231a905a1f864bdc633dMolecular Recognition of PNA-Containing Hybrids: Spontaneous Assembly of Helical Cyanine Dye Aggregates on PNA TemplatesSmith, Jeffrey O.; Olson, Darren A.; Armitage, Bruce A.Journal of the American Chemical Society (1999), 121 (12), 2686-2695CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Sym. cyanine dyes contg. benzothiazole groups have been shown to bind with high affinity to a variety of PNA-contg. hybrids, including PNA/DNA duplexes, a PNA/PNA duplex, and a bisPNA/DNA triplex. Binding of a dicarbocyanine dye results in a 114 nm hypsochromic shift of the main visible absorption band. CD spectropolarimetry reveals exciton coupling between multiple chromophores bound to the same PNA/DNA or PNA/PNA duplex, demonstrating binding of the dye as an aggregate. A continuous variations expt. indicates that the dye binds as a 6(±1):1 complex with a 12 base pair PNA/DNA duplex. The dye aggregate forms in a highly cooperative manner and exhibits a temp.-dependent self-assembly behavior which is independent of the PNA/DNA hybridization event. Expts. with mismatched and parallel duplexes demonstrate a strong preference for a continuous, antiparallel helix as a template on which to assemble the helical dye aggregate. Successful binding of the dye to the duplex and triplex indicates that dyes assoc. with one another in the minor groove of the template. The 114 nm shift in absorption causes an instantaneous visible color change from blue to purple, providing a convenient method for detecting PNA hybridization with its complementary target sequence.
- 64Wang, M. M.; Silva, G. L.; Armitage, B. A. DNA-Templated Formation of a Helical Cyanine Dye J-Aggregate. J. Am. Chem. Soc. 2000, 122, 9977– 9986, DOI: 10.1021/ja002184nGoogle Scholar64https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXmsl2jtrk%253D&md5=e2fd6590d3cdebe8008455435bd756b9DNA-Templated Formation of a Helical Cyanine Dye J-AggregateWang, Miaomiao; Silva, Gloria L.; Armitage, Bruce A.Journal of the American Chemical Society (2000), 122 (41), 9977-9986CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)UV-vis and CD spectroscopy reveal that a tri-cationic cyanine dye spontaneously assembles into a helical J-aggregate in the presence of a double-helical DNA template. The stability of the J-aggregate is strongly dependent on the dye concn. and DNA length in a manner that reflects a high degree of cooperativity in formation of the aggregate. Slight changes in environmental conditions such as temp. and ionic strength result in interconversion between J- and H-aggregates. The aggregate likely consists of dimeric units assembled in an offset, face-to-face orientation within the minor groove of the DNA template, analogous to an earlier report of H-aggregation on DNA by a related cyanine dye. A model is proposed that relates the two aggregate structures by translation of one monomer from a given dimer along the floor of the minor groove. This translation requires adjacent monomers to also translate, leading to the obsd. cooperativity.
- 65Chowdhury, A.; Wachsmann-Hogiu, S.; Bangal, P. R.; Raheem, I.; Peteanu, L. A. Characterization of Chiral H and J Aggregates of Cyanine Dyes Formed by DNA Templating Using Stark and Fluorescence Spectroscopies. J. Phys. Chem. B 2001, 105, 12196– 12201, DOI: 10.1021/jp012825gGoogle Scholar65https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3MXnslaqsLw%253D&md5=4b1ece4397b0e87c5b10ee7af6ce24c2Characterization of Chiral H and J Aggregates of Cyanine Dyes Formed by DNA Templating Using Stark and Fluorescence SpectroscopiesChowdhury, Arindam; Wachsmann-Hogiu, Sebastian; Bangal, Prakriti R.; Raheem, Izzat; Peteanu, Linda A.Journal of Physical Chemistry B (2001), 105 (48), 12196-12201CODEN: JPCBFK; ISSN:1089-5647. (American Chemical Society)A series of studies is presented to characterize the photophys. properties of a novel type of aggregate formed by the spontaneous noncovalent assembly of numerous cofacial dimers of cyanine dyes (DiSC3+(5)) to the minor groove of poly(dI-dC) DNA. The dimensions of these helical aggregates, first synthesized and characterized by Armitage and co-workers (J. Am. Chem. Soc. 2000, 122, 9977-9986), are restricted to the width of the dye dimer because of steric constraints in the minor groove, though the length of the aggregate can extend essentially for the full length of the DNA template. These unique species exhibit both H- and J-type absorption bands that are shifted from the absorption max. of the monomeric dye by +1650 and -1275 cm-1, resp., because of the stacking interactions between the dyes composing the dimers. Addnl. splittings are seen because of head-to-head interactions between adjacent dye dimers. Here, we present the low-temp. (77 K) absorption, fluorescence, and electroabsorption spectra of these aggregates as well as measurements of the fluorescence lifetime of the monomer and of the J-type emission at 10°. The electroabsorption measurements yield values of the av. difference polarizability on excitation, 〈Δα〉, for the H and J bands of -74 and -34 Å3, resp. These are between 2 and 6 times larger than that of the monomer. Both bands exhibit similar values for the difference dipole moment on excitation |.vector.Δμ| of between 0.6 and 0.7 D that are somewhat smaller than that of the monomer (1.1 D). The absorption and fluorescence expts. show that the line width of the J band is ∼4 times narrower than the exptl. fwhm of the DiSC3+(5) monomer while the fluorescence decay of the aggregate is roughly a factor of 2 faster. Implications of all of these measurements for detg. the no. of dyes that are excited cooperatively upon light absorption are discussed.
- 66Garoff, R. A.; Litzinger, E. A.; Connor, R. E.; Fishman, I.; Armitage, B. A. Helical Aggregation of Cyanine Dyes on DNA Templates: Effect of Dye Structure on Formation of Homo- and Heteroaggregates. Langmuir 2002, 18, 6330– 6337, DOI: 10.1021/la025742fGoogle Scholar66https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38Xkt12ktL0%253D&md5=cbea8e8f28c50beaab8edebe57226c87Helical Aggregation of Cyanine Dyes on DNA Templates: Effect of Dye Structure on Formation of Homo- and HeteroaggregatesGaroff, Rachel A.; Litzinger, Elizabeth A.; Connor, Rebecca E.; Fishman, Irene; Armitage, Bruce A.Langmuir (2002), 18 (16), 6330-6337CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)UV-visible and CD spectroscopic expts. were used to characterize DNA-templated helical aggregates formed from a variety of sym., cationic cyanine dyes. Two types of electronic couplings can be obsd. in these aggregates: face-to-face interactions between dye monomers and end-to-end interactions between dye dimers. The face-to-face interactions yield approx. 4-fold stronger couplings due to greater orbital overlap. Variation of the heterocyclic groups on the dye reveals that aggregation on DNA follows the following trend: quinoline > benzothiazole > benzoxazole > dimethylindole. This trend follows the tendency of these dyes to aggregate in aq. soln. Within the benzothiazole class of dyes, a dicarbocyanine dye (pentamethine bridge) aggregates much more readily than the carbocyanine (trimethine bridge) analog. However, a tricarbocyanine dye (heptamethine bridge) aggregates less readily than the dicarbocyanine, in contrast to their relative tendency to aggregate in water. In addn., heteroaggregates in which two different dyes assoc. cofacially on the DNA template can be synthesized.
- 67Chowdhury, A.; Yu, L. P.; Raheem, I.; Peteanu, L.; Liu, L. A.; Yaron, D. J. Stark Spectroscopy of Size-Selected Helical H-Aggregates of a Cyanine Dye Templated by Duplex DNA. Effect of Exciton Coupling on Electronic Polarizabilities. J. Phys. Chem. A 2003, 107, 3351– 3362, DOI: 10.1021/jp021866pGoogle Scholar67https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXjs1Wjsr4%253D&md5=a46e6448fa72931769d34008571eab00Stark Spectroscopy of Size-Selected Helical H-Aggregates of a Cyanine Dye Templated by Duplex DNA. Effect of Exciton Coupling on Electronic PolarizabilitiesChowdhury, Arindam; Yu, Liping; Raheem, Izzat; Peteanu, Linda; Liu, L. Angela; Yaron, David J.Journal of Physical Chemistry A (2003), 107 (18), 3351-3362CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)Stark spectroscopy (electroabsorption) is used to study the variation of electronic properties with the size of helical H-aggregates that are formed by the spontaneous noncovalent assembly of co-facial dimers of the cyanine dye (DiSC2(5)) into the minor groove of double-helical DNA. The unique and important property of these aggregates, first synthesized and characterized by Armitage and co-workers (J. Am. Chem. Soc. 1999, 121, 2987), is that their size is controlled by the properties of the DNA template. Specifically, the length of the aggregate formed is detd. by the length of the DNA template and its width along the π stacking dimension is restricted to that of the dye dimer due to steric constraints in the minor groove. Results for aggregates consisting of 1, 2, 5, and ∼35 adjacent dimers bound to DNA are presented here. The absorption maxima of these species exhibit a large blue shift (1750 cm-1) from that of the monomer due to the face-to-face interactions within the dimers. Relatively weak (330-650 cm-1) secondary splittings are also seen that arise from end-to-end interactions between adjacent dimers on the chain. The av. change in polarizability on excitation (〈Δα〉) is found to double when two dyes form a stacked dimer whereas no further increase in 〈Δα〉 is seen as the chain length is increased. Semiempirical (INDO-SCI) calcns. yield exciton coupling energies that are consistent with expt. However, 〈Δα〉 is predicted to increase toward more pos. values on dimerization while the reverse trend is seen exptl. Nonetheless, both expt. and theory find that 〈Δα〉 is unaffected by higher aggregation.
- 68Hannah, K. C.; Armitage, B. A. DNA-Templated Assembly of Helical Cyanine Dye Aggregates: A Supramolecular Chain Polymerization. Acc. Chem. Res. 2004, 37, 845– 853, DOI: 10.1021/ar030257cGoogle Scholar68https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXnt12hu7s%253D&md5=e765802296ac18eb6a7b1f8c6c0accdaDNA-Templated Assembly of Helical Cyanine Dye Aggregates: A Supramolecular Chain PolymerizationHannah, Kristen C.; Armitage, Bruce A.Accounts of Chemical Research (2004), 37 (11), 845-853CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)A review. Sym. cationic cyanine dyes assemble in cooperative fashion into helical supramol. polymers using DNA as a template. The dyes assemble into cofacial dimers within the minor groove of the DNA and assembly of one dimer facilitates assembly of addnl. dimers directly adjacent to the first. Growth of the polymer ceases when the end of the DNA is reached or when the DNA sequence blocks dimerization of the dye. Thus, this process can be thought of as a supramol. analog of a chain polymn. This Account describes how polymn. depends on the dye structure and DNA sequence and also summarizes the interesting optical properties exhibited by these chiral, helical materials.
- 69Tomlinson, A.; Frezza, B.; Kofke, M.; Wang, M. M.; Armitage, B. A.; Yaron, D. A Structural Model for Cyanine Dyes Templated into the Minor Groove of DNA. Chem. Phys. 2006, 325, 36– 47, DOI: 10.1016/j.chemphys.2005.10.007Google Scholar69https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28Xltlemtbw%253D&md5=383623147ba79f8da37f99bc3d0dc867A structural model for cyanine dyes templated into the minor groove of DNATomlinson, Aimee; Frezza, Brian; Kofke, Matthew; Wang, Miaomiao; Armitage, Bruce A.; Yaron, DavidChemical Physics (2006), 325 (1), 36-47CODEN: CMPHC2; ISSN:0301-0104. (Elsevier B.V.)3,3-Diethylthiadicarbocyanine (DiSC2(5)) is a monocationic dye which forms cofacial dimers that insert into the minor groove of DNA [J. Seifert, R. Conner, S. Kushon, M. Wang, B. Armitage, J. Am. Chem. Soc. 121 (1999) 2987]. These dyes self-assemble into long helical aggregates in AT-rich regions with the dimers aligned in an end-to-end fashion. A model is presented that allows for the construction of large helical aggregates with continuously variable structural parameters. The spectra or excited states are computed using a direct INDO single CI (SCI) method. Results are reported for both H- and J-type aggregates ranging in size from 2 to 6 dimers. A more approx. model based on transition charge densities enables calcns. of larger aggregates. These models are used to derive structural parameters of both H- and J-type aggregates from the available spectral data, resulting in a new structural model for J-type aggregation in these systems.
- 70Stadler, A. L.; Renikuntla, B. R.; Yaron, D.; Fang, A. S.; Armitage, B. A. Substituent Effects on the Assembly of Helical Cyanine Dye Aggregates in the Minor Groove of a DNA Template. Langmuir 2011, 27, 1472– 1479, DOI: 10.1021/la104329cGoogle Scholar70https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhsF2ms7zM&md5=1757566507c3fba6f583bffffb042ca5Substituent Effects on the Assembly of Helical Cyanine Dye Aggregates in the Minor Groove of a DNA TemplateStadler, Andrea L.; Renikuntla, Babu Rao; Yaron, David; Fang, Adam S.; Armitage, Bruce A.Langmuir (2011), 27 (4), 1472-1479CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)Double-helical DNA was used as a template for the assembly of helical cyanine dye aggregates. The aggregates consist of cofacial dimers aligned end-to-end in the minor groove of the DNA. The effect of methoxy or fluoro substituents placed on the periphery of the cyanine dye heterocycles on aggregation both in water and on the DNA template was studied by UV-vis and CD spectroscopy. Methoxy groups were found to be stronger promoters of aggregation than fluoro, and a dimethoxy dye exhibited a higher propensity to aggregate compared with an unsym. methoxy/fluoro dye. Semiempirical calcns. supported the exptl. observation of methoxy substitution favoring aggregation. These results indicate that dispersion and hydrophobic effects contribute more to dimerization/aggregation than do electron donor-acceptor effects.
- 71Banal, J. L.; Kondo, T.; Veneziano, R.; Bathe, M.; Schlau-Cohen, G. S. Photophysics of J-Aggregate-Mediated Energy Transfer on DNA. J. Phys. Chem. Lett. 2017, 8, 5827– 5833, DOI: 10.1021/acs.jpclett.7b01898Google Scholar71https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhvVSmtLfN&md5=f0f639202fe61210725aaff89ff9080cPhotophysics of J-Aggregate-Mediated Energy Transfer on DNABanal, James L.; Kondo, Toru; Veneziano, Remi; Bathe, Mark; Schlau-Cohen, Gabriela S.Journal of Physical Chemistry Letters (2017), 8 (23), 5827-5833CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)Achieving nanoscale spatial and electronic control over the formation of dye aggregates is a major synthetic challenge due to their typically inhomogeneous self-assembly, which limits control over their higher-order organization. To address these challenges, synthetic DNA-templated pseudoisocyanine (PIC) J-aggregates were recently introduced. However, the dependence of the photophysics of the superradiant exciton on the underlying DNA template length and the impact of static disorder on energy transfer through these PIC J-aggregates remain unknown. Here, we examine the delocalization length progression of superradiant PIC excitons by varying the length of poly-A DNA tracts that templates PIC J-aggregates. We then investigate the energy transfer efficiency from PIC J-aggregates with DNA duplex template length, which we found to be limited by static disorder. Utilizing the self-assembled and selective formation of superradiant excitons on DNA provides a platform to det. the function of delocalized excitons in the context of nanoscale energy transport.
- 72Boulais, É.; Sawaya, N. P. D.; Veneziano, R.; Andreoni, A.; Banal, J. L.; Kondo, T.; Mandal, S.; Lin, S.; Schlau-Cohen, G. S.; Woodbury, N. W. Programmed Coherent Coupling in a Synthetic DNA-Based Excitonic Circuit. Nat. Mater. 2018, 17, 159– 166, DOI: 10.1038/nmat5033Google Scholar72https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhsl2qtrrN&md5=0cc78d472a07d50e26ac243e9ef3c07aProgrammed coherent coupling in a synthetic DNA-based excitonic circuitBoulais, Etienne; Sawaya, Nicolas P. D.; Veneziano, Remi; Andreoni, Alessio; Banal, James L.; Kondo, Toru; Mandal, Sarthak; Lin, Su; Schlau-Cohen, Gabriela S.; Woodbury, Neal W.; Yan, Hao; Aspuru-Guzik, Alan; Bathe, MarkNature Materials (2018), 17 (2), 159-166CODEN: NMAACR; ISSN:1476-1122. (Nature Research)Natural light-harvesting systems spatially organize densely packed chromophore aggregates using rigid protein scaffolds to achieve highly efficient, directed energy transfer. Here, we report a synthetic strategy using rigid DNA scaffolds to similarly program the spatial organization of densely packed, discrete clusters of cyanine dye aggregates with tunable absorption spectra and strongly coupled exciton dynamics present in natural light-harvesting systems. We 1st characterize the range of dye-aggregate sizes that can be templated spatially by A-tracts of B-form DNA while retaining coherent energy transfer. We then use structure-based modeling and quantum dynamics to guide the rational design of higher-order synthetic circuits consisting of multiple discrete dye aggregates within a DX-tile. These programmed circuits exhibit excitonic transport properties with prominent CD, superradiance, and fast delocalized exciton transfer, consistent with our quantum dynamics predictions. This bottom-up strategy offers a versatile approach to the rational design of strongly coupled excitonic circuits using spatially organized dye aggregates for use in coherent nanoscale energy transport, artificial light-harvesting, and nanophotonics.
- 73Nicoli, F.; Roos, M. K.; Hemmig, E. A.; Di Antonio, M.; de Vivie-Riedle, R.; Liedl, T. Proximity-Induced H-Aggregation of Cyanine Dyes on DNA-Duplexes. J. Phys. Chem. A 2016, 120, 9941– 9947, DOI: 10.1021/acs.jpca.6b10939Google Scholar73https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XitVajtrnL&md5=adeda33f095d31ac502a29cfe0ed1fc4Proximity-Induced H-Aggregation of Cyanine Dyes on DNA-DuplexesNicoli, Francesca; Roos, Matthias K.; Hemmig, Elisa A.; Di Antonio, Marco; de Vivie-Riedle, Regina; Liedl, TimJournal of Physical Chemistry A (2016), 120 (50), 9941-9947CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)A wide variety of org. dyes form, under certain conditions, clusters known as J- and H-aggregates. Cyanine dyes are such a class of mols. where the spatial proximity of several dyes leads to overlapping electron orbitals and thus to the creation of a new energy landscape compared to that of the individual units. Here, the authors created artificial H-aggregates of exactly 2 Cy3 dyes by covalently linking them to a DNA mol. with controlled sub-nanometer distances. The absorption spectra of these coupled systems exhibited a blue-shifted peak, whose intensity varied depending on the distance between the dyes and the rigidity of the DNA template. Simulated vibrational resolved spectra, based on MO theory, excellently reproduced the exptl. obsd. features. CD spectroscopy addnl. revealed distinct signals, which indicated a chiral arrangement of the dye mols. Mol. dynamics simulations of a Cy3-Cy3 construct including a 14-base pair DNA sequence verified chiral stacking of the dye mols.
- 74Markova, L. I.; Malinovskii, V. L.; Patsenker, L. D.; Häner, R. J- Vs. H-Type Assembly: Pentamethine Cyanine (Cy5) as a near-IR Chiroptical Reporter. Chem. Commun. 2013, 49, 5298– 5300, DOI: 10.1039/c3cc42103aGoogle Scholar74https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXns1ags7w%253D&md5=1deebeaee79fddc66a914704c4cda2d5J- vs. H-type assembly: pentamethine cyanine (Cy5) as a near-IR chiroptical reporterMarkova, Larysa I.; Malinovskii, Vladimir L.; Patsenker, Leonid D.; Haener, RobertChemical Communications (Cambridge, United Kingdom) (2013), 49 (46), 5298-5300CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)The DNA-enabled dimerization of pentamethine cyanine (Cy5) dyes was studied by optical methods. The value of cyanine as a chiroptical reporter using a monomer-to-dimer switch is demonstrated. The specific shape of the CD signal and its high intensity are a result of J-type assembly.
- 75Probst, M.; Langenegger, S. M.; Häner, R. A Modular LHC Built on the DNA Three-Way Junction. Chem. Commun. 2014, 50, 159– 161, DOI: 10.1039/C3CC47490AGoogle Scholar75https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvVKjtLjF&md5=e7b616c5bbd54019a2f7d679c95b0faeA modular LHC built on the DNA three-way junctionProbst, Markus; Langenegger, Simon M.; Haener, RobertChemical Communications (Cambridge, United Kingdom) (2014), 50 (2), 159-161CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)A light-harvesting complex composed of a π-stacked multichromophoric array in a DNA three-way junction is described. The modular design allows for a ready exchange of non-covalently attached energy acceptors.
- 76Markova, L. I.; Malinovskii, V. L.; Patsenker, L. D.; Häner, R. Synthesis and Properties of Squaraine-Modified DNA. Org. Biomol. Chem. 2012, 10, 8944– 8947, DOI: 10.1039/c2ob26787jGoogle Scholar76https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhsF2qtLrO&md5=8732fa38727e27d7ae3c903140475f37Synthesis and properties of squaraine-modified DNAMarkova, Larysa I.; Malinovskii, Vladimir L.; Patsenker, Leonid D.; Haener, RobertOrganic & Biomolecular Chemistry (2012), 10 (45), 8944-8947CODEN: OBCRAK; ISSN:1477-0520. (Royal Society of Chemistry)The incorporation of squaraines into DNA via the phosphoramidite approach is described. High molar absorptivity, environment-sensitive fluorescence properties and intense CD effects render squaraines valuable building blocks for DNA-based optical probes and nanostructures.
- 77Malinovskii, V. L.; Wenger, D.; Häner, R. Nucleic Acid-Guided Assembly of Aromatic Chromophores. Chem. Soc. Rev. 2010, 39, 410– 422, DOI: 10.1039/B910030JGoogle Scholar77https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXht1Wltbk%253D&md5=08466f4cf2fe78034fa5d557f165b162Nucleic acid-guided assembly of aromatic chromophoresMalinovskii, Vladimir L.; Wenger, Daniel; Haner, RobertChemical Society Reviews (2010), 39 (2), 410-422CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)A review. The rational formation of arom. chromophore arrays is an intriguing challenge since ordered collectives of chromophores possess properties that are largely different from those of the individual mols. Therefore, nucleic acids are increasingly used as scaffolds for the construction of multi-chromophore arrays. This tutorial review provides an introduction to the field of nucleic acid-guided chromophore assemblies for non-specialists and a ref. point for those familiar with the area by highlighting the recent developments and describing some of the spectroscopic methods used for the study of oligonucleotide-chromophore conjugates.
- 78Li, S.; Langenegger, S. M.; Häner, R. Control of Aggregation-Induced Emission by DNA Hybridization. Chem. Commun. 2013, 49, 5835– 5837, DOI: 10.1039/c3cc42706dGoogle Scholar78https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXovFWmsb8%253D&md5=7a887296c7703b48626e68e4159eb9deControl of aggregation-induced emission by DNA hybridizationLi, Shaoguang; Langenegger, Simon M.; Haener, RobertChemical Communications (Cambridge, United Kingdom) (2013), 49 (52), 5835-5837CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)Aggregation-induced emission (AIE) was studied by hybridization of dialkynyl-tetraphenylethylene (DATPE) modified DNA strands. Mol. aggregation and fluorescence of DATPEs are controlled by duplex formation.
- 79Häner, R.; Samain, F.; Malinovskii, V. L. DNA-Assisted Self-Assembly of Pyrene Foldamers. Chem. - Eur. J. 2009, 15, 5701– 5708, DOI: 10.1002/chem.200900369Google Scholar79https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXms1ekt7Y%253D&md5=8f2f19743d8c01098697b301b2b1f9f9DNA-Assisted Self-Assembly of Pyrene FoldamersHaner, Robert; Samain, Florent; Malinovskii, Vladimir L.Chemistry - A European Journal (2009), 15 (23), 5701-5708, S5701/1-S5701/8CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)Folding in the tides: Upon hybridization, pyrene mols. assemble through interstrand stacking interactions to form double-stranded, helical structures. Structural organization of the pyrene mols. is an intrinsic property of the oligoaryl part and takes place independently of the sequence of the attached DNA. Pyrene helicity is most pronounced in a bi-segmental chimera, in which a DNA stem is present only at one end of the pyrene section. The self-organization of oligopyrene foldamers is described. Bi- and tri-segmental oligomers composed of nucleotides and non-nucleosidic, achiral pyrene monomers form double-stranded helical structures, as shown by absorbance, fluorescence, and CD spectroscopy. The mixed nature of alternating arom. and phosphate groups ensures water soly. which, in turn, favors folding of the arom. units. Pyrene mols. also assemble though interstrand stacking interactions. Structural organization of the pyrene units is an intrinsic property of the oligoaryl part and takes place independently from the sequence of the attached DNA. Chirality transfer from DNA to the pyrene segment leads to formation of a double helix, in which neighboring pyrene units are, in the present case, twisted in a right-handed manner. Pyrene helicity is most pronounced in a bi-segmental chimera, in which a DNA stem is present only at one end of the pyrene section.
- 80Garo, F.; Häner, R. A DNA-Based Light-Harvesting Antenna. Angew. Chem., Int. Ed. 2012, 51, 916– 919, DOI: 10.1002/anie.201103295Google Scholar80https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhsF2ksr%252FL&md5=a19402b55d0c8841a7bcdb7296022e66A DNA-Based Light-Harvesting AntennaGaro, Florian; Haener, RobertAngewandte Chemie, International Edition (2012), 51 (4), 916-919, S916/1-S916/23CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)A DNA-based light-harvesting antenna consists of an array of π-stacked phenanthrene chromophores (light collecting antenna), and an exciplex forming pyrene (the energy collection center), and a DNA double helix (the supramol. scaffold). Up to 8 phenantherens were used for light collection. The no. of photons emitted by the phenanthrene-pyrene exciplex is proportional to to the no. of light absorbing chromophores.
- 81Adeyemi, O. O.; Malinovskii, V. L.; Biner, S. M.; Calzaferri, G.; Häner, R. Photon Harvesting by Excimer-Forming Multichromophores. Chem. Commun. 2012, 48, 9589– 9591, DOI: 10.1039/c2cc34183bGoogle Scholar81https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xht12qsrjN&md5=9ad61ebfb509cb71b74ed02b84b60198Photon harvesting by excimer-forming multichromophoresAdeyemi, Oliver O.; Malinovskii, Vladimir L.; Biner, Sarah M.; Calzaferri, Gion; Haener, RobertChemical Communications (Cambridge, United Kingdom) (2012), 48 (77), 9589-9591CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)A light-harvesting system based on a DNA-organized oligopyrene-cyanine complex is described. Energy transfer from the pyrene units to the cyanine dye was found to proceed via FRET from locally confined excimers to the acceptor.
- 82Asanuma, H.; Fujii, T.; Kato, T.; Kashida, H. Coherent Interactions of Dyes Assembled on DNA. J. Photochem. Photobiol., C 2012, 13, 124– 135, DOI: 10.1016/j.jphotochemrev.2012.04.002Google Scholar82https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XntVWhtbk%253D&md5=a6cea5584e14c9a209e452cc91db26a2Coherent interactions of dyes assembled on DNAAsanuma, Hiroyuki; Fujii, Taiga; Kato, Tomohiro; Kashida, HiromuJournal of Photochemistry and Photobiology, C: Photochemistry Reviews (2012), 13 (2), 124-135CODEN: JPPCAF; ISSN:1389-5567. (Elsevier B.V.)A review. The optical behavior of an organized dye assembly is different from that of the isolated dye; this difference is explained using mol. exciton theory. The theory predicts that mutual orientation, the no. of dyes in the cluster, and combinations of different dyes should display given characteristic spectroscopic behaviors due to coherent interactions. Comparison of theor. predictions with exptl. results has been limited so far. One of the reasons is the absence of a rigid and well-organized system that can control the orientation and size of the dye assembly. Recently, the DNA duplex has been used to assemble chromophores in a programmed manner. Use of DNA allows organized dye assembly with a given size and particular orientation. In this review, we evaluate the spectroscopic behavior of the H-type aggregate based on mol. exciton theory and compare it with actual dye assembly with DNA duplex. Furthermore, we demonstrate the importance of coherent interactions on the obsd. optical properties of dyes assembled in a DNA duplex.
- 83Kashida, H.; Asanuma, H. Preparation of Supramolecular Chromophoric Assemblies Using a DNA Duplex. Phys. Chem. Chem. Phys. 2012, 14, 7196– 7204, DOI: 10.1039/c2cp40520bGoogle Scholar83https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XmtlGjur4%253D&md5=e2b7b27633b41e6894fa6348f8a7e4f2Preparation of supramolecular chromophoric assemblies using a DNA duplexKashida, Hiromu; Asanuma, HiroyukiPhysical Chemistry Chemical Physics (2012), 14 (20), 7196-7204CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)A review with refs. and new materials are presented . Organization of supramol. assemblies of chromophores with precisely-controlled orientation and sequence remains challenging. Nucleic acids with complementary base sequences spontaneously form double-helical structures. Therefore, covalent attachment of chromophores to DNA or RNA can be used to control assembly and orientation of chromophores. In this perspective, we first review our recent work on the assemblies of fluorophores (pyrene and perylene) by using natural base pairs. The interaction between dyes can be strictly controlled by means of cluster and interstrand wedge motifs. We then discuss novel artificial base pairs that can suppress the interaction between fluorophores and nucleobases. We incorporated a cyclohexane moiety into DNA, and showed that these artificial base pairs suppressed the electron-hole transfer between fluorophores and nucleobases and enhanced the quantum yields of fluorophores. These base pairs can potentially be used to accumulate fluorophores inside DNA duplexes without decreasing quantum yields.
- 84Cunningham, P. D.; Kim, Y. C.; Diaz, S. A.; Buckhout-White, S.; Mathur, D.; Medintz, I. L.; Melinger, J. S. Optical Properties of Vibronically Coupled Cy3 Dimers on DNA Scaffolds. J. Phys. Chem. B 2018, 122, 5020– 5029, DOI: 10.1021/acs.jpcb.8b02134Google Scholar84https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXosVelsLk%253D&md5=9184938ca1825373bfa592846d1f534cOptical Properties of Vibronically Coupled Cy3 Dimers on DNA ScaffoldsCunningham, Paul D.; Kim, Young C.; Diaz, Sebastian A.; Buckhout-White, Susan; Mathur, Divita; Medintz, Igor L.; Melinger, Joseph S.Journal of Physical Chemistry B (2018), 122 (19), 5020-5029CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)The effect of electronic coupling on the optical properties of Cy3 dimers attached to DNA duplexes was examine as a function of base pair (bp) sepn. using steady-state and time-resolved spectroscopy. For close Cy3-Cy3 sepns., 0 and 1 bp between dyes, intermediate to strong electronic coupling is revealed by modulation of the absorption and fluorescence properties including spectral band shape, peak wavelength, and excited-state lifetime. Using a vibronic exciton model, the authors est. coupling strengths of 150 and 266 cm-1 for the 1 and 0 bp sepns., resp., which are comparable to those found in natural light-harvesting complexes. For the strongest electronic coupling (0 bp sepn.), the absorption band shape is strongly affected by the base pairs that surround the dyes, where more strongly H-bonded G-C pairs produce a red shifted absorption spectrum consistent with a J-type dimer. This effect is studied theor. using mol. dynamics simulation, which predicts an in-line dye configuration that is consistent with the exptl. J-type spectrum. When the Cy3 dimers are in a std. aq. buffer, the presence of relatively strong electronic coupling is accompanied by decreased fluorescence lifetime, suggesting that it promotes nonradiative relaxation in cyanine dyes. The use of a viscous solvent can suppress this nonradiative recombination and restore the dimer fluorescent emission. Ultrafast transient absorption measurements of Cy3 dimers in both std. aq. buffer and viscous glycerol buffer suggest that sufficiently strong electronic coupling increases the probability of excited-state relaxation through a dark state that is related to Cy3 torsional motion.
- 85Mazuski, R. J.; Díaz, S. A.; Wood, R. E.; Lloyd, L. T.; Klein, W. P.; Mathur, D.; Melinger, J. S.; Engel, G. S.; Medintz, I. L. Ultrafast Excitation Transfer in Cy5 DNA Photonic Wires Displays Dye Conjugation and Excitation Energy Dependency. J. Phys. Chem. Lett. 2020, 4163– 4172, DOI: 10.1021/acs.jpclett.0c01020Google Scholar85https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXovVGltLY%253D&md5=72480da3ab7165fe5a6e5566d4c2f798Ultrafast Excitation Transfer in Cy5 DNA Photonic Wires Displays Dye Conjugation and Excitation Energy DependencyMazuski, Richard J.; Diaz, Sebastian A.; Wood, Ryan E.; Lloyd, Lawson T.; Klein, William P.; Mathur, Divita; Melinger, Joseph S.; Engel, Gregory S.; Medintz, Igor L.Journal of Physical Chemistry Letters (2020), 11 (10), 4163-4172CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)DNA scaffolds enable base-pair-specific positioning of fluorescent mols., allowing for nanometer-scale precision in controlling multidye interactions. Expanding on this concept, DNA-based mol. photonic wires (MPWs) allow for light harvesting and directional propagation of photonic energy on the nanometer scale. The most common MPW examples exploit Forster resonance energy transfer (FRET), and FRET between the same dye species (HomoFRET) was recently shown to increase the distance and efficiency at which MPWs can function. Although increased proximity between adjacent fluorophores can be used to increase the energy transfer efficiency, FRET assumptions break down as the distance between the dye mols. becomes comparable to their size (~ 2 nm). Here the authors compare dye conjugation with single vs. dimer Cy5 dye repeats as HomoFRET MPW components on a double-crossover DNA scaffold. At room temp. (RT) under low-light conditions, end-labeled uncoupled dye mols. provide optimal transfer, while the Cy5 dimers show ultrafast (<100 ps) nonradiative decay that severely limits their functionality. Of particular interest is the observation that through increased excitation fluence as well as cryogenic temps., the dimeric MPW shows suppression of the ultrafast decay, demonstrating fluorescence lifetimes similar to the single Cy5 MPWs. This work points to the complex dynamic capabilities of dye-based nanophotonic networks, where dye positioning and interactions can become crit., and could be used to extend the lengths and complexities of such dye-DNA devices, enabling multiparameter nanophotonic circuitry.
- 86Asanuma, H.; Shirasuka, K.; Takarada, T.; Kashida, H.; Komiyama, M. DNA-Dye Conjugates for Controllable H Aggregation(1). J. Am. Chem. Soc. 2003, 125, 2217– 2223, DOI: 10.1021/ja021153kGoogle Scholar86https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXovFyksg%253D%253D&md5=b246e2945f9373813aaa52558532a241DNA-Dye Conjugates for Controllable H* AggregationAsanuma, Hiroyuki; Shirasuka, Kenji; Takarada, Tohru; Kashida, Hiromu; Komiyama, MakotoJournal of the American Chemical Society (2003), 125 (8), 2217-2223CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Methyl red H* aggregate of predetd. size is successfully synthesized from the DNA conjugate involving multiple Methyl red moieties in sequence. In the single stranded state, hypsochromicity monotonically increases with the no. of incorporated dyes: the peak max. of the conjugate involving six Me Reds appears at 415 nm, and the shift is as great as 69 nm (3435 cm-1) with respect to the monomeric transition. This large hypsochromicity accompanied by the narrowing of the band clearly demonstrates that H* aggregate is formed in the single strand. H* aggregation is further promoted at higher ionic strength. Upon addn. of complementary DNA below the Tm, however, this H* band disappears and a new peak appears at 448 nm, indicating that aggregated structure is changed by the duplex formation. This spectral change is completely reversible so that the H* band at 415 nm appears again above Tm. Thus, aggregated structure can be reversibly controlled by the formation and dissocn. of the DNA duplex.
- 87Kashida, H.; Asanuma, H.; Komiyama, M. Alternating Hetero H Aggregation of Different Dyes by Interstrand Stacking from Two DNA-Dye Conjugates. Angew. Chem., Int. Ed. 2004, 43, 6522– 6525, DOI: 10.1002/anie.200460870Google Scholar87https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXhtFajsbzJ&md5=b19b4a369ce2680d59da4518cf52933cAlternating hetero H aggregation of different dyes by interstrand stacking from two DNA-dye conjugatesKashida, Hiromu; Asanuma, Hiroyuki; Komiyama, MakotoAngewandte Chemie, International Edition (2004), 43 (47), 6522-6525CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)Seeing red: Aggregates in which methyl red and naphthyl red moieties are stacked alternately in a DNA duplex have been prepd. by hybridization of two DNA-dye conjugates. A sharp absorption band appears at 478 nm, which is different from that of the individual dyes. A strong CD effect is also induced by the interstrand heterostacking of the dyes.
- 88Kashida, H.; Tanaka, M.; Baba, S.; Sakamoto, T.; Kawai, G.; Asanuma, H.; Komiyama, M. Covalent Incorporation of Methyl Red Dyes into Double-Stranded DNA for Their Ordered Clustering. Chem. - Eur. J. 2006, 12, 777– 784, DOI: 10.1002/chem.200500111Google Scholar88https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XosFWjsg%253D%253D&md5=c8ba061f33fcadb8642675e33f15ef9aCovalent incorporation of Methyl Red dyes into double-stranded DNA for their ordered clusteringKashida, Hiromu; Tanaka, Masayuki; Baba, Seiki; Sakamoto, Taiichi; Kawai, Gota; Asanuma, Hiroyuki; Komiyama, MakotoChemistry - A European Journal (2006), 12 (3), 777-784CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)An ordered dye cluster of Me Reds was formed in double-stranded DNA by hybridizing two cDNA-dye conjugates, each involving a Methyl red moiety on a threoninol linker and a 1,3-propanediol spacer arranged alternately in the middle of the DNA sequence. In the duplex, Me Reds from each strand were axially stacked antiparallel to each other, as detd. from NMR anal. This clustering of Me Reds induced distinct changes in both UV/Vis and CD spectra. Single-stranded DNA-Methyl red conjugates on D-threoninol linkers and (1,3-propanediol) spacers exhibited broad absorption spectra with λmax at around 480 nm, and almost no CD was obsd. at around the absorption max. of Methyl red. However, as Me Reds were clustered by hybridization, λmax shifted towards shorter wavelengths with respect to its monomeric transition. This hypsochromic shift increased as the no. of Methyl red mols. increased. Furthermore, a pos. couplet was also strongly induced here. These dye clusters are H-aggregates, in which mol. excitons are coupled. The pos. couplet demonstrates that the clusters on D-threoninol form a right-handed helix. In contrast, the induced CD became much weaker with Methyl red on L-threoninol, which intrinsically prefers counterclockwise winding. Thus, mutual orientation of the stacked dye mols. was controlled by the chirality of the linker.
- 89Ikeda, S.; Okamoto, A. Hybridization-Sensitive On-Off DNA Probe: Application of the Exciton Coupling Effect to Effective Fluorescence Quenching. Chem. - Asian J. 2008, 3, 958– 968, DOI: 10.1002/asia.200800014Google Scholar89https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXnsVGlsb4%253D&md5=a29d7fd5191e896eef42c9ced9c6cc35Hybridization-sensitive on-off DNA probe: application of the exciton coupling effect to effective fluorescence quenchingIkeda, Shuji; Okamoto, AkimitsuChemistry - An Asian Journal (2008), 3 (6), 958-968CODEN: CAAJBI; ISSN:1861-4728. (Wiley-VCH Verlag GmbH & Co. KGaA)The design of dyes that emit fluorescence only when they recognize the target mol., i.e., chem. for the effective quenching of free dyes, must play a significant role in the development of the next generation of functional fluorescent dyes. On the basis of this concept, we designed a doubly fluorescence-labeled nucleoside. Two thiazole orange dyes were covalently linked to a single nucleotide in a DNA probe. An absorption band at approx. 480 nm appeared strongly when the probe was in a single-stranded state, whereas an absorption band at approx. 510 nm became predominant when the probe was hybridized with the complementary strand. The shift in the absorption bands shows the existence of an excitonic interaction caused by the formation of an H aggregate between dyes, and as a result, emission from the probe before hybridization was suppressed. Dissocn. of aggregates by hybridization with the complementary strand resulted in the disruption of the excitonic interaction and strong emission from the hybrid. This clear change in fluorescence intensity that is dependent on hybridization is useful for visible gene anal.
- 90Fujii, T.; Kashida, H.; Asanuma, H. Analysis of Coherent Heteroclustering of Different Dyes by Use of Threoninol Nucleotides for Comparison with the Molecular Exciton Theory. Chem. - Eur. J. 2009, 15, 10092– 10102, DOI: 10.1002/chem.200900962Google Scholar90https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXht1amtrbO&md5=e6fc3d38bd14395a53a165b7db13b435Analysis of Coherent Heteroclustering of Different Dyes by Use of Threoninol Nucleotides for Comparison with the Molecular Exciton TheoryFujii, Taiga; Kashida, Hiromu; Asanuma, HiroyukiChemistry - A European Journal (2009), 15 (39), 10092-10102, S10092/1-S10092/12CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)To test the mol. exciton theory for heterodimeric chromophores, various heterodimers and clusters, in which two different dyes were stacked alternately, were prepd. by hybridizing two oligodeoxyribonucleotides (ODNs), each of which tethered a different dye on D-threoninol at the center of the strand. NMR analyses revealed that two different dyes from each strand were stacked antiparallel to each other in the duplex, and were located adjacent to the 5'-side of a natural nucleobase. The spectroscopic behavior of these heterodimers was systematically examd. as a function of the difference in the wavelength of the dye absorption maxima (Δλmax). We found that the absorption spectrum of the heterodimer was significantly different from that of the simple sum of each monomeric dye in the single strand. When azobenzene and Methyl red, which have λmax at 336 and 480 nm, resp., in the single strand (Δλmax=144 nm), were assembled on ODNs, the band derived from azobenzene exhibited a small hyperchromism, whereas the band from Methyl red showed hypochromism and both bands shifted to a longer wavelength (bathochromism). These hyper- and hypochromisms were further enhanced in a heterodimer derived from 4'-methylthioazobenzene and Methyl red, which had a much smaller Δλmax (82 nm; λmax=398 and 480 nm in the single-strand, resp.). With a combination of 4'-dimethylamino-2-nitroazobenzene and Methyl red, which had an even smaller Δλmax (33 nm), a single sharp absorption band that was apparently different from the sum of the single-stranded spectra was obsd. These changes in the intensity of the absorption band could be explained by the mol. exciton theory, which has been mainly applied to the spectral behavior of H- and/or J-aggregates composed of homo dyes. However, the bathochromic band shifts obsd. at shorter wavelengths did not agree with the hypsochromism predicted by the theory. Thus, these data exptl. verify the mol. exciton theory of heterodimerization. This coherent coupling among the heterodimers could also partly explain the bathochromicity and hypochromicity that were obsd. when the dyes were intercalated into the duplex.
- 91Hara, Y.; Fujii, T.; Kashida, H.; Sekiguchi, K.; Liang, X.; Niwa, K.; Takase, T.; Yoshida, Y.; Asanuma, H. Coherent Quenching of a Fluorophore for the Design of a Highly Sensitive in-Stem Molecular Beacon. Angew. Chem., Int. Ed. 2010, 49, 5502– 5506, DOI: 10.1002/anie.201001459Google Scholar91https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXps1Chtrk%253D&md5=e06d2a7a33ec1412da37721fac0729f7Coherent Quenching of a Fluorophore for the Design of a Highly Sensitive In-Stem Molecular BeaconHara, Yuichi; Fujii, Taiga; Kashida, Hiromu; Sekiguchi, Koji; Liang, Xingguo; Niwa, Kosuke; Takase, Tomokazu; Yoshida, Yasuko; Asanuma, HiroyukiAngewandte Chemie, International Edition (2010), 49 (32), 5502-5506, S5502/1-S5502/14CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)Fluorescence-labeled oligonucleotides provide powerful tools for highly sensitive, sequence-specific detection of target DNA/RNA. One practical problem with the use of these fluorescent probes is background emission intensity in the absence of the target, because background emission, as well as scattered light of excitation due to a small Stokes shift, critically affects probe sensitivity. Suppression of background emission is particularly important for the design of a highly sensitive mol. beacon (MB); that is a hairpin oligonucleotide dual-labeled at both 5'- and 3'-termini with a fluorophore and a quencher. The use of D-threoninol as a scaffold facilitated dimerization or clustering of the dyes in the duplex. We have utilized this base surrogate (threoninol nucleotide) to develop a new in stem mol. beacon (ISMB) in which both fluorophore (perylene) and quencher (anthraquinone) on D-threoninols are incorporated into the stem region as a pseudo base pair. Herein, we used Thiazole Orange (TO) and pentamethylindocarbocyanine (Cy3) as fluorophores. These results strongly suggest that coherency between the fluorophore and the quencher and also direct contact of the fluorophore-quencher pair significantly contribute to effective quenching. We chose NR or MR as a quencher of Cy3 to design an ISMB targeting the survivin gene. Excitonic interaction (coherency) was utilized to design a highly sensitive ISMB. Based on the results of a systematic study, we conclude that minimizing the Δλmax maximizes quenching efficiency due to maximization of coherency.
- 92Ruedas-Rama, M. J.; Alvarez-Pez, J. M.; Orte, A. Formation of Stable BOBO-3 H-Aggregate Complexes Hinders DNA Hybridization. J. Phys. Chem. B 2010, 114, 9063– 9071, DOI: 10.1021/jp103131rGoogle Scholar92https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXnvVeis7k%253D&md5=218c1b1d135df5c224d6960a25b58494Formation of Stable BOBO-3 H-Aggregate Complexes Hinders DNA HybridizationRuedas-Rama, Maria J.; Alvarez-Pez, Jose M.; Orte, AngelJournal of Physical Chemistry B (2010), 114 (27), 9063-9071CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)In recent works, the authors have been studying the photophysics and binding properties of the trimethine cyanine homodimer dye BOBO-3, a DNA intercalative fluorophore that shows an important fluorescence enhancement upon binding to double-stranded DNA. During studying the interactions of the dye with single-stranded homo-oligonucleotides the authors detected the apparition of an addnl. absorption band centered on 466 nm. The large hypsochromic effect and the fact that direct excitation of this band resulted in negligible fluorescence emission are characteristic properties of an H-type mol. aggregate. The authors study the properties of this H-aggregate, and obtain by Principal Component Anal. the spectral shape and assocn. const. of the complex. The H-aggregate complex shows very unique features. On one hand, the nucleotide bases cytosine or adenine are crucially involved in the formation of the aggregate. The authors describe here that at least six consecutive cytidine nucleosides are required to properly form the BOBO-3 H-aggregate complex. However, the formation of such a stable complex prevents hybridization of the bases involved with their complementary strands. This phenomenon draws important conclusions on the anomalously high stability of the BOBO-3 H-aggregate complex. To the best of the authors' knowledge, this is the first time such a stable H-aggregate of a dimeric cyanine dye facilitated by specific nucleotide bases in single strands has been reported.
- 93Ruedas-Rama, M. J.; Orte, A.; Martin-Domingo, M. C.; Castello, F.; Talavera, E. M.; Alvarez-Pez, J. M. Interaction of YOYO-3 with Different DNA Templates to Form H-Aggregates. J. Phys. Chem. B 2014, 118, 6098– 6106, DOI: 10.1021/jp5022888Google Scholar93https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXotFCksbw%253D&md5=45b9d637f16709b29a2c8afdf8b870cfInteraction of YOYO-3 with Different DNA Templates to Form H-AggregatesRuedas-Rama, Maria J.; Orte, Angel; Martin-Domingo, Maria C.; Castello, F.; Talavera, Eva. M.; Alvarez-Pez, Jose M.Journal of Physical Chemistry B (2014), 118 (23), 6098-6106CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)Homodimeric cyanine dyes are DNA intercalators that display a large enhancement of fluorescence emission when bound to double-stranded DNA. However, other different interaction modes are possible, such as H-type mol. aggregates of the dye, templated by the nucleic acid. In this paper, we study in depth the formation of nonfluorescent H-aggregates of the cyanine homodimer YOYO-3 with two different DNA templates using absorption and both steady-state and time-resolved fluorescence spectroscopy. First, a nonfluorescent YOYO-3 H-aggregate complex was found to form in single-stranded polycytidine chains, resulting in the appearance of a new absorption band at approx. 500 nm. The specific interaction of cytosine bases suggests the involvement of the C-rich i-motif in facilitating the formation of the H-aggregate complex. Second, the interaction of YOYO-3 with double-stranded poly(A·T) tracts also led to the appearance of a new absorption band at approx. 500 nm, and hence of a different type of H-aggregate. We found that the aggregate is formed mainly in double-stranded regions with consecutive adenine bases in the same strand (and thymine bases in the complementary strand). These poly(A·T) tracts provide narrow minor grooves and enhanced electrostatic neg. potential to promote the aggregation of the neg. charged cyanine. As the YOYO-3 H-aggregates are nonfluorescent, our results provide an important basis to quant. understand the fluorescence emission of this cyanine dye in the presence of DNA strands.
- 94Kringle, L.; Sawaya, N. P. D.; Widom, J.; Adams, C.; Raymer, M. G.; Aspuru-Guzik, A.; Marcus, A. H. Temperature-Dependent Conformations of Exciton-Coupled Cy3 Dimers in Double-Stranded DNA. J. Chem. Phys. 2018, 148, 085101 DOI: 10.1063/1.5020084Google Scholar94https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXjsF2lsLo%253D&md5=d0e3621a6fce8bb238ab1d340aed91e9Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNAKringle, Loni; Sawaya, Nicolas P. D.; Widom, Julia; Adams, Carson; Raymer, Michael G.; Aspuru-Guzik, Alan; Marcus, Andrew H.Journal of Chemical Physics (2018), 148 (8), 085101/1-085101/13CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)Understanding the properties of electronically interacting mol. chromophores, which involve internally coupled electronic-vibrational motions, is important to the spectroscopy of many biol. relevant systems. Here, we applied linear absorption, CD, and 2-dimensional fluorescence spectroscopy to study the polarized collective excitations of excitonically coupled cyanine-3 dimers (Cy3)2 that were rigidly positioned within the opposing sugar-phosphate backbones of the double-stranded region of a double-stranded (ds)-single-stranded (ss) DNA fork construct. We showed that the exciton-coupling strength of the (Cy3)2-DNA construct could be systematically varied with temp. below the double-stranded-single-stranded (ds-ss) DNA denaturation transition. We interpreted the spectroscopic measurements in terms of the Holstein vibronic dimer model, from which we obtained information about the local conformation of the (Cy3)2 dimer, as well as the degree of static disorder experienced by the Cy3 monomer and the (Cy3)2 dimer probe locally within their resp. DNA duplex environments. The properties of the (Cy3)2-DNA construct we detd. suggested that it may be employed as a useful model system to test fundamental concepts of protein-DNA interactions and the role of electronic-vibrational coherence in electronic energy migration within exciton-coupled biomol. arrays. (c) 2018 American Institute of Physics.
- 95Heussman, D.; Kittell, J.; Kringle, L.; Tamimi, A.; von Hippel, P. H.; Marcus, A. H. Measuring Local Conformations and Conformational Disorder of (Cy3)(2) Dimer Labeled DNA Fork Junctions Using Absorbance, Circular Dichroism and Two-Dimensional Fluorescence Spectroscopy. Faraday Discuss. 2019, 216, 211– 235, DOI: 10.1039/C8FD00245BGoogle Scholar95https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhvFemsbY%253D&md5=7918548ea017a0dd7459869fc61e1fb9Measuring local conformations and conformational disorder of (Cy3)2 dimer labeled DNA fork junctions using absorbance, circular dichroism and two-dimensional fluorescence spectroscopyHeussman, Dylan; Kittell, Justin; Kringle, Loni; Tamimi, Amr; von Hippel, Peter H.; Marcus, Andrew H.Faraday Discussions (2019), 216 (Ultrafast Photoinduced Energy and Charge Transfer), 211-235CODEN: FDISE6; ISSN:1359-6640. (Royal Society of Chemistry)The sugar-phosphate backbone of DNA near single-stranded (ss)-double-stranded (ds) junctions likely fluctuates within a broad distribution of conformations to permit the proper binding of genome regulatory proteins that function at these sites. In this work we use absorbance, CD (CD), and two-dimensional fluorescence spectroscopy (2DFS) to study the local conformations and conformational disorder within chromophore-labeled DNA constructs. These constructs employ dimers of the fluorescent chromophore Cy3 that are site-specifically incorporated into the sugar-phosphate backbones of DNA strands at ss-ds DNA fork junctions. We show that these data can be analyzed to det. the local conformations of the (Cy3)2 dimer, and the degree of conformational disorder. Our anal. employs an essential-state Holstein-Frenkel Hamiltonian model, which takes into account the internal electronic-vibrational motions within each Cy3 chromophore, and the resonant electronic interaction that couples the two chromophores together. Our results suggest that this approach may be applied generally to understand local backbone conformation and conformational disorder at ss-ds DNA fork junctions.
- 96Albinsson, B.; Hannestad, J. K.; Börjesson, K. Functionalized DNA Nanostructures for Light Harvesting and Charge Separation. Coord. Chem. Rev. 2012, 256, 2399– 2413, DOI: 10.1016/j.ccr.2012.02.024Google Scholar96https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XktlCisb0%253D&md5=37e76c0155636177b1d5fb1a4b799164Functionalized DNA nanostructures for light harvesting and charge separationAlbinsson, Bo; Hannestad, Jonas K.; Boerjesson, KarlCoordination Chemistry Reviews (2012), 256 (21-22), 2399-2413CODEN: CCHRAM; ISSN:0010-8545. (Elsevier B.V.)A review. Mimicking natural photosynthesis by covalently arranging antenna and charge sepn. units is a formidable task. Many such beautiful supramol. complexes have been designed and synthesized with large efforts, some of which are presented in this special issue. The ability to predict relative position of and electronic coupling between the active components in covalent arrays is quite high but there are two obvious drawbacks with the covalent approach. Firstly, as the size grows the complexity of the org. synthesis increases and secondly, sensitivity to light-induced damage becomes a major issue if covalent bonds are broken. Self-assembly of the photoactive components should, in principle, provide a soln. to both these issues but generally the ability to predict position and electronic coupling is too low to have the designed properties needed for a functional artificial photosynthetic complex. Here, we present an approach of using DNA as a template for arranging both charge sepn. units and antenna mols. that govern long-range energy transfer. Of particular interest is the ability of DNA to function as a scaffold for chromophores, either through covalent attachment, or through non-covalent assocn. by means of intercalation or grove binding. Using controlled positioning of dyes, multichromophoric assemblies can be created, capable of long range communication through multi-step energy transfer. This facilitates creation of DNA-based photonic devices for both light harvesting and directed information transfer. The channeled excitation energy can be transformed site specifically to chem. energy by charge sepn. of DNA linked porphyrins. A two phase system is discussed, in which the DNA is located in buffered soln. whereas the hydrophobic porphyrins, responsible for the charge sepn. reaction, are located in the lipid bilayer of liposomes or supported lipid bilayers.
- 97Probst, M.; Wenger, D.; Biner, S. M.; Häner, R. The DNA Three-Way Junction as a Mould for Tripartite Chromophore Assembly. Org. Biomol. Chem. 2012, 10, 755– 759, DOI: 10.1039/C1OB06400BGoogle Scholar97https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhs1OqsLjF&md5=08cd8df0cc17559ac33a13dcc9502423The DNA three-way junction as a mould for tripartite chromophore assemblyProbst, Markus; Wenger, Daniel; Biner, Sarah M.; Haener, RobertOrganic & Biomolecular Chemistry (2012), 10 (4), 755-759CODEN: OBCRAK; ISSN:1477-0520. (Royal Society of Chemistry)The DNA three-way junction serves as a scaffold for the mol. organization of non-nucleosidic alkynylpyrene and perylenediimide chromophores located at the branch point of the structure. Depending on the compn. of the tripartite assembly, the constructs possess distinct spectroscopic properties, ranging from monomer or excimer fluorescence to completely quenched tripartite aggregates.
- 98Seeman, N. C. Nucleic Acid Junctions and Lattices. J. Theor. Biol. 1982, 99, 237– 247, DOI: 10.1016/0022-5193(82)90002-9Google Scholar98https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL3sXhtlWhuw%253D%253D&md5=82c15bbb6dadb9b373d9da1a68ba23e3Nucleic acid junctions and latticesSeeman, Nadrian C.Journal of Theoretical Biology (1982), 99 (2), 237-47CODEN: JTBIAP; ISSN:0022-5193.It is possible to generate sequences of oligomeric nucleic acids which will preferentially assoc. to form migrationally immobile junctions, rather than linear duplexes. These structures are predicted on the maximization of Watson-Crick base pairing and the lack of sequence symmetry customarily found in their analogs in living systems. Criteria which oligonucleotide sequences must fulfill to yield these junction structures are presented. The generable junctions are nexuses, from which 3-8 double helices may emanate. Each junction may be treated as a macromol. valence cluster, and individual clusters may be linked together directly, or with pieces of linear DNA interspersed between them. This covalent linkage can be done with enormous specificity, using sticky-ended ligation techniques. It appears to be possible to generate covalently joined 3-dimensional networks of nucleic acids which are periodic in connectivity and perhaps in space.
- 99Kallenbach, N. R.; Ma, R.-I.; Seeman, N. C. An Immobile Nucleic Acid Junction Constructed from Oligonucleotides. Nature 1983, 305, 829– 831, DOI: 10.1038/305829a0Google Scholar99https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2cXmtlKjug%253D%253D&md5=fda00f282f58e8a89d4b6921380ac914An immobile nucleic acid junction constructed from oligonucleotidesKallenbach, Neville R.; Ma, Rong Ine; Seeman, Nadrian C.Nature (London, United Kingdom) (1983), 305 (5937), 829-31CODEN: NATUAS; ISSN:0028-0836.A stable tetrameric junction complex formed from 4 hexadecadeoxyribonucleotides was characterized by electrophoresis and UV spectroscopy. The stoichiometry of the complex was 1:1:1:1, and the structure of the complex was distinct from linear duplex DNA. The relative stability of the different complexes of strands 1-4 was assessed by thermal denaturation studies monitored by hyperchromism at 260 nm. The hyperchromism in the junction was twice that in the same concn. of pairs, strongly suggesting that the complex was closed with 4 arms nearly intact. The increase in junction stability, reflected in the higher melting temp., further strenghtened this argument. Thus, it is possible to design and synthesize immoble nucleic acid junctions by using optimization procedures.
- 100Cannon, B. L.; Kellis, D. L.; Patten, L. K.; Davis, P. H.; Lee, J.; Graugnard, E.; Yurke, B.; Knowlton, W. B. Coherent Exciton Delocalization in a Two-State DNA-Templated Dye Aggregate System. J. Phys. Chem. A 2017, 121, 6905– 6916, DOI: 10.1021/acs.jpca.7b04344Google Scholar100https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtlCgu7rJ&md5=d9b8d6c559a7f393cdc9f41c437252cbCoherent Exciton Delocalization in a Two-State DNA-Templated Dye Aggregate SystemCannon, Brittany L.; Kellis, Donald L.; Patten, Lance K.; Davis, Paul H.; Lee, Jeunghoon; Graugnard, Elton; Yurke, Bernard; Knowlton, William B.Journal of Physical Chemistry A (2017), 121 (37), 6905-6916CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)Coherent exciton delocalization in dye aggregate systems gives rise to a variety of intriguing optical phenomena, including J- and H-aggregate behavior and Davydov splitting. Systems that exhibit coherent exciton delocalization at room temp. are of interest for the development of artificial light-harvesting devices, colorimetric detection schemes, and quantum computers. A simple dye system templated by DNA that exhibits tunable optical properties is reported. At low salt and DNA concns., a DNA duplex with 2 internally functionalized Cy5 dyes (i.e., dimer) persists and displays predominantly J-aggregate behavior. Increasing the salt and/or DNA concns. was found to promote coupling between 2 of the DNA duplexes via branch migration, thus forming a 4-armed junction (i.e., tetramer) with H-aggregate behavior. This H-tetramer aggregate exhibits a surprisingly large Davydov splitting in its absorbance spectrum that produces a visible color change of the soln. from cyan to violet and gives clear evidence of coherent exciton delocalization.
- 101Cannon, B. L.; Patten, L. K.; Kellis, D. L.; Davis, P. H.; Lee, J.; Graugnard, E.; Yurke, B.; Knowlton, W. B. Large Davydov Splitting and Strong Fluorescence Suppression: An Investigation of Exciton Delocalization in DNA-Templated Holliday Junction Dye Aggregates. J. Phys. Chem. A 2018, 122, 2086– 2095, DOI: 10.1021/acs.jpca.7b12668Google Scholar101https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXisFars7c%253D&md5=399901c74716501ecbb121f1ab2dbbb6Large Davydov Splitting and Strong Fluorescence Suppression: An Investigation of Exciton Delocalization in DNA-Templated Holliday Junction Dye AggregatesCannon, Brittany L.; Patten, Lance K.; Kellis, Donald L.; Davis, Paul H.; Lee, Jeunghoon; Graugnard, Elton; Yurke, Bernard; Knowlton, William B.Journal of Physical Chemistry A (2018), 122 (8), 2086-2095CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)Exciton delocalization in dye aggregate systems is a phenomenon that is revealed by spectral features, such as Davydov splitting, J- and H-aggregate behavior, and fluorescence suppression. Using DNA as an architectural template to assemble dye aggregates enables specific control of the aggregate size and dye type, proximal and precise positioning of the dyes within the aggregates, and a method for constructing large, modular 2- and 3-dimensional arrays. Here, the authors report on dye aggregates, organized via an immobile Holliday junction DNA template, that exhibit large Davydov splitting of the absorbance spectrum (125 nm, 397.5 meV), J- and H-aggregate behavior, and near-complete suppression of the fluorescence emission (∼97.6% suppression). Because of the unique optical properties of the aggregates, the dye aggregate system is a viable candidate as a sensitive absorbance and fluorescence optical reporter. DNA-templated aggregates exhibiting exciton delocalization may find application in optical detection and imaging, light-harvesting, photovoltaics, optical information processing, and quantum computing.
- 102Davydov, A. Theory of Absorption Spectra of Molecular Crystals. Ukr. J. Phys. 2008, 53, 69– 70Google ScholarThere is no corresponding record for this reference.
- 103Stennett, E. M. S.; Ciuba, M. A.; Levitus, M. Photophysical Processes in Single Molecule Organic Fluorescent Probes. Chem. Soc. Rev. 2014, 43, 1057– 1075, DOI: 10.1039/C3CS60211GGoogle Scholar103https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtlalu7k%253D&md5=0feda28a3a1e28546b6d47fd2f5134f2Photophysical processes in single molecule organic fluorescent probesStennett, Elana M. S.; Ciuba, Monika A.; Levitus, MarciaChemical Society Reviews (2014), 43 (4), 1057-1075CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)A review. The use of org. fluorescent probes in biochem. and biophys. applications of single mol. spectroscopy and fluorescence microscopy techniques continues to increase. As single mol. measurements become more quant. and new developments in super-resoln. imaging allow researchers to image biol. materials with unprecedented resoln., it is becoming increasingly important to understand how the properties of the probes influence the signals measured in these expts. In this review, we focus on the photochem. and photophys. processes of org. fluorophores that affect the properties of fluorescence emission. This includes photobleaching, quenching, and the formation of non-emissive (dark) states that result in fluorescence blinking in a variety of timescales. These processes, if overlooked, can result in an erroneous interpretation of the data. Understanding their phys. origins, on the other hand, allows researchers to design expts. and interpret results so that the max. amt. of information about the system of interest can be extd. from fluorescence signals.
- 104Demchenko, A. P. Photobleaching of Organic Fluorophores: Quantitative Characterization, Mechanisms, Protection. Methods Appl. Fluoresc. 2020, 8, 022001 DOI: 10.1088/2050-6120/ab7365Google Scholar104https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXit1SitLvN&md5=8b8dcec15d31fb8036562976e5e7ba18Photobleaching of organic fluorophores: quantitative characterization, mechanisms, protectionDemchenko, Alexander P.Methods and Applications in Fluorescence (2020), 8 (2), 022001CODEN: MAFEB2; ISSN:2050-6120. (IOP Publishing Ltd.)A review. Photochem. stability is one of the most important parameters that det. the usefulness of org. dyes in different applications. This Review addresses key factors that det. the dye photostability. It is shown that photodegrdn. can follow different oxygen-dependent and oxygenindependent mechanisms and may involve both 1S1-3T1 and higher-energy 1Sn-3Tn excited states. Their involvement and contribution depends on dye structure, medium conditions, irradn. power. Fluorescein, rhodamine, BODIPY and cyanine dyes, as well as conjugated polymers are discussed as selected examples illustrating photobleaching mechanisms. The strategies for modulating and improving the photostability are overviewed. They include the improvement of fluorophore design, particularly by attaching protective and anti-fading groups, creating proper medium conditions in liq., solid and nanoscale environments. The special conditions for biol. labeling, sensing and imaging are outlined.
- 105Yagi, S.; Nakazumi, H. Heterocyclic Polymethine Dyes. Topics in Heterocyclic Chemistry; Strekowski, L., Ed.; Springer-Verlag: Berlin, Heidelberg, 2008; Vol. 14, pp 133– 181.Google ScholarThere is no corresponding record for this reference.
- 106Terpetsching, E.; Szmacinski, H.; Lakowicz, J. R. Synthesis, Spectral Properties and Photostabilities of Symmetrical and Unsymmetrical Squaraines - a New Class of Fluorophores with Long-Wavelength Excitation and Emission. Anal. Chim. Acta 1993, 282, 633– 641, DOI: 10.1016/0003-2670(93)80128-8Google ScholarThere is no corresponding record for this reference.
- 107Terpetschnig, E.; Lakowicz, J. R. Synthesis and Characterization of Unsymmetrical Squaraines - a New Class of Cyanine Dyes. Dyes Pigm. 1993, 21, 227– 234, DOI: 10.1016/0143-7208(93)85016-SGoogle Scholar107https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK3sXlsVWitbo%253D&md5=eca395fc1b31965ee53bae34f5c3e1feSynthesis and characterization of unsymmetrical squaraines: a new class of cyanine dyesTerpetschnig, Ewald; Lakowicz, Joseph R.Dyes and Pigments (1993), 21 (3), 227-34CODEN: DYPIDX; ISSN:0143-7208.A new class of unsym. cyanine dyes and their precursors was synthesized, and characterized with the aid of 1H-NMR, IR, and mass spectroscopy. The dyes exhibit high m.ps., poor soly. in org. solvents and absorption max. in the range 640-670 nm with high extinction coeffs.
- 108Markova, L. I.; Terpetschnig, E. A.; Patsenker, L. D. Comparison of a Series of Hydrophilic Squaraine and Cyanine Dyes for Use as Biological Labels. Dyes Pigm. 2013, 99, 561– 570, DOI: 10.1016/j.dyepig.2013.06.022Google Scholar108https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhslWqu7fN&md5=870916e3216d93eb5697f48e45d42d43Comparison of a series of hydrophilic squaraine and cyanine dyes for use as biological labelsMarkova, Larysa I.; Terpetschnig, Ewald A.; Patsenker, Leonid D.Dyes and Pigments (2013), 99 (3), 561-570CODEN: DYPIDX; ISSN:0143-7208. (Elsevier Ltd.)Unlike cyanine dyes, which are widely used as fluorescent probes and labels for biomedical applications squaraine dyes are less investigated. A series of monoreactive, water-sol., squaraine dyes with two arom. sulfo groups and up to 3 sulfobutyl groups was synthesized and the spectral properties of these dyes were compared to dicarbocyanines of identical structure. Compared to the cyanines in aq. solns. the squaraine dyes absorb and emit at shorter wavelengths (630-636 nm/639-645 nm vs. 647-653 nm/665-672 nm), have higher molar absorptivities (284,000-333,000 M-1 cm-1vs. 242,000-260,000 M-1 cm-1), lower fluorescence quantum yields (4.3-9.4% vs. 27-32%) and lower fluorescence lifetimes (0.2-0.3 ns vs. 1.0-1.2 ns) but the quantum yields and lifetimes substantially increase when bound to proteins (Bovine Serum Albumin (BSA) or antibodies, IgG (IgG)). Squaraines with two arom. sulfo groups show no aggregation tendency up to concns. of 2 × 10-4 M while the corresponding cyanine dye is free of aggregation up to 5 × 10-4 M. The increase in the no. of sulfobutyl groups bears a strong influence on the aggregation tendency of both dye classes upon covalent labeling to BSA and IgG resulting in increased quantum yields and lifetimes of the protein conjugates. Compared to cyanines, squaraine dyes exhibit higher photostabilities and much higher sensitivity of the quantum yields and fluorescence lifetimes toward the microenvironment and are therefore better suited as fluorescence sensors.
- 109Treibs, A.; Jacob, K. Cyclotrimethine Dyes Derived from Squaric Acid. Angew. Chem., Int. Ed. 1965, 4, 694, DOI: 10.1002/anie.196506941Google ScholarThere is no corresponding record for this reference.
- 110Jiang, J. Q.; Sun, C. L.; Shi, Z. F.; Zhang, H. L. Squaraines as Light-Capturing Materials in Photovoltaic Cells. RSC Adv. 2014, 4, 32987– 32996, DOI: 10.1039/C4RA03972FGoogle Scholar110https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtFeqsbrO&md5=d98f9dd4e8d4549d8a1293e9ec73518dSquaraines as light-capturing materials in photovoltaic cellsJiang, Jian-Qiao; Sun, Chun-Lin; Shi, Zi-Fa; Zhang, Hao-LiRSC Advances (2014), 4 (62), 32987-32996CODEN: RSCACL; ISSN:2046-2069. (Royal Society of Chemistry)Photovoltaic cells are considered to be one of the most promising renewable energy sources of the 21st century. In particular, dye-sensitized solar cells (DSSCs) and org. photovoltaic devices (OPVs) are potentially the most economical and environmentally friendly ones. Squaraine (SQ) has intense absorption at 600-850 nm, exactly where sun flux is the most abundant. Furthermore, various substituents on SQ cores provide great possibilities for different mol.-design strategies. These characters make SQs ideal candidates for new DSSCs and OPVs. In response to the rapid development of SQ-based solar cells, a panorama of these ongoing studies is presented here, including the general synthetic routes of SQs and the various SQs used in DSSCs and OPVs. Our discussions are focused on the diverse mol. designs of SQs used in DSSCs and OPVs. The design strategies to acquire better light-harvesting abilities are also provided here, as well as the principles behind these strategies.
- 111Khopkar, S.; Shankarling, G. Synthesis, Photophysical Properties and Applications of NIR Absorbing Unsymmetrical Squaraines: A Review. Dyes Pigm. 2019, 170, 107645 DOI: 10.1016/j.dyepig.2019.107645Google Scholar111https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhtlaqtrvE&md5=9a8c4fa195ca8a2bdd45f120fd5f2ad6Synthesis, photophysical properties and applications of NIR absorbing unsymmetrical squaraines: A reviewKhopkar, Sushil; Shankarling, GanapatiDyes and Pigments (2019), 170 (), 107645CODEN: DYPIDX; ISSN:0143-7208. (Elsevier Ltd.)A review. Unsym. squarylium dyes (unsym. squaraines) represent one of the most promising class of squaraine chem., due to their outstanding photophys. properties, including absorption in NIR region, good intramol. charge transfer, high molar absorption coeffs. and tunable electrochem. properties. These properties making them extremely useful for photovoltaic as well as biomedical applications. Moreover, the synthesis of unsym. squarylium dyes is excellent for modifying their absorption and emission wavelength by changing suitable arom. or heterocyclic moiety. There is no collective review for unsym. squaraines in the literature therefore we are presenting this review detailing their synthetic methodologies reported for different classes of unsym. squaraines and their applications comprising dye sensitized solar cells (DSSCs), small mol. org. solar cells (OSCs), photodynamic therapy (PDT), chemosensors and fluorescence probes.
- 112Sreejith, S.; Carol, P.; Parayalil, C.; Ayyappanpillai, A. Squaraine Dyes: A. Mine of Molecular Materials. J. Mater. Chem. 2008, 18, 264– 274, DOI: 10.1039/B707734CGoogle Scholar112https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXitVOlsw%253D%253D&md5=63f8290c39ec8d69db1f09a5a31a6acbSquaraine dyes: a mine of molecular materialsSreejith, Sivaramapanicker; Carol, Priya; Chithra, Parayalil; Ajayaghosh, AyyappanpillaiJournal of Materials Chemistry (2008), 18 (3), 264-274CODEN: JMACEP; ISSN:0959-9428. (Royal Society of Chemistry)A review. This feature article highlights the recent developments in the field of squaraine chem. Attempts were made to address the relevance of squaraine dyes as a class of functional org. materials useful for electronic and photonic applications. Due to the synthetic access of a variety of squaraine dyes with structural variations and due to the strong absorption and emission properties which respond to the surrounding medium, these dyes were receiving significant attention. Therefore, squaraine dyes were extensively studied in recent years, from both fundamental and technol. viewpoints.
- 113Xia, G. M.; Wang, H. M. Squaraine Dyes: The Hierarchical Synthesis and Its Application in Optical Detection. J. Photochem. Photobiol., C 2017, 31, 84– 113, DOI: 10.1016/j.jphotochemrev.2017.03.001Google Scholar113https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXlsVahuro%253D&md5=d5799c10c8cf356eb8c0647d9af22503Squaraine dyes: The hierarchical synthesis and its application in optical detectionXia, Guomin; Wang, HongmingJournal of Photochemistry and Photobiology, C: Photochemistry Reviews (2017), 31 (), 84-113CODEN: JPPCAF; ISSN:1389-5567. (Elsevier B.V.)Squaraine dyes, a four-membered ring system with structural rigidity, possess unique photoelec. properties and are marked by their exceptionally sharp and intense absorption assocd. with a strong fluorescent emission in soln. These favorable characteristics have prompted their exploitation in a no. of state of the art applications including photocond., data storage, light-emitting field-effect transistors, solar cells and fluorescent histol. probes. In this review, we first summarize the recently proposed novel methods in the synthesis of these versatile derivs. Subsequently, their extensive applications in the prevalent optical detection of the surrounding medium such as ions, pH, thiol-based compds., biomols. and cell over the past decades are covered and discussed. In addn., different categories for the synthesis and sensing mechanisms for various squaric acid-based chemo-/bio- sensors are illustrated. Finally, the challenges and opportunities in the synthesis and application of these derivs. are also briefly discussed.
- 114Ilina, K.; MacCuaig, W. M.; Laramie, M.; Jeouty, J. N.; McNally, L. R.; Henary, M. Squaraine Dyes: Molecular Design for Different Applications and Remaining Challenges. Bioconjugate Chem. 2020, 31, 194– 213, DOI: 10.1021/acs.bioconjchem.9b00482Google Scholar114https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhsVygtbjI&md5=077585c8218d55863400be59a0dedd3dSquaraine Dyes: Molecular Design for Different Applications and Remaining ChallengesIlina, Kristina; MacCuaig, William M.; Laramie, Matthew; Jeouty, Jannatun N.; McNally, Lacey R.; Henary, MagedBioconjugate Chemistry (2020), 31 (2), 194-213CODEN: BCCHES; ISSN:1043-1802. (American Chemical Society)A review. Squaraine dyes are a class of org. dyes with strong and narrow absorption bands in the near-IR. Despite high molar absorptivities and fluorescence quantum yields, these dyes were less explored than other dye scaffolds due to their susceptibility to nucleophilic attack. Recent strategies in probe design including encapsulation, conjugation to biomols., and new synthetic modifications have seen squaraine dyes emerging into the forefront of biomedical imaging and other applications. Herein, we provide a concise overview of (1) the synthesis of sym. and unsym. squaraine dyes, (2) the relation between structure and photophys. properties of squaraine dyes, and (3) current applications of squaraine dyes in the literature. Given the recent successes at overcoming the limitations of squaraine dyes, they show high potential in biol. imaging, in photodynamic and photothermal therapies, and as mol. sensors.
- 115Würthner, F.; Kaiser, T. E.; Saha-Moller, C. R. J-Aggregates: From Serendipitous Discovery to Supramolecular Engineering of Functional Dye Materials. Angew. Chem., Int. Ed. 2011, 50, 3376– 3410, DOI: 10.1002/anie.201002307Google Scholar115https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXktFWmtL0%253D&md5=a4da0f17b4afad13f6aee2509b919f60J-Aggregates: From Serendipitous Discovery to Supramolecular Engineering of Functional Dye MaterialsWuerthner, Frank; Kaiser, Theo E.; Saha-Moeller, Chantu R.Angewandte Chemie, International Edition (2011), 50 (15), 3376-3410CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)A review. J-aggregates are of significant interest for org. materials conceived by supramol. approaches. Their discovery in the 1930s represents one of the most important milestones in dye chem. as well as the germination of supramol. chem. The intriguing optical properties of J-aggregates as well as their prospect for applications have motivated scientists to become involved in this field, and numerous contributions have been published. This Review provides an overview on the J-aggregates of a broad variety of dyes well as their potential applications. Thus, this Review is intended to be of interest to the supramol., photochem., and materials science communities.
- 116Mayerhöffer, U.; Wurthner, F. Cooperative Self-Assembly of Squaraine Dyes. Chem. Sci. 2012, 3, 1215– 1220, DOI: 10.1039/c2sc00996jGoogle ScholarThere is no corresponding record for this reference.
- 117Röhr, M. I. S.; Marciniak, H.; Hoche, J.; Schreck, M. H.; Ceymann, H.; Mitric, R.; Lambert, C. Exciton Dynamics from Strong to Weak Coupling Limit Illustrated on a Series of Squaraine Dimers. J. Phys. Chem. C 2018, 122, 8082– 8093, DOI: 10.1021/acs.jpcc.8b00847Google ScholarThere is no corresponding record for this reference.
- 118Malý, P.; Lüttig, J.; Mueller, S.; Schreck, M.; Lambert, C.; Brixner, T. Coherently and Fluorescence-Detected Two-Dimensional Electronic Spectroscopy: Direct Comparison on Squaraine Dimers. Phys. Chem. Chem. Phys. 2020, 21222– 21237, DOI: 10.1039/D0CP03218BGoogle Scholar118https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhsleksbvE&md5=44835ab4fda0a7fad6bc4ec5bbd58554Coherently and fluorescence-detected two-dimensional electronic spectroscopy: direct comparison on squaraine dimersMaly, Pavel; Luettig, Julian; Mueller, Stefan; Schreck, Maximilian H.; Lambert, Christoph; Brixner, TobiasPhysical Chemistry Chemical Physics (2020), 22 (37), 21222-21237CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)Optical two-dimensional electronic spectroscopy (2DES) is now widely utilized to study excitonic structure and dynamics of a broad range of systems, from mols. to solid state. Besides the traditional exptl. implementation using phase matching and coherent signal field detection, action-based approaches that detect incoherent signals such as fluorescence have been gaining popularity in recent years. While incoherent detection extends the range of applicability of 2DES, the obsd. spectra are not equiv. to the coherently detected ones. This raises questions about their interpretation and the sensitivity of the technique. Here we directly compare, both exptl. and theor., four-wave mixing coherently and fluorescence-detected 2DES of a series of squaraine dimers of increasing electronic coupling. All expts. are qual. well reproduced by a Frenkel exciton model with secular Redfield theory description of excitation dynamics. We contrast the spectral features and the sensitivities of both techniques with respect to exciton energies, delocalization, coherent and dissipative dynamics, and exciton-exciton annihilation. Discussing the fundamental and practical differences, we demonstrate the degree of complementarity of the techniques.
- 119Huff, J. S.; Davis, P. H.; Christy, A.; Kellis, D. L.; Kandadai, N.; Toa, Z. S. D.; Scholes, G. D.; Yurke, B.; Knowlton, W. B.; Pensack, R. D. DNA-Templated Aggregates of Strongly Coupled Cyanine Dyes: Nonradiative Decay Governs Exciton Lifetimes. J. Phys. Chem. Lett. 2019, 10, 2386– 2392, DOI: 10.1021/acs.jpclett.9b00404Google Scholar119https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXnvFCns70%253D&md5=c3f0644cabd5620350138d249ece4e87DNA-Templated Aggregates of Strongly Coupled Cyanine Dyes: Nonradiative Decay Governs Exciton LifetimesHuff, Jonathan S.; Davis, Paul H.; Christy, Allison; Kellis, Donald L.; Kandadai, Nirmala; Toa, Zi S. D.; Scholes, Gregory D.; Yurke, Bernard; Knowlton, William B.; Pensack, Ryan D.Journal of Physical Chemistry Letters (2019), 10 (10), 2386-2392CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)Mol. excitons were used in a variety of applications including light harvesting, optoelectronics, and nanoscale computing. Controlled aggregation via covalent attachment of dyes to DNA templates is a promising aggregate assembly technique that enables the design of extended dye networks. However, there are few studies of exciton dynamics in DNA-templated dye aggregates. The authors report time-resolved excited-state dynamics measurements of two cyanine-based dye aggregates, a J-like dimer and an H-like tetramer, formed through DNA-templating of covalently attached dyes. Time-resolved fluorescence and transient absorption indicate that nonradiative decay, as internal conversion, dominates the aggregate ground state recovery dynamics, with singlet exciton lifetimes on the order of tens of picoseconds for the aggregates vs. nanoseconds for the monomer. These results highlight the importance of circumventing nonradiative decay pathways in the future design of DNA-templated dye aggregates.
- 120Spano, F. C. Analysis of the Uv/Vis and Cd Spectral Line Shapes of Carotenoid Assemblies: Spectral Signatures of Chiral H-Aggregates. J. Am. Chem. Soc. 2009, 131, 4267– 4278, DOI: 10.1021/ja806853vGoogle Scholar120https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXisl2ktLg%253D&md5=70ccb019beee1ff29b70f8f68a72e5c8Analysis of the UV/Vis and CD Spectral Line Shapes of Carotenoid Assemblies: Spectral Signatures of Chiral H-AggregatesSpano, Frank C.Journal of the American Chemical Society (2009), 131 (12), 4267-4278CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Using vibronic exciton theory we evaluate the absorption and CD spectra of lutein (I; R = H) and lutein diacetate (I; R = Ac) aggregates, which have previously been described as card-packed H-aggregates and head-to-tail J-aggregates, resp. The dramatically different spectral line shapes for both aggregates are shown to arise from strongly and weakly coupled H-aggregates consisting of helical arrays of chromophores. For lutein (I; R = H), the aggregates consist of tightly packed stacks of individual carotenoid mols., while lutein diacetate (I; R = Ac) aggregates resemble nematic liq. crystals. For both aggregates the agreement between expt. and theory is excellent. Anal. expressions for the absorption and CD spectra are presented, highlighting the spectral signatures of weakly coupled H (and J)-aggregation arising from distortions in the single-mol. Franck-Condon progression.
- 121Liang, K. N.; Farahat, M. S.; Perlstein, J.; Law, K. Y.; Whitten, D. G. Exciton Interactions in Nonconjugated Squaraine Dimers. Mechanisms for Coupling and Consequences for Photophysics and Photochemistry. J. Am. Chem. Soc. 1997, 119, 830– 831, DOI: 10.1021/ja962091zGoogle Scholar121https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXitFSqug%253D%253D&md5=bdb5ea64f28746e3b4c9d04c4b14dfd9Exciton Interactions in Flexible and Semirigid Nonconjugated Squaraine Dimers. Mechanisms for Coupling and Consequences for Photophysics and PhotochemistryLiang, Kangning; Farahat, Mohammad S.; Perlstein, Jerry; Law, Kock-Yee; Whitten, David G.Journal of the American Chemical Society (1997), 119 (4), 830-831CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)A study are reported of exciton coupling in a series of bissquaraines linked by a simple polymethylene spacers and more restricted xylyl sepd. squaraines and in relatively rigid doubly bridged squaraines. The study shows that at least two types of exciton-coupled states are detectable, the relative prominence of each depending on the specific bissquaraine structure and on solvent. The study also shows that in flexible systems the ready accessibility of different dimer (aggregate) structures can have significant effects on the squaraine photophysics which in turn affects photoreactivity.
- 122Kühn, O.; Renger, T.; May, V. Theory of Exciton-Vibrational Dynamics in Molecular Dimers. Chem. Phys. 1996, 204, 99– 114, DOI: 10.1016/0301-0104(95)00448-3Google Scholar122https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XitVSkt7k%253D&md5=dc3f84fef08bb9b2f79d463f469ad58fTheory of exciton-vibrational dynamics in molecular dimersKuehn, Oliver; Renger, Thomas; May, VolkhardChemical Physics (1996), 204 (1), 99-114CODEN: CMPHC2; ISSN:0301-0104. (Elsevier)The exciton transfer in a mol. dimer embedded in a condensed medium is studied theor. To include coherent vibrational dynamics a single effective mode per monomer is split off from the whole set of vibrational degrees of freedom of the dimer and the environment. The remaining modes are treated as a heat bath. To study the dissipative exciton transfer dynamics the d. matrix formalism is applied. Choosing an appropriate exciton-vibrational basis set with respect to the 2 effective modes the theory is formulated in the related state representation. The general approach is applied to the exciton motion in a chlorophyll a/b dimer of the light-harvesting complex of the photosystem II of higher plants. The complex dynamic behavior following an ultrafast optical excitation in the absorption region of the chlorophyll b monomer is studied.
- 123Holstein, T. Studies of Polaron Motion: Part I. The Molecular-Crystal Model. Ann. Phys. 1959, 8, 325– 342, DOI: 10.1016/0003-4916(59)90002-8Google Scholar123https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaF3cXpsFejsQ%253D%253D&md5=47b19defdd3c86c62c9bfcf15ff2fc13Polaron motion. I. Molecular-crystal modelHolstein, T.Annals of Physics (San Diego, CA, United States) (1959), 8 (), 325-42CODEN: APNYA6; ISSN:0003-4916.A unidimensional mol.-crystal model of the polaron (electron plus its induced crystal lattice deformation) is developed. This is equiv. to the continuum-polarization model for polarons with dimensions large compared to the lattice spacing.
- 124Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. UCSF Chimera - a Visualization System for Exploratory Research and Analysis. J. Comput. Chem. 2004, 25, 1605– 1612, DOI: 10.1002/jcc.20084Google Scholar124https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXmvVOhsbs%253D&md5=944b175f440c1ff323705987cf937ee7UCSF Chimera-A visualization system for exploratory research and analysisPettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.; Couch, Gregory S.; Greenblatt, Daniel M.; Meng, Elaine C.; Ferrin, Thomas E.Journal of Computational Chemistry (2004), 25 (13), 1605-1612CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale mol. assemblies such as viral coats, and Collab., which allows researchers to share a Chimera session interactively despite being at sep. locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and assocd. structures; ViewDock, for screening docked ligand orientations; Movie, for replaying mol. dynamics trajectories; and Vol. Viewer, for display and anal. of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.
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Abstract
Figure 1
Figure 1. (a) Representative example of the chemical structure of cyanine dye Cy5, where R and R′ are sites of attachment to DNA through phosphoramidite linkers. (b) Representative example of the chemical structure of core-substituted indolenine squaraine dye, where X = O, S, NR1, C(CN)2; R is a site of attachment to DNA through a serinol linker; and R1 is an alkyl (also see Figure S1). (c) Asymmetric DNA sequences to assemble immobile Holliday junctions; complementary regions of ssDNA are color-coded: for example, the purple region of strand A is complementary to the purple region of strand D, and the green region of strand A is complementary to the green region of strand B, and so on. (d) Schematic representation of dye monomer, dimers, and a tetramer in four-armed duplex DNA junctions (Holliday junctions) where squaraine dyes are depicted as blue dots. As discussed in Sections S3 and S10, the DNA HJ may exist primarily in a stacked conformation. ssDNA strands used to assemble DNA HJ are labeled as A, B, C, and D.
Figure 2
Figure 2. (a, c, e, g) Acquired steady-state absorption spectra of the DNA–Square 660 dye constructs in 1× TBE, 15 mM MgCl2 at room temperature (dotted lines) and theoretical absorption spectra derived from KRM modeling (solid lines). The DNA–dye construct concentration was 1.5 μM. The insets show a schematic representation of dye monomer, dimers, and tetramer constructs in DNA HJs. (b, d, f, h) Acquired CD spectra of the DNA–Square 660 dye constructs in 1× TBE, 15 mM MgCl2 at room temperature (dotted lines) and theoretical CD spectra derived from KRM modeling (solid lines). The DNA–dye construct concentration was 1.5 μM.
Figure 3
Figure 3. Molecular models of the Square 660 core region adjacent dimer SQ-BC and transverse dimer SQ-AC. The side view shows a J1,2 parameter, in meV, a center-to-center distance R, in Å, and a slip angle θs, in degree. The oblique view shows oblique angle α, in degree, as an angle between vectors 1 and 2 if their centers are superimposed. Note that the fitting procedure determines the position and orientation of the long axes of the Square 660 dyes but not the rotation of the dye core around its long axis. As such, the dye core rotations were arbitrarily chosen.
Figure 4
Figure 4. Molecular model of the Square 660 core region tetramer SQ-ABCD. The side view shows Jm,n parameter between each pair of dyes, in meV, and slip angles θs, in degree. The oblique view shows a center-to-center distance R, in Å, and oblique angle α, in degree.
References
This article references 124 other publications.
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- 4Roden, J.; Eisfeld, A. Anomalous Strong Exchange Narrowing in Excitonic Systems. J. Chem. Phys. 2011, 134, 034901 DOI: 10.1063/1.35287184https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXmvFajtQ%253D%253D&md5=e2bac707e3a16930bfb0cfa5e0136614Anomalous strong exchange narrowing in excitonic systemsRoden, Jan; Eisfeld, AlexanderJournal of Chemical Physics (2011), 134 (3), 034901/1-034901/8CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)Exchange narrowing in the absorption spectrum of a chain of monomers, which are coupled via resonant dipole-dipole interaction, was studied theor. The individual (uncoupled) monomers exhibit a broad absorption line shape due to the coupling to an environment consisting of a continuum of vibrational modes. Upon increasing the interaction between the monomers, the absorption spectrum of the chain narrows. For a non-Markovian environment with a Lorentzian spectral d., a narrowing of the peak width full width at half max. (FWHM) by a factor 1/N, where N is the no. of monomers were found. This is much stronger than the usual 1/√N narrowing. For a Markovian environment no exchange narrowing at all occurs. The relation of different measures of the width (FWHM, std. deviation) is discussed. (c) 2011 American Institute of Physics.
- 5Fidder, H.; Knoester, J.; Wiersma, D. A. Optical Properties of Disordered Molecular Aggregates: A Numerical Study. J. Chem. Phys. 1991, 95, 7880– 7890, DOI: 10.1063/1.4613175https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK38XjtVajtQ%253D%253D&md5=ebe0291b4f881d781f29e6323cf5e12aOptical properties of disordered molecular aggregates: a numerical studyFidder, Henk; Knoester, Jasper; Wiersma, Douwe A.Journal of Chemical Physics (1991), 95 (11), 7880-90CODEN: JCPSA6; ISSN:0021-9606.Results are presented of numerical simulations on optical properties of linear mol. aggregates with diagonal and off-diagonal disorder. In contrast to previous studies, off-diagonal disorder is introduced indirectly through Gaussian randomness in the mol. positions; this results in a strongly asym. distribution for the interactions. Moreover, there is no restriction to nearest-neighbor interactions. There is simultaneous focus on several optical observables (absorption linewidth and line shift and superradiant behavior) and on the d. and the localization behavior of the eigenstates (Frenkel excitons). The dependence of these optical properties on the disorder is investigated and expressed in terms of simple power laws. For off-diagonal disorder, such a study has not been performed before. In the case of diagonal disorder, in particular, the superradiant decay rate of the aggregates may be strongly affected by the inclusion of non-nearest-neighbor interactions. Recent results of absorption line shape, superradiant emission, and resonance light-scattering measurements on pseudoisocyanine aggregates can be understood on the basis of these calcns.
- 6Vaitekonis, S.; Trinkunas, G.; Valkunas, L. Red Chlorophylls in the Exciton Model of Photosystem I. Photosynth. Res. 2005, 86, 185– 201, DOI: 10.1007/s11120-005-2747-x6https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXhtVWls73I&md5=4bd6b5640f8c4828743db6dfd4a7103fRed Chlorophylls in the Exciton Model of Photosystem IVaitekonis, Sarunas; Trinkunas, Gediminas; Valkunas, LeonasPhotosynthesis Research (2005), 86 (1-2), 185-201CODEN: PHRSDI; ISSN:0166-8595. (Springer)Structural arrangement of pigment mols. of Photosystem I of photosynthetic cyanobacterium Synechococcus elongatus is used for theor. modeling of the excitation energy spectrum. It is demonstrated that a straightforward application of the exciton theory with the assumption of the same mol. transition energy does not describe the red side of the absorption spectrum. Since the inhomogeneity in the mol. transition energies caused by a dispersive interaction with the mol. surrounding cannot be identified directly from the structural model, the evolutionary search procedure is used for fitting the low temp. absorption and CD spectra. As a result, one dimer, three trimers and one tetramer of chlorophyll mols. responsible for the red side of the absorption spectrum with their assignment to the spectroscopically established three bands at 708, 714 and 719 nm are detd. All of them are found to be situated not in the very close vicinity of the reaction center but are encircling it almost at the same distance. In order to explain the unusual broadening on the red side of the spectrum the exciton state mixing with the charge transfer (CT) states is considered. It is shown that two effects can be distinguished as caused by mixing of those states: (i) the oscillator strength borrowing by the CT state from the exciton transition and (ii) the borrowing of the high d. of the CT state by the exciton state. The intermol. vibrations between two counter-charged mols. det. the high d. in the CT state. From the broad red absorption wing it is concluded that the CT state should be the lowest state in the complexes under consideration. Such mixing effect enables resolving the diversity in the mol. transition energies as detd. by different theor. approaches.
- 7Abramavicius, D.; Mukamel, S. Exciton Delocalization and Transport in Photosystem I of Cyanobacteria Synechococcus Elongates: Simulation Study of Coherent Two-Dimensional Optical Signals. J. Phys. Chem. B 2009, 113, 6097– 6108, DOI: 10.1021/jp811339p7https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXktFWltb0%253D&md5=fe2ceed4b62c141ca2ed541f52494f74Exciton delocalization and transport in Photosystem I of cyanobacterium Synechococcus elongatus: Simulation study of coherent two-dimensional optical signalsAbramavicius, Darius; Mukamel, ShaulJournal of Physical Chemistry B (2009), 113 (17), 6097-6108CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)Electronic excitations and the optical properties of the photosynthetic complex PSI are analyzed using an effective exciton model developed by Vaitekonis et al. [Photosynth. Res.2005, 86, 185]. States of the reaction center, the linker states, the highly delocalized antenna states and the red states are identified and assigned in absorption and CD spectra by taking into account the spectral distribution of d. of exciton states, exciton delocalization length, and participation ratio in the reaction center. Signatures of exciton cooperative dynamics in nonchiral and chirality-induced two-dimensional (2D) photon-echo signals are identified. Nonchiral signals show resonances assocd. with the red, the reaction center, and the bulk antenna states as well as transport between them. Spectrally overlapping contributions of the linker and the delocalized antenna states are clearly resolved in the chirality-induced signals. Strong correlations are obsd. between the delocalized antenna states, the linker states, and the RC states. The active space of the complex covering the RC, the linker, and the delocalized antenna states is common to PSI complexes in bacteria and plants.
- 8Abramavicius, D.; Palmieri, B.; Mukamel, S. Extracting Single and Two-Exciton Couplings in Photosynthetic Complexes by Coherent Two-Dimensional Electronic Spectra. Chem. Phys. 2009, 357, 79– 84, DOI: 10.1016/j.chemphys.2008.10.0108https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXitVSisLg%253D&md5=be185e45c2c041c6b8c28ea0375ff417Extracting single and two-exciton couplings in photosynthetic complexes by coherent two-dimensional electronic spectraAbramavicius, Darius; Palmieri, Benoit; Mukamel, ShaulChemical Physics (2009), 357 (1-3), 79-84CODEN: CMPHC2; ISSN:0301-0104. (Elsevier B.V.)Signatures of "strong" J and "weak" K exciton couplings in the nonlinear femtosecond optical response of the FMO photosynthetic complex are identified. The two types of couplings originate from interactions of mol. transition charge dipoles and change of mol. permanent dipoles in their ground and excited states, resp. We demonstrate that by combining various two-dimensional optical signals it should be possible to invert spectroscopic data to reconstruct the full exciton Hamiltonian (energies and couplings).
- 9Abramavicius, D.; Palmieri, B.; Voronine, D. V.; Šanda, F.; Mukamel, S. Coherent Multidimensional Optical Spectroscopy of Excitons in Molecular Aggregates; Quasiparticle Versus Supermolecule Perspectives. Chem. Rev. 2009, 109, 2350– 2408, DOI: 10.1021/cr800268n9https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXls1GltLw%253D&md5=19f94fb7600ed1c26eeb196b5e2705a5Coherent Multidimensional Optical Spectroscopy of Excitons in Molecular Aggregates; Quasiparticle versus Supermolecule PerspectivesAbramavicius, Darius; Palmieri, Benoit; Voronine, Dmitri V.; Sanda, Frantisek; Mukamel, ShaulChemical Reviews (Washington, DC, United States) (2009), 109 (6), 2350-2408CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review.
- 10McRae, E. G.; Kasha, M. The Molecular Exciton Model. In Physical Processes in Radiation Biology; Augenstein, L.; Mason, R.; Rosenberg, B., Eds.; Academic Press: New York, 1964; pp 23– 42.There is no corresponding record for this reference.
- 11Hestand, N. J.; Spano, F. C. Determining the Spatial Coherence of Excitons from the Photoluminescence Spectrum in Charge-Transfer J-Aggregates. Chem. Phys. 2016, 481, 262– 271, DOI: 10.1016/j.chemphys.2016.06.00511https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtV2nu7jK&md5=8e9c69e654a4e6b8c411c12e52f245e1Determining the spatial coherence of excitons from the photoluminescence spectrum in charge-transfer J-aggregatesHestand, Nicholas J.; Spano, Frank C.Chemical Physics (2016), 481 (), 262-271CODEN: CMPHC2; ISSN:0301-0104. (Elsevier B.V.)The importance of spatial coherence in energy and charge transfer processes in biol. systems and photovoltaic devices has been hotly debated over the past several years. While larger spatial coherences are thought to benefit transport, a clear correlation has yet to be established, partly because a simple and accurate measure of the coherence length has remained elusive. Previously, it was shown that the no. of coherently connected chromophores, NCoh, can be detd. directly from the ratio (SR) of the 0-0 and 0-1 vibronic line strengths in the photoluminescence (PL) spectrum. The relation NCoh = λ20SR, where λ20 is the assocd. monomeric Huang-Rhys parameter, was derived in the Frenkel exciton limit. Here, it is shown that SR remains a highly accurate measure of coherence for systems characterized by significant charge transfer interactions (e.g. conjugated π-stacked systems). The only requirement is that the exciton band curvature must be pos., as in a J-aggregate.
- 12Hestand, N. J.; Spano, F. C. Molecular Aggregate Photophysics Beyond the Kasha Model: Novel Design Principles for Organic Materials. Acc. Chem. Res. 2017, 50, 341– 350, DOI: 10.1021/acs.accounts.6b0057612https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhvVSms7s%253D&md5=ae2fb7f835d1839ea6375df6dcd917d5Molecular Aggregate Photophysics beyond the Kasha Model: Novel Design Principles for Organic MaterialsHestand, Nicholas J.; Spano, Frank C.Accounts of Chemical Research (2017), 50 (2), 341-350CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)A review. The transport and photophys. properties of org. mol. aggregates, films, and crystals continue to receive widespread attention, driven mainly by expanding com. applications involving display and wearable technols. as well as the promise of efficient, large-area solar cells. The main blueprint for understanding how mol. packing impacts photophys. properties was drafted over 5 decades ago by Michael Kasha. K. showed that the Coulombic coupling between 2 mols., as detd. by the alignment of their transition dipoles, induces energetic shifts in the main absorption spectral peak and changes in the radiative decay rate when compared to uncoupled mols. In H-aggregates, the transition dipole moments align side-by-side leading to a spectral blue-shift and suppressed radiative decay rate, while in J-aggregates, the transition dipole moments align head-to-tail leading to a spectral red shift and an enhanced radiative decay rate. Although many examples of H- and J-aggregates were discovered, there are also many unconventional aggregates, which are not understood within the confines of Kasha's theory. Examples include nanopillars of 7,8,15,16-tetraazaterrylene, as well as several perylene-based dyes, which exhibit so-called H- to J-aggregate transformations. Such aggregates are typically characterized by significant wave function overlap between neighboring MOs of small (∼4 Å) intermol. distances, such as those found in rylene π-stacks and oligoacene herringbone lattices. Wave function overlap facilitates charge-transfer which creates an effective short-range exciton coupling that can also induce J- or H-aggregate behavior, depending on the sign. Unlike Coulomb coupling, short-range coupling is extremely sensitive to small (sub-Å) transverse displacements between neighboring chromophores. For perylene chromophores, the sign of the short-range coupling changes several times as 2 mols. are slipped from a side-by-side to head-to-tail configuration, in marked contrast to the sign of the Coulomb coupling, which changes only once. Such sensitivity allows J- to H-aggregate interconversions over distances several times smaller than those predicted by Kasha's theory. Since the total coupling drives exciton transport and photophys. properties, interference between the short- and long-range (Coulomb) couplings, as manifest by their relative signs and magnitudes, gives rise to a host of new aggregate types, referred to as HH, HJ, JH, and JJ aggregates, with distinct photophys. properties. An extreme example is the null HJ-aggregate in which total destructive interference leads to absorption line shapes practically identical to uncoupled mols. The severely compromised exciton bandwidth effectively shuts down energy transport. The new aggregates types described herein can be exploited for electronic materials design. The enhanced exciton bandwidth and weakly emissive properties of HH-aggregates make them ideal candidates for solar cell absorbers, while the enhanced charge mobility and strong emissive behavior of JJ-aggregates makes them excellent candidates for light-emitting diodes.
- 13Hestand, N. J.; Spano, F. C. Expanded Theory of H- and J-Molecular Aggregates: The Effects of Vibronic Coupling and Intermolecular Charge Transfer. Chem. Rev. 2018, 118, 7069– 7163, DOI: 10.1021/acs.chemrev.7b0058113https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXns1Cjurc%253D&md5=eb65f01278db2b376e55512f42ee286fExpanded Theory of H- and J-Molecular Aggregates: Effects of Vibronic Coupling and Intermolecular Charge TransferHestand, Nicholas J.; Spano, Frank C.Chemical Reviews (Washington, DC, United States) (2018), 118 (15), 7069-7163CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. The electronic excited states of mol. aggregates and their photophys. signatures have long fascinated spectroscopists and theoreticians alike since the advent of Frenkel exciton theory almost 90 years ago. The influence of mol. packing on basic optical probes like absorption and photoluminescence was originally worked out by Kasha for aggregates dominated by Coulombic intermol. interactions, eventually leading to the classification of J- and H-aggregates. This review outlines advances made in understanding the relationship between aggregate structure and photophysics when vibronic coupling and intermol. charge transfer are incorporated. An assortment of packing geometries is considered from the humble mol. dimer to more exotic structures including linear and bent aggregates, two-dimensional herringbone and "HJ" aggregates, and chiral aggregates. The interplay between long-range Coulomb coupling and short-range charge-transfer-mediated coupling strongly depends on the aggregate architecture leading to a wide array of photophys. behaviors.
- 14Zhong, C.; Bialas, D.; Collison, C. J.; Spano, F. C. Davydov Splitting in Squaraine Dimers. J. Phys. Chem. C 2019, 123, 18734– 18745, DOI: 10.1021/acs.jpcc.9b0529714https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhsVWjurzO&md5=937cb0798772723adb4a00bbb161da44Davydov Splitting in Squaraine DimersZhong, Chuwei; Bialas, David; Collison, Christopher J.; Spano, Frank C.Journal of Physical Chemistry C (2019), 123 (30), 18734-18745CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)The essential states model (ESM) for donor-acceptor-donor (D-A-D) chromophores is used to explore absorption and photoluminescence (PL) in mol. dimers composed of centrosym. and non-centrosym. squaraine mols. The spectral line shapes and shifts relative to the monomer spectrum are due to an interesting interplay between three-center charge distributions responsible for ground- and excited-state (permanent) dipole and quadrupole moments and two-center charge distributions responsible for transition dipole moments. The Davydov splitting is sensitive only to the interactions between the (extended) transition dipoles , whereas the permanent dipole-dipole and quadruple-quadrupole interactions impact the midpoint frequency of the two Davydov components, leading to a generally asym. splitting relative to the peak monomer transition frequency. The theory accurately reproduces the steady-state absorption and PL line shapes recently obtained for covalently bound squaraine dimers. The ESM also predicts an extreme type of non-Kasha behavior, where both Davydov components are blue-shifted above the monomer transition frequency.
- 15Abramavicius, D.; Mukamel, S. Exciton Dynamics in Chromophore Aggregates with Correlated Environment Fluctuations. J. Chem. Phys. 2011, 134, 174504– 174510, DOI: 10.1063/1.357945515https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXlslCmu7o%253D&md5=8b093609c81cd3cd62cf54f3deb09816Exciton dynamics in chromophore aggregates with correlated environment fluctuationsAbramavicius, Darius; Mukamel, ShaulJournal of Chemical Physics (2011), 134 (17), 174504/1-174504/10CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)The effects of correlated mol. transition energy fluctuations in mol. aggregates on the d. matrix dynamics, and their signatures in the optical response are studied. Correlated fluctuations do not affect single-exciton dynamics and can be described as a nonlocal contribution to the spectral broadening, which appears as a multiplicative factor in the time-domain response function. Intraband coherences are damped only by uncorrelated transition energy fluctuations. The signal can then be expressed as a spectral convolution of a local contribution of the uncorrelated fluctuations and the nonlocal contribution of the correlated fluctuations. (c) 2011 American Institute of Physics.
- 16Mirkovic, T.; Ostroumov, E. E.; Anna, J. M.; van Grondelle, R.; Govindjee; Scholes, G. D. Light Absorption and Energy Transfer in the Antenna Complexes of Photosynthetic Organisms. Chem. Rev. 2017, 117, 249– 293, DOI: 10.1021/acs.chemrev.6b0000216https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtFyit7vI&md5=7201884bb63ab70347f79f951ff3369aLight absorption and energy transfer in the antenna complexes of photosynthetic organismsMirkovic, Tihana; Ostroumov, Evgeny E.; Anna, Jessica M.; van Grondelle, Rienk; Govindjee; Scholes, Gregory D.Chemical Reviews (Washington, DC, United States) (2017), 117 (2), 249-293CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. The process of photosynthesis is initiated by the capture of sunlight by a network of light-absorbing mols. (chromophores), which are also responsible for the subsequent funneling of the excitation energy to the reaction centers. Through evolution, genetic drift, and speciation, photosynthetic organisms have discovered many solns. for light harvesting. In this review, we describe the underlying photophys. principles by which this energy is absorbed, as well as the mechanisms of electronic excitation energy transfer (EET). First, optical properties of the individual pigment chromophores present in light-harvesting antenna complexes are introduced, and then we examine the collective behavior of pigment-pigment and pigment-protein interactions. The description of energy transfer, in particular multichromophoric antenna structures, is shown to vary depending on the spatial and energetic landscape, which dictates the relative coupling strength between constituent pigment mols. In the latter half of the article, we focus on the light-harvesting complexes of purple bacteria as a model to illustrate the present understanding of the synergetic effects leading to EET optimization of light-harvesting antenna systems while exploring the structure and function of the integral chromophores. We end this review with a brief overview of the energy-transfer dynamics and pathways in the light-harvesting antennas of various photosynthetic organisms.
- 17Spano, F. C. The Spectral Signatures of Frenkel Polarons in H- and J-Aggregates. Acc. Chem. Res. 2010, 43, 429– 439, DOI: 10.1021/ar900233v17https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhsFKgurzL&md5=a66d2effbaf73a403bf00e6e198efe0aThe Spectral Signatures of Frenkel Polarons in H- and J-AggregatesSpano, Frank C.Accounts of Chemical Research (2010), 43 (3), 429-439CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)A review. Electronic excitations in small aggregates, thin films, and crystals of conjugated org. mols. play a fundamental role in the operation of a wide array of org.-based devices including solar cells, transistors, and light-emitting diodes. Such excitations, or excitons, are generally spread out over several mols.: a balance between the delocalizing influence of resonant intermol. coupling and the localizing influence of static and dynamic disorder dets. the coherence range of the exciton. Because of the soft nature of org. materials, significant nuclear relaxation in the participating mols. also accompanies the electronic excitations. To properly understand energy or charge transport, 1 must treat intermol. (excitonic) coupling, electron-vibrational coupling, and disorder on equal footing. In this Account, the authors review the key elements of a theor. approach based on a multiparticle representation that describes electronic excitations in org. materials as vibronic excitations surrounded by a field of vibrational excitations. Such composite excitations are appropriately called Frenkel excitonic polarons. For many conjugated mols., the bulk of the nuclear reorganization energy following electronic excitation arises from the elongation of a sym. vinyl stretching mode with energy ∼1400 cm-1. To appreciate the impact of aggregation, the authors study how the vibronic progression of this mode, which dominates the isolated (solvated) mol. absorption and emission spectra, is distorted when mols. are close enough to interact with each other. As the authors demonstrate in this Account, the nature of the distortion provides a wealth of information about how the mols. are packed, the strength of the excitonic interactions between mols., the no. of mols. that are coherently coupled, and the nature of the disorder. The aggregation-induced deviations from the Poissonian distribution of vibronic peak intensities take on 2 extremes identified with ideal H- and J-aggregates. The sign of the nearest neighbor electronic coupling, pos. for H and neg. for J, distinguishes the 2 basic aggregate forms. For several decades, researchers have known that H-aggregates exhibit blue-shifted absorption spectra and are subradiant while J-aggregates exhibit the opposite behavior (red shifted absorption and superradiance). However, the exact inclusion of exciton-vibrational coupling reveals several more distinguishing traits between the 2 aggregate types: in H(J)-aggregates the ratio of the 1st 2 vibronic peak intensities in the absorption spectrum decreases (increases) with increasing excitonic coupling, while the ratio of the 0-0 to 0-1 emission intensities increases (decreases) with disorder and increases (decreases) with increasing temp. These 2 extreme behaviors provide the framework for understanding absorption and emission in more complex morphologies, such as herringbone packing in oligo(phenylene vinylene)s, oligothiophenes and polyacene crystals, as well as the polymorphic packing arrangements obsd. in carotenoids.
- 18Renger, T.; May, V.; Kühn, O. Ultrafast Excitation Energy Transfer Dynamics in Photosynthetic Pigment–Protein Complexes. Phys. Rep. 2001, 343, 137– 254, DOI: 10.1016/S0370-1573(00)00078-818https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3MXhsVemsrs%253D&md5=50ce79c52301b5d9908904b28e57471aUltrafast excitation energy transfer dynamics in photosynthetic pigment-protein complexesRenger, T.; May, V.; Kuhn, O.Physics Reports (2001), 343 (3), 137-254CODEN: PRPLCM; ISSN:0370-1573. (Elsevier Science B.V.)A review contg. 239 refs. Photosynthetically active membranes of certain bacteria and higher plants contain antenna systems which surround the reaction center to increase its absorption cross section for the incoming sun light. The excitation energy created in the antenna pigments is transferred via an exciton mechanism to the reaction center where charge sepn. takes place. Sub-picosecond laser spectroscopy makes it possible to follow the initial dynamic events of excitation energy (exciton) motion and exciton relaxation in real time. On the other hand, the success of structure resoln. opened the door to the microscopic understanding of spectroscopic data and to an appreciation of the structure-function relationship realized in different systems. Here, it will be demonstrated how the combination of microscopically based theor. models and numerical simulations pave the road from spectroscopic data to a deeper understanding of the functionality of photosynthetic antenna systems. The d. matrix technique is introduced as the theor. tool providing a unified description of the processes which follow ultrafast laser excitation. This includes in particular coherent exciton motion, vibrational coherences, exciton relaxation, and exciton localization. It can be considered as a major result of recent investigations that a theor. model of intermediate complexity was shown to be suitable to explain a variety of expts. on different photosynthetic antenna systems. We start with introducing the structural components of antenna systems and discuss their general function. In the second part the formulation of the appropriate theor. model as well as the simulation of optical spectra is reviewed in detail. Emphasis is put on the mapping of the complex protein structure and its hierarchy of dynamic phenomena onto models of static and dynamic disorder. In particular, it is shown that the protein spectral d. plays a key role in characterizing excitation energy dissipation. The theor. concepts are illustrated in the third part by results of numerical simulations of linear and nonlinear optical expts. for three types of antennae: the peripheral light-harvesting complex 2 of purple bacteria, the Fenna-Mathew-Olson complex of green bacteria, and the light-harvesting complex of photosystem II of green plants.
- 19Schulze, J.; Kühn, O. Explicit Correlated Exciton-Vibrational Dynamics of the FMO Complex. J. Phys. Chem. B 2015, 119, 6211– 6216, DOI: 10.1021/acs.jpcb.5b0392819https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXnsVeisL0%253D&md5=da605f66b2c7c7f4bee69f2068dcaa36Explicit Correlated Exciton-Vibrational Dynamics of the FMO ComplexSchulze, J.; Kuehn, O.Journal of Physical Chemistry B (2015), 119 (20), 6211-6216CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)The coupled exciton-vibrational dynamics of a three-site model of the Fenna-Matthews-Olson complex is investigated using the numerically exact multilayer multiconfiguration time-dependent Hartree approach. Thereby the specific coupling of the vibrational modes to local electronic transitions is adapted from a discretized exptl. spectral d. The soln. of the resulting time-dependent Schr.ovrddot.odinger equation including three electronic and 450 vibrational degrees of freedom is analyzed in terms of excitonic populations and coherences. Emphasis is put onto the role of specific ranges of vibrational frequencies. It is obsd. that modes between 160 and 300 cm-1 are responsible for the sub-picosecond population and coherence decay. Further, it is found that a mean-field approach with respect to the vibrational degrees of freedom is not applicable.
- 20Tretiak, S.; Mukamel, S. Density Matrix Analysis and Simulation of Electronic Excitations in Conjugated and Aggregated Molecules. Chem. Rev. 2002, 102, 3171– 3212, DOI: 10.1021/cr010125220https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XmsFSqtbY%253D&md5=e786f9963e003aaac58850d89142c063Density Matrix Analysis and Simulation of Electronic Excitations in Conjugated and Aggregated MoleculesTretiak, Sergei; Mukamel, ShaulChemical Reviews (Washington, DC, United States) (2002), 102 (9), 3171-3212CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. A discussion is presented on the collective electronic oscillator (CEO) formalism, electronic coherence sizes underlying the optical response of conjugated mols., optical response in chromophore aggregates.
- 21Richter, M.; Ahn, K. J.; Knorr, A.; Schliwa, A.; Bimberg, D.; Madjet, M. E.-A.; Renger, T. Theory of Excitation Transfer in Coupled Nanostructures – from Quantum Dots to Light Harvesting Complexes. Phys. Status Solidi B 2006, 243, 2302– 2310, DOI: 10.1002/pssb.20066805321https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XovFOisLs%253D&md5=b56c66a0de8f80a2b37e4f4eb677b832Theory of excitation transfer in coupled nanostructures. From quantum dots to light harvesting complexesRichter, Marten; Ahn, Kwang Jun; Knorr, Andreas; Schliwa, Andrei; Bimberg, Dieter; El-Amine Madjet, Mohamed; Renger, ThomasPhysica Status Solidi B: Basic Solid State Physics (2006), 243 (10), 2302-2310CODEN: PSSBBD; ISSN:0370-1972. (Wiley-VCH Verlag GmbH)Spatially localized but electromagnetically coupled electrons are model systems for excitation transfer on nanoscales. A unified description of coupled semiconductor quantum dots and coupled chlorophylls in light harvesting complexes is presented, considering Coulomb interaction including excitonic Foerster-coupling and (bi-) excitonic shifts as well as electron-phonon interaction. Linear absorption spectra are calcd. and principles for the description of third order optical nonlinearities are outlined.
- 22Asanuma, H.; Fujii, T.; Kato, T.; Kashida, H. Coherent Interactions of Dyes Assembled on DNA. J. Photochem. Photobiol., C 2012, 13, 124– 135, DOI: 10.1016/j.jphotochemrev.2012.04.00222https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XntVWhtbk%253D&md5=a6cea5584e14c9a209e452cc91db26a2Coherent interactions of dyes assembled on DNAAsanuma, Hiroyuki; Fujii, Taiga; Kato, Tomohiro; Kashida, HiromuJournal of Photochemistry and Photobiology, C: Photochemistry Reviews (2012), 13 (2), 124-135CODEN: JPPCAF; ISSN:1389-5567. (Elsevier B.V.)A review. The optical behavior of an organized dye assembly is different from that of the isolated dye; this difference is explained using mol. exciton theory. The theory predicts that mutual orientation, the no. of dyes in the cluster, and combinations of different dyes should display given characteristic spectroscopic behaviors due to coherent interactions. Comparison of theor. predictions with exptl. results has been limited so far. One of the reasons is the absence of a rigid and well-organized system that can control the orientation and size of the dye assembly. Recently, the DNA duplex has been used to assemble chromophores in a programmed manner. Use of DNA allows organized dye assembly with a given size and particular orientation. In this review, we evaluate the spectroscopic behavior of the H-type aggregate based on mol. exciton theory and compare it with actual dye assembly with DNA duplex. Furthermore, we demonstrate the importance of coherent interactions on the obsd. optical properties of dyes assembled in a DNA duplex.
- 23Czikklely, V.; Forsterling, H. D.; Kuhn, H. Extended Dipole Model for Aggregates of Dye Molecules. Chem. Phys. Lett. 1970, 6, 207– 210, DOI: 10.1016/0009-2614(70)80220-2There is no corresponding record for this reference.
- 24Jelley, E. E. Spectral Absorption and Fluorescence of Dyes in the Molecular State. Nature 1936, 138, 1009– 1010, DOI: 10.1038/1381009a024https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaA2sXht1Gmtg%253D%253D&md5=cc8df78b75b185f7d9581cdddde20711Spectral absorption and fluorescence of dyes in the molecular stateJelley, Edwin E.Nature (London, United Kingdom) (1936), 138 (), 1009-10CODEN: NATUAS; ISSN:0028-0836.Resonance radiation was observed in suspensions of several dyes. Three general methods of prepn. each cause the dye to pass from the dissocd. state in true soln., through a transitory mol. state which exhibits a characteristic absorption and fluorescence, to the cryst. state. The effect is shown strikingly by 1,1'-diethyl-ψ-cyanine chloride. The methods: (1) A concd. soln. in a strongly polar solvent (PhNO2, pyridine) is rapidly dild. with a nonpolar or feebly polar liquid (ligroin, CCl4, C6H6, PhMe, xylene). (2) The dye is dissolved in a strongly polar substance (such as benzophenone) which is crystd. by a sudden chilling, some of the dye remaining molecularly dispersed in the solid. The position of the band depends on the salt of the dye, but not on the dispersing solid. The sharp absorption band is not dichroic (not a function of the vibrational direction); absorption bands of the cryst. dye are strongly dichroic. The method is general for salts of basic dyes. (3) A soln. in MeOH or EtOH is added to 5 M NaCl. A strong fluorescence at 577 mμ and an absorption band at 574 mμ develop. The absorption and fluorescence disappear reversibly at 60°; a similar reversibility occurs on varying the alc. concn. In each of the 3 methods a transient mol. absorption occurs, with a duration from less than a sec. to a few weeks. The fluorescence is unpolarized. In adsorbed dyes (walls of the containing vessel, filter paper, cotton wool, kaolin) the effect sometimes lasts a min. or so, and then disappears rapidly. A similar type of narrow absorption band assocd. with fluorescence of about the same wave length occurs in the ruby: synthetic rubies are made by a process which corresponds to method (2).
- 25Jelley, E. E. Molecular, Nematic and Crystal States of I: I-Diethyl--Cyanine Chloride. Nature 1937, 139, 631, DOI: 10.1038/139631b025https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaA2sXjt1Cmsw%253D%253D&md5=9c7189699c679fb051e243c2b5f8ed8fMolecular, nematic and crystal states of 1,1'-diethyl-ψ-cyanine chlorideJelley, Edwin E.Nature (London, United Kingdom) (1937), 139 (), 631-2CODEN: NATUAS; ISSN:0028-0836.cf. C. A. 31, 1703.6. By use of spectrographic, ultramicroscopic and streaming birefringence methods in the study of dispersions of 1,1'-diethyl-ψ-cyanine chloride in NaCl solns., it is shown that the dye passes from the dissocd. state through a mol. phase of very brief duration to form very thin threads. These threads are cryst. in the direction of their length only, and correspond to the nematic type of liquid crystal. The abnormal viscosity noted by Scheibe, Kandler and Ecker (C. A. 31, 3785.6) is due, not to a reversible polymerization of the dye ions, but to nematic aggregates of dye mols.
- 26Scheibe, G. ÜBer Die VeräNderlichkeit Der Absorptionsspektren in LöSungen Und Die Nebenvalenzen Als Ihre Ursache. Angew. Chem. 1937, 50, 212– 219, DOI: 10.1002/ange.1937050110326https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaA2sXislegsg%253D%253D&md5=f3123e579aa0f24544a5c349698a3dbdThe variation of absorption spectra in solutions and the side valences as its causeScheibe, G.Angewandte Chemie (1937), 50 (), 212-19CODEN: ANCEAD; ISSN:0044-8249.A comprehensive treatise with forty-five references.
- 27Koepke, J.; Hu, X.; Muenke, C.; Schulten, K.; Michel, H. The Crystal Structure of the Light-Harvesting Complex II (B800-850) from Rhodospirillum Molischianum. Structure 1996, 4, 581– 597, DOI: 10.1016/S0969-2126(96)00063-927https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XjsVKlsb4%253D&md5=35997bc28f1daaaa4db29192b3131ca0The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianumKoepke, Juergen; Hu, Xiche; Muenke, Cornelia; Schulten, Klaus; Michel, HartmutStructure (London) (1996), 4 (5), 581-597CODEN: STRUE6; ISSN:0969-2126. (Current Biology)The light-harvesting complexes II (LH-2s) are integral membrane proteins that form ring-like structures, oligomers of αβ-heterodimers, in the photosynthetic membranes of purple bacteria. They contain a large no. of chromophores organized optimally for light absorption and rapid light energy migration. Recently, the structure of the nonameric LH-2 of Rhodopseudomonas acidophila has been detd.; we report here the crystal structure of the octameric LH-2 from Rhodospirillum molischianum. The unveiling of similarities and differences in the architecture of these proteins may provide valuable insight into the efficient energy transfer mechanisms of bacterial photosynthesis. The crystal structure of LH-2 from Rs. molischianum has been detd. by mol. replacement at 2.4 Å resoln. using X-ray diffraction. The crystal structure displays two concentric cylinders of sixteen membrane-spanning helical subunits, contg. two rings of bacteriochlorophyll-a (BChl-a) mols. One ring comprises sixteen B850 BChl-as perpendicular to the membrane plane and the other eight B800 BChl-as that are nearly parallel to the membrane plane; eight membrane-spanning lycopenes (the major carotenoid in this complex) stretch out between the B800 and B850 BCHl-as. The B800 BChl-as exhibit a different ligation from that of Rps. acidophila (aspartate is the Mg ligand as opposed to formyl-methionine in Rps. acidophila). The light-harvesting complexes from different bacteria assume various ring sizes. In LH-2 of Rs. molischianum, the Qy transition dipole moments of neighboring B850 and B800 BChl-as are nearly parallel to each other, i.e., they are optimally aligned for Foerster exciton transfer. Dexter energy transfer between these chlorophylls is also possible through interactions mediated by lycopenes and B850 BChl-a phytyl tails; the B800 BChl-a and one of the two B850 BChl-as assocd. with each heterodimeric unit are in van der Waals distance to a lycopene, such that singlet and triplet energy transfer between lycopene and the BChl-as can occur by the Dexter mechanism. The ring structure of the B850 BChl-as is optimal for light energy transfer in that it samples all spatial absorption and emission characteristics and places all oscillator strength into energetically low lying, thermally accessible exciton states.
- 28Chachisvilis, M.; Kuhn, O.; Pullerits, T.; Sundstrom, V. Excitons in Photosynthetic Purple Bacteria: Wavelike Motion or Incoherent Hopping?. J. Phys. Chem. B 1997, 101, 7275– 7283, DOI: 10.1021/jp963360a28https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXlsVSns70%253D&md5=ced8c8f2acdfa49361576a1a2e327445Excitons in photosynthetic purple bacteria: Wavelike motion or incoherent hopping?Chachisvilis, Mirianas; Kuehn, Oliver; Pullerits, Tonu; Sundstroem, VillyJournal of Physical Chemistry B (1997), 101 (37), 7275-7283CODEN: JPCBFK; ISSN:1089-5647. (American Chemical Society)The authors have studied excitation energy transfer in the photosynthetic antenna systems LH1 and LH2 of purple bacteria. Femtosecond pump-probe expts. are combined with computer simulations using the recently established crystal structure of these systems to assess the nature of excitation motion. The authors have measured the transient absorption kinetics and spectra of the LH1 and LH2 complexes in the temp. range from 4.2 to 296 K with femtosecond time resoln. The calcns. based on the Pauli master equation disagreed with exptl. measured population and anisotropy kinetics, suggesting that the simple model of excitation hopping between bacteriochlorophyll a mols. is not a proper description for energy transport in LH1 and LH2. As a next step, the authors have used the exciton theory to reproduce the transient absorption spectra of LH2, and we found that the coherence length of the exciton in B850 of LH2 1.5 ps after excitation of B800 is 4 ± 1.
- 29Hu, X.; Damjanovic, A.; Ritz, T.; Schulten, K. Architecture and Mechanism of the Light-Harvesting Apparatus of Purple Bacteria. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 5935– 5941, DOI: 10.1073/pnas.95.11.593529https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1cXjtlKgs74%253D&md5=725f4350878a0c1db38538e554361c6cArchitecture and mechanism of the light-harvesting apparatus of purple bacteriaHu, Xiche; Damjanovic, Ana; Ritz, Thorsten; Schulten, KlausProceedings of the National Academy of Sciences of the United States of America (1998), 95 (11), 5935-5941CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Photosynthetic organisms fuel their metab. with light energy and have developed for this purpose an efficient app. for harvesting sunlight. The at. structure of the app., as it evolved in purple bacteria, has been constructed through a combination of x-ray crystallog., electron microscopy, and modeling. The detailed structure and overall architecture reveals a hierarchical aggregate of pigments that utilizes, as shown through femtosecond spectroscopy and quantum physics, elegant and efficient mechanisms for primary light absorption and transfer of electronic excitation toward the photosynthetic reaction center.
- 30Jonas, D. M.; Lang, M. J.; Nagasawa, Y.; Joo, T.; Fleming, G. R. Pump-Probe Polarization Anisotropy Study of Femtosecond Energy Transfer within the Photosynthetic Reaction Center of Rhodobacter Sphaeroides R26. J. Phys. Chem. A 1996, 100, 12660– 12673, DOI: 10.1021/jp960708t30https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XjvFCit7w%253D&md5=54891085ed6983477104cdca1c659002Pump-Probe Polarization Anisotropy Study of Femtosecond Energy Transfer within the Photosynthetic Reaction Center of Rhodobacter sphaeroides R26Jonas, David M.; Lang, Matthew J.; Nagasawa, Yutaka; Joo, Taiha; Fleming, Graham R.Journal of Physical Chemistry (1996), 100 (30), 12660-12673CODEN: JPCHAX; ISSN:0022-3654. (American Chemical Society)The energy transfer from the accessory bacteriochlorophylls (B) to the special pair (P) in the photosynthetic reaction center has been time resolved with pump-probe polarization anisotropy measurements using 20-25 fs duration pulses near 800 nm. The expts. were carried out at low pulse energies (500 pJ in a 34 μm spot), low repetition rates (5 kHz), and high sample flow velocities (100 cm/s) to avoid artifacts from satn. and photoexcitation of incompletely relaxed reaction centers. The pump excitation corresponds to 1.4 × 106 photons/μm2: the "satn. intensity" for the charge sepn. quantum yield is 3 × 107 photons/μm2. Magic angle pump-probe transients can be satisfactorily fit as biexponential, with an ∼120 fs bleach decay followed by a 2.8 ps bleach rise. (An ∼400 fs bleach decay seen in several previous expts. arises from unrelaxed reaction centers.) The initial pump-probe anisotropy is 0.4 and decays with an ∼80 fs time const., which we attribute to dipole reorientation by electronic energy transfer. Simultaneous kinetic modeling of the parallel, perpendicular, and magic angle pump-probe transients using the reaction center structure and dipole orientations is consistent with energy transfer proceeding in two steps: ∼80 fs electronic energy transfer from the accessory bacteriochlorophylls to the upper exciton component of the special pair (B → P+) followed by an ∼150 fs internal conversion from the upper exciton component to the lower exciton component of the special pair (P+ → P-). Finally, charge sepn. after electron transfer from P- to H causes an electrochromic (Stark) shift of B and produces the 2.8 ps bleach rise. The two-step energy transfer model is supported by the observation of weak quantum beat oscillations (125 cm-1 and 227 cm-1) with near-zero anisotropy in the pump-probe signals. The near-zero anisotropy is only consistent with pump-probe signals from P+ species created by energy transfer from B. The ∼80 fs B → P+ energy transfer is so rapid that it sets vibrational wave packets in motion on the special pair. Because B → P energy transfer is more rapid than conventional energy transfer rates, it may be more appropriate to think of energy transfer between pigments in the reaction center as an intermediate case between energy transfer among sep. pigments and internal conversion within a single supermol.
- 31Arpin, P. C.; Turner, D. B.; McClure, S. D.; Jumper, C. C.; Mirkovic, T.; Challa, J. R.; Lee, J.; Teng, C. Y.; Green, B. R.; Wilk, K. E. Spectroscopic Studies of Cryptophyte Light Harvesting Proteins: Vibrations and Coherent Oscillations. J. Phys. Chem. B 2015, 119, 10025– 10034, DOI: 10.1021/acs.jpcb.5b0470431https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtFyru7nO&md5=2b38e1b9a1e52da45733ea0c3e743352Spectroscopic Studies of Cryptophyte Light Harvesting Proteins: Vibrations and Coherent OscillationsArpin, Paul C.; Turner, Daniel B.; McClure, Scott D.; Jumper, Chanelle C.; Mirkovic, Tihana; Challa, J. Reddy; Lee, Joohyun; Teng, Chang Ying; Green, Beverley R.; Wilk, Krystyna E.; Curmi, Paul M. G.; Hoef-Emden, Kerstin; McCamant, David W.; Scholes, Gregory D.Journal of Physical Chemistry B (2015), 119 (31), 10025-10034CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)The first step of photosynthesis is the absorption of light by antenna complexes. Recent studies of light-harvesting complexes using two-dimensional electronic spectroscopy have revealed interesting coherent oscillations. Some contributions to those coherences are assigned to electronic coherence and therefore have implications for theories of energy transfer. To assign these femtosecond data and to gain insight into the interplay among electronic and vibrational resonances, we need detailed information on vibrations and coherences in the excited electronic state compared to the ground electronic state. Here, we used broad-band transient absorption and femtosecond stimulated Raman spectroscopies to record ground- and excited-state coherences in four related photosynthetic proteins: PC577 from Hemiselmis pacifica CCMP706, PC612 from Hemiselmis virescens CCAC 1635 B, PC630 from Chroomonas CCAC 1627 B (marine), and PC645 from Chroomonas mesostigmatica CCMP269. Two of those proteins (PC630 and PC645) have strong electronic coupling while the other two proteins (PC577 and PC612) have weak electronic coupling between the chromophores. We report vibrational spectra for the ground and excited electronic states of these complexes as well as an anal. of coherent oscillations obsd. in the broad-band transient absorption data.
- 32Brixner, T.; Hildner, R.; Kohler, J.; Lambert, C.; Wurthner, F. Exciton Transport in Molecular Aggregates - from Natural Antennas to Synthetic Chromophore Systems. Adv. Energy Mater. 2017, 7, 1700236 DOI: 10.1002/aenm.201700236There is no corresponding record for this reference.
- 33Graugnard, E.; Kellis, D. L.; Bui, H.; Barnes, S.; Kuang, W.; Lee, J.; Hughes, W. L.; Knowlton, W. B.; Yurke, B. DNA-Controlled Excitonic Switches. Nano Lett. 2012, 12, 2117– 2122, DOI: 10.1021/nl300433633https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XjsVSrt7o%253D&md5=b1d332b925c3578e90db2a452b15ef7aDNA-Controlled Excitonic SwitchesGraugnard, Elton; Kellis, Donald L.; Bui, Hieu; Barnes, Stephanie; Kuang, Wan; Lee, Jeunghoon; Hughes, William L.; Knowlton, William B.; Yurke, BernardNano Letters (2012), 12 (4), 2117-2122CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)Fluorescence resonance energy transfer (FRET) is a promising means of enabling information processing in nanoscale devices, but dynamic control over exciton pathways is required. Here, we demonstrate the operation of two complementary switches consisting of diffusive FRET transmission lines in which exciton flow is controlled by DNA. Repeatable switching is accomplished by the removal or addn. of fluorophores through toehold-mediated strand invasion. In principle, these switches can be networked to implement any Boolean function.
- 34Cannon, B. L.; Kellis, D. L.; Davis, P. H.; Lee, J.; Kuang, W.; Hughes, W. L.; Graugnard, E.; Yurke, B.; Knowlton, W. B. Excitonic and Logic Gates on DNA Brick Nanobreadboards. ACS Photonics 2015, 2, 398– 404, DOI: 10.1021/ph500444d34https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXivFSrtrc%253D&md5=508e9646c05bd709bf29547e2a71f2d7Excitonic AND Logic Gates on DNA Brick NanobreadboardsCannon, Brittany L.; Kellis, Donald L.; Davis, Paul H.; Lee, Jeunghoon; Kuang, Wan; Hughes, William L.; Graugnard, Elton; Yurke, Bernard; Knowlton, William B.ACS Photonics (2015), 2 (3), 398-404CODEN: APCHD5; ISSN:2330-4022. (American Chemical Society)A promising application of DNA self-assembly is the fabrication of chromophore-based excitonic devices. DNA brick assembly is a compelling method for creating programmable nanobreadboards on which chromophores may be rapidly and easily repositioned to prototype new excitonic devices, optimize device operation, and induce reversible switching. Using DNA nanobreadboards, the authors demonstrated each of these functions through the construction and operation of two different excitonic AND logic gates. The modularity and high chromophore d. achievable via this brick-based approach provide a viable path toward developing information processing and storage systems.
- 35Kellis, D. L.; Rehn, S. M.; Cannon, B. L.; Davis, P. H.; Graugnard, E.; Lee, J.; Yurke, B.; Knowlton, W. B. DNA-Mediated Excitonic Upconversion FRET Switching. New J. Phys. 2015, 17, 115007 DOI: 10.1088/1367-2630/17/11/11500735https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XpsFyksr4%253D&md5=34809198b6a387fbe13f5ccdffe14daeDNA-mediated excitonic upconversion FRET switchingKellis, Donald L.; Rehn, Sarah M.; Cannon, Brittany L.; Davis, Paul H.; Graugnard, Elton; Lee, Jeunghoon; Yurke, Bernard; Knowlton, William B.New Journal of Physics (2015), 17 (Nov.), 115007/1-115007/11CODEN: NJOPFM; ISSN:1367-2630. (IOP Publishing Ltd.)Excitonics is a rapidly expanding field of nanophotonics in which the harvesting of photons, ensuing creation and transport of excitons via F.ovrddot.orster resonant energy transfer (FRET), and subsequent charge sepn. or photon emission has led to the demonstration of excitonic wires, switches, Boolean logic and light harvesting antennas for many applications. FRET funnels excitons down an energy gradient resulting in energy loss with each step along the pathway. Conversely, excitonic energy upconversion via upconversion nanoparticles (UCNPs), although currently inefficient, serves as an energy ratchet to boost the exciton energy. Although FRET-based upconversion has been demonstrated, it suffers from low FRET efficiency and lacks the ability to modulate the FRET.Wehave engineered an upconversion FRET-based switch by combining lanthanide-doped UCNPs and fluorophores that demonstrates excitonic energy upconversion by nearly a factor of 2, an excited state donor to acceptor FRET efficiency of nearly 25%, and an acceptor fluorophore quantum efficiency that is close to unity. These findings offer a promising path for energy upconversion in nanophotonic applications including artificial light harvesting, excitonic circuits, photovoltaics, nanomedicine, and optoelectronics.
- 36Wang, S. Y.; Lebeck, A. R.; Dwyer, C. Nanoscale Resonance Energy Transfer-Based Devices for Probabilistic Computing. IEEE Micro 2015, 35, 72– 84, DOI: 10.1109/MM.2015.124There is no corresponding record for this reference.
- 37Sawaya, N. P. D.; Rappoport, D.; Tabor, D. P.; Aspuru-Guzik, A. Excitonics: A Set of Gates for Molecular Exciton Processing and Signaling. ACS Nano 2018, 12, 6410– 6420, DOI: 10.1021/acsnano.8b0058437https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhtFKlsrbI&md5=78778908f0ed9dd660e61c3fde263f5bExcitonics: A Set of Gates for Molecular Exciton Processing and SignalingSawaya, Nicolas P. D.; Rappoport, Dmitrij; Tabor, Daniel P.; Aspuru-Guzik, AlanACS Nano (2018), 12 (7), 6410-6420CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)Regulating energy transfer pathways through materials is a central goal of nanotechnol., as a greater degree of control is crucial for developing sensing, spectroscopy, microscopy, and computing applications. Such control necessitates a toolbox of actuation methods that can direct energy transfer based on user input. A proposal is introduced for a mol. exciton gate, analogous to a traditional transistor, for regulating exciton flow in chromophoric systems. The gate may be activated with an input of light or an input flow of excitons. The proposal relies on excitation migration via the 2nd excited singlet (S2) state of the gate mol. It exhibits the following features, only a subset of which are present in previous exciton switching schemes: ps time scale actuation, amplification/gain behavior, and a lack of mol. rearrangement. The device can be used to produce universal binary logic or amplification of an exciton current, providing an excitonic platform with several potential uses, including signal processing for microscopy and spectroscopy methods that implement tunable exciton flux.
- 38Ostroverkhova, O. Organic Optoelectronic Materials: Mechanisms and Applications. Chem. Rev. 2016, 116, 13279– 13412, DOI: 10.1021/acs.chemrev.6b0012738https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xhs1egsLnM&md5=4ab815e1951d3749bf2a5bbd93106a9bOrganic Optoelectronic Materials: Mechanisms and ApplicationsOstroverkhova, OksanaChemical Reviews (Washington, DC, United States) (2016), 116 (22), 13279-13412CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. Org. (opto)electronic materials have received considerable attention due to their applications in thin-film-transistors, light-emitting diodes, solar cells, sensors, photorefractive devices, and many others. The technol. promises include low cost of these materials and the possibility of their room-temp. deposition from soln. on large-area and/or flexible substrates. The article reviews the current understanding of the phys. mechanisms that det. the (opto)electronic properties of high-performance org. materials. The focus of the review is on photoinduced processes and on electronic properties important for optoelectronic applications relying on charge carrier photogeneration. Addnl., it highlights the capabilities of various exptl. techniques for characterization of these materials, summarizes top-of-the-line device performance, and outlines recent trends in the further development of the field. The properties of materials based both on small mols. and on conjugated polymers are considered, and their applications in org. solar cells, photodetectors, and photorefractive devices are discussed.
- 39Bardeen, C. J. The Structure and Dynamics of Molecular Excitons. Annu. Rev. Phys. Chem. 2014, 65, 127– 148, DOI: 10.1146/annurev-physchem-040513-10365439https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtVKjtLvM&md5=476fafa72e54b9775dd1be2c85d785d1The structure and dynamics of molecular excitonsBardeen, Christopher J.Annual Review of Physical Chemistry (2014), 65 (), 127-148CODEN: ARPLAP; ISSN:0066-426X. (Annual Reviews)A review. The photophys. behavior of org. semiconductors is governed by their excitonic states. In this review, I classify the three different exciton types (Frenkel singlet, Frenkel triplet, and charge transfer) typically encountered in org. semiconductors. Exptl. challenges that arise in the study of solid-state org. systems are discussed. The steady-state spectroscopy of intermol. delocalized Frenkel excitons is described, using cryst. tetracene as an example. I consider the problem of a localized exciton diffusing in a disordered matrix in detail, and exptl. results on conjugated polymers and model systems suggest that energetic disorder leads to subdiffusive motion. Multiexciton processes such as singlet fission and triplet fusion are described, emphasizing the role of spin state coherence and magnetic fields in studying singlet ↔ triplet pair interconversion. Singlet fission provides an example of how all three types of excitons (triplet, singlet, and charge transfer) may interact to produce useful phenomena for applications such as solar energy conversion.
- 40Eisfeld, A.; Briggs, J. S. The J-Band of Organic Dyes: Lineshape and Coherence Length. Chem. Phys. 2002, 281, 61– 70, DOI: 10.1016/S0301-0104(02)00594-340https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XkvFChtLs%253D&md5=4ec746cf9b355203250cab9a08377c2eThe J-band of organic dyes: lineshape and coherence lengthEisfeld, Alexander; Briggs, John S.Chemical Physics (2002), 281 (1), 61-70CODEN: CMPHC2; ISSN:0301-0104. (Elsevier Science B.V.)Self-organized J-aggregates of dye mols., known for >60 yr, are emerging as remarkably versatile quantum systems with applications in photog., opto-electronics, solar cells, photobiol. and as supra-mol. fibers. Recently there was much effort to achieve quantum entanglement and coherence on the nanoscale in atom traps and quantum dot aggregates (for use in quantum computing). The excitonic state of the J-aggregate is a textbook case of mesoscopic quantum coherence and entanglement. The establishment of coherence can literally be seen since the dye changes color dramatically on aggregation due to strong shifts in the absorption spectrum. In a simple theory the shifts and shapes of optical absorption spectra upon aggregation to a polymer are reproduced, and the coherence length of quantum entanglement of monomer wavefunctions are calcd.
- 41Thilagam, A. Entanglement Dynamics of J-Aggregate Systems. J. Phys. A: Math. Theor. 2011, 44, 135306 DOI: 10.1088/1751-8113/44/13/135306There is no corresponding record for this reference.
- 42Sarovar, M.; Ishizaki, A.; Fleming, G. R.; Whaley, K. B. Quantum Entanglement in Photosynthetic Light-Harvesting Complexes. Nat. Phys. 2010, 6, 462– 467, DOI: 10.1038/nphys165242https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXmslChsbw%253D&md5=31b0159b3b3e627fc121cb1ecc45cc2dQuantum entanglement in photosynthetic light-harvesting complexesSarovar, Mohan; Ishizaki, Akihito; Fleming, Graham R.; Whaley, K. BirgittaNature Physics (2010), 6 (6), 462-467CODEN: NPAHAX; ISSN:1745-2473. (Nature Publishing Group)Light-harvesting components of photosynthetic organisms are complex, coupled, many-body quantum systems, in which electronic coherence has recently been shown to survive for relatively long timescales, despite the decohering effects of their environments. Here, we analyze entanglement in multichromophoric light-harvesting complexes, and establish methods for quantification of entanglement by describing necessary and sufficient conditions for entanglement and by deriving a measure of global entanglement. These methods are then applied to the Fenna-Matthews-Olson protein to ext. the initial state and temp. dependencies of entanglement. We show that, although the Fenna-Matthews-Olson protein in natural conditions largely contains bipartite entanglement between dimerized chromophores, a small amt. of long-range and multipartite entanglement should exist even at physiol. temps. This constitutes the first rigorous quantification of entanglement in a biol. system. Finally, we discuss the practical use of entanglement in densely packed mol. aggregates such as light-harvesting complexes.
- 43Thilagam, A. Quantum Information Processing Attributes of J-Aggregates; World Scientific Publishing Company: Singapore, 2012; Vol. 2.There is no corresponding record for this reference.
- 44Ball, P. Physics of Life: The Dawn of Quantum Biology. Nature 2011, 474, 272– 274, DOI: 10.1038/474272a44https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXnsFOqsLc%253D&md5=5bc81aac8b360e7b6a9c4c7d062b94c5Physics of life: The dawn of quantum biologyBall, PhilipNature (London, United Kingdom) (2011), 474 (7351), 272-274CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)The key to practical quantum computing and high-efficiency solar cells may lie in the messy green world outside the physics lab.
- 45Lloyd, S. Quantum Coherence in Biological Systems. J. Phys.: Conf. Ser. 2011, 302, 012037 DOI: 10.1088/1742-6596/302/1/01203745https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtFSku7bP&md5=bc97885fd5a4bd840afc0289bd52da4cQuantum coherence in biological systemsLloyd, SethJournal of Physics: Conference Series (2011), 302 (), 012037/1-012037/5CODEN: JPCSDZ; ISSN:1742-6588. (Institute of Physics Publishing)A review. This paper reviews the role of quantum mechanics in biol. systems, and shows how the interplay between coherence and decoherence can strongly enhance quantum transport in photosynthesis.
- 46Vickerstaff, T.; Lemin, D. R. Aggregation of Dyes in Aqueous Solution. Nature 1946, 157, 373, DOI: 10.1038/157373a046https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaH28XhvV2jtw%253D%253D&md5=ba143cf6c2223197f59b645708c653aeAggregation of dyes in aqueous solutionVickerstaff, T.; Lemin, D. R.Nature (London, United Kingdom) (1946), 157 (), 373CODEN: NATUAS; ISSN:0028-0836.The work of Rabinovitch and Epstein (C.A. 35, 1294.7) on the absorption spectrum of methylene blue 0.002-0.000,002 M was repeated. They reported an absorption band at 6560 A., which decreases in intensity, and one at 6000 A., which increases in intensity, both with increasing concn. Higher extinction coeffs. than those of Rabinovitch and Epstein were found. The second absorption band not only increases in intensity with concn., but also shifts continuously toward shorter wave lengths; at 0.0025 M, the peak is at 6050 A.; at 0.0313 M, it is at 5850 A. This shows that a soln. of methylene blue is not a simple mixt. of monomer and dimer, but contains higher polymers, particularly at higher concns. This is supported by the data of Lange and Herre (C.A. 32, 4051.1) and Sheppard and Geddes (C.A. 39, 866.9).
- 47Dickinson, H. O. The Aggregation of Cyanine Dyes in Aqueous Solution. Trans. Faraday Soc. 1947, 43, 486– 491, DOI: 10.1039/tf947430048647https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaH1cXht1ygtw%253D%253D&md5=4ccf8fb32ca5788cfb3bfb2cc3f105b8Aggregation of cyanine dyes in aqueous solutionDickinson, H. O.Transactions of the Faraday Society (1947), 43 (), 486-91CODEN: TFSOA4; ISSN:0014-7672.The absorption and photographic sensitizing properties of 2-ethyl-2'-methylpseudocyanine chloride and Isoquinoline Red have been examd. The degree of aggregation of both dyes in aq. soln. has been detd. by osmotic pressure and elec. conductance measurements. The degree of aggregation appears to be fairly const. over the range of concn. studied. The absorption and sensitizing properties of the two dyes have been related to their degree of aggregation.
- 48Heyne, B. Self-Assembly of Organic Dyes in Supramolecular Aggregates. Photochem. Photobiol. Sci. 2016, 15, 1103– 1114, DOI: 10.1039/C6PP00221H48https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xhtleit7vP&md5=b61bbc375d19b8a6ff20e8f02a4b9396Self-assembly of organic dyes in supramolecular aggregatesHeyne, BelindaPhotochemical & Photobiological Sciences (2016), 15 (9), 1103-1114CODEN: PPSHCB; ISSN:1474-905X. (Royal Society of Chemistry)Many scientists probably consider dye aggregation in soln. a curse. Here, the adjective "many" should be stressed, as some other researchers thrive on forcing dyes to aggregate in soln. This perspective paper is certainly not meant to be a comprehensive review on the topic. However, for people intrigued by this pervasive phenomenon, I will try to offer a general picture on the self-assembly of dyes into supramol. aggregates by presenting and discussing key information on their thermodn., kinetics, and optical changes. More recent topics will be introduced, such as the impact of external stimuli on dye aggregation, with a particular focus on ion specific effects. Finally, aggregation-induced emission will also be examd.
- 49Engel, G. S.; Calhoun, T. R.; Read, E. L.; Ahn, T. K.; Mancal, T.; Cheng, Y. C.; Blankenship, R. E.; Fleming, G. R. Evidence for Wavelike Energy Transfer through Quantum Coherence in Photosynthetic Systems. Nature 2007, 446, 782– 786, DOI: 10.1038/nature0567849https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXktVeqt78%253D&md5=7b4589af9ac8747b5412060efac43428Evidence for wavelike energy transfer through quantum coherence in photosynthetic systemsEngel, Gregory S.; Calhoun, Tessa R.; Read, Elizabeth L.; Ahn, Tae-Kyu; Mancal, Tomas; Cheng, Yuan-Chung; Blankenship, Robert E.; Fleming, Graham R.Nature (London, United Kingdom) (2007), 446 (7137), 782-786CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centers, where long term energy storage is initiated. The energy transfer mechanism is often described by semiclassical models that invoke 'hopping' of excited-state populations along discrete energy levels. Two-dimensional Fourier transform electronic spectroscopy has mapped these energy levels and their coupling in the Fenna-Matthews-Olson (FMO) bacteriochlorophyll complex, which is found in green S bacteria and acts as an energy 'wire' connecting a large peripheral light-harvesting antenna, the chlorosome, to the reaction center. The spectroscopic data clearly document the dependence of the dominant energy transport pathways on the spatial properties of the excited-state wavefunctions of the whole bacteriochlorophyll complex. But the intricate dynamics of quantum coherence, which has no classical analog, was largely neglected in the analyses-even though electronic energy transfer involving oscillatory populations of donors and acceptors was 1st discussed >70 years ago, and electronic quantum beats arising from quantum coherence in photosynthetic complexes were predicted and indirectly obsd. Here the authors extend previous two-dimensional electronic spectroscopy studies of the FMO bacteriochlorophyll complex, and obtain direct evidence for remarkably long-lived electronic quantum coherence playing an important part in energy transfer processes within this system. The quantum coherence manifests itself in characteristic, directly observable quantum beating signals among the excitons within the Chlorobium tepidum FMO complex at 77 K. This wavelike characteristic of the energy transfer within the photosynthetic complex can explain its extreme efficiency, in that it allows the complexes to sample vast areas of phase space to find the most efficient path.
- 50Lee, H.; Cheng, Y. C.; Fleming, G. R. Coherence Dynamics in Photosynthesis: Protein Protection of Excitonic Coherence. Science 2007, 316, 1462– 1465, DOI: 10.1126/science.114218850https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXmtFSjsbs%253D&md5=ad1e8c76789a04846ce844220a8e5c3dCoherence Dynamics in Photosynthesis: Protein Protection of Excitonic CoherenceLee, Hohjai; Cheng, Yuan-Chung; Fleming, Graham R.Science (Washington, DC, United States) (2007), 316 (5830), 1462-1465CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)The role of quantum coherence in promoting the efficiency of the initial stages of photosynthesis is an open and intriguing question. We performed a two-color photon echo expt. on a bacterial reaction center that enabled direct visualization of the coherence dynamics in the reaction center. The data revealed long-lasting coherence between two electronic states that are formed by mixing of the bacteriopheophytin and accessory bacteriochlorophyll excited states. This coherence can only be explained by strong correlation between the protein-induced fluctuations in the transition energy of neighboring chromophores. Our results suggest that correlated protein environments preserve electronic coherence in photosynthetic complexes and allow the excitation to move coherently in space, enabling highly efficient energy harvesting and trapping in photosynthesis.
- 51Scholes, G. D.; Fleming, G. R.; Olaya-Castro, A.; van Grondelle, R. Lessons from Nature About Solar Light Harvesting. Nat. Chem. 2011, 3, 763– 774, DOI: 10.1038/nchem.114551https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXht1ajurzF&md5=356439ff0cf14151e1c943af885f5cddLessons from nature about solar light harvestingScholes, Gregory D.; Fleming, Graham R.; Olaya-Castro, Alexandra; van Grondelle, RienkNature Chemistry (2011), 3 (10), 763-774CODEN: NCAHBB; ISSN:1755-4330. (Nature Publishing Group)A review. Solar fuel prodn. often starts with the energy from light being absorbed by an assembly of mols.; this electronic excitation is subsequently transferred to a suitable acceptor. For example, in photosynthesis, antenna complexes capture sunlight and direct the energy to reaction centers that then carry out the assocd. chem. In this Review, we describe the principles learned from studies of various natural antenna complexes and suggest how to elucidate strategies for designing light-harvesting systems. We envisage that such systems will be used for solar fuel prodn., to direct and regulate excitation energy flow using mol. organizations that facilitate feedback and control, or to transfer excitons over long distances. Also described are the notable properties of light-harvesting chromophores, spatial-energetic landscapes, the roles of excitonic states and quantum coherence, as well as how antennas are regulated and photoprotected.
- 52Scholes, G. D. Quantum Biology Coherence in Photosynthesis. Nat. Phys. 2011, 7, 448– 449, DOI: 10.1038/nphys201352https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXmvVarsLc%253D&md5=96fd2be3e321c27b173bb704888e912fCoherence in photosynthesisScholes, Gregory D.Nature Physics (2011), 7 (6), 448-449CODEN: NPAHAX; ISSN:1745-2473. (Nature Publishing Group)A review. Evidence has accumulated that quantum coherence plays a role in photosynthesis. A better understanding of this process might help us design more efficient solar cells to harness the Sun's energy.
- 53Fassioli, F.; Dinshaw, R.; Arpin, P. C.; Scholes, G. D. Photosynthetic Light Harvesting: Excitons and Coherence. J. R. Soc., Interface 2014, 11, 20130901 DOI: 10.1098/rsif.2013.090153https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXmtV2rsrY%253D&md5=1ccc7148540392efb762f7496411895bPhotosynthetic light harvesting: excitons and coherenceFassioli, Francesca; Dinshaw, Rayomond; Arpin, Paul C.; Scholes, Gregory D.Journal of the Royal Society, Interface (2014), 11 (92), 20130901/1-20130901/22CODEN: JRSICU; ISSN:1742-5689. (Royal Society)A review. Photosynthesis begins with light harvesting, where specialized pigment-protein complexes transform sunlight into electronic excitations delivered to reaction centers to initiate charge sepn. There is evidence that quantum coherence between electronic excited states plays a role in energy transfer. In this review, we discuss how quantum coherence manifests in photosynthetic light harvesting and its implications. We begin by examg. the concept of an exciton, an excited electronic state delocalized over several spatially sepd. mols., which is the most widely available signature of quantum coherence in light harvesting. We then discuss recent results concerning the possibility that quantum coherence between electronically excited states of donors and acceptors may give rise to a quantum coherent evolution of excitations, modifying the traditional incoherent picture of energy transfer. Key to this (partially) coherent energy transfer appears to be the structure of the environment, in particular the participation of non-equil. vibrational modes. We discuss the open questions and controversies regarding quantum coherent energy transfer and how these can be addressed using new exptl. techniques.
- 54Dill, K. A.; MacCallum, J. L. The Protein-Folding Problem, 50 Years On. Science 2012, 338, 1042– 1046, DOI: 10.1126/science.121902154https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xhs12itrnF&md5=bd73e6103d437b24594ce4cd86ad25dcThe protein-folding problem, 50 years onDill, Ken A.; MacCallum, Justin L.Science (Washington, DC, United States) (2012), 338 (6110), 1042-1046CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)A review. The protein-folding problem was 1st posed about one half-century ago. The term refers to 3 broad questions: (1) What is the phys. code by which an amino acid sequence dictates a protein's native structure (2) How can proteins fold so fast and (3) Can one devise a computer algorithm to predict protein structures from their sequences. Here, the authors review progress on these problems. In a few cases, computer simulations of the phys. forces in chem. detailed models have now achieved the accurate folding of small proteins. It has been learned that proteins fold rapidly because random thermal motions cause conformational changes leading energetically downhill toward the native structure, a principle that is captured in funnel-shaped energy landscapes. And thanks in part to the large Protein Data Bank of known structures, predicting protein structures is now far more successful than was thought possible in earlier days. What began as 3 questions of basic science one half-century ago has now grown into the full-fledged research field of protein phys. science.
- 55Yeates, T. O. Geometric Principles for Designing Highly Symmetric Self-Assembling Protein Nanomaterials. Annu. Rev. Biophys. 2017, 46, 23– 42, DOI: 10.1146/annurev-biophys-070816-03392855https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXksVCqsLw%253D&md5=733660019538f9c9ecaf9c0bcb217702Geometric Principles for Designing Highly Symmetric Self-Assembling Protein NanomaterialsYeates, Todd O.Annual Review of Biophysics (2017), 46 (), 23-42CODEN: ARBNCV; ISSN:1936-122X. (Annual Reviews)A review. Emerging protein design strategies are enabling the creation of diverse, self-assembling supramol. structures with precision on the at. scale. The design possibilities include various types of architectures: finite cages or shells, essentially unbounded two-dimensional and three-dimensional arrays (i.e., crystals), and linear or tubular filaments. In nature, structures of those types are generally sym., and, accordingly, symmetry provides a powerful guide for developing new design approaches. Recent design studies have produced numerous protein assemblies in close agreement with geometric specifications. For certain design approaches, a complete list of allowable symmetry combinations that can be used for construction has been articulated, opening a path to a rich diversity of geometrically defined protein materials. Future challenges include improving and elaborating on current strategies and endowing designed protein nanomaterials with properties useful in nanomedicine and material science applications.
- 56Huang, P. S.; Boyken, S. E.; Baker, D. The Coming of Age of De Novo Protein Design. Nature 2016, 537, 320– 327, DOI: 10.1038/nature1994656https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhsFajsrzL&md5=4627161c32d649123f680281b78adbe4The coming of age of de novo protein designHuang, Po-Ssu; Boyken, Scott E.; Baker, DavidNature (London, United Kingdom) (2016), 537 (7620), 320-327CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)A review. There are 20200 possible amino acid sequences for a 200-residue protein, of which the natural evolutionary process has sampled only an infinitesimal subset. De novo protein design explores the full sequence space, guided by the phys. principles that underlie protein folding. Computational methodol. has advanced to the point that a wide range of structures can be designed from scratch with at.-level accuracy. Almost all protein engineering so far has involved the modification of naturally occurring proteins; it should now be possible to design new functional proteins from the ground up to tackle current challenges in biomedicine and nanotechnol.
- 57Bale, J. B.; Gonen, S.; Liu, Y.; Sheffler, W.; Ellis, D.; Thomas, C.; Cascio, D.; Yeates, T. O.; Gonen, T.; King, N. P. Accurate Design of Megadalton-Scale Two-Component Icosahedral Protein Complexes. Science 2016, 353, 389– 394, DOI: 10.1126/science.aaf881857https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtFyit7bI&md5=830c50306546812190a79aa995396a76Accurate design of megadalton-scale two-component icosahedral protein complexesBale, Jacob B.; Gonen, Shane; Liu, Yuxi; Sheffler, William; Ellis, Daniel; Thomas, Chantz; Cascio, Duilio; Yeates, Todd O.; Gonen, Tamir; King, Neil P.; Baker, DavidScience (Washington, DC, United States) (2016), 353 (6297), 389-394CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)Nature provides many examples of self- and co-assembling protein-based mol. machines, including icosahedral protein cages that serve as scaffolds, enzymes, and compartments for essential biochem. reactions and icosahedral virus capsids, which encapsidate and protect viral genomes and mediate entry into host cells. Inspired by these natural materials, the authors report the computational design and exptl. characterization of co-assembling, two-component, 120-subunit icosahedral protein nanostructures with mol. wts. (1.8 to 2.8 megadaltons) and dimensions (24 to 40 nm in diam.) comparable to those of small viral capsids. Electron microscopy, small-angle x-ray scattering, and x-ray crystallog. show that 10 designs spanning three distinct icosahedral architectures form materials closely matching the design models. In vitro assembly of icosahedral complexes from independently purified components occurs rapidly, at rates comparable to those of viral capsids, and enables controlled packaging of mol. cargo through charge complementarity. The ability to design megadalton-scale materials with at.-level accuracy and controllable assembly opens the door to a new generation of genetically programmable protein-based mol. machines.
- 58Wei, B.; Dai, M.; Yin, P. Complex Shapes Self-Assembled from Single-Stranded DNA Tiles. Nature 2012, 485, 623– 626, DOI: 10.1038/nature1107558https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XnvVyltb4%253D&md5=9c59d1bb62366c9cbbced30e889ed821Complex shapes self-assembled from single-stranded DNA tilesWei, Bryan; Dai, Mingjie; Yin, PengNature (London, United Kingdom) (2012), 485 (7400), 623-626CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)Programmed self-assembly of strands of nucleic acid has proved highly effective for creating a wide range of structures with desired shapes. A particularly successful implementation is DNA origami, in which a long scaffold strand is folded by hundreds of short auxiliary strands into a complex shape. Modular strategies are in principle simpler and more versatile and have been used to assemble DNA or RNA tiles into periodic and algorithmic two-dimensional lattices, extended ribbons and tubes, three-dimensional crystals, polyhedra and simple finite two-dimensional shapes. But creating finite yet complex shapes from a large no. of uniquely addressable tiles remains challenging. Here we solve this problem with the simplest tile form, a single-stranded tile (SST) that consists of a 42-base strand of DNA composed entirely of concatenated sticky ends and that binds to four local neighbors during self-assembly. Although ribbons and tubes with controlled circumferences have been created using the SST approach, we extend it to assemble complex two-dimensional shapes and tubes from hundreds (in some cases more than one thousand) distinct tiles. Our main design feature is a self-assembled rectangle that serves as a mol. canvas, with each of its constituent SST strands-folded into a 3 nm-by-7 nm tile and attached to four neighboring tiles-acting as a pixel. A desired shape, drawn on the canvas, is then produced by one-pot annealing of all those strands that correspond to pixels covered by the target shape; the remaining strands are excluded. We implement the strategy with a master strand collection that corresponds to a 310-pixel canvas, and then use appropriate strand subsets to construct 107 distinct and complex two-dimensional shapes, thereby establishing SST assembly as a simple, modular and robust framework for constructing nanostructures with prescribed shapes from short synthetic DNA strands.
- 59Ke, Y.; Ong, L. L.; Shih, W. M.; Yin, P. Three-Dimensional Structures Self-Assembled from DNA Bricks. Science 2012, 338, 1177– 1183, DOI: 10.1126/science.122726859https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xhslans7bP&md5=bb760600ffabe6af4759019dbd22226fThree-Dimensional Structures Self-Assembled from DNA BricksKe, Yonggang; Ong, Luvena L.; Shih, William M.; Yin, PengScience (Washington, DC, United States) (2012), 338 (6111), 1177-1183CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)We describe a simple and robust method to construct complex three-dimensional (3D) structures by using short synthetic DNA strands that we call "DNA bricks". In one-step annealing reactions, bricks with hundreds of distinct sequences self-assemble into prescribed 3D shapes. Each 32-nucleotide brick is a modular component; it binds to four local neighbors and can be removed or added independently. Each 8-base pair interaction between bricks defines a voxel with dimensions of 2.5 by 2.5 by 2.7 nm, and a master brick collection defines a "mol. canvas" with dimensions of 10 by 10 by 10 voxels. By selecting subsets of bricks from this canvas, we constructed a panel of 102 distinct shapes exhibiting sophisticated surface features, as well as intricate interior cavities and tunnels.
- 60Rothemund, P. W. K. Folding DNA to Create Nanoscale Shapes and Patterns. Nature 2006, 440, 297– 302, DOI: 10.1038/nature0458660https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XitlKgu7g%253D&md5=583caefdda9b1deb5d3f2ef78d9e6ecbFolding DNA to create nanoscale shapes and patternsRothemund, Paul W. K.Nature (London, United Kingdom) (2006), 440 (7082), 297-302CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)'Bottom-up fabrication', which exploits the intrinsic properties of atoms and mols. to direct their self-organization, is widely used to make relatively simple nanostructures. A key goal for this approach is to create nanostructures of high complexity, matching that routinely achieved by 'top-down' methods. The self-assembly of DNA mols. provides an attractive route towards this goal. Here the author describe a simple method for folding long, single-stranded DNA mols. into arbitrary two-dimensional shapes. The design for a desired shape is made by raster-filling the shape with a 7-kilobase single-stranded scaffold and by choosing over 200 short oligonucleotide 'staple strands' to hold the scaffold in place. Once synthesized and mixed, the staple and scaffold strands self-assemble in a single step. The resulting DNA structures are roughly 100 nm in diam. and approx. desired shapes such as squares, disks and five-pointed stars with a spatial resoln. of 6 nm. Because each oligonucleotide can serve as a 6-nm pixel, the structures can be programmed to bear complex patterns such as words and images on their surfaces. Finally, individual DNA structures can be programmed to form larger assemblies, including extended periodic lattices and a hexamer of triangles (which constitutes a 30-megadalton mol. complex).
- 61Seeman, N. C. DNA in a Material World. Nature 2003, 421, 427– 431, DOI: 10.1038/nature0140661https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXisFGqtLk%253D&md5=a8e40994e5ea08a665aab18697196e62DNA in a material worldSeeman, Nadrian C.Nature (London, United Kingdom) (2003), 421 (6921, Suppl.), 427-431CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)The specific bonding of DNA base pairs provides the chem. foundation for genetics. This powerful mol. recognition system can be used in nanotechnol. to direct the assembly of highly structured materials with specific nanoscale features, as well as in DNA computation to process complex information. The exploitation of DNA for material purposes presents a new chapter in the history of the mol.
- 62Seifert, J. L.; Connor, R. E.; Kushon, S. A.; Wang, M.; Armitage, B. A. Spontaneous Assembly of Helical Cyanine Dye Aggregates on DNA Nanotemplates. J. Am. Chem. Soc. 1999, 121, 2987– 2995, DOI: 10.1021/ja984279j62https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1MXhvV2qtbc%253D&md5=ac33b8b50aa9ce58894e6f3f96db44e7Spontaneous Assembly of Helical Cyanine Dye Aggregates on DNA NanotemplatesSeifert, Jennifer L.; Connor, Rebecca E.; Kushon, Stuart A.; Wang, Miaomiao; Armitage, Bruce A.Journal of the American Chemical Society (1999), 121 (13), 2987-2995CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)3,3'-Diethylthiadicarbocyanine (DiSC2(5)) is a sym. cationic cyanine dye consisting of two N-ethylated benzothiazole groups linked by a pentamethine bridge. Spectroscopic anal. indicates dimerization of the dye in the presence of duplex DNA sequences consisting of alternating adenine/thymine (A/T) or inosine/cytosine (I/C) residues, based on the following observations: (i) the absorption max. shifts from 647 to 590 nm, (ii) exciton splitting is obsd. in the induced CD spectrum, and (iii) fluorescence from the dye is strongly quenched. Dimerization on I/C, but not G/C sequences indicates that the cyanine dimers insert into the minor groove, a conclusion that is supported by viscometric anal. Spectroscopic studies with short synthetic oligonucleotide duplexes demonstrate that dimerization is highly cooperative: binding of one dimer greatly facilitates binding of a second dimer. For longer binding sites, this cooperativity leads to the formation of extended helical cyanine dye aggregates consisting of dimers aligned in an end-to-end fashion within the minor groove of the DNA. The DNA structure strictly controls the dimensions of the aggregate, permitting distinction between inter- and intradimer interactions.
- 63Smith, J. O.; Olson, D. A.; Armitage, B. A. Molecular Recognition of PNA-Containing Hybrids: Spontaneous Assembly of Helical Cyanine Dye Aggregates on PNA Templates. J. Am. Chem. Soc. 1999, 121, 2686– 2695, DOI: 10.1021/ja983755363https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1MXhslektrc%253D&md5=9d19337b31d6231a905a1f864bdc633dMolecular Recognition of PNA-Containing Hybrids: Spontaneous Assembly of Helical Cyanine Dye Aggregates on PNA TemplatesSmith, Jeffrey O.; Olson, Darren A.; Armitage, Bruce A.Journal of the American Chemical Society (1999), 121 (12), 2686-2695CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Sym. cyanine dyes contg. benzothiazole groups have been shown to bind with high affinity to a variety of PNA-contg. hybrids, including PNA/DNA duplexes, a PNA/PNA duplex, and a bisPNA/DNA triplex. Binding of a dicarbocyanine dye results in a 114 nm hypsochromic shift of the main visible absorption band. CD spectropolarimetry reveals exciton coupling between multiple chromophores bound to the same PNA/DNA or PNA/PNA duplex, demonstrating binding of the dye as an aggregate. A continuous variations expt. indicates that the dye binds as a 6(±1):1 complex with a 12 base pair PNA/DNA duplex. The dye aggregate forms in a highly cooperative manner and exhibits a temp.-dependent self-assembly behavior which is independent of the PNA/DNA hybridization event. Expts. with mismatched and parallel duplexes demonstrate a strong preference for a continuous, antiparallel helix as a template on which to assemble the helical dye aggregate. Successful binding of the dye to the duplex and triplex indicates that dyes assoc. with one another in the minor groove of the template. The 114 nm shift in absorption causes an instantaneous visible color change from blue to purple, providing a convenient method for detecting PNA hybridization with its complementary target sequence.
- 64Wang, M. M.; Silva, G. L.; Armitage, B. A. DNA-Templated Formation of a Helical Cyanine Dye J-Aggregate. J. Am. Chem. Soc. 2000, 122, 9977– 9986, DOI: 10.1021/ja002184n64https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXmsl2jtrk%253D&md5=e2fd6590d3cdebe8008455435bd756b9DNA-Templated Formation of a Helical Cyanine Dye J-AggregateWang, Miaomiao; Silva, Gloria L.; Armitage, Bruce A.Journal of the American Chemical Society (2000), 122 (41), 9977-9986CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)UV-vis and CD spectroscopy reveal that a tri-cationic cyanine dye spontaneously assembles into a helical J-aggregate in the presence of a double-helical DNA template. The stability of the J-aggregate is strongly dependent on the dye concn. and DNA length in a manner that reflects a high degree of cooperativity in formation of the aggregate. Slight changes in environmental conditions such as temp. and ionic strength result in interconversion between J- and H-aggregates. The aggregate likely consists of dimeric units assembled in an offset, face-to-face orientation within the minor groove of the DNA template, analogous to an earlier report of H-aggregation on DNA by a related cyanine dye. A model is proposed that relates the two aggregate structures by translation of one monomer from a given dimer along the floor of the minor groove. This translation requires adjacent monomers to also translate, leading to the obsd. cooperativity.
- 65Chowdhury, A.; Wachsmann-Hogiu, S.; Bangal, P. R.; Raheem, I.; Peteanu, L. A. Characterization of Chiral H and J Aggregates of Cyanine Dyes Formed by DNA Templating Using Stark and Fluorescence Spectroscopies. J. Phys. Chem. B 2001, 105, 12196– 12201, DOI: 10.1021/jp012825g65https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3MXnslaqsLw%253D&md5=4b1ece4397b0e87c5b10ee7af6ce24c2Characterization of Chiral H and J Aggregates of Cyanine Dyes Formed by DNA Templating Using Stark and Fluorescence SpectroscopiesChowdhury, Arindam; Wachsmann-Hogiu, Sebastian; Bangal, Prakriti R.; Raheem, Izzat; Peteanu, Linda A.Journal of Physical Chemistry B (2001), 105 (48), 12196-12201CODEN: JPCBFK; ISSN:1089-5647. (American Chemical Society)A series of studies is presented to characterize the photophys. properties of a novel type of aggregate formed by the spontaneous noncovalent assembly of numerous cofacial dimers of cyanine dyes (DiSC3+(5)) to the minor groove of poly(dI-dC) DNA. The dimensions of these helical aggregates, first synthesized and characterized by Armitage and co-workers (J. Am. Chem. Soc. 2000, 122, 9977-9986), are restricted to the width of the dye dimer because of steric constraints in the minor groove, though the length of the aggregate can extend essentially for the full length of the DNA template. These unique species exhibit both H- and J-type absorption bands that are shifted from the absorption max. of the monomeric dye by +1650 and -1275 cm-1, resp., because of the stacking interactions between the dyes composing the dimers. Addnl. splittings are seen because of head-to-head interactions between adjacent dye dimers. Here, we present the low-temp. (77 K) absorption, fluorescence, and electroabsorption spectra of these aggregates as well as measurements of the fluorescence lifetime of the monomer and of the J-type emission at 10°. The electroabsorption measurements yield values of the av. difference polarizability on excitation, 〈Δα〉, for the H and J bands of -74 and -34 Å3, resp. These are between 2 and 6 times larger than that of the monomer. Both bands exhibit similar values for the difference dipole moment on excitation |.vector.Δμ| of between 0.6 and 0.7 D that are somewhat smaller than that of the monomer (1.1 D). The absorption and fluorescence expts. show that the line width of the J band is ∼4 times narrower than the exptl. fwhm of the DiSC3+(5) monomer while the fluorescence decay of the aggregate is roughly a factor of 2 faster. Implications of all of these measurements for detg. the no. of dyes that are excited cooperatively upon light absorption are discussed.
- 66Garoff, R. A.; Litzinger, E. A.; Connor, R. E.; Fishman, I.; Armitage, B. A. Helical Aggregation of Cyanine Dyes on DNA Templates: Effect of Dye Structure on Formation of Homo- and Heteroaggregates. Langmuir 2002, 18, 6330– 6337, DOI: 10.1021/la025742f66https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38Xkt12ktL0%253D&md5=cbea8e8f28c50beaab8edebe57226c87Helical Aggregation of Cyanine Dyes on DNA Templates: Effect of Dye Structure on Formation of Homo- and HeteroaggregatesGaroff, Rachel A.; Litzinger, Elizabeth A.; Connor, Rebecca E.; Fishman, Irene; Armitage, Bruce A.Langmuir (2002), 18 (16), 6330-6337CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)UV-visible and CD spectroscopic expts. were used to characterize DNA-templated helical aggregates formed from a variety of sym., cationic cyanine dyes. Two types of electronic couplings can be obsd. in these aggregates: face-to-face interactions between dye monomers and end-to-end interactions between dye dimers. The face-to-face interactions yield approx. 4-fold stronger couplings due to greater orbital overlap. Variation of the heterocyclic groups on the dye reveals that aggregation on DNA follows the following trend: quinoline > benzothiazole > benzoxazole > dimethylindole. This trend follows the tendency of these dyes to aggregate in aq. soln. Within the benzothiazole class of dyes, a dicarbocyanine dye (pentamethine bridge) aggregates much more readily than the carbocyanine (trimethine bridge) analog. However, a tricarbocyanine dye (heptamethine bridge) aggregates less readily than the dicarbocyanine, in contrast to their relative tendency to aggregate in water. In addn., heteroaggregates in which two different dyes assoc. cofacially on the DNA template can be synthesized.
- 67Chowdhury, A.; Yu, L. P.; Raheem, I.; Peteanu, L.; Liu, L. A.; Yaron, D. J. Stark Spectroscopy of Size-Selected Helical H-Aggregates of a Cyanine Dye Templated by Duplex DNA. Effect of Exciton Coupling on Electronic Polarizabilities. J. Phys. Chem. A 2003, 107, 3351– 3362, DOI: 10.1021/jp021866p67https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXjs1Wjsr4%253D&md5=a46e6448fa72931769d34008571eab00Stark Spectroscopy of Size-Selected Helical H-Aggregates of a Cyanine Dye Templated by Duplex DNA. Effect of Exciton Coupling on Electronic PolarizabilitiesChowdhury, Arindam; Yu, Liping; Raheem, Izzat; Peteanu, Linda; Liu, L. Angela; Yaron, David J.Journal of Physical Chemistry A (2003), 107 (18), 3351-3362CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)Stark spectroscopy (electroabsorption) is used to study the variation of electronic properties with the size of helical H-aggregates that are formed by the spontaneous noncovalent assembly of co-facial dimers of the cyanine dye (DiSC2(5)) into the minor groove of double-helical DNA. The unique and important property of these aggregates, first synthesized and characterized by Armitage and co-workers (J. Am. Chem. Soc. 1999, 121, 2987), is that their size is controlled by the properties of the DNA template. Specifically, the length of the aggregate formed is detd. by the length of the DNA template and its width along the π stacking dimension is restricted to that of the dye dimer due to steric constraints in the minor groove. Results for aggregates consisting of 1, 2, 5, and ∼35 adjacent dimers bound to DNA are presented here. The absorption maxima of these species exhibit a large blue shift (1750 cm-1) from that of the monomer due to the face-to-face interactions within the dimers. Relatively weak (330-650 cm-1) secondary splittings are also seen that arise from end-to-end interactions between adjacent dimers on the chain. The av. change in polarizability on excitation (〈Δα〉) is found to double when two dyes form a stacked dimer whereas no further increase in 〈Δα〉 is seen as the chain length is increased. Semiempirical (INDO-SCI) calcns. yield exciton coupling energies that are consistent with expt. However, 〈Δα〉 is predicted to increase toward more pos. values on dimerization while the reverse trend is seen exptl. Nonetheless, both expt. and theory find that 〈Δα〉 is unaffected by higher aggregation.
- 68Hannah, K. C.; Armitage, B. A. DNA-Templated Assembly of Helical Cyanine Dye Aggregates: A Supramolecular Chain Polymerization. Acc. Chem. Res. 2004, 37, 845– 853, DOI: 10.1021/ar030257c68https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXnt12hu7s%253D&md5=e765802296ac18eb6a7b1f8c6c0accdaDNA-Templated Assembly of Helical Cyanine Dye Aggregates: A Supramolecular Chain PolymerizationHannah, Kristen C.; Armitage, Bruce A.Accounts of Chemical Research (2004), 37 (11), 845-853CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)A review. Sym. cationic cyanine dyes assemble in cooperative fashion into helical supramol. polymers using DNA as a template. The dyes assemble into cofacial dimers within the minor groove of the DNA and assembly of one dimer facilitates assembly of addnl. dimers directly adjacent to the first. Growth of the polymer ceases when the end of the DNA is reached or when the DNA sequence blocks dimerization of the dye. Thus, this process can be thought of as a supramol. analog of a chain polymn. This Account describes how polymn. depends on the dye structure and DNA sequence and also summarizes the interesting optical properties exhibited by these chiral, helical materials.
- 69Tomlinson, A.; Frezza, B.; Kofke, M.; Wang, M. M.; Armitage, B. A.; Yaron, D. A Structural Model for Cyanine Dyes Templated into the Minor Groove of DNA. Chem. Phys. 2006, 325, 36– 47, DOI: 10.1016/j.chemphys.2005.10.00769https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28Xltlemtbw%253D&md5=383623147ba79f8da37f99bc3d0dc867A structural model for cyanine dyes templated into the minor groove of DNATomlinson, Aimee; Frezza, Brian; Kofke, Matthew; Wang, Miaomiao; Armitage, Bruce A.; Yaron, DavidChemical Physics (2006), 325 (1), 36-47CODEN: CMPHC2; ISSN:0301-0104. (Elsevier B.V.)3,3-Diethylthiadicarbocyanine (DiSC2(5)) is a monocationic dye which forms cofacial dimers that insert into the minor groove of DNA [J. Seifert, R. Conner, S. Kushon, M. Wang, B. Armitage, J. Am. Chem. Soc. 121 (1999) 2987]. These dyes self-assemble into long helical aggregates in AT-rich regions with the dimers aligned in an end-to-end fashion. A model is presented that allows for the construction of large helical aggregates with continuously variable structural parameters. The spectra or excited states are computed using a direct INDO single CI (SCI) method. Results are reported for both H- and J-type aggregates ranging in size from 2 to 6 dimers. A more approx. model based on transition charge densities enables calcns. of larger aggregates. These models are used to derive structural parameters of both H- and J-type aggregates from the available spectral data, resulting in a new structural model for J-type aggregation in these systems.
- 70Stadler, A. L.; Renikuntla, B. R.; Yaron, D.; Fang, A. S.; Armitage, B. A. Substituent Effects on the Assembly of Helical Cyanine Dye Aggregates in the Minor Groove of a DNA Template. Langmuir 2011, 27, 1472– 1479, DOI: 10.1021/la104329c70https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhsF2ms7zM&md5=1757566507c3fba6f583bffffb042ca5Substituent Effects on the Assembly of Helical Cyanine Dye Aggregates in the Minor Groove of a DNA TemplateStadler, Andrea L.; Renikuntla, Babu Rao; Yaron, David; Fang, Adam S.; Armitage, Bruce A.Langmuir (2011), 27 (4), 1472-1479CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)Double-helical DNA was used as a template for the assembly of helical cyanine dye aggregates. The aggregates consist of cofacial dimers aligned end-to-end in the minor groove of the DNA. The effect of methoxy or fluoro substituents placed on the periphery of the cyanine dye heterocycles on aggregation both in water and on the DNA template was studied by UV-vis and CD spectroscopy. Methoxy groups were found to be stronger promoters of aggregation than fluoro, and a dimethoxy dye exhibited a higher propensity to aggregate compared with an unsym. methoxy/fluoro dye. Semiempirical calcns. supported the exptl. observation of methoxy substitution favoring aggregation. These results indicate that dispersion and hydrophobic effects contribute more to dimerization/aggregation than do electron donor-acceptor effects.
- 71Banal, J. L.; Kondo, T.; Veneziano, R.; Bathe, M.; Schlau-Cohen, G. S. Photophysics of J-Aggregate-Mediated Energy Transfer on DNA. J. Phys. Chem. Lett. 2017, 8, 5827– 5833, DOI: 10.1021/acs.jpclett.7b0189871https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhvVSmtLfN&md5=f0f639202fe61210725aaff89ff9080cPhotophysics of J-Aggregate-Mediated Energy Transfer on DNABanal, James L.; Kondo, Toru; Veneziano, Remi; Bathe, Mark; Schlau-Cohen, Gabriela S.Journal of Physical Chemistry Letters (2017), 8 (23), 5827-5833CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)Achieving nanoscale spatial and electronic control over the formation of dye aggregates is a major synthetic challenge due to their typically inhomogeneous self-assembly, which limits control over their higher-order organization. To address these challenges, synthetic DNA-templated pseudoisocyanine (PIC) J-aggregates were recently introduced. However, the dependence of the photophysics of the superradiant exciton on the underlying DNA template length and the impact of static disorder on energy transfer through these PIC J-aggregates remain unknown. Here, we examine the delocalization length progression of superradiant PIC excitons by varying the length of poly-A DNA tracts that templates PIC J-aggregates. We then investigate the energy transfer efficiency from PIC J-aggregates with DNA duplex template length, which we found to be limited by static disorder. Utilizing the self-assembled and selective formation of superradiant excitons on DNA provides a platform to det. the function of delocalized excitons in the context of nanoscale energy transport.
- 72Boulais, É.; Sawaya, N. P. D.; Veneziano, R.; Andreoni, A.; Banal, J. L.; Kondo, T.; Mandal, S.; Lin, S.; Schlau-Cohen, G. S.; Woodbury, N. W. Programmed Coherent Coupling in a Synthetic DNA-Based Excitonic Circuit. Nat. Mater. 2018, 17, 159– 166, DOI: 10.1038/nmat503372https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhsl2qtrrN&md5=0cc78d472a07d50e26ac243e9ef3c07aProgrammed coherent coupling in a synthetic DNA-based excitonic circuitBoulais, Etienne; Sawaya, Nicolas P. D.; Veneziano, Remi; Andreoni, Alessio; Banal, James L.; Kondo, Toru; Mandal, Sarthak; Lin, Su; Schlau-Cohen, Gabriela S.; Woodbury, Neal W.; Yan, Hao; Aspuru-Guzik, Alan; Bathe, MarkNature Materials (2018), 17 (2), 159-166CODEN: NMAACR; ISSN:1476-1122. (Nature Research)Natural light-harvesting systems spatially organize densely packed chromophore aggregates using rigid protein scaffolds to achieve highly efficient, directed energy transfer. Here, we report a synthetic strategy using rigid DNA scaffolds to similarly program the spatial organization of densely packed, discrete clusters of cyanine dye aggregates with tunable absorption spectra and strongly coupled exciton dynamics present in natural light-harvesting systems. We 1st characterize the range of dye-aggregate sizes that can be templated spatially by A-tracts of B-form DNA while retaining coherent energy transfer. We then use structure-based modeling and quantum dynamics to guide the rational design of higher-order synthetic circuits consisting of multiple discrete dye aggregates within a DX-tile. These programmed circuits exhibit excitonic transport properties with prominent CD, superradiance, and fast delocalized exciton transfer, consistent with our quantum dynamics predictions. This bottom-up strategy offers a versatile approach to the rational design of strongly coupled excitonic circuits using spatially organized dye aggregates for use in coherent nanoscale energy transport, artificial light-harvesting, and nanophotonics.
- 73Nicoli, F.; Roos, M. K.; Hemmig, E. A.; Di Antonio, M.; de Vivie-Riedle, R.; Liedl, T. Proximity-Induced H-Aggregation of Cyanine Dyes on DNA-Duplexes. J. Phys. Chem. A 2016, 120, 9941– 9947, DOI: 10.1021/acs.jpca.6b1093973https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XitVajtrnL&md5=adeda33f095d31ac502a29cfe0ed1fc4Proximity-Induced H-Aggregation of Cyanine Dyes on DNA-DuplexesNicoli, Francesca; Roos, Matthias K.; Hemmig, Elisa A.; Di Antonio, Marco; de Vivie-Riedle, Regina; Liedl, TimJournal of Physical Chemistry A (2016), 120 (50), 9941-9947CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)A wide variety of org. dyes form, under certain conditions, clusters known as J- and H-aggregates. Cyanine dyes are such a class of mols. where the spatial proximity of several dyes leads to overlapping electron orbitals and thus to the creation of a new energy landscape compared to that of the individual units. Here, the authors created artificial H-aggregates of exactly 2 Cy3 dyes by covalently linking them to a DNA mol. with controlled sub-nanometer distances. The absorption spectra of these coupled systems exhibited a blue-shifted peak, whose intensity varied depending on the distance between the dyes and the rigidity of the DNA template. Simulated vibrational resolved spectra, based on MO theory, excellently reproduced the exptl. obsd. features. CD spectroscopy addnl. revealed distinct signals, which indicated a chiral arrangement of the dye mols. Mol. dynamics simulations of a Cy3-Cy3 construct including a 14-base pair DNA sequence verified chiral stacking of the dye mols.
- 74Markova, L. I.; Malinovskii, V. L.; Patsenker, L. D.; Häner, R. J- Vs. H-Type Assembly: Pentamethine Cyanine (Cy5) as a near-IR Chiroptical Reporter. Chem. Commun. 2013, 49, 5298– 5300, DOI: 10.1039/c3cc42103a74https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXns1ags7w%253D&md5=1deebeaee79fddc66a914704c4cda2d5J- vs. H-type assembly: pentamethine cyanine (Cy5) as a near-IR chiroptical reporterMarkova, Larysa I.; Malinovskii, Vladimir L.; Patsenker, Leonid D.; Haener, RobertChemical Communications (Cambridge, United Kingdom) (2013), 49 (46), 5298-5300CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)The DNA-enabled dimerization of pentamethine cyanine (Cy5) dyes was studied by optical methods. The value of cyanine as a chiroptical reporter using a monomer-to-dimer switch is demonstrated. The specific shape of the CD signal and its high intensity are a result of J-type assembly.
- 75Probst, M.; Langenegger, S. M.; Häner, R. A Modular LHC Built on the DNA Three-Way Junction. Chem. Commun. 2014, 50, 159– 161, DOI: 10.1039/C3CC47490A75https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvVKjtLjF&md5=e7b616c5bbd54019a2f7d679c95b0faeA modular LHC built on the DNA three-way junctionProbst, Markus; Langenegger, Simon M.; Haener, RobertChemical Communications (Cambridge, United Kingdom) (2014), 50 (2), 159-161CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)A light-harvesting complex composed of a π-stacked multichromophoric array in a DNA three-way junction is described. The modular design allows for a ready exchange of non-covalently attached energy acceptors.
- 76Markova, L. I.; Malinovskii, V. L.; Patsenker, L. D.; Häner, R. Synthesis and Properties of Squaraine-Modified DNA. Org. Biomol. Chem. 2012, 10, 8944– 8947, DOI: 10.1039/c2ob26787j76https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhsF2qtLrO&md5=8732fa38727e27d7ae3c903140475f37Synthesis and properties of squaraine-modified DNAMarkova, Larysa I.; Malinovskii, Vladimir L.; Patsenker, Leonid D.; Haener, RobertOrganic & Biomolecular Chemistry (2012), 10 (45), 8944-8947CODEN: OBCRAK; ISSN:1477-0520. (Royal Society of Chemistry)The incorporation of squaraines into DNA via the phosphoramidite approach is described. High molar absorptivity, environment-sensitive fluorescence properties and intense CD effects render squaraines valuable building blocks for DNA-based optical probes and nanostructures.
- 77Malinovskii, V. L.; Wenger, D.; Häner, R. Nucleic Acid-Guided Assembly of Aromatic Chromophores. Chem. Soc. Rev. 2010, 39, 410– 422, DOI: 10.1039/B910030J77https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXht1Wltbk%253D&md5=08466f4cf2fe78034fa5d557f165b162Nucleic acid-guided assembly of aromatic chromophoresMalinovskii, Vladimir L.; Wenger, Daniel; Haner, RobertChemical Society Reviews (2010), 39 (2), 410-422CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)A review. The rational formation of arom. chromophore arrays is an intriguing challenge since ordered collectives of chromophores possess properties that are largely different from those of the individual mols. Therefore, nucleic acids are increasingly used as scaffolds for the construction of multi-chromophore arrays. This tutorial review provides an introduction to the field of nucleic acid-guided chromophore assemblies for non-specialists and a ref. point for those familiar with the area by highlighting the recent developments and describing some of the spectroscopic methods used for the study of oligonucleotide-chromophore conjugates.
- 78Li, S.; Langenegger, S. M.; Häner, R. Control of Aggregation-Induced Emission by DNA Hybridization. Chem. Commun. 2013, 49, 5835– 5837, DOI: 10.1039/c3cc42706d78https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXovFWmsb8%253D&md5=7a887296c7703b48626e68e4159eb9deControl of aggregation-induced emission by DNA hybridizationLi, Shaoguang; Langenegger, Simon M.; Haener, RobertChemical Communications (Cambridge, United Kingdom) (2013), 49 (52), 5835-5837CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)Aggregation-induced emission (AIE) was studied by hybridization of dialkynyl-tetraphenylethylene (DATPE) modified DNA strands. Mol. aggregation and fluorescence of DATPEs are controlled by duplex formation.
- 79Häner, R.; Samain, F.; Malinovskii, V. L. DNA-Assisted Self-Assembly of Pyrene Foldamers. Chem. - Eur. J. 2009, 15, 5701– 5708, DOI: 10.1002/chem.20090036979https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXms1ekt7Y%253D&md5=8f2f19743d8c01098697b301b2b1f9f9DNA-Assisted Self-Assembly of Pyrene FoldamersHaner, Robert; Samain, Florent; Malinovskii, Vladimir L.Chemistry - A European Journal (2009), 15 (23), 5701-5708, S5701/1-S5701/8CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)Folding in the tides: Upon hybridization, pyrene mols. assemble through interstrand stacking interactions to form double-stranded, helical structures. Structural organization of the pyrene mols. is an intrinsic property of the oligoaryl part and takes place independently of the sequence of the attached DNA. Pyrene helicity is most pronounced in a bi-segmental chimera, in which a DNA stem is present only at one end of the pyrene section. The self-organization of oligopyrene foldamers is described. Bi- and tri-segmental oligomers composed of nucleotides and non-nucleosidic, achiral pyrene monomers form double-stranded helical structures, as shown by absorbance, fluorescence, and CD spectroscopy. The mixed nature of alternating arom. and phosphate groups ensures water soly. which, in turn, favors folding of the arom. units. Pyrene mols. also assemble though interstrand stacking interactions. Structural organization of the pyrene units is an intrinsic property of the oligoaryl part and takes place independently from the sequence of the attached DNA. Chirality transfer from DNA to the pyrene segment leads to formation of a double helix, in which neighboring pyrene units are, in the present case, twisted in a right-handed manner. Pyrene helicity is most pronounced in a bi-segmental chimera, in which a DNA stem is present only at one end of the pyrene section.
- 80Garo, F.; Häner, R. A DNA-Based Light-Harvesting Antenna. Angew. Chem., Int. Ed. 2012, 51, 916– 919, DOI: 10.1002/anie.20110329580https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhsF2ksr%252FL&md5=a19402b55d0c8841a7bcdb7296022e66A DNA-Based Light-Harvesting AntennaGaro, Florian; Haener, RobertAngewandte Chemie, International Edition (2012), 51 (4), 916-919, S916/1-S916/23CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)A DNA-based light-harvesting antenna consists of an array of π-stacked phenanthrene chromophores (light collecting antenna), and an exciplex forming pyrene (the energy collection center), and a DNA double helix (the supramol. scaffold). Up to 8 phenantherens were used for light collection. The no. of photons emitted by the phenanthrene-pyrene exciplex is proportional to to the no. of light absorbing chromophores.
- 81Adeyemi, O. O.; Malinovskii, V. L.; Biner, S. M.; Calzaferri, G.; Häner, R. Photon Harvesting by Excimer-Forming Multichromophores. Chem. Commun. 2012, 48, 9589– 9591, DOI: 10.1039/c2cc34183b81https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xht12qsrjN&md5=9ad61ebfb509cb71b74ed02b84b60198Photon harvesting by excimer-forming multichromophoresAdeyemi, Oliver O.; Malinovskii, Vladimir L.; Biner, Sarah M.; Calzaferri, Gion; Haener, RobertChemical Communications (Cambridge, United Kingdom) (2012), 48 (77), 9589-9591CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)A light-harvesting system based on a DNA-organized oligopyrene-cyanine complex is described. Energy transfer from the pyrene units to the cyanine dye was found to proceed via FRET from locally confined excimers to the acceptor.
- 82Asanuma, H.; Fujii, T.; Kato, T.; Kashida, H. Coherent Interactions of Dyes Assembled on DNA. J. Photochem. Photobiol., C 2012, 13, 124– 135, DOI: 10.1016/j.jphotochemrev.2012.04.00282https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XntVWhtbk%253D&md5=a6cea5584e14c9a209e452cc91db26a2Coherent interactions of dyes assembled on DNAAsanuma, Hiroyuki; Fujii, Taiga; Kato, Tomohiro; Kashida, HiromuJournal of Photochemistry and Photobiology, C: Photochemistry Reviews (2012), 13 (2), 124-135CODEN: JPPCAF; ISSN:1389-5567. (Elsevier B.V.)A review. The optical behavior of an organized dye assembly is different from that of the isolated dye; this difference is explained using mol. exciton theory. The theory predicts that mutual orientation, the no. of dyes in the cluster, and combinations of different dyes should display given characteristic spectroscopic behaviors due to coherent interactions. Comparison of theor. predictions with exptl. results has been limited so far. One of the reasons is the absence of a rigid and well-organized system that can control the orientation and size of the dye assembly. Recently, the DNA duplex has been used to assemble chromophores in a programmed manner. Use of DNA allows organized dye assembly with a given size and particular orientation. In this review, we evaluate the spectroscopic behavior of the H-type aggregate based on mol. exciton theory and compare it with actual dye assembly with DNA duplex. Furthermore, we demonstrate the importance of coherent interactions on the obsd. optical properties of dyes assembled in a DNA duplex.
- 83Kashida, H.; Asanuma, H. Preparation of Supramolecular Chromophoric Assemblies Using a DNA Duplex. Phys. Chem. Chem. Phys. 2012, 14, 7196– 7204, DOI: 10.1039/c2cp40520b83https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XmtlGjur4%253D&md5=e2b7b27633b41e6894fa6348f8a7e4f2Preparation of supramolecular chromophoric assemblies using a DNA duplexKashida, Hiromu; Asanuma, HiroyukiPhysical Chemistry Chemical Physics (2012), 14 (20), 7196-7204CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)A review with refs. and new materials are presented . Organization of supramol. assemblies of chromophores with precisely-controlled orientation and sequence remains challenging. Nucleic acids with complementary base sequences spontaneously form double-helical structures. Therefore, covalent attachment of chromophores to DNA or RNA can be used to control assembly and orientation of chromophores. In this perspective, we first review our recent work on the assemblies of fluorophores (pyrene and perylene) by using natural base pairs. The interaction between dyes can be strictly controlled by means of cluster and interstrand wedge motifs. We then discuss novel artificial base pairs that can suppress the interaction between fluorophores and nucleobases. We incorporated a cyclohexane moiety into DNA, and showed that these artificial base pairs suppressed the electron-hole transfer between fluorophores and nucleobases and enhanced the quantum yields of fluorophores. These base pairs can potentially be used to accumulate fluorophores inside DNA duplexes without decreasing quantum yields.
- 84Cunningham, P. D.; Kim, Y. C.; Diaz, S. A.; Buckhout-White, S.; Mathur, D.; Medintz, I. L.; Melinger, J. S. Optical Properties of Vibronically Coupled Cy3 Dimers on DNA Scaffolds. J. Phys. Chem. B 2018, 122, 5020– 5029, DOI: 10.1021/acs.jpcb.8b0213484https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXosVelsLk%253D&md5=9184938ca1825373bfa592846d1f534cOptical Properties of Vibronically Coupled Cy3 Dimers on DNA ScaffoldsCunningham, Paul D.; Kim, Young C.; Diaz, Sebastian A.; Buckhout-White, Susan; Mathur, Divita; Medintz, Igor L.; Melinger, Joseph S.Journal of Physical Chemistry B (2018), 122 (19), 5020-5029CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)The effect of electronic coupling on the optical properties of Cy3 dimers attached to DNA duplexes was examine as a function of base pair (bp) sepn. using steady-state and time-resolved spectroscopy. For close Cy3-Cy3 sepns., 0 and 1 bp between dyes, intermediate to strong electronic coupling is revealed by modulation of the absorption and fluorescence properties including spectral band shape, peak wavelength, and excited-state lifetime. Using a vibronic exciton model, the authors est. coupling strengths of 150 and 266 cm-1 for the 1 and 0 bp sepns., resp., which are comparable to those found in natural light-harvesting complexes. For the strongest electronic coupling (0 bp sepn.), the absorption band shape is strongly affected by the base pairs that surround the dyes, where more strongly H-bonded G-C pairs produce a red shifted absorption spectrum consistent with a J-type dimer. This effect is studied theor. using mol. dynamics simulation, which predicts an in-line dye configuration that is consistent with the exptl. J-type spectrum. When the Cy3 dimers are in a std. aq. buffer, the presence of relatively strong electronic coupling is accompanied by decreased fluorescence lifetime, suggesting that it promotes nonradiative relaxation in cyanine dyes. The use of a viscous solvent can suppress this nonradiative recombination and restore the dimer fluorescent emission. Ultrafast transient absorption measurements of Cy3 dimers in both std. aq. buffer and viscous glycerol buffer suggest that sufficiently strong electronic coupling increases the probability of excited-state relaxation through a dark state that is related to Cy3 torsional motion.
- 85Mazuski, R. J.; Díaz, S. A.; Wood, R. E.; Lloyd, L. T.; Klein, W. P.; Mathur, D.; Melinger, J. S.; Engel, G. S.; Medintz, I. L. Ultrafast Excitation Transfer in Cy5 DNA Photonic Wires Displays Dye Conjugation and Excitation Energy Dependency. J. Phys. Chem. Lett. 2020, 4163– 4172, DOI: 10.1021/acs.jpclett.0c0102085https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXovVGltLY%253D&md5=72480da3ab7165fe5a6e5566d4c2f798Ultrafast Excitation Transfer in Cy5 DNA Photonic Wires Displays Dye Conjugation and Excitation Energy DependencyMazuski, Richard J.; Diaz, Sebastian A.; Wood, Ryan E.; Lloyd, Lawson T.; Klein, William P.; Mathur, Divita; Melinger, Joseph S.; Engel, Gregory S.; Medintz, Igor L.Journal of Physical Chemistry Letters (2020), 11 (10), 4163-4172CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)DNA scaffolds enable base-pair-specific positioning of fluorescent mols., allowing for nanometer-scale precision in controlling multidye interactions. Expanding on this concept, DNA-based mol. photonic wires (MPWs) allow for light harvesting and directional propagation of photonic energy on the nanometer scale. The most common MPW examples exploit Forster resonance energy transfer (FRET), and FRET between the same dye species (HomoFRET) was recently shown to increase the distance and efficiency at which MPWs can function. Although increased proximity between adjacent fluorophores can be used to increase the energy transfer efficiency, FRET assumptions break down as the distance between the dye mols. becomes comparable to their size (~ 2 nm). Here the authors compare dye conjugation with single vs. dimer Cy5 dye repeats as HomoFRET MPW components on a double-crossover DNA scaffold. At room temp. (RT) under low-light conditions, end-labeled uncoupled dye mols. provide optimal transfer, while the Cy5 dimers show ultrafast (<100 ps) nonradiative decay that severely limits their functionality. Of particular interest is the observation that through increased excitation fluence as well as cryogenic temps., the dimeric MPW shows suppression of the ultrafast decay, demonstrating fluorescence lifetimes similar to the single Cy5 MPWs. This work points to the complex dynamic capabilities of dye-based nanophotonic networks, where dye positioning and interactions can become crit., and could be used to extend the lengths and complexities of such dye-DNA devices, enabling multiparameter nanophotonic circuitry.
- 86Asanuma, H.; Shirasuka, K.; Takarada, T.; Kashida, H.; Komiyama, M. DNA-Dye Conjugates for Controllable H Aggregation(1). J. Am. Chem. Soc. 2003, 125, 2217– 2223, DOI: 10.1021/ja021153k86https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXovFyksg%253D%253D&md5=b246e2945f9373813aaa52558532a241DNA-Dye Conjugates for Controllable H* AggregationAsanuma, Hiroyuki; Shirasuka, Kenji; Takarada, Tohru; Kashida, Hiromu; Komiyama, MakotoJournal of the American Chemical Society (2003), 125 (8), 2217-2223CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Methyl red H* aggregate of predetd. size is successfully synthesized from the DNA conjugate involving multiple Methyl red moieties in sequence. In the single stranded state, hypsochromicity monotonically increases with the no. of incorporated dyes: the peak max. of the conjugate involving six Me Reds appears at 415 nm, and the shift is as great as 69 nm (3435 cm-1) with respect to the monomeric transition. This large hypsochromicity accompanied by the narrowing of the band clearly demonstrates that H* aggregate is formed in the single strand. H* aggregation is further promoted at higher ionic strength. Upon addn. of complementary DNA below the Tm, however, this H* band disappears and a new peak appears at 448 nm, indicating that aggregated structure is changed by the duplex formation. This spectral change is completely reversible so that the H* band at 415 nm appears again above Tm. Thus, aggregated structure can be reversibly controlled by the formation and dissocn. of the DNA duplex.
- 87Kashida, H.; Asanuma, H.; Komiyama, M. Alternating Hetero H Aggregation of Different Dyes by Interstrand Stacking from Two DNA-Dye Conjugates. Angew. Chem., Int. Ed. 2004, 43, 6522– 6525, DOI: 10.1002/anie.20046087087Alternating hetero H aggregation of different dyes by interstrand stacking from two DNA-dye conjugatesKashida, Hiromu; Asanuma, Hiroyuki; Komiyama, Mak