Single-Color Isomer-Resolved Spectroscopy
- Grite L. AbmaGrite L. AbmaRadboud University, Institute for Molecules and Materials, Heijendaalseweg 135, 6525 AJ Nijmegen, The NetherlandsMore by Grite L. Abma
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- Dries KleuskensDries KleuskensRadboud University, Institute for Molecules and Materials, Heijendaalseweg 135, 6525 AJ Nijmegen, The NetherlandsMore by Dries Kleuskens
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- Siwen WangSiwen WangRadboud University, Institute for Molecules and Materials, Heijendaalseweg 135, 6525 AJ Nijmegen, The NetherlandsMore by Siwen Wang
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- Michiel BalsterMichiel BalsterRadboud University, Institute for Molecules and Materials, Heijendaalseweg 135, 6525 AJ Nijmegen, The NetherlandsMore by Michiel Balster
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- Andre van RoijAndre van RoijRadboud University, Institute for Molecules and Materials, Heijendaalseweg 135, 6525 AJ Nijmegen, The NetherlandsMore by Andre van Roij
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- Niek JanssenNiek JanssenRadboud University, Institute for Molecules and Materials, Heijendaalseweg 135, 6525 AJ Nijmegen, The NetherlandsMore by Niek Janssen
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- Daniel A. Horke*Daniel A. Horke*E-mail: [email protected]Radboud University, Institute for Molecules and Materials, Heijendaalseweg 135, 6525 AJ Nijmegen, The NetherlandsMore by Daniel A. Horke
Abstract

Structural isomers, such as conformers or tautomers, are of significant importance across chemistry and biology, as they can have different functionalities. In gas-phase experiments using molecular beams, formation of many different isomers cannot be prevented, and their presence significantly complicates the assignment of spectral lines. Current isomer-resolved spectroscopic techniques heavily rely on theoretical calculations or make use of elaborate double-resonance schemes. We show here that isomer-resolved spectroscopy can also be performed using a single tunable laser. In particular, we demonstrate single-color isomer-resolved spectroscopy by utilizing electrostatic deflection to spatially separate the isomers. We show that for 3-aminophenol we can spatially separate the syn and anti conformers and use these pure samples to perform high-resolution REMPI spectroscopy, making the assignment of transitions to a particular isomer trivial, without any additional a priori information. This approach allows one to add isomer specificity to any molecular-beam-based experiment.
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*Disclaimer
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License Summary*
You are free to share (copy and redistribute) this article in any medium or format and to adapt (remix, transform, and build upon) the material for any purpose, even commercially within the parameters below:
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Attribution (BY): Credit must be given to the creator.
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I. Introduction
Figure 1

Figure 1. Structures and permanent dipole moments of syn and anti 3-aminophenol.
II. Methods
III. Results and Discussion
Figure 2

Figure 2. Resonance enhanced multiphoton ionization spectra of 3-aminophenol. (a) Measured in the middle of the molecular beam without deflection fields, containing a mixture of syn and anti conformers. (b) At the most deflected edge of the molecular beam, containing a pure sample of syn 3-aminophenol. (c) Mixture spectrum with the pure syn spectrum subtracted (green), as well as the spectrum collected at the undeflected edge containing a nearly pure sample of anti conformers (red).
Figure 3

Figure 3. Measured molecular beam intensity of syn (blue) and anti 3-aminophenol (red) as a function of laser height (data points), and matching trajectory simulations (solid lines), yielding a rotational temperature of 1.3 K. The inset shows the relative purity of the syn conformer across the deflected molecular beam. The vertical lines show the positions at which the resonance enhanced multiphoton ionization spectra for the pure syn (right) and anti (left) conformers were measured.
Figure 4

Figure 4. Zoom-in of the spectral region 34 800 cm–1 to 35 000 cm–1 for the spectra shown in Figure 2, highlighting the purity of the produced molecular beams and the trivial assignment of lines to conformers.
IV. Conclusion
Supporting Information
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jpca.2c02277.
Detailed description of the experimental setup and list of observed spectral lines (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 work was supported by The Netherlands Organization for Scientific Research (NWO) under grant numbers STU.019.009, 712.018.004, and VI-VIDI-193.037, as well as the Spectroscopy of Cold Molecules Department and the Institute for Molecules and Materials of Radboud University Nijmegen. Computational parts of this work were carried out on the Dutch national e-infrastructure with the support of SURF Cooperative.
References
This article references 26 other publications.
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- 14Chang, Y.-P.; Horke, D. A.; Trippel, S.; Küpper, J. Spatially-controlled complex molecules and their applications. Int. Rev. Phys. Chem. 2015, 34, 557– 590, DOI: 10.1080/0144235X.2015.1077838Google Scholar14https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhslensb7O&md5=a9fe710737d3d0b5049a3598e26e403eSpatially-controlled complex molecules and their applicationsChang, Yuan-Pin; Horke, Daniel A.; Trippel, Sebastian; Kuepper, JochenInternational Reviews in Physical Chemistry (2015), 34 (4), 557-590CODEN: IRPCDL; ISSN:0144-235X. (Taylor & Francis Ltd.)The understanding of mol. structure and function is at the very heart of the chem. and mol. sciences. Expts. that allow for the creation of structurally pure samples and the investigation of their mol. dynamics and chem. function have developed tremendeously over the last few decades, although 'there's plenty of room at the bottom' for better control as well as further applications. Here, we describe the use of inhomogeneous elec. fields for the manipulation of neutral mols. in the gas-phase, i.e. for the sepn. of complex mols. according to size, structural isomer, and quantum state. For these complex mols., all quantum states are strong-field seeking, requiring dynamic fields for their confinement. Current applications of these controlled samples are summarised and interesting future applications discussed.
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- 16de Nijs, A. J.; Bethlem, H. L. On deflection fields, weak-focusing and strong-focusing storage rings for polar molecules. Phys. Chem. Chem. Phys. 2011, 13, 19052– 8, DOI: 10.1039/c1cp21477bGoogle Scholar16https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtlerurfJ&md5=d3dc2455f094298e670685ab8c933dfcOn deflection fields, weak-focusing and strong-focusing storage rings for polar moleculesde Nijs, Adrian J.; Bethlem, Hendrick L.Physical Chemistry Chemical Physics (2011), 13 (42), 19052-19058CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)In this paper, we analyze elec. deflection fields for polar mols. in terms of a multipole expansion and derive a simple but rather insightful expression for the force on the mols. Ideally, a deflection field exerts a strong, const. force in one direction, while the force in the other directions is zero. We show how, by a proper choice of the expansion coeffs., this ideal can be best approximated. We present a design for a practical electrode geometry based on this anal. By bending such a deflection field into a circle, a simple storage ring can be created; the direct analog of a weak-focusing cyclotron for charged particles. We show that for realistic parameters a weak-focusing ring is only stable for mols. with a very low velocity. A strong-focusing (alternating-gradient) storage ring can be created by arranging many straight deflection fields in a circle and by alternating the sign of the hexapole term between adjacent deflection fields. The acceptance of this ring is numerically calcd. for realistic parameters. Such a storage ring might prove useful in expts. looking for an EDM of elementary particles.
- 17Eppink, A. T. J. B.; Parker, D. H. Velocity map imaging of ions and electrons using electrostatic lenses: Application in photoelectron and photofragment ion imaging of molecular oxygen. Rev. Sci. Instrum. 1997, 68, 3477– 3484, DOI: 10.1063/1.1148310Google Scholar17https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXmtVantLo%253D&md5=a83796aa42f608d71271f5d397906508Velocity map imaging of ions and electrons using electrostatic lenses: Application in photoelectron and photofragment ion imaging of molecular oxygenEppink, Andre T. J. B.; Parker, David H.Review of Scientific Instruments (1997), 68 (9), 3477-3484CODEN: RSINAK; ISSN:0034-6748. (American Institute of Physics)The application of electrostatic lenses is demonstrated to give a substantial improvement of the two-dimensional (2D) ion/electron imaging technique. This combination of ion lens optics and 2D detection makes "velocity map imaging" possible, i.e., all particles with the same initial velocity vector are mapped onto the same point on the detector. Whereas the more common application of grid electrodes leads to transmission redn., severe trajectory deflections and blurring due to the non-point source geometry, these problems are avoided with open lens electrodes. A three-plate assembly with aperture electrodes has been tested and its properties are compared with those of grid electrodes. The photodissocn. processes occurring in mol. oxygen following the two-photon 3dπ(3Σ1g-)(v=2, N=2)←X(3Σg-) Rydberg excitation around 225 nm are presented here to show the improvement in spatial resoln. in the ion and electron images. Simulated trajectory calcns. show good agreement with expt. and support the appealing properties of this velocity mapping technique.
- 18Chang, Y.-P.; Filsinger, F.; Sartakov, B.; Küpper, J. CMIstark: Python package for the Stark-effect calculation and symmetry classification of linear, symmetric and asymmetric top wavefunctions in dc electric fields. Comput. Phys. Commun. 2014, 185, 339– 349, DOI: 10.1016/j.cpc.2013.09.001Google Scholar18https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsFWrsbfM&md5=1fb3973e5cfe2a1728d92b26e036a2d1CMIstark: Python package for the Stark-effect calculation and symmetry classification of linear, symmetric and asymmetric top wavefunctions in dc electric fieldsChang, Yuan-Pin; Filsinger, Frank; Sartakov, Boris G.; Kuepper, JochenComputer Physics Communications (2014), 185 (1), 339-349CODEN: CPHCBZ; ISSN:0010-4655. (Elsevier B.V.)The Controlled Mol. Imaging group (CMI) at the Center for Free Electron Laser Science (CFEL) has developed the CMISTARK software to calc., view, and analyze the energy levels of adiabatic Stark energy curves of linear, sym. top and asym. top mols. The program exploits the symmetry of the Hamiltonian to generate fully labeled adiabatic Stark energy curves. CMISTARK is written in Python and easily extendable, while the core numerical calcns. make use of machine optimized BLAS and LAPACK routines. Calcd. energies are stored in HDF5 files for convenient access and programs to ext. ASCII data or to generate graphical plots are provided.
- 19Xie, Y.; Su, H.; Tzeng, W. B. Rotamers of m-aminophenol cation studied by mass analyzed threshold ionization spectroscopy and theoretical calculations. Chem. Phys. Lett. 2004, 394, 182– 187, DOI: 10.1016/j.cplett.2004.07.005Google Scholar19https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXmt1WmtrY%253D&md5=267aace472f74dc4383721ab31e3ae19Rotamers of m-aminophenol cation studied by mass analyzed threshold ionization spectroscopy and theoretical calculationsXie, Yan; Su, Huawei; Tzeng, Wen BihChemical Physics Letters (2004), 394 (1-3), 182-187CODEN: CHPLBC; ISSN:0009-2614. (Elsevier B.V.)The vibrationally resolved spectra of selected rotamers of m-aminophenol were recorded by mass analyzed threshold ionization spectroscopy in connection with two-color resonant two-photon excitation scheme. The adiabatic ionization energies of the cis and trans rotamers are 61,460 ± 5 and 61,734 ± 5 cm-1, resp. The frequencies of modes 1 (breathing) and 18a (in-plane CH bending) are 744 and 1097 cm-1 for the cis, and 736 and 1104 cm-1 for the trans rotamer, resp. Different orientation of the OH with respect to the NH2 substituent only slightly influences these two modes.
- 20Yatsyna, V.; Bakker, D. J.; Feifel, R.; Rijs, A. M.; Zhaunerchyk, V. aminophenol isomers unraveled by conformer-specific far-IR action spectroscopy. Phys. Chem. Chem. Phys. 2016, 18, 6275– 6283, DOI: 10.1039/C5CP07426FGoogle Scholar20https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhslWms78%253D&md5=0a0e3fc1a6232682b779d8a785d09f90Aminophenol isomers unraveled by conformer-specific far-IR action spectroscopyYatsyna, Vasyl; Bakker, Daniel J.; Feifel, Raimund; Rijs, Anouk M.; Zhaunerchyk, VitaliPhysical Chemistry Chemical Physics (2016), 18 (8), 6275-6283CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)Spectroscopic studies of mol. structure can strongly benefit from extending the conventional mid-IR range to the far-IR and THz regions, as low-frequency mol. vibrations provide unique fingerprints and high sensitivity to intra- and intermol. interactions. The gas-phase conformer specific far-IR spectra of aminophenol isomers, recorded in the spectral range of 220-800 cm-1 at the free-electron laser lab. FELIX in Nijmegen (the Netherlands), are reported. Many distinct far-IR vibrational signatures which are specific for the mol. structure of the different aminophenol isomers are revealed and assigned. The obsd. far-IR transitions of the NH2 wagging (inversion) motion were treated with a double-min. harmonic well potential model that has enabled us to obtain the inversion barrier values. Also, the limitations and capability of conventional DFT frequency calcns. to describe the far-IR vibrational modes are discussed.
- 21Shinozaki, M.; Sakai, M.; Yamaguchi, S.; Fujioka, T.; Fujii, M. S1 ←S0 electronic spectrum of jet-cooled m-aminophenol. Phys. Chem. Chem. Phys. 2003, 5, 5044– 5050, DOI: 10.1039/B309461HGoogle Scholar21https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXosFWjuro%253D&md5=be9a4f49f48724391c13c36afae97778S1-S0 Electronic spectrum of jet-cooled m-aminophenolShinozaki, Minako; Sakai, Makoto; Yamaguchi, Shigeru; Fujioka, Tomoo; Fujii, MasaakiPhysical Chemistry Chemical Physics (2003), 5 (22), 5044-5050CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)The S1 and S0 states of m-aminophenol were studied using laser induced fluorescence and dispersed fluorescence spectroscopy in a supersonic jet. The dispersed fluorescence spectra, obtained by exciting the bands at 34,109 and 34,469 cm-1, show the same vibronic structure, which suggests the coexistence of rotational isomers in m-aminophenol. A quantum chem. calcn. also supports the coexistence of rotational isomers. From the relative intensities in the spectrum and the calcd. stabilization energies of isomers, the bands are assigned to the origin of the cis- and trans-isomers, resp. The dispersed fluorescence spectra obtained by exciting the S1 vibronic bands were analyzed by comparing with the calcd. vibrational frequencies and IR and Raman spectra. From the anal., the S1 vibronic bands were assigned. A 1-to-one correspondence between the S1 and S0 vibrations is broken, and vibrational mixing due to Fermi resonance or the Duschinsky effect is suggested.
- 22Even, U.; Jortner, J.; Noy, D.; Lavie, N.; Cossart-Magos, N. Cooling of large molecules below 1 K and He clusters formation. J. Chem. Phys. 2000, 112, 8068– 8071, DOI: 10.1063/1.481405Google Scholar22https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXivVOis7g%253D&md5=6576ae146fc6673305338fd88ad9f70fCooling of large molecules below 1 K and He clusters formationEven, U.; Jortner, J.; Noy, D.; Lavie, N.; Cossart-Magos, C.Journal of Chemical Physics (2000), 112 (18), 8068-8071CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)We present here the design details of a high-pressure pulsed valve that generates intense supersonic jets. The measured rotational contours of aniline indicate that temps. <0.5 K can be achieved before the formation of clusters with the He carrier gas. The spectral shifts and vibronic structure of anthracene-Hen clusters (n = 1-6) are showing some surprising features.
- 23Hutzler, N. R.; Lu, H.-I.; Doyle, J. M. The buffer gas beam: An intense, cold, and slow source for atoms and molecules. Chem. Rev. 2012, 112, 4803– 4827, DOI: 10.1021/cr200362uGoogle Scholar23https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XmslKju7g%253D&md5=a056b57a331197fc5d4097b68c8db443The Buffer Gas Beam: An Intense, Cold, and Slow Source for Atoms and MoleculesHutzler, Nicholas R.; Lu, Hsin-I.; Doyle, John M.Chemical Reviews (Washington, DC, United States) (2012), 112 (9), 4803-4827CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. The authors discuss the properties of buffer gas beams, compare them with more std. beam techniques, and discuss both existing and proposed applications. The ability of this technique to deliver cold, slow, and intense beams of atoms and mols., including those that are difficult to produce with effusive or supersonic techniques, is fueling adoption of this technique for a wide range of applications. However, this beam prodn. technique is still relatively new and has not been as thoroughly characterized and developed as others.
- 24Liu, J.; Koenig, J. L. Data Processing Techniques to Extract Pure-Component Spectra from Mixture Spectra and Their Application to Polymeric Systems. Anal. Chem. 1987, 59, 2609– 2615, DOI: 10.1021/ac00148a017Google Scholar24https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2sXlsFGis74%253D&md5=4336746e7721abbaf3d81c76adbc70cfData processing techniques to extract pure-component spectra from mixture spectra and their application to polymeric systemsLiu, Juwhan; Koenig, Jack L.Analytical Chemistry (1987), 59 (21), 2609-15CODEN: ANCHAM; ISSN:0003-2700.A nonlinear optimization technique was developed to ext. pure-component spectra from the mixt. spectra. The absorbances of the pure spectra and the concns. are variables to be optimized in the algorithm proposed. As constraints, nonnegativities of absorbances and concns. are applied where the concns. are used in terms of fractions. Through tests, three "pure" rotational isomer spectra of poly(ethylene terephthalate) were obtained. A least-squares procedure was utilized to expand the scope of the proposed method. This technique was applicable to all systems described by the Beer-Lambert law.
- 25Trippel, S.; Chang, Y.-P.; Stern, S.; Mullins, T.; Holmegaard, L.; Küpper, J. Spatial separation of state- and size-selected neutral clusters. Phys. Rev. A 2012, 86, 033202, DOI: 10.1103/PhysRevA.86.033202Google Scholar25https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhsF2isrrF&md5=9f89a2e46ca1524f4242603f49c7f46bSpatial separation of state- and size-selected neutral clustersTrippel, Sebastian; Chang, Yuan-Pin; Stern, Stephan; Mullins, Terry; Holmegaard, Lotte; Kuepper, JochenPhysical Review A: Atomic, Molecular, and Optical Physics (2012), 86 (3-A), 033202/1-033202/6CODEN: PLRAAN; ISSN:1050-2947. (American Physical Society)We demonstrate the spatial sepn. of the prototypical indole(H2O) clusters from the various species present in the supersonic expansion of mixts. of indole and water. The major mol. constituents of the resulting mol. beam are H2O, indole, indole(H2O), and indole(H2O)2. It is a priori not clear whether such floppy systems are amenable to strong manipulation using elec. fields. Here, we have exploited the cold supersonic mol. beam and the electrostatic deflector to sep. indole(H2O) from the other mol. species as well as the helium seed gas. The exptl. results are quant. explained by trajectory simulations, which also demonstrate that the quantum-state selectivity of the process leads to samples of indole(H2O) in low-lying rotational states. The prepd. clean samples of indole(H2O) are ideally suited for investigations of the stereodynamics of this complex system, including time-resolved half-collision and diffraction expts. of fixed-in-space clusters. Our findings clearly demonstrate that the hydrogen bonded indole(H2O) complex behaves as a rigid mol. under our exptl. conditions and that it can be strongly deflected.
- 26Franz, J.; Gianturco, F. A. Low-Energy Positron Scattering from DNA Nucleobases: The Effects from Permanent Dipoles. Eur. Phys. J. D 2014, 68, 279, DOI: 10.1140/epjd/e2014-50072-0Google ScholarThere is no corresponding record for this reference.
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Abstract
Figure 1
Figure 1. Structures and permanent dipole moments of syn and anti 3-aminophenol.
Figure 2
Figure 2. Resonance enhanced multiphoton ionization spectra of 3-aminophenol. (a) Measured in the middle of the molecular beam without deflection fields, containing a mixture of syn and anti conformers. (b) At the most deflected edge of the molecular beam, containing a pure sample of syn 3-aminophenol. (c) Mixture spectrum with the pure syn spectrum subtracted (green), as well as the spectrum collected at the undeflected edge containing a nearly pure sample of anti conformers (red).
Figure 3
Figure 3. Measured molecular beam intensity of syn (blue) and anti 3-aminophenol (red) as a function of laser height (data points), and matching trajectory simulations (solid lines), yielding a rotational temperature of 1.3 K. The inset shows the relative purity of the syn conformer across the deflected molecular beam. The vertical lines show the positions at which the resonance enhanced multiphoton ionization spectra for the pure syn (right) and anti (left) conformers were measured.
Figure 4
Figure 4. Zoom-in of the spectral region 34 800 cm–1 to 35 000 cm–1 for the spectra shown in Figure 2, highlighting the purity of the produced molecular beams and the trivial assignment of lines to conformers.
References
ARTICLE SECTIONSThis article references 26 other publications.
- 1Chang, Y.-P.; Długołȩcki, K.; Küpper, J.; Rösch, D.; Wild, D.; Willitsch, S. Specific Chemical Reactivities of Spatially Separated 3-Aminophenol Conformers with Cold Ca+ Ions. Science 2013, 342, 98– 101, DOI: 10.1126/science.1242271Google Scholar1https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsFelsbzF&md5=16d1cac0fd5d89aac0c4cf800e488222Specific Chemical Reactivities of Spatially Separated 3-Aminophenol Conformers with Cold Ca+ IonsChang, Yuan-Pin; Dlugolecki, Karol; Kuepper, Jochen; Roesch, Daniel; Wild, Dieter; Willitsch, StefanScience (Washington, DC, United States) (2013), 342 (6154), 98-101CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)Many mols. exhibit multiple rotational isomers (conformers) that interconvert thermally and are difficult to isolate. Consequently, a precise characterization of their role in chem. reactions proved challenging. The authors have probed the reactivity of specific conformers by using an exptl. technique based on their spatial sepn. in a mol. beam by electrostatic deflection. The sepd. conformers react with a target of Coulomb-crystd. ions in a trap. In the reaction of Ca+ with 3-aminophenol, a twofold larger rate const. for the cis compared with the trans conformer (differentiated by the O-H bond orientation) were found. This result is explained by conformer-specific differences in the long-range ion-mol. interaction potentials. Approach demonstrates the possibility of controlling reactivity through selection of conformational states.
- 2Champenois, E. G. Conformer-Specific Photochemistry Imaged in Real Space and Time. Science 2021, 374, 178– 182, DOI: 10.1126/science.abk3132Google Scholar2https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXit1eqsbnP&md5=ec20347af136a96070ee94bf6cf4908dConformer-specific photochemistry imaged in real space and timeChampenois, E. G.; Sanchez, D. M.; Yang, J.; Nunes, J. P. Figueira; Attar, A.; Centurion, M.; Forbes, R.; Guhr, M.; Hegazy, K.; Ji, F.; Saha, S. K.; Liu, Y.; Lin, M.-F.; Luo, D.; Moore, B.; Shen, X.; Ware, M. R.; Wang, X. J.; Martinez, T. J.; Wolf, T. J. A.Science (Washington, DC, United States) (2021), 374 (6564), 178-182CODEN: SCIEAS; ISSN:1095-9203. (American Association for the Advancement of Science)Conformational isomers (conformers) of mols. play a decisive role in biol. and org. chem. However, exptl. methods for investigating chem. reaction dynamics are typically not conformer sensitive. We report on a gas-phase mega eV ultrafast electron diffraction investigation of a-phellandrene undergoing an electrocyclic ring-opening reaction. We directly imaged the evolution of a specific set of a-phellandrene conformers into the product isomer predicted by the Woodward-Hoffmann rules in real space and time. Our exptl. results are in quant. agreement with nonadiabatic quantum mol. dynamics simulations, which provide considerable detail of how conformation influences the time scale and quantum efficiency of photoinduced ring-opening reactions.
- 3Dill, K. A.; MacCallum, J. L. The Protein-Folding Problem, 50 Years On. Science 2012, 338, 1042– 1046, DOI: 10.1126/science.1219021Google Scholar3https://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.
- 4Godfrey, P. D.; Brown, R. D. Shape of Glycine. J. Am. Chem. Soc. 1995, 117, 2019– 2023, DOI: 10.1021/ja00112a015Google Scholar4https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2MXjs1CmsLw%253D&md5=56345df6afc9c0759d313ee2542bfe4dShape of GlycineGodfrey, Peter D.; Brown, Ronald D.Journal of the American Chemical Society (1995), 117 (7), 2019-23CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Using a Stark-modulated free-expansion jet spectrometer, the authors have measured and subsequently analyzed the rotational spectra of the two 13C, the 15N, and the methylene-d2 isotopomers of the amino acid glycine conformers 1 and 2 and of the N,O-d3 isotopomer for conformer 2. The structural implications of the derived rotational consts., in light of published geometric parameters from elaborate post-Hartree-Fock ab initio calcns., have led to the conclusion that both of these conformers have rP structures of Cs symmetry. A twisted C1 symmetry modification of conformer 2, designated 3, is the favored prediction of elaborate ab initio calcns., but the effect of the zero-point twisting vibration would give either conformation an rP geometry of Cs symmetry. Thus there is no discrepancy between theory and expt. From a sensitive survey scan of the spectrum of the main isotopomer, an upper limit of 1/5 has been set for the abundance of the theor. conformer 4 relative to 2. This result appears to be in conflict with the most elaborate ab initio calcns., which give 4 as energetically similar to 2 and may point to the importance of conformational relaxation during the jet expansion for higher energy conformers that have suitably low barriers to isomerization.
- 5Godfrey, P. D.; Brown, R. D.; Rodgers, F. M. The Missing Conformers of Glycine and Alanine: Relaxation in Seeded Supersonic Jets. J. Mol. Struct. 1996, 376, 65– 81, DOI: 10.1016/0022-2860(95)09065-7Google Scholar5https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XhsVaqsLw%253D&md5=c14e19f4a27403ab8964c5bc5179cae1The missing conformers of glycine and alanine: relaxation in seeded supersonic jetsGodfrey, Peter D.; Brown, Ronald D.; Rodgers, Fiona M.Journal of Molecular Structure (1996), 376 (), 65-81CODEN: JMOSB4; ISSN:0022-2860. (Elsevier)Certain conformers of glycine and alanine that are predicted by ab initio calcns. to be among those of the lowest energy have not been detected in jet spectroscopy studies of these amino acids, although others of similar or higher predicted energy are obsd. Selective conformational relaxation of the missing conformers to lower energy species during the free jet expansion, broadly consistent with the criteria established by R. S. Ruoff et al. (1990) and by P. Felder and H. H. Geunthard (1982), has been found to provide a satisfactory explanation. Relevant regions of the mol. potential energy hypersurface have been modeled via ab initio calcns. [MP2/6-31G(d,p)] and these show that glycine conformers 4 and 7 can relax to conformer 1, leading to the conclusion, in accordance with observation, that only the latter and conformer 2 should be detected in the jet. In the case of alanine, the ab initio study of the mol. potential energy hypersurface has yielded revised data on predicted spectroscopic consts. for some conformers. Because of the combined effects of relaxation and conformational coalescence through large-amplitude vibrational motion, the revised data do not change the interpretation of the previous spectroscopic study of alanine. The barrier sepg. conformers 2 and 3 is predicted to be no more than 129 cm-1, so that in addn. conformer 1, only a single addnl. coalesced conformer (2,3), undergoing a large-amplitude motion in a double-min. potential, is expected to appear in the jet spectrum rather than two sep. species. The ab initio calcns. on alanine indicate that conformers 4 and 5 are sepd. by a low energy barrier and a similarly low barrier separates conformer 4 from the much lower energy conformer 1. The resulting coalesced conformer (4,5) is effectively a "ledge" on one wall of the potential well contg. conformer 1, and is occupied via an excited vibrational state of conformer 1. In this light, the coalesced conformer (4,5) is not expected to be obsd. in the jet, as the vibrational relaxation of low-frequency vibrational modes is known to be very efficient in free jet expansions. Overall, no conflicts are found to remain between the exptl. observations of jet spectra and the ab initio calcns. for glycine and alanine, provided that the scope of such calcns. is broadened from a narrower focus on equil. structures to consideration of the potential hypersurface. This approach should be important in the correct interpretation of the spectra of other multi-conformational species in free jet expansions.
- 6Barone, V.; Biczysko, M.; Bloino, J.; Puzzarini, C. Glycine Conformers: A Never-Ending Story?. Phys. Chem. Chem. Phys. 2013, 15, 1358– 1363, DOI: 10.1039/C2CP43884DGoogle Scholar6https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsVCqug%253D%253D&md5=b501f7ccc117bad20d69c86c48814560Glycine conformers: a never-ending story?Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Puzzarini, CristinaPhysical Chemistry Chemical Physics (2013), 15 (5), 1358-1363CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)The structure and vibrational spectra of a marginally stable conformer of glycine (usually referred to as VIp or ttc) recently detected in low-temp. matrixes have been characterized by a state-of-the-art computational approach allowing an overall quality for bond distances, rotational consts., conformational enthalpies and vibrational frequencies well within the chem. accuracy. The high accuracy of the computational results allows us to draw a fully consistent interpretation of the available exptl. data and to obtain a more complete characterization of an elusive glycine conformer.
- 7Robertson, E. G.; Simons, J. P. Getting into shape: Conformational and supramolecular landscapes in small biomolecules and their hydrated clusters. Phys. Chem. Chem. Phys. 2001, 3, 1– 18, DOI: 10.1039/b008225mGoogle Scholar7https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXovFSgurY%253D&md5=73875e11c28ca6c604205d9a5fb6ca1dGetting into shape: Conformational and supramolecular landscapes in small biomolecules and their hydrated clustersRobertson, Evan G.; Simons, John P.Physical Chemistry Chemical Physics (2001), 3 (1), 1-18CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)A review, with 171 refs. The last few years have seen a very rapid growth in understanding the influence of non-bonded, particularly hydrogen-bonded interactions, on the shapes and conformations of flexible mols., including those of pharmacol. or biol. importance, and of the supramol. structures of their hydrated clusters. This has come about through the combination of a wide range of newly developed spectroscopic strategies, many of which are laser-based, coupled with powerful and widely available ab initio codes for structural computation. The consequent rapid growth of a new link between the worlds of chem. and biophysics is surveyed in a review which introduces the range of present strategies, their origins, and their application to studies of neurotransmitters, amides and peptides, amino acids and nucleic acid bases. It concludes with a prospectus for the future.
- 8Dian, B. C.; Clarkson, J. R.; Zwier, T. S. Direct Measurement of Energy Thresholds to Conformational Isomerization in Tryptamine. Science 2004, 303, 1169– 1173, DOI: 10.1126/science.1093731Google Scholar8https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXhsVWgtLc%253D&md5=b92b6927f1a123a20750b361eaf59b6eDirect Measurement of Energy Thresholds to Conformational Isomerization in TryptamineDian, Brian C.; Clarkson, Jasper R.; Zwier, Timothy S.Science (Washington, DC, United States) (2004), 303 (5661), 1169-1173CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)Stimulated emission pumping (SEP)-hole filling spectroscopy and SEP-induced population transfer spectroscopy have been used to place narrow bounds on the energy thresholds for isomerization between individual reactant-product isomer pairs involving the seven conformational min. of tryptamine. The thresholds for isomerizing conformer A to all six other conformations divided into three groups at 750 wavenumbers (cm-1) (A → B, F), 1000 cm-1 [A → C(2)], and 1280 to 1320 cm-1 [A → D, E, and C(1)]. The appearance of the first band and the absence of the band below it were used to place upper and lower bounds to the barrier heights for each process. The thresholds for A → B and B → A isomerizations were also combined to det. the relative energies of these two lowest energy min. The combined data from all X → Y isomerizations identify important isomerization pathways on the potential energy surface linking the min.
- 9Snoek, L. C.; Robertson, E. G.; Kroemer, R. T.; Simons, J. P. Conformational landscapes in amino acids: Infrared and ultraviolet ion-dip spectroscopy of phenylalanine in the gas phase. Chem. Phys. Lett. 2000, 321, 49– 56, DOI: 10.1016/S0009-2614(00)00320-1Google Scholar9https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXisFems7k%253D&md5=2486894079d1a64ade09d1482086f685Conformational landscapes in amino acids: infrared and ultraviolet ion-dip spectroscopy of phenylalanine in the gas phaseSnoek, L. C.; Robertson, E. G.; Kroemer, R. T.; Simons, J. P.Chemical Physics Letters (2000), 321 (1,2), 49-56CODEN: CHPLBC; ISSN:0009-2614. (Elsevier Science B.V.)A full structural assignment of the most stable conformers of phenylalanine, based upon a combination of UV and IR ion-dip spectroscopy of the jet-cooled amino acid, coupled with high-level ab-initio computation is presented. The results are discussed in relation to aliph. amino acids to highlight the importance of ring side-chain interactions. The question of zwitterion formation is also discussed.
- 10Bakker, J. M.; Mac Aleese, L.; Meijer, G.; von Helden, G. Fingerprint IR spectroscopy to probe amino acid conformations in the gas phase. Phys. Rev. Lett. 2003, 91, 203003, DOI: 10.1103/PhysRevLett.91.203003Google Scholar10https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXovF2mtbg%253D&md5=ae93ee38a07e1ff12429298c81a49c71Fingerprint IR Spectroscopy to Probe Amino Acid Conformations in the Gas PhaseBakker, Joost M.; Mac Aleese, Luke; Meijer, Gerard; von Helden, GertPhysical Review Letters (2003), 91 (20), 203003/1-203003/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)The IR absorption spectra are reported of different conformational isomers of gas phase amino acid mols. in the mol. fingerprint region of 330-1500 cm-1. The IR absorption spectra for 3 conformers of the amino acid tryptophan show absorption bands that uniquely identify the conformational structure of the mol. and that are well matched by d. functional theory calcns. The present observations hold great promise for future identification of conformational folding of larger mols. by their IR absorption characteristics.
- 11de Vries, M. S.; Hobza, P. Gas-Phase Spectroscopy of Biomolecular Building Blocks. Annu. Rev. Phys. Chem. 2007, 58, 585– 612, DOI: 10.1146/annurev.physchem.57.032905.104722Google Scholar11https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXlslSit7Y%253D&md5=7d018c406624c9f6e19913c9a15ab5faGas-phase spectroscopy of biomolecular building blocksde Vries, Mattanjah S.; Hobza, PavelAnnual Review of Physical Chemistry (2007), 58 (), 585-612CODEN: ARPLAP; ISSN:0066-426X. (Annual Reviews Inc.)A review. Gas-phase spectroscopy lends itself ideally to the study of isolated mols. and provides important data for comparison with theory. In recent years, we have seen enormous progress in the study of biomol. building blocks in the gas phase. The motivation for such work is threefold:. (a) It is important to distinguish between intrinsic mol. properties and properties that result from the biol. environment. (b) Gas-phase spectroscopy of clusters provides insights into fundamental interactions and into microsolvation. (c) Gas-phase data support quantum-chem. calcns. This review focuses on the current status of (poly)amino acids and DNA bases. Recent results help elucidate structure and hydrogen-bonded interactions, as well as showcase a successful interplay between theory and expt.
- 12van Geenen, F. A. M. G.; Kranenburg, R. F.; van Asten, A. C.; Martens, J.; Oomens, J.; Berden, G. Isomer-Specific Two-Color Double-Resonance IR2MS3 Ion Spectroscopy Using a Single Laser: Application in the Identification of Novel Psychoactive Substances. Anal. Chem. 2021, 93, 2687– 2693, DOI: 10.1021/acs.analchem.0c05042Google Scholar12https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhsValu7Y%253D&md5=6a9f515352b62ef2fe9b1a1833d88274Isomer-Specific Two-Color Double-Resonance IR2MS3 Ion Spectroscopy Using a Single Laser: Application in the Identification of Novel Psychoactive Substancesvan Geenen, Fred A. M. G.; Kranenburg, Ruben F.; van Asten, Arian C.; Martens, Jonathan; Oomens, Jos; Berden, GielAnalytical Chemistry (Washington, DC, United States) (2021), 93 (4), 2687-2693CODEN: ANCHAM; ISSN:0003-2700. (American Chemical Society)The capability of an ion trap mass spectrometer to store ions for an arbitrary amt. of time allows the use of a single IR laser to perform two-color double resonance IR-IR spectroscopic expts. on mass-to-charge (m/z) selected ions. In this single-laser IR2MS3 scheme, one IR laser frequency is used to remove a selected set of isomers from the total trapped ion population and the second IR laser frequency, from the same laser, is used to record the IR spectrum of the remaining precursor ions. This yields isomer-specific vibrational spectra of the m/z-selected ions, which can reveal the structure and identity of the initially co-isolated isomeric species. The use of a single laser greatly reduces the exptl. complexity of two-color IR2MS3 and enhances its application in fields employing anal. MS. In this work, we demonstrate the methodol. by acquiring single-laser IR2MS3 spectra in a forensic context, identifying two previously unidentified isomeric novel psychoactive substances (NPS) from a sample that was confiscated by the Amsterdam Police.
- 13Filsinger, F.; Küpper, J.; Meijer, G.; Hansen, J. L.; Maurer, J.; Nielsen, J. H.; Holmegaard, L.; Stapelfeldt, H. Pure samples of individual conformers: the separation of stereo-isomers of complex molecules using electric fields. Angew. Chem., Int. Ed. 2009, 48, 6900– 6902, DOI: 10.1002/anie.200902650Google Scholar13https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhtVOrtrvF&md5=fe37488447b221fe78e7765b7b5979a9Pure samples of individual conformers: The separation of stereoisomers of complex molecules using electric fieldsFilsinger, Frank; Kuepper, Jochen; Meijer, Gerard; Hansen, Jonas L.; Maurer, Jochen; Nielsen, Jens H.; Holmegaard, Lotte; Stapelfeldt, HenrikAngewandte Chemie, International Edition (2009), 48 (37), 6900-6902CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)The authors demonstrate that electrostatic deflection, a classic mol. beam manipulation method that dates back to the 1920s, allows the spatial sepn. of the conformers of a neutral mol. when it is applied to intense beams of rotationally cold mols. produced by a state-of-the-art pulsed supersonic expansion source. The cis and trans conformers of 3-aminophenol are used herein as prototypical structural isomers of complex mols. From the precisely known rotational consts. and dipole moments, the energies of the rotational states of cis-3-aminophenol and trans-3-aminophenol are calcd. as a function of elec. field strength.
- 14Chang, Y.-P.; Horke, D. A.; Trippel, S.; Küpper, J. Spatially-controlled complex molecules and their applications. Int. Rev. Phys. Chem. 2015, 34, 557– 590, DOI: 10.1080/0144235X.2015.1077838Google Scholar14https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhslensb7O&md5=a9fe710737d3d0b5049a3598e26e403eSpatially-controlled complex molecules and their applicationsChang, Yuan-Pin; Horke, Daniel A.; Trippel, Sebastian; Kuepper, JochenInternational Reviews in Physical Chemistry (2015), 34 (4), 557-590CODEN: IRPCDL; ISSN:0144-235X. (Taylor & Francis Ltd.)The understanding of mol. structure and function is at the very heart of the chem. and mol. sciences. Expts. that allow for the creation of structurally pure samples and the investigation of their mol. dynamics and chem. function have developed tremendeously over the last few decades, although 'there's plenty of room at the bottom' for better control as well as further applications. Here, we describe the use of inhomogeneous elec. fields for the manipulation of neutral mols. in the gas-phase, i.e. for the sepn. of complex mols. according to size, structural isomer, and quantum state. For these complex mols., all quantum states are strong-field seeking, requiring dynamic fields for their confinement. Current applications of these controlled samples are summarised and interesting future applications discussed.
- 15Even, U. Pulsed Supersonic Beams from High Pressure Source: Simulation Results and Experimental Measurements. Adv. Chem. 2014, 2014, 636042, DOI: 10.1155/2014/636042Google ScholarThere is no corresponding record for this reference.
- 16de Nijs, A. J.; Bethlem, H. L. On deflection fields, weak-focusing and strong-focusing storage rings for polar molecules. Phys. Chem. Chem. Phys. 2011, 13, 19052– 8, DOI: 10.1039/c1cp21477bGoogle Scholar16https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtlerurfJ&md5=d3dc2455f094298e670685ab8c933dfcOn deflection fields, weak-focusing and strong-focusing storage rings for polar moleculesde Nijs, Adrian J.; Bethlem, Hendrick L.Physical Chemistry Chemical Physics (2011), 13 (42), 19052-19058CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)In this paper, we analyze elec. deflection fields for polar mols. in terms of a multipole expansion and derive a simple but rather insightful expression for the force on the mols. Ideally, a deflection field exerts a strong, const. force in one direction, while the force in the other directions is zero. We show how, by a proper choice of the expansion coeffs., this ideal can be best approximated. We present a design for a practical electrode geometry based on this anal. By bending such a deflection field into a circle, a simple storage ring can be created; the direct analog of a weak-focusing cyclotron for charged particles. We show that for realistic parameters a weak-focusing ring is only stable for mols. with a very low velocity. A strong-focusing (alternating-gradient) storage ring can be created by arranging many straight deflection fields in a circle and by alternating the sign of the hexapole term between adjacent deflection fields. The acceptance of this ring is numerically calcd. for realistic parameters. Such a storage ring might prove useful in expts. looking for an EDM of elementary particles.
- 17Eppink, A. T. J. B.; Parker, D. H. Velocity map imaging of ions and electrons using electrostatic lenses: Application in photoelectron and photofragment ion imaging of molecular oxygen. Rev. Sci. Instrum. 1997, 68, 3477– 3484, DOI: 10.1063/1.1148310Google Scholar17https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXmtVantLo%253D&md5=a83796aa42f608d71271f5d397906508Velocity map imaging of ions and electrons using electrostatic lenses: Application in photoelectron and photofragment ion imaging of molecular oxygenEppink, Andre T. J. B.; Parker, David H.Review of Scientific Instruments (1997), 68 (9), 3477-3484CODEN: RSINAK; ISSN:0034-6748. (American Institute of Physics)The application of electrostatic lenses is demonstrated to give a substantial improvement of the two-dimensional (2D) ion/electron imaging technique. This combination of ion lens optics and 2D detection makes "velocity map imaging" possible, i.e., all particles with the same initial velocity vector are mapped onto the same point on the detector. Whereas the more common application of grid electrodes leads to transmission redn., severe trajectory deflections and blurring due to the non-point source geometry, these problems are avoided with open lens electrodes. A three-plate assembly with aperture electrodes has been tested and its properties are compared with those of grid electrodes. The photodissocn. processes occurring in mol. oxygen following the two-photon 3dπ(3Σ1g-)(v=2, N=2)←X(3Σg-) Rydberg excitation around 225 nm are presented here to show the improvement in spatial resoln. in the ion and electron images. Simulated trajectory calcns. show good agreement with expt. and support the appealing properties of this velocity mapping technique.
- 18Chang, Y.-P.; Filsinger, F.; Sartakov, B.; Küpper, J. CMIstark: Python package for the Stark-effect calculation and symmetry classification of linear, symmetric and asymmetric top wavefunctions in dc electric fields. Comput. Phys. Commun. 2014, 185, 339– 349, DOI: 10.1016/j.cpc.2013.09.001Google Scholar18https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsFWrsbfM&md5=1fb3973e5cfe2a1728d92b26e036a2d1CMIstark: Python package for the Stark-effect calculation and symmetry classification of linear, symmetric and asymmetric top wavefunctions in dc electric fieldsChang, Yuan-Pin; Filsinger, Frank; Sartakov, Boris G.; Kuepper, JochenComputer Physics Communications (2014), 185 (1), 339-349CODEN: CPHCBZ; ISSN:0010-4655. (Elsevier B.V.)The Controlled Mol. Imaging group (CMI) at the Center for Free Electron Laser Science (CFEL) has developed the CMISTARK software to calc., view, and analyze the energy levels of adiabatic Stark energy curves of linear, sym. top and asym. top mols. The program exploits the symmetry of the Hamiltonian to generate fully labeled adiabatic Stark energy curves. CMISTARK is written in Python and easily extendable, while the core numerical calcns. make use of machine optimized BLAS and LAPACK routines. Calcd. energies are stored in HDF5 files for convenient access and programs to ext. ASCII data or to generate graphical plots are provided.
- 19Xie, Y.; Su, H.; Tzeng, W. B. Rotamers of m-aminophenol cation studied by mass analyzed threshold ionization spectroscopy and theoretical calculations. Chem. Phys. Lett. 2004, 394, 182– 187, DOI: 10.1016/j.cplett.2004.07.005Google Scholar19https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXmt1WmtrY%253D&md5=267aace472f74dc4383721ab31e3ae19Rotamers of m-aminophenol cation studied by mass analyzed threshold ionization spectroscopy and theoretical calculationsXie, Yan; Su, Huawei; Tzeng, Wen BihChemical Physics Letters (2004), 394 (1-3), 182-187CODEN: CHPLBC; ISSN:0009-2614. (Elsevier B.V.)The vibrationally resolved spectra of selected rotamers of m-aminophenol were recorded by mass analyzed threshold ionization spectroscopy in connection with two-color resonant two-photon excitation scheme. The adiabatic ionization energies of the cis and trans rotamers are 61,460 ± 5 and 61,734 ± 5 cm-1, resp. The frequencies of modes 1 (breathing) and 18a (in-plane CH bending) are 744 and 1097 cm-1 for the cis, and 736 and 1104 cm-1 for the trans rotamer, resp. Different orientation of the OH with respect to the NH2 substituent only slightly influences these two modes.
- 20Yatsyna, V.; Bakker, D. J.; Feifel, R.; Rijs, A. M.; Zhaunerchyk, V. aminophenol isomers unraveled by conformer-specific far-IR action spectroscopy. Phys. Chem. Chem. Phys. 2016, 18, 6275– 6283, DOI: 10.1039/C5CP07426FGoogle Scholar20https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhslWms78%253D&md5=0a0e3fc1a6232682b779d8a785d09f90Aminophenol isomers unraveled by conformer-specific far-IR action spectroscopyYatsyna, Vasyl; Bakker, Daniel J.; Feifel, Raimund; Rijs, Anouk M.; Zhaunerchyk, VitaliPhysical Chemistry Chemical Physics (2016), 18 (8), 6275-6283CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)Spectroscopic studies of mol. structure can strongly benefit from extending the conventional mid-IR range to the far-IR and THz regions, as low-frequency mol. vibrations provide unique fingerprints and high sensitivity to intra- and intermol. interactions. The gas-phase conformer specific far-IR spectra of aminophenol isomers, recorded in the spectral range of 220-800 cm-1 at the free-electron laser lab. FELIX in Nijmegen (the Netherlands), are reported. Many distinct far-IR vibrational signatures which are specific for the mol. structure of the different aminophenol isomers are revealed and assigned. The obsd. far-IR transitions of the NH2 wagging (inversion) motion were treated with a double-min. harmonic well potential model that has enabled us to obtain the inversion barrier values. Also, the limitations and capability of conventional DFT frequency calcns. to describe the far-IR vibrational modes are discussed.
- 21Shinozaki, M.; Sakai, M.; Yamaguchi, S.; Fujioka, T.; Fujii, M. S1 ←S0 electronic spectrum of jet-cooled m-aminophenol. Phys. Chem. Chem. Phys. 2003, 5, 5044– 5050, DOI: 10.1039/B309461HGoogle Scholar21https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXosFWjuro%253D&md5=be9a4f49f48724391c13c36afae97778S1-S0 Electronic spectrum of jet-cooled m-aminophenolShinozaki, Minako; Sakai, Makoto; Yamaguchi, Shigeru; Fujioka, Tomoo; Fujii, MasaakiPhysical Chemistry Chemical Physics (2003), 5 (22), 5044-5050CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)The S1 and S0 states of m-aminophenol were studied using laser induced fluorescence and dispersed fluorescence spectroscopy in a supersonic jet. The dispersed fluorescence spectra, obtained by exciting the bands at 34,109 and 34,469 cm-1, show the same vibronic structure, which suggests the coexistence of rotational isomers in m-aminophenol. A quantum chem. calcn. also supports the coexistence of rotational isomers. From the relative intensities in the spectrum and the calcd. stabilization energies of isomers, the bands are assigned to the origin of the cis- and trans-isomers, resp. The dispersed fluorescence spectra obtained by exciting the S1 vibronic bands were analyzed by comparing with the calcd. vibrational frequencies and IR and Raman spectra. From the anal., the S1 vibronic bands were assigned. A 1-to-one correspondence between the S1 and S0 vibrations is broken, and vibrational mixing due to Fermi resonance or the Duschinsky effect is suggested.
- 22Even, U.; Jortner, J.; Noy, D.; Lavie, N.; Cossart-Magos, N. Cooling of large molecules below 1 K and He clusters formation. J. Chem. Phys. 2000, 112, 8068– 8071, DOI: 10.1063/1.481405Google Scholar22https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXivVOis7g%253D&md5=6576ae146fc6673305338fd88ad9f70fCooling of large molecules below 1 K and He clusters formationEven, U.; Jortner, J.; Noy, D.; Lavie, N.; Cossart-Magos, C.Journal of Chemical Physics (2000), 112 (18), 8068-8071CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)We present here the design details of a high-pressure pulsed valve that generates intense supersonic jets. The measured rotational contours of aniline indicate that temps. <0.5 K can be achieved before the formation of clusters with the He carrier gas. The spectral shifts and vibronic structure of anthracene-Hen clusters (n = 1-6) are showing some surprising features.
- 23Hutzler, N. R.; Lu, H.-I.; Doyle, J. M. The buffer gas beam: An intense, cold, and slow source for atoms and molecules. Chem. Rev. 2012, 112, 4803– 4827, DOI: 10.1021/cr200362uGoogle Scholar23https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XmslKju7g%253D&md5=a056b57a331197fc5d4097b68c8db443The Buffer Gas Beam: An Intense, Cold, and Slow Source for Atoms and MoleculesHutzler, Nicholas R.; Lu, Hsin-I.; Doyle, John M.Chemical Reviews (Washington, DC, United States) (2012), 112 (9), 4803-4827CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. The authors discuss the properties of buffer gas beams, compare them with more std. beam techniques, and discuss both existing and proposed applications. The ability of this technique to deliver cold, slow, and intense beams of atoms and mols., including those that are difficult to produce with effusive or supersonic techniques, is fueling adoption of this technique for a wide range of applications. However, this beam prodn. technique is still relatively new and has not been as thoroughly characterized and developed as others.
- 24Liu, J.; Koenig, J. L. Data Processing Techniques to Extract Pure-Component Spectra from Mixture Spectra and Their Application to Polymeric Systems. Anal. Chem. 1987, 59, 2609– 2615, DOI: 10.1021/ac00148a017Google Scholar24https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2sXlsFGis74%253D&md5=4336746e7721abbaf3d81c76adbc70cfData processing techniques to extract pure-component spectra from mixture spectra and their application to polymeric systemsLiu, Juwhan; Koenig, Jack L.Analytical Chemistry (1987), 59 (21), 2609-15CODEN: ANCHAM; ISSN:0003-2700.A nonlinear optimization technique was developed to ext. pure-component spectra from the mixt. spectra. The absorbances of the pure spectra and the concns. are variables to be optimized in the algorithm proposed. As constraints, nonnegativities of absorbances and concns. are applied where the concns. are used in terms of fractions. Through tests, three "pure" rotational isomer spectra of poly(ethylene terephthalate) were obtained. A least-squares procedure was utilized to expand the scope of the proposed method. This technique was applicable to all systems described by the Beer-Lambert law.
- 25Trippel, S.; Chang, Y.-P.; Stern, S.; Mullins, T.; Holmegaard, L.; Küpper, J. Spatial separation of state- and size-selected neutral clusters. Phys. Rev. A 2012, 86, 033202, DOI: 10.1103/PhysRevA.86.033202Google Scholar25https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhsF2isrrF&md5=9f89a2e46ca1524f4242603f49c7f46bSpatial separation of state- and size-selected neutral clustersTrippel, Sebastian; Chang, Yuan-Pin; Stern, Stephan; Mullins, Terry; Holmegaard, Lotte; Kuepper, JochenPhysical Review A: Atomic, Molecular, and Optical Physics (2012), 86 (3-A), 033202/1-033202/6CODEN: PLRAAN; ISSN:1050-2947. (American Physical Society)We demonstrate the spatial sepn. of the prototypical indole(H2O) clusters from the various species present in the supersonic expansion of mixts. of indole and water. The major mol. constituents of the resulting mol. beam are H2O, indole, indole(H2O), and indole(H2O)2. It is a priori not clear whether such floppy systems are amenable to strong manipulation using elec. fields. Here, we have exploited the cold supersonic mol. beam and the electrostatic deflector to sep. indole(H2O) from the other mol. species as well as the helium seed gas. The exptl. results are quant. explained by trajectory simulations, which also demonstrate that the quantum-state selectivity of the process leads to samples of indole(H2O) in low-lying rotational states. The prepd. clean samples of indole(H2O) are ideally suited for investigations of the stereodynamics of this complex system, including time-resolved half-collision and diffraction expts. of fixed-in-space clusters. Our findings clearly demonstrate that the hydrogen bonded indole(H2O) complex behaves as a rigid mol. under our exptl. conditions and that it can be strongly deflected.
- 26Franz, J.; Gianturco, F. A. Low-Energy Positron Scattering from DNA Nucleobases: The Effects from Permanent Dipoles. Eur. Phys. J. D 2014, 68, 279, DOI: 10.1140/epjd/e2014-50072-0Google ScholarThere is no corresponding record for this reference.
Supporting Information
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Detailed description of the experimental setup and list of observed spectral lines (PDF)
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