Behavior of Trapped Molecules in Lantern-Like Carcerand SuperphanesClick to copy article linkArticle link copied!
- Andrzej EilmesAndrzej EilmesFaculty of Chemistry, Jagiellonian University in Kraków, Gronostajowa 2, PL-30 387 Krakow, PolandMore by Andrzej Eilmes
- Mirosław Jabłoński*Mirosław Jabłoński*Email: [email protected]. Phone: +48 (56) 611-4695.Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, PL-87 100 Torun, PolandMore by Mirosław Jabłoński
Abstract
Superphanes are a group of organic molecules from the cyclophane family. They are characterized by the presence of two parallel benzene rings joined together by six bridges. If these bridges are sufficiently long, the superphane cavity can be large enough to trap small molecules or ions. Using ab initio (time scale of 80 ps) and classical (up to 200 ns) molecular dynamics (MD) methods, we study the behavior of five fundamental molecules (M = H2O, NH3, HF, HCN, MeOH) encapsulated inside the experimentally reported lantern-like superphane and its two derivatives featuring slightly modified side bridges. The main focus is studying the dynamics of hydrogen bonds between the trapped M molecule and the imino nitrogen atoms of the side chains of the host superphane. The length of the N···H hydrogen bond increases in the following order: HF < HCN < H2O < MeOH < NH3. The mobility of the trapped molecule and its preferred position inside the superphane cage depend not only on the type of this molecule but also largely on the in/out conformational arrangement of the imino nitrogens in the side chains of the superphane. Their inward-pointing positions allow the formation of strong N···H hydrogen bonds. For this reason, these nitrogens are the preferred sites of interaction. The mobility of the molecules and their residence times on each side of the superphane have been explained by referring to the symmetry and conformation of the given superphane cage. All force field MD simulations have shown that the encapsulated molecule remained inside the superphane cage for 200 ns without any escape event to the outside. Moreover, our simulations based on some endohedral complexes in the water box also showed no exchange event. Thus, the superphanes we study are true carcerand molecules. We attribute this property to the hydrophobic side chains and their pinwheel arrangement, which makes the side walls of the studied superphanes fairly impenetrable to small molecules.
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Attribution (BY): Credit must be given to the creator.
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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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Introduction
Figure 1
Figure 1. Side and top views of the [26](1,2,3,4,5,6) (a) and [36](1,2,3,4,5,6) (b) superphanes.
Figure 2
Figure 2. Side and top views of the lantern-like superphane 1 synthesized by Qing He’s group. (42)
Figure 3
Figure 3. Side and top views of the superphane synthesized by Badjić et al. (47)
Figure 4
Figure 4. Side chains in superphanes 1, 2, and 3. Hydrogen atoms participating in hydrogen bonds with the guest molecule are labeled as follows: Hi─imino H atom, Hc─central H atom.
Figure 5
Figure 5. Superphanes 2 and 3.
Computational Methodology
Results and Discussion
Conformation of Superphane Cages
Figure 6
Figure 6. Positions of inward pointing N atoms (marked by orange spheres) in the initial structures of superphanes 1–3. Hydrogen atoms are not shown.
Figure 7
Figure 7. Definitions of C–C–C–N dihedral angles used to trace the conformations at N atoms in superphane 1 (a), superphane 2 (b), and superphane 3 (c); small values of the angle correspond to in conformations, whereas large absolute values indicate out conformations (d).
Figure 8
Figure 8. Evolution of conformations at the four nitrogen atoms inward-pointing in the initial structures during the AIMD simulations for empty superphane cages 1–3. Nitrogen atoms at the bottom and the top of the cage are labeled “b” and “t”, respectively.
Figure 9
Figure 9. Conformations at the nitrogen atoms in MD simulations for empty superphane cages 1–3. Each line corresponds to one N atom. Nitrogen atoms at the bottom and the top of the cage are labeled “b” and “t”, respectively.
Figure 10
Figure 10. Conformations at the nitrogen atoms in MD simulations for HF encapsulated in 1–3. Each line corresponds to one N atom. Nitrogen atoms at the bottom and the top of the cage are labeled “b” and “t”, respectively.
Dynamics of Encapsulated Molecules
Figure 11
Figure 11. Distributions of N···H distances obtained in MD simulations for M@1.
Figure 12
Figure 12. Distributions of the distances between the H atom of M and the center of the superphane cage obtained in the FF MD simulations for M@1–M@3.
Figure 13
Figure 13. Probabilities of interaction with a water hydrogen atom for individual nitrogen atoms at the bottom (blue) or the top (cyan) of the 1–3 superphane cages.
Figure 14
Figure 14. Statistics of residence times for H2O in the cages 1–3 obtained from the FF MD simulations. Note the scale difference between panels.
system | tbottom, ps | ttop, ps |
---|---|---|
H2O@1 | 684 | 703 |
HF@1 | ||
HCN@1 | ||
MeOH@1 | 6890 | 8220 |
NH3@1 | 9.2 | 9.3 |
H2O@2 | 142 | 10 |
HF@2 | ||
HCN@2 | 2387 | 31 |
MeOH@2 | 248 | 57 |
NH3@2 | 2 | 1 |
H2O@3 | 27 | 27 |
HF@3 | 1334 | 1224 |
HCN@3 | 510 | 553 |
MeOH@3 | 200 | 198 |
NH3@3 | 4.2 | 4.1 |
Results averaged over three trajectories.
M | 1 | 2 | 3 |
---|---|---|---|
H2O | –12.1 | –10.3 | –8.0 |
HF | –15.7 | –14.9 | –9.8 |
HCN | –15.2 | –14.9 | –11.4 |
MeOH | –16.9 | –15.6 | –13.4 |
HH3 | –7.8 | –6.8 | –6.0 |
Results averaged over three trajectories.
Tightness of the Cage
Figure 15
Figure 15. A sample snapshot of the solvated H2O@1 at the end of the FF MD simulations with the encapsulated water molecule shown as sticks and the solvating molecules shown as gray lines (a); evolution of the dO-center distance (b); and its distributions at the beginning and at the end of the trajectory (c).
Conclusions
Supporting Information
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jcim.4c01040.
Figures showing evolution of conformations at the four initially inward pointing N atoms in H2O@n during the AIMD simulations, conformations at the nitrogen atoms in MD simulations for H2O encapsulated in 1–3, definitions of dN···H, dH-center and dO-center distances, and FF parameters and input structures (in the Tinker v7 format) for M@n (n = 1, 2, 3; M = H2O, HF, HCN, NH3, MeOH) (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
We gratefully acknowledge Polish high-performance computing infrastructure PL-Grid (HPC Centre ACK Cyfronet AGH) for providing computer facilities within computational grant no. PLG/2023/016895.
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- 22Meno, T.; Sako, K.; Suenaga, M.; Mouri, M.; Shinmyozu, T.; Inazu, T.; Takemura, H. Conformational analysis of [3.3.3](1,3,5)cyclophane systems. Can. J. Chem. 1990, 68, 440– 445, DOI: 10.1139/v90-067Google ScholarThere is no corresponding record for this reference.
- 23Shinmyozu, T.; Hirakida, M.; Kusumoto, S.; Tomonou, M.; Inazu, T.; Rudziński, J. M. Synthesis of [35](1,2,3,4,5)Cyclophane. Chem. Lett. 1994, 23, 669– 672, DOI: 10.1246/cl.1994.669Google ScholarThere is no corresponding record for this reference.
- 24Caramori, G. F.; Galembeck, S. E.; Laali, K. K. A Computational Study of [2.2]Cyclophanes. J. Org. Chem. 2005, 70, 3242– 3250, DOI: 10.1021/jo047864dGoogle Scholar24https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXisFOgt70%253D&md5=6a5e8e03d5c16465efcad7cad4c800cbA Computational Study of [2.2]CyclophanesCaramori, Giovanni F.; Galembeck, Sergio E.; Laali, Kenneth K.Journal of Organic Chemistry (2005), 70 (8), 3242-3250CODEN: JOCEAH; ISSN:0022-3263. (American Chemical Society)A computational study of isomeric [2.2]cyclophanes, [2.2]paracyclophane 1, [2.2]metacyclophane 2, and [2.2]metaparacyclophane 3, was carried out. For 1, geometry optimizations performed by various methods at different basis sets showed that MP2/6-31+G(d,p) and B3PW91/6-31+G(d,p) provide the best results in comparison to the x-ray data. Compd. 1 has D2 symmetry with distorted bridges. A conformational search was performed for [2.2]cyclophanes 2 and 3. Each cyclophane exists in two conformations which have different energies in the case of 3 but are degenerate in the case of 2. Relative energies and strain energies at the bridges follow the same order, indicating that the relief of bridge tension and repulsion between π clouds are detg. factors for the stability of [2.2]cyclophanes. Through a decompn. of strain energy, both the rings or the bridges can absorb strain, but it depends on the conformer of butane that is considered in the calcn. of SE(br). Changes in aromaticity of these compds. were evaluated by NICS and HOMA and were compared with benzene and xylenes dimers as models. Despite distortions from planarity and shortening and lengthening of the C-C bonds relative to the mean, the Ph rings are arom. NICS suggests a concn. of electronic d. between the rings as a result of bridging process. Computed MK, NPA, and GAPT charges were compared for the isomeric cyclophanes. The GIAO chem. shifts were calcd. and indicate that 1 has a larger diamagnetic anisotropy than the other isomers.
- 25Caramori, G. F.; Galembeck, S. E. Computational Study about Through-Bond and Through-Space Interactions in [2.2]Cyclophanes. J. Phys. Chem. A 2007, 111, 1705– 1712, DOI: 10.1021/jp066863hGoogle Scholar25https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXhsFOktbk%253D&md5=4b153e3e4894fe9356e5676d5a00ffb9Computational Study about Through-Bond and Through-Space Interactions in [2.2]CyclophanesCaramori, Giovanni F.; Galembeck, Sergio E.Journal of Physical Chemistry A (2007), 111 (9), 1705-1712CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)An anal. of the electron d., obtained by B3PW91/6-31+G(d,p), B3LYP/6-31+G(d,p), and MP2/6-31+G(d,p) for [2,2]cyclophane isomers, [2.2]paracyclophane, anti-[2.2]metacyclophane, syn-[2.2]metacyclophane, and [2.2]metaparacyclophane, was made through natural bond orbitals (NBO), natural steric anal. (NSA), and atoms in mols. (AIM) methods and through anal. of frontier MOs. NBO indicates that all compds. present through-bond interactions, but only the conformers of [2.2]metacyclophane present significant through-space interactions. The last interactions are obsd. in AIM anal. and by the plots of MOs. AIM indicates that these through-space interactions are closed-shell ones, and they stabilize the conformers. In contrast, all isomers present through-bond and through-space repulsive interactions. In addn., the at. properties, computed over the at. basins, showed that the position of the bridges and the relative displacement of the rings can affect the at. charges, the first at. moments, and the at. vols.
- 26Dodziuk, H.; Szymański, S.; Jaźwiński, J.; Ostrowski, M.; Demissie, T. B.; Ruud, K.; Kuś, P.; Hopf, H.; Lin, S.-T. Structure and NMR Spectra of Some [2.2]Paracyclophanes. The Dilemma of [2.2]Paracyclophane Symmetry. J. Phys. Chem. A 2011, 115, 10638– 10649, DOI: 10.1021/jp205693aGoogle Scholar26https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtFelu73F&md5=3cad57e454b879ffb27001f6fd27e90eStructure and NMR Spectra of Some [2.2]Paracyclophanes. The Dilemma of [2.2]Paracyclophane SymmetryDodziuk, Helena; Szymanski, Slawomir; Jazwinski, Jaroslaw; Ostrowski, Maciej; Demissie, Taye Beyene; Ruud, Kenneth; Kus, Piotr; Hopf, Henning; Lin, Shaw-TaoJournal of Physical Chemistry A (2011), 115 (38), 10638-10649CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)D. functional theory (DFT) quantum chem. calcns. of the structure and NMR parameters for highly strained hydrocarbon [2.2]paracyclophane 1 and its three derivs. are presented. The calcd. NMR parameters are compared with the exptl. ones. By least-squares fitting of the 1H spectra, almost all JHH coupling consts. could be obtained with high accuracy. Theor. vicinal JHH couplings in the aliph. bridges, calcd. using different basis sets (6-311G(d,p), and Huz-IV) reproduce the exptl. values with essentially the same root-mean-square error of ∼1.3 Hz, regardless of the basis set used. These discrepancies could be in part due to a considerable impact of rovibrational effects on the obsd. JHH couplings, since the latter show a measurable dependence on temp. Because of the lasting literature controversies concerning the symmetry of parent compd. 1, D2h vs. D2, a crit. anal. of the relevant literature data is carried out. The symmetry issue is prone to confusion because, according to some literature claims, the two hypothetical enantiomeric D2 structures of 1 could be sepd. by a very low energy barrier that would explain the occurrence of rovibrational effects on the obsd. vicinal JHH couplings. However, the D2h symmetry of 1 with a flat energy min. could also account for these effects.
- 27Fujitsuka, M.; Miyazaki, T.; Lu, C.; Shinmyozu, T.; Majima, T. Multistep Electron Transfer Systems Containing [2.2]- or [3.3]Paracyclophane. J. Phys. Chem. A 2016, 120, 1184– 1189, DOI: 10.1021/acs.jpca.5b11766Google Scholar27https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XitFeru7Y%253D&md5=f07abb306dd08911fed5ac60b90fbe10Multistep Electron Transfer Systems Containing [2.2]- or [3.3]ParacyclophaneFujitsuka, Mamoru; Miyazaki, Takaaki; Lu, Chao; Shinmyozu, Teruo; Majima, TetsuroJournal of Physical Chemistry A (2016), 120 (8), 1184-1189CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)Paracyclophanes (PCPs), which exhibit interesting properties due to their transannular interactions, have been employed as a spacer in various electron transfer (ET) systems. In the present work, we investigated ET processes in dyads and triads contg. [2.2]PCP or [3.3]PCP as donors to study their properties in multistep ET processes. The dyad mols. of PCP and 1,8-naphthalimide (NI) as a photosensitizing electron acceptor exhibited charge sepn. (CS) upon excitation of NI. In addn., triads of NI, PCP, and carbazole showed charge shift after an initial CS, thus confirming multistep ET. In this study, we demonstrated that use of [3.3]PCP in place of [2.2]PCP enhanced the initial CS rate. Lower oxidn. potentials and a smaller reorganization energy for [3.3]PCP are shown to be key factors for this enhanced CS rate. Both of these properties are closely related to the strained structure of PCP; hence, the present results demonstrate the importance of strain in ET chem.
- 28Matsuiwa, K.; Hayashi, S.; Nakanishi, W. Dynamic and Static Behavior of Intramolecular π–π Interactions in [2.2]- and [3.3]Cyclophanes, Elucidated by QTAIM Dual Functional Analysis with QC Calculations. ChemistrySelect 2017, 2, 1774– 1782, DOI: 10.1002/slct.201602047Google ScholarThere is no corresponding record for this reference.
- 29Majerz, I.; Dziembowska, T. What Is the Main Feature Distinguishing the Through-Space Interactions in Cyclophanes from Their Aliphatic Analogues?. ACS Omega 2020, 5, 22314– 22324, DOI: 10.1021/acsomega.0c02671Google Scholar29https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhs1GgtbnO&md5=7df816f4787696b0c22447fc74b60547What Is the Main Feature Distinguishing the Through-Space Interactions in Cyclophanes from Their Aliphatic Analogues?Majerz, Irena; Dziembowska, TeresaACS Omega (2020), 5 (35), 22314-22324CODEN: ACSODF; ISSN:2470-1343. (American Chemical Society)Classical cyclophanes with two benzene rings have been compared with cyclophanes with one benzene ring replaced with an aliph. part and aliph. compds., which are cyclophane analogs. Anal. of geometry, at. charges, and arom. and steric energy and investigation of intramol. noncovalent interactions and charge mobility show that there is no special feature that distinguishes the classical cyclophanes from aliph. analogs, so the definition of cyclophanes can be extended to other compds.
- 30Zhang, X.-X.; Li, J.; Niu, Y.-Y. A Review of Crystalline Multibridged Cyclophane Cages: Synthesis, Their Conformational Behavior, and Properties. Molecules 2022, 27, 7083, DOI: 10.3390/molecules27207083Google ScholarThere is no corresponding record for this reference.
- 31Nogita, R.; Matohara, K.; Yamaji, M.; Oda, T.; Sakamoto, Y.; Kumagai, T.; Lim, C.; Yasutake, M.; Shimo, T.; Jefford, C. W.; Shinmyozu, T. Photochemical Study of [33](1,3,5)Cyclophane and Emission Spectral Properties of [3n]Cyclophanes (n = 2–6). J. Am. Chem. Soc. 2004, 126, 13732– 13741, DOI: 10.1021/ja030032xGoogle Scholar31https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXnvFGgsL4%253D&md5=b1c761658dd686cf02d58a4736f7dd13Photochemical Study of [33](1,3,5)Cyclophane and Emission Spectral Properties of [3n]Cyclophanes (n = 2-6)Nogita, Rika; Matohara, Kumi; Yamaji, Minoru; Oda, Takuma; Sakamoto, Youichi; Kumagai, Tsutomu; Lim, Chultack; Yasutake, Mikio; Shimo, Tetsuro; Jefford, Charles W.; Shinmyozu, TeruoJournal of the American Chemical Society (2004), 126 (42), 13732-13741CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Photochem. reaction of [33](1,3,5)cyclophane 2, which is a photoprecursor for the formation of propella[33]prismane 18, was studied using a sterilizing lamp (254 nm). Upon photolysis in dry and wet CH2Cl2 or MeOH in the presence of 2 mol/L aq. HCl soln., the cyclophane 2 afforded novel cage compds. comprised of new skeletons, tetracyclo[6.3.1.0.2,704,11]dodeca-5,9-diene 43, hexacyclo[6.4.0.0.2,60.4,110.5,1009,12]dodecane 44, and pentacyclo[6.4.0.0.2,60.4,1105,10]dodecane 45. All of these products were confirmed by the x-ray structural analyses. A possible mechanism for the formation of these photoproducts via the hexaprismane deriv. 18 is proposed. The photophys. properties in the excited state of the [3n]cyclophanes ([3n]CP, n = 2-6) were investigated by measuring the emission spectra and detg. the quantum yields and lifetimes of the fluorescence. All [3n]CPs show excimeric fluorescence without a monomeric one. The lifetime of the excimer fluorescence becomes gradually longer with the increasing no. of the trimethylene bridges. The [3n]CPs also shows excimeric phosphorescence spectra without vibrational structures for n = 2, 4, and 5, while phosphorescence is absent for n = 3 and 6. With an increase in symmetry of the benzene skeleton in the [33]- and [36]CPs, the probability of the radiation (phosphorescence) process from the lowest triplet state may drastically decrease. Electronic supplementary information (ESI) is available at http://pubs.acs.org and contains alternative mechanism of single electron-transfer, crystal packing diagrams, and summary of crystallog. data and refinement details.
- 32Fujitsuka, M.; Tojo, S.; Shinmyozu, T.; Majima, T. Intramolecular dimer radical anions of [3n] cyclophanes: transannular distance dependent stabilization energy. Chem. Commun. 2009, 1553– 1555, DOI: 10.1039/b810122aGoogle ScholarThere is no corresponding record for this reference.
- 33Ghasemabadi, P. G.; Yao, T.; Bodwell, G. J. Cyclophanes containing large polycyclic aromatic hydrocarbons. Chem. Soc. Rev. 2015, 44, 6494– 6518, DOI: 10.1039/C5CS00274EGoogle Scholar33https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXptFOqs7g%253D&md5=134750980b78cb5345923017e39f55a0Cyclophanes containing large polycyclic aromatic hydrocarbonsGhasemabadi, Parisa Ghods; Yao, Tieguang; Bodwell, Graham J.Chemical Society Reviews (2015), 44 (18), 6494-6518CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)A review. Although a very large no. cyclophanes has been reported, only a very small proportion of them contain polycyclic arom. systems that can be thought of as 'large', i.e. with ≥4 rings. Such cyclophanes, illuminating both the chem. that was used to synthesize them and what was learned from studying them were highlighted. Context for the main body was provided by the careful consideration of the anatomy of a cyclophane and the classification of general synthetic approaches. The subsequent sections covered eleven different PAHs and are organized primarily according to increasing size of the arom. system, starting with pyrene (C16, the only large polycyclic arom. system to have been incorporated into numerous cyclophanes) and ending with hexabenzo[bc,ef,hi,kl,no,qr]coronene (C42).
- 34Jabłoński, M. Bond Paths Between Distant Atoms Do Not Necessarily Indicate Dominant Interactions. J. Comput. Chem. 2018, 39, 2183– 2195, DOI: 10.1002/jcc.25532Google Scholar34https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhvV2jsbfF&md5=72bd87bc238812e3840a9070a701dd62Bond paths between distant atoms do not necessarily indicate dominant interactionsJablonski, MiroslawJournal of Computational Chemistry (2018), 39 (26), 2183-2195CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)The goal of the article is to revive discussion on the interpretation of bond paths linking distant atoms, particularly tracing weak interactions in dimers. According to the Pendas' concept of privileged exchange channel, a bond path is formed between this pair of competing atoms, which is assocd. with larger value of the exchange energy. We point out that, due to the short-range nature of the exchange energy, bond paths linking distant atoms clearly become doubtful indicators of dominant intermol. interactions, particularly if some other characteristics (geometric, spectroscopic, based on electrostatic parameters, etc.) indicate other intermol. interactions as dominant. Several such cases are thoroughly investigated. We show that electrostatic parameters are much more reliable indicators of dominant intermol. interactions than bond paths. Then, we pay attention that the presence of ("unexpected", i.e., not necessarily indicating dominant intermol. interactions) bond paths between pairs of atoms featuring highly expanded charge distributions can be easily explained by visual exploration of isodensity contour plots. As always pointing in the direction of the steepest increase, the gradient vector of the electron d. favors areas of its high values gaining higher exchange energy, yet being blind to highly electron deficient areas nearby, which, however, can quite often be involved in dominant intermol. interactions as strongly suggested by many other bonding anal. We also suggest that an interat. component of Hellmann-Feynman force would most likely be the most reliable indicator of attractive or repulsive character of individual interat. interaction. © 2018 Wiley Periodicals, Inc.
- 35Jabłoński, M. On the Uselessness of Bond Paths Linking Distant Atoms and on the Violation of the Concept of Privileged Exchange Channels. ChemistryOpen 2019, 8, 497– 507, DOI: 10.1002/open.201900109Google Scholar35https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXosFKitr4%253D&md5=3c4c2268d8fc8a4e35bf6ef5e5900c5aOn the Uselessness of Bond Paths Linking Distant Atoms and on the Violation of the Concept of Privileged Exchange ChannelsJablonski, MiroslawChemistryOpen (2019), 8 (4), 497-507CODEN: CHOPCK; ISSN:2191-1363. (Wiley-VCH Verlag GmbH & Co. KGaA)We refer to frequently used determinants suggesting dominant interactions between distant atoms in various dimers. First of all, we show, against the still-prevailling opinion, that, in general, bond paths have nothing in common with dominant intermol. interactions and therefore they are useless in such cases. Quite the contrary, reliable information about dominant intermol. interactions can be obtained by means of electrostatic potential maps, which very convincingly explain mutual orientation of mols. in a dimer. For the first time, numerous examples of interactions that violate both the concept of privileged exchange channels proposed by Pendas and his collaborators as well as inequalities obtained by Tognetti and Joubert for the β parameter related to secondary interactions are presented. The possible cause of this violation is suggested. We also show that the so-called counterintuitive bond paths result from quite natural behavior of the electron d. gradient vector, i. e. searching for those areas of space that are characterized by large values of electron d. or the most expanded its distributions.
- 36Jabłoński, M. Counterintuitive bond paths: An intriguing case of the C(NO2)3– ion. Chem. Phys. Lett. 2020, 759, 137946, DOI: 10.1016/j.cplett.2020.137946Google ScholarThere is no corresponding record for this reference.
- 37Jabłoński, M. The physical nature of the ultrashort spike–ring interaction in iron maiden molecules. J. Comput. Chem. 2022, 43, 1206– 1220, DOI: 10.1002/jcc.26879Google ScholarThere is no corresponding record for this reference.
- 38Jabłoński, M. The Ultrashort Spike–Ring Interaction in Substituted Iron Maiden Molecules. Molecules 2023, 28, 2244, DOI: 10.3390/molecules28052244Google ScholarThere is no corresponding record for this reference.
- 39Bader, R. F. W. Atoms in Molecules: A Quantum Theory; Oxford University Press: New York, USA, 1990.Google ScholarThere is no corresponding record for this reference.
- 40Popelier, P. L. A. Atoms in Molecules: An Introduction; Longman: Singapore, 2000.Google ScholarThere is no corresponding record for this reference.
- 41Matta, C. F.; Boyd, R. J. The Quantum Theory of Atoms in Molecules; Wiley VCH: Weinheim, Germany, 2007.Google ScholarThere is no corresponding record for this reference.
- 42Li, A.; Xiong, S.; Zhou, W.; Zhai, H.; Liu, Y.; He, Q. Superphane: A new lantern-like receptor for encapsulation of a water dimer. Chem. Commun. 2021, 57, 4496– 4499, DOI: 10.1039/D1CC01158HGoogle Scholar42https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXos1elt7c%253D&md5=66490622fd05bbcaaa2ac7431976490eSuperphane: a new lantern-like receptor for encapsulation of a water dimerLi, Aimin; Xiong, Shenglun; Zhou, Wei; Zhai, Huijuan; Liu, Yuanchu; He, QingChemical Communications (Cambridge, United Kingdom) (2021), 57 (37), 4496-4499CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)A new superphane I, featuring an aesthetically pleasing structure, was successfully obtained via one-pot synthesis of a hexakis-amine and m-phthalaldehyde in a [2+6] manner. It proved capable of entrapping a water dimer within its cavity as inferred from the mass spectroscopy, crystallog. anal., NMR spectroscopy, and theor. calcns.
- 43Li, A.; Liu, Y.; Zhou, W.; Jiang, Y.; He, Q. Superphanes: Facile and efficient preparation, functionalization and unique properties. Tetrahedron Chem 2022, 1, 100006, DOI: 10.1016/j.tchem.2022.100006Google ScholarThere is no corresponding record for this reference.
- 44Zhou, W.; Li, A.; Gale, P. A.; He, Q. A highly selective superphane for ReO4– recognition and extraction. Cell Rep. Phys. Sci. 2022, 3, 100875, DOI: 10.1016/j.xcrp.2022.100875Google ScholarThere is no corresponding record for this reference.
- 45Zhou, W.; Wang, F.; Li, A.; Bai, S.; Feng, X.; He, Q. A Superphane-based carcerand for arsenic detoxification via imprisoning arsenate. Cell Rep. Phys. Sci. 2023, 4, 101295, DOI: 10.1016/j.xcrp.2023.101295Google Scholar45https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3sXktV2jsLg%253D&md5=9e98d5d1a63dfe7eb6353b10b66bdd80A Superphane-based carcerand for arsenic detoxification via imprisoning arsenateZhou, Wei; Wang, Fei; Li, Aimin; Bai, Silei; Feng, Xinxin; He, QingCell Reports Physical Science (2023), 4 (3), 101295CODEN: CRPSF5; ISSN:2666-3864. (Elsevier Inc.)Carcerands, special mol. constructs with enclosed interiors as a new phase of matter, have attracted immense interest because of their unique structures, physicochem. properties, and potential applications in many aspects, e.g., targeted drug delivery. However, carcerands for imprisoning, inter alia, anions of interest represent an unmet challenge. Herein, we report the design and synthesis of a superphane-based carcerand 1, featuring up to 18 anion binding sites and a fully enclosed interior space. Carcerand 1 is found capable of incarcerating H2PO4- anion, yielding an anion carceplex 5, as inferred from crystallog. anal., 1H NMR (NMR) spectroscopy, and diffusion-ordered NMR spectroscopy (DOSY), as well as mol. dynamics simulations. More importantly, highly toxic arsenate anion was also imprisoned within carcerand 1, offering the arsenate carceplex 6 that proved nontoxic compared with free arsenate or peripherally bound arsenate in the HEK293T cell line.
- 46Zhou, W.; Li, A.; Zhou, M.; Xu, Y.; Zhang, Y.; He, Q. Nonporous amorphous superadsorbents for highly effective and selective adsorption of iodine in water. Nat. Commun. 2023, 14, 5388, DOI: 10.1038/s41467-023-41056-5Google Scholar46https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3sXhvVKhtrvM&md5=7ce0755635ae382a098365850447766eNonporous amorphous superadsorbents for highly effective and selective adsorption of iodine in waterZhou, Wei; Li, Aimin; Zhou, Min; Xu, Yiyao; Zhang, Yi; He, QingNature Communications (2023), 14 (1), 5388CODEN: NCAOBW; ISSN:2041-1723. (Nature Portfolio)Adsorbents widely utilized for environmental remediation, water purifn., and gas storage have been usually reported to be either porous or cryst. materials. In this contribution, we report the synthesis of two covalent org. superphane cages, that are utilized as the nonporous amorphous superadsorbents for aq. iodine adsorption with the record-breaking iodine adsorption capability and selectivity. In the static adsorption system, the cages exhibit iodine uptake capacity of up to 8.41 g g-1 in I2 aq. soln. and 9.01 g g-1 in I3- (KI/I2) aq. soln., resp., even in the presence of a large excess of competing anions. In the dynamic flow-through expt., the aq. iodine adsorption capability for I2 and I3- can reach up to 3.59 and 5.79 g g-1, resp. Moreover, these two superphane cages are able to remove trace iodine in aq. media from ppm level (5.0 ppm) down to ppb level concn. (as low as 11 ppb). Based on a binding-induced adsorption mechanism, such nonporous amorphous mol. materials prove superior to all existing porous adsorbents. This study can open up a new avenue for development of state-of-the-art adsorption materials for practical uses with conceptionally new nonporous amorphous superadsorbents (NAS).
- 47Xie, H.; Finnegan, T. J.; Liyana Gunawardana, V. W.; Pavlović, R. Z.; Moore, C. E.; Badjić, J. D. A Hexapodal Capsule for the Recognition of Anions. J. Am. Chem. Soc. 2021, 143, 3874– 3880, DOI: 10.1021/jacs.0c12329Google Scholar47https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXlsVCjtr4%253D&md5=ec3fafd54ea81865e9dd4b38d703f65bA Hexapodal Capsule for the Recognition of AnionsXie, Han; Finnegan, Tyler J.; Liyana Gunawardana, Vageesha W.; Pavlovic, Radoslav Z.; Moore, Curtis E.; Badjic, Jovica D.Journal of the American Chemical Society (2021), 143 (10), 3874-3880CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)We herein describe the prepn., characterization, and recognition characteristics of novel hexapodal capsule 1 composed of two benzenes joined by six hydrogen bonding (HB) groups to encircle space. This barrel-shaped host was obtained by reversible imine condensation of hexakis-aldehyde 2 and hexakis-amine 3 in the presence of oxyanions or halides acting as templates. Fascinatingly, capsule 1 includes 18 HB donating (Csp2-H and N-H) and 12 HB accepting groups (C=O and C=N) surrounding a binding pocket (78 Å3). In this regard, the complexation of fluoride, chloride, carbonate, sulfate, and hydrogen phosphate was probed by NMR spectroscopy (DMSO) and X-ray diffraction anal. to disclose the adaptive nature of 1 undergoing an adjustment of its conformation to complement each anionic guest. Furthermore, the rate by which encapsulated chloride was substituted by sulfate or hydrogen phosphate was slow (>7 days) while the stability of [SO4⊂1]2- was greatest in the series with Ka > 107 M-1 in highly competitive DMSO. With facile access to 1, the stage is set to probe this modular, polyvalent, and novel host to further improve the extn. of tetrahedral oxyanions from waste and the environment or control their chem. in living systems.
- 48Xie, H.; Gunawardana, V. W. L.; Finnegan, T. J.; Xie, W.; Badjić, J. D. Picking on Carbonate: Kinetic Selectivity in the Encapsulation of Anions. Angew. Chem., Int. Ed. 2022, 61, e202116518 DOI: 10.1002/anie.202116518Google Scholar48https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XisFKgtLo%253D&md5=0011dd70b5f35e0d91d23b2f4a8c29fbPicking on Carbonate: Kinetic Selectivity in the Encapsulation of AnionsXie, Han; Gunawardana, Vageesha W. Liyana; Finnegan, Tyler J.; Xie, William; Badjic, Jovica D.Angewandte Chemie, International Edition (2022), 61 (12), e202116518CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)Supramol. hosts bind to inorg. anions at a fast rate and select them in proportion with thermodn. stability of the corresponding [anion⊂host] complexes, forming in a reversible manner. In this study, we describe the action of hexapodal capsule 1 and its remarkable ability to select anions based on a large span of rates by which they enter this host. The thermodn. affinity of 1 toward eighteen anions extends over eight orders of magnitude (0<Ka<108 M-1; 1H NMR spectroscopy). The capsule would retain CO32- (Ka=107 M-1) for hours in the presence of eleven competing anions, including stronger binding SO42-, HAsO42- and HPO42- (Ka=107-108 M-1). The obsd. selection resulted from 1 possessing narrow apertures (ca. 3x6 S) comparable in size to anions (d=3.5-7.1 S) slowing down the encapsulation to last from seconds to days. The unorthodox mode of action of 1 sets the stage for creating hosts that pick anions by their ability to access the host.
- 49Oh, J. H.; Kim, J. H.; Kim, D. S.; Han, H. J.; Lynch, V. M.; Sessler, J. L.; Kim, S. K. Synthesis and Anion Recognition Features of a Molecular Cage Containing Both Hydrogen Bond Donors and Acceptors. Org. Lett. 2019, 21, 4336– 4339, DOI: 10.1021/acs.orglett.9b01515Google Scholar49https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhtVeit7rO&md5=a08603d33a84901f45f0716ecb438cffSynthesis and Anion Recognition Features of a Molecular Cage Containing Both Hydrogen Bond Donors and AcceptorsOh, Ju Hyun; Kim, Jeong Hyeon; Kim, Dong Sub; Han, Hye Jin; Lynch, Vincent M.; Sessler, Jonathan L.; Kim, Sung KukOrganic Letters (2019), 21 (11), 4336-4339CODEN: ORLEF7; ISSN:1523-7052. (American Chemical Society)A mol. cage, macrobicycle, contg. amide and pyrrole groups as hydrogen-bonding donors and imine groups as hydrogen-bonding acceptors has been synthesized. The macrobicycle was found to recognize tetrahedral oxyanions with high affinities, such as H2PO4-, HSO4-, SO42-, and HP2O73-, as well as the spherical halide anions, in chloroform. A single-crystal X-ray diffraction anal. revealed that the macrobicycle formed a 1:1 complex with H2PO4- in the solid state.
- 50Zhao, X.; Xiong, S.; Zhang, J.; Pu, J.; Ding, W.; Chen, X.; He, Q.; Zhang, Z. A hexapyrrolic molecular cage and the anion-binding studies in chloroform. J. Mol. Struct. 2023, 1293, 136232, DOI: 10.1016/j.molstruc.2023.136232Google ScholarThere is no corresponding record for this reference.
- 51Li, A.; Liu, Y.; Luo, K.; He, Q. CO2 Capture in Liquid Phase and Room-Temperature Release and Concentration Using Mechanical Power. CCS Chem. 2024, DOI: 10.31635/ccschem.024.202404292Google ScholarThere is no corresponding record for this reference.
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- 52Jabłoński, M. Characteristics of Intermolecular Interactions between Encapsulated Molecules and the Lantern-Like Carcerand Superphanes. Molecules 2024, 29, 601, DOI: 10.3390/molecules29030601Google ScholarThere is no corresponding record for this reference.
- 53Chai, J.-D.; Head-Gordon, M. Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections. Phys. Chem. Chem. Phys. 2008, 10, 6615– 6620, DOI: 10.1039/b810189bGoogle Scholar53https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhtlCksbfO&md5=c7848f8bf050e11972d438aaebd68fdfLong-range corrected hybrid density functionals with damped atom-atom dispersion correctionsChai, Jeng-Da; Head-Gordon, MartinPhysical Chemistry Chemical Physics (2008), 10 (44), 6615-6620CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)We report re-optimization of a recently proposed long-range cor. (LC) hybrid d. functional [J.-D. Chai and M. Head-Gordon, J. Chem. Phys., 2008, 128, 084106] to include empirical atom-atom dispersion corrections. The resulting functional, ωB97X-D yields satisfactory accuracy for thermochem., kinetics, and non-covalent interactions. Tests show that for non-covalent systems, ωB97X-D shows slight improvement over other empirical dispersion-cor. d. functionals, while for covalent systems and kinetics it performs noticeably better. Relative to our previous functionals, such as ωB97X, the new functional is significantly superior for non-bonded interactions, and very similar in performance for bonded interactions.
- 54Hohenberg, P.; Kohn, W. Inhomogeneous Electron Gas. Phys. Rev. 1964, 136, B864– B871, DOI: 10.1103/PhysRev.136.B864Google ScholarThere is no corresponding record for this reference.
- 55Parr, R. G.; Yang, W. Density-Functional Theory of Atoms and Molecules; Oxford University Press: New York, NY, USA, 1989.Google ScholarThere is no corresponding record for this reference.
- 56Jensen, F. Introduction to Computational Chemistry; John Wiley & Sons Ltd.: Chichester, UK, 2007.Google ScholarThere is no corresponding record for this reference.
- 57Pritchard, B. P.; Altarawy, D.; Didier, B.; Gibson, T. D.; Windus, T. L. New Basis Set Exchange: An Open, Up-to-Date Resource for the Molecular Sciences Community. J. Chem. Inf. Model. 2019, 59, 4814– 4820, DOI: 10.1021/acs.jcim.9b00725Google Scholar57https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhvFCksrfJ&md5=fb809621ce47a29aad4b762c80365c22New Basis Set Exchange: An Open, Up-to-Date Resource for the Molecular Sciences CommunityPritchard, Benjamin P.; Altarawy, Doaa; Didier, Brett; Gibson, Tara D.; Windus, Theresa L.Journal of Chemical Information and Modeling (2019), 59 (11), 4814-4820CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)A review. The Basis Set Exchange (BSE) has been a prominent fixture in the quantum chem. community. First publicly available in 2007, it is recognized by both users and basis set creators as the de facto source for information related to basis sets. This popular resource has been rewritten, utilizing modern software design and best practices. The basis set data has been sepd. into a stand-alone library with an accessible API, and the Web site has been updated to use the current generation of web development libraries. The general layout and workflow of the Web site is preserved, while helpful features requested by the user community have been added. Overall, this design should increase adaptability and lend itself well into the future as a dependable resource for the computational chem. community. This article will discuss the decision to rewrite the BSE, the new architecture and design, and the new features that have been added.
- 58TeraChem. PetaChem. Version 1.9; LLC: Los Altos Hills, CA, USA, 2021.Google ScholarThere is no corresponding record for this reference.
- 59Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. J. Am. Chem. Soc. 1996, 118, 11225– 11236, DOI: 10.1021/ja9621760Google Scholar59https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XmtlOitrs%253D&md5=fef2924a69421881390282aa309ae91bDevelopment and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic LiquidsJorgensen, William L.; Maxwell, David S.; Tirado-Rives, JulianJournal of the American Chemical Society (1996), 118 (45), 11225-11236CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)The parametrization and testing of the OPLS all-atom force field for org. mols. and peptides are described. Parameters for both torsional and nonbonded energetics have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER all-atom force field. The torsional parameters were detd. by fitting to rotational energy profiles obtained from ab initio MO calcns. at the RHF/6-31G*//RHF/6-31G* level for more than 50 org. mols. and ions. The quality of the fits was high with av. errors for conformational energies of less than 0.2 kcal/mol. The force-field results for mol. structures are also demonstrated to closely match the ab initio predictions. The nonbonded parameters were developed in conjunction with Monte Carlo statistical mechanics simulations by computing thermodn. and structural properties for 34 pure org. liqs. including alkanes, alkenes, alcs., ethers, acetals, thiols, sulfides, disulfides, aldehydes, ketones, and amides. Av. errors in comparison with exptl. data are 2% for heats of vaporization and densities. The Monte Carlo simulations included sampling all internal and intermol. degrees of freedom. It is found that such non-polar and monofunctional systems do not show significant condensed-phase effects on internal energies in going from the gas phase to the pure liqs.
- 60Allinger, N. L.; Yuh, Y. H.; Lii, J. H. Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 1. J. Am. Chem. Soc. 1989, 111, 8551– 8566, DOI: 10.1021/ja00205a001Google Scholar60https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL1MXmtlWmsLo%253D&md5=e35207cdf829f8f78f2fdd6908887401Molecular mechanics. The MM3 force field for hydrocarbons. 1Allinger, Norman L.; Yuh, Young H.; Lii, Jenn HueiJournal of the American Chemical Society (1989), 111 (23), 8551-66CODEN: JACSAT; ISSN:0002-7863.A new mol. mechanics force field (called MM3) for the treatment of aliph. hydrocarbons has been developed and is presented here. This force field will enable one to calc. the structures and energies, including heats of formation, conformational energies, and rotational barriers, for hydrocarbons more accurately than was possible with earlier force fields. In addn. to simple mols., a great many highly strained mols. have been studied, and the results are almost always of exptl. accuracy.
- 61Frisch, M. J.; Gaussian 09. Revision D.01; Gaussian, Inc.: Wallingford, CT, USA, 2013.Google ScholarThere is no corresponding record for this reference.
- 62Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 1983, 79, 926– 935, DOI: 10.1063/1.445869Google Scholar62https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL3sXksF2htL4%253D&md5=a1161334e381746be8c9b15a5e56f704Comparison of simple potential functions for simulating liquid waterJorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.; Impey, Roger W.; Klein, Michael L.Journal of Chemical Physics (1983), 79 (2), 926-35CODEN: JCPSA6; ISSN:0021-9606.Classical Monte Carlo simulations were carried out for liq. H2O in the NPT ensemble at 25° and 1 atm using 6 of the simpler intermol. potential functions for the dimer. Comparisons were made with exptl. thermodn. and structural data including the neutron diffraction results of Thiessen and Narten (1982). The computed densities and potential energies agree with expt. except for the original Bernal-Fowler model, which yields an 18% overest. of the d. and poor structural results. The discrepancy may be due to the correction terms needed in processing the neutron data or to an effect uniformly neglected in the computations. Comparisons were made for the self-diffusion coeffs. obtained from mol. dynamics simulations.
- 63Ponder, J. W. Tinker - Software Tools for Molecular Design . Version 7.1.3, 2015.Google ScholarThere is no corresponding record for this reference.
- 64Bussi, G.; Donadio, D.; Parrinello, M. Canonical Sampling through Velocity Rescaling. J. Chem. Phys. 2007, 126, 014101, DOI: 10.1063/1.2408420Google Scholar64https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXosVCltg%253D%253D&md5=9c182b57bfc65bca6be23c8c76b4be77Canonical sampling through velocity rescalingBussi, Giovanni; Donadio, Davide; Parrinello, MicheleJournal of Chemical Physics (2007), 126 (1), 014101/1-014101/7CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)The authors present a new mol. dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains const. during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. The authors illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liq. phases. Its performance is excellent and largely independent of the thermostat parameter also with regard to the dynamic properties.
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Abstract
Figure 1
Figure 1. Side and top views of the [26](1,2,3,4,5,6) (a) and [36](1,2,3,4,5,6) (b) superphanes.
Figure 2
Figure 2. Side and top views of the lantern-like superphane 1 synthesized by Qing He’s group. (42)
Figure 3
Figure 3. Side and top views of the superphane synthesized by Badjić et al. (47)
Figure 4
Figure 4. Side chains in superphanes 1, 2, and 3. Hydrogen atoms participating in hydrogen bonds with the guest molecule are labeled as follows: Hi─imino H atom, Hc─central H atom.
Figure 5
Figure 5. Superphanes 2 and 3.
Figure 6
Figure 6. Positions of inward pointing N atoms (marked by orange spheres) in the initial structures of superphanes 1–3. Hydrogen atoms are not shown.
Figure 7
Figure 7. Definitions of C–C–C–N dihedral angles used to trace the conformations at N atoms in superphane 1 (a), superphane 2 (b), and superphane 3 (c); small values of the angle correspond to in conformations, whereas large absolute values indicate out conformations (d).
Figure 8
Figure 8. Evolution of conformations at the four nitrogen atoms inward-pointing in the initial structures during the AIMD simulations for empty superphane cages 1–3. Nitrogen atoms at the bottom and the top of the cage are labeled “b” and “t”, respectively.
Figure 9
Figure 9. Conformations at the nitrogen atoms in MD simulations for empty superphane cages 1–3. Each line corresponds to one N atom. Nitrogen atoms at the bottom and the top of the cage are labeled “b” and “t”, respectively.
Figure 10
Figure 10. Conformations at the nitrogen atoms in MD simulations for HF encapsulated in 1–3. Each line corresponds to one N atom. Nitrogen atoms at the bottom and the top of the cage are labeled “b” and “t”, respectively.
Figure 11
Figure 11. Distributions of N···H distances obtained in MD simulations for M@1.
Figure 12
Figure 12. Distributions of the distances between the H atom of M and the center of the superphane cage obtained in the FF MD simulations for M@1–M@3.
Figure 13
Figure 13. Probabilities of interaction with a water hydrogen atom for individual nitrogen atoms at the bottom (blue) or the top (cyan) of the 1–3 superphane cages.
Figure 14
Figure 14. Statistics of residence times for H2O in the cages 1–3 obtained from the FF MD simulations. Note the scale difference between panels.
Figure 15
Figure 15. A sample snapshot of the solvated H2O@1 at the end of the FF MD simulations with the encapsulated water molecule shown as sticks and the solvating molecules shown as gray lines (a); evolution of the dO-center distance (b); and its distributions at the beginning and at the end of the trajectory (c).
References
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- 1Sekine, Y.; Brown, M.; Boekelheide, V. [2.2.2.2.2.2](1,2,3,4,5,6)Cyclophane: Superphane. J. Am. Chem. Soc. 1979, 101, 3126– 3127, DOI: 10.1021/ja00505a0531https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaE1MXktlyqu74%253D&md5=8acf676e2e7e13bd6aec6c28c98693bc[2.2.2.2.2.2](1,2,3,4,5,6)Cyclophane: superphaneSekine, Y.; Brown, M.; Boekelheide, V.Journal of the American Chemical Society (1979), 101 (11), 3126-7CODEN: JACSAT; ISSN:0002-7863.The prepn. of [2.2.2.2.2.2](1,2,3,4,5,6)cyclophane (I), which for many years has posed a major synthetic challenge, is described as is also a first example of the [2.2.2.2](1,2,3,4)cyclophane series (II) and this, plus its accompanying communication, complete all of the possible isomers of [2n] cyclophanes. The synthetic methods described have a great potential for prepg. a wide variety of compds.
- 2El-tamany, S.; Hopf, H. Eine zweite Synthese von [26](1,2,3,4,5,6)Cyclophan (Superphan). Chem. Ber. 1983, 116, 1682– 1685, DOI: 10.1002/cber.19831160444There is no corresponding record for this reference.
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- 5Sekine, Y.; Boekelheide, V. A Study of the Synthesis and Properties of [26](1,2,3,4,5,6)Cyclophane (Superphane). J. Am. Chem. Soc. 1981, 103, 1777– 1785, DOI: 10.1021/ja00397a0325https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL3MXhvFWktb0%253D&md5=5287b6df2bd997f47fee18b9c9d322f3A study of the synthesis and properties of [26](1,2,3,4,5,6)cyclophane (superphane)Sekine, Yasuo; Boekelheide, V.Journal of the American Chemical Society (1981), 103 (7), 1777-85CODEN: JACSAT; ISSN:0002-7863.A synthesis of [26](1,2,3,4,5,6)cyclophane (I) is described. This mol., the ultimate in a multibridged [2n]cyclophane, was given the trivial name superphane and was synthesized in ten steps starting from 2,4,5-trimethylbenzyl chloride. X-ray anal. shows superphane to be a highly sym. (D6h) mol. with the benzene decks being planar hexagons sepd. by 2.624 Å. The 1H NMR spectrum of superphane shows a singlet at δ 2.98 and the 13C NMR spectrum singlets at δ 144.2 and 32.2, reflecting this high degree of symmetry. Superphane does exhibit the Birch redn. and undergoes electrophilic attack by alkyl cations and benzylic substitution with N-bromosuccinimide. Although superphane readily forms a charge-transfer complex with TCNE, it does not give the normal, Diels-Alder, barrelene-type adduct with either TCNE or dicyanoacetylene. In the presence of AlCl3 superphane reacts with dicyanoacetylene to form an unusual structure involving formation of novel intramol. bonds.
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- 7Jabłoński, M. Does the Presence of a Bond Path Really Mean Interatomic Stabilization? The Case of the Ng@Superphane (Ng = He, Ne, Ar, and Kr) Endohedral Complexes. Symmetry 2021, 13, 2241, DOI: 10.3390/sym13122241There is no corresponding record for this reference.
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- 10Sakamoto, Y.; Miyoshi, N.; Hirakida, M.; Kusumoto, S.; Kawase, H.; Rudzinski, J. M.; Shinmyozu, T. Syntheses, Structures, and Transannular π–π Interactions of Multibridged [3n]Cyclophanes. J. Am. Chem. Soc. 1996, 118, 12267– 12275, DOI: 10.1021/ja961944k10https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XmvV2gu7Y%253D&md5=d0e4b40f8aa0a9474c8b82e954029b56Syntheses, Structures, and Transannular π-π Interactions of Multibridged [3n]Cyclophanes1Sakamoto, Youichi; Miyoshi, Naomi; Hirakida, Mihoko; Kusumoto, Shirou; Kawase, Haruo; Rudzinski, Jerzy M.; Shinmyozu, TeruoJournal of the American Chemical Society (1996), 118 (49), 12267-12275CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)The syntheses, conformational study, and transannular π-π interaction of multibridged [3n]cyclophanes including the ultimate member of this series, [36](1,2,3,4,5,6)cyclophane I, were described. The stepwise construction of trimethylene bridges starting from [33](1,3,5)cyclophane led to the synthesis of I. The variable-temp. 1H NMR study (CD2Cl2) and mol. mechanics calcns. (MM3) of five-bridged analog of I revealed the most stable conformer, the relative stability order of the three stable isomers, and energy barriers for the trimethylene bridge inversion. A similar variable temp. 1H NMR study (toluene-d8) of I suggested the presence of a trimethylene bridge inversion process between two C6h conformers. The charge transfer (CT) bands of the complexes of multibridged [3n]cyclophanes with tetracyanoethylene (TCNE) show significant bathochromic shifts with the increase in the no. of the bridges, and this is mainly attributed to the effective hyperconjugation between the benzyl hydrogens and the benzene rings. The CT band of the TCNE-I complex (728 nm) is the longest wavelength among those of the TCNE complexes of [m.n]cyclophanes and multibridged benzenophanes.
- 11Hori, K.; Sentou, W.; Shinmyozu, T. Ab Initio Molecular Orbital Study on Inversion Mechanism of Trimethylene Bridges of [33](1,3,5)- and [36](1,2,3,4,5,6) Cyclophanes. Tetrahedron Lett. 1997, 38, 8955– 8958, DOI: 10.1016/S0040-4039(97)10361-6There is no corresponding record for this reference.
- 12Bettinger, H. F.; Schleyer, P. v. R.; Schaefer III, H. F. [36](1,2,3,4,5,6)Cyclophane–A Molecular Pinwheel and Its Correlated Inversion: NMR and Energetic Considerations. J. Am. Chem. Soc. 1998, 120, 1074– 1075, DOI: 10.1021/ja972217812https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1cXmvFWhug%253D%253D&md5=45bd7abf6f27f7de90399b1985f3355d[36](1,2,3,4,5,6)Cyclophane-A Molecular Pinwheel and Its Correlated Inversion: NMR and Energetic ConsiderationsBettinger, Holger F.; Schleyer, Paul v. R.; Schaefer, Henry F., IIIJournal of the American Chemical Society (1998), 120 (5), 1074-1075CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Various theor. methods (mol. mechanics, semiempirical MO, ab initio MO, DFT) predicted that the title compd. I possesses intramol. distance of 2.9-3.0 Å between the two benzene rings compared with 3.35 Å in graphite; thus the π electrons in the space between the rings must repel the rings away from each other. As a consequence, the CCC trimethylene bond angle is 120° and the arom. CC bonds in I are stretched by 0.01 Å with respect to benzene. The ring-closed prismane deriv. of I (II) (propella[36]prismane) is 110.8 kcal/mol higher in energy than arom. I despite its six addnl. CC bonds. Transition structures and min. on the potential energy surface for degenerate conformational inversion of I are identified, and the sequential flipping process is favored over a synchronous mechanism involving a D6h structure.
- 13Yasutake, M.; Sakamoto, Y.; Onaka, S.; Sako, K.; Tatemitsu, H.; Shinmyozu, T. Crystal structural properties of a pinwheel compound: [36](1,2,3,4,5,6)cyclophane. Tetrahedron Lett. 2000, 41, 7933– 7938, DOI: 10.1016/S0040-4039(00)01384-813https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXotVGrsbg%253D&md5=f075e21e6c4f2fe7011e2b36ab316bacMultibridged [3n]cyclophanes. Part 12. Crystal structural properties of a pinwheel compound: [36](1,2,3,4,5,6)cyclophaneYasutake, Mikio; Sakamoto, Youichi; Onaka, Satoru; Sako, Katsuya; Tatemitsu, Hitoshi; Shinmyozu, TeruoTetrahedron Letters (2000), 41 (41), 7933-7938CODEN: TELEAY; ISSN:0040-4039. (Elsevier Science Ltd.)In the crystal structures of [36](1,2,3,4,5,6)cyclophane 1 and the 1:TCNQ (1:1) complex, the cyclophane moiety is obsd. as the D6h structure because of the disorder of the mols. with C6h symmetry. In contrast, the C6h structure is obsd. in the crystals of the 1:TCNQ-F4 (1:1) complex, and the complex shows an alternating donor-acceptor stacking with partial donor-acceptor overlap.
- 14Yasutake, M.; Koga, T.; Sakamoto, Y.; Komatsu, S.; Zhou, M.; Sako, K.; Tatemitsu, H.; Onaka, S.; Aso, Y.; Inoue, S.; Shinmyozu, T. An Alternative Synthetic Route of [35](1,2,3,4,5)Cyclophane, and Structural Properties of Multibridged [3n]Cyclophanes and Their Charge-Transfer Complexes in the Solid State. J. Am. Chem. Soc. 2002, 124, 10136– 10145, DOI: 10.1021/ja012363k14https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XlslKjsLg%253D&md5=20042d8d07165d4a25fe250830dd0edbMultibridged [3n]cyclophanes, part 13. An Alternative Synthetic Route of [35](1,2,3,4,5)Cyclophane, and Structural Properties of Multibridged [3n]Cyclophanes and Their Charge-Transfer Complexes in the Solid StateYasutake, Mikio; Koga, Toru; Sakamoto, Youichi; Komatsu, Shingo; Zhou, Ming; Sako, Katsuya; Tatemitsu, Hitoshi; Onaka, Satoru; Aso, Yoshio; Inoue, Shinobu; Shinmyozu, TeruoJournal of the American Chemical Society (2002), 124 (34), 10136-10145CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)To develop an improved synthetic route to [36](1,2,3,4,5,6)cyclophane (CP) (I), a more practical synthetic route to [35](1,2,3,4,5)CP than the original one was developed, which started from [32](1,3)CP via [34](1,2,4,5)CP. The fundamental structural parameters of [3n]CPs (n = 3-6) in the solid state were elucidated, and the obsd. structures were in good agreement with the most stable conformers in soln. and those predicted by the theor. calcns. In the case of I, the most stable C6h structure was obsd. in the crystal structure of the I-TCNQ-F4 (1:1) complex, whereas the highly strained structure with a D6h symmetry was obsd. in the crystal structure of I and the I-TCNQ-benzene (1:1:1) complex because of a severe disorder problem. [3n]CPs (n > 3) showed reversible redox processes, and I (+0.39 V vs Fc/Fc+, Cl2CHCHCl2) showed the lowest first half-wave oxidn. potential [E1/2 (I)] in [3n]CPs. The E1/2 (I) data support the strong donating ability of I and its lower homologs. This is attributed to their mol. structures where effective hyperconjugation between the benzyl hydrogens and benzene ring is possible. By taking advantage of the strong electron-donating ability of [3n]CPs, their CT complexes with TCNE, TCNQ, and TCNQ-F4 were prepd., and their crystal structural properties were examd. The single-crystal cond. data of the CT complexes indicated that the TCNQ-F4 complexes showed higher conductivities than the corresponding TCNQ complexes mainly due to a larger charge sepn. Among the [3n]CP-TCNQ complexes, the [33](1,3,5)CP-TCNQ-F4 (1:1) complex showed the highest cond. (10-4 S cm-1), and this was ascribed to the formation of an infinite column of partially overlapped acceptors with a short acceptor-acceptor distance, while the formation of such a column was not obsd. in the I-TCNQ-F4 complex. Although the conductivities of the cyclophane-CT complexes are much lower than those of the TTF related complexes, this study successfully provides the basic knowledge for understanding the CT interactions in the solid state.
- 15Jabłoński, M. Bader’s Topological Bond Path Does Not Necessarily Indicate Stabilizing Interaction–Proof Studies Based on the Ng@[3n]cyclophane Endohedral Complexes. Molecules 2023, 28, 6353, DOI: 10.3390/molecules28176353There is no corresponding record for this reference.
- 16Modern Cyclophane Chemistry; Gleiter, R., Hopf, H., Eds.; Wiley VCH: Weinheim, Germany, 2004.There is no corresponding record for this reference.
- 17Gleiter, R.; Kratz, D. “Super” Phanes. Acc. Chem. Res. 1993, 26, 311– 318, DOI: 10.1021/ar00030a003There is no corresponding record for this reference.
- 18Schirch, P. F. T.; Boekelheide, V. [2.2.2.2.2](1,2,3,4,5)Cyclophane. J. Am. Chem. Soc. 1979, 101, 3125– 3126, DOI: 10.1021/ja00505a052There is no corresponding record for this reference.
- 19Kleinschroth, J.; Hopf, H. The Chemical Behavior of Multibridged [2n]Cyclophanes. Angew. Chem., Int. Ed. Engl. 1982, 21, 469– 480, DOI: 10.1002/anie.198204691There is no corresponding record for this reference.
- 20Spanget-Larsen, J. Electronic states of the [2n]cyclophanes. Theoret. Chim. Acta (Berl.) 1983, 64, 187– 203, DOI: 10.1007/BF0055139620https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2cXhsFGqsLg%253D&md5=af39b4d80b296122e0b1e572cfe8c10eElectronic states of the [2n]cyclophanesSpanget-Larsen, JensTheoretica Chimica Acta (1983), 64 (3), 187-203CODEN: TCHAAM; ISSN:0040-5744.Low-energy singlet and triplet states for a series of [2n]cyclophanes are discussed in terms of the results of a simple model calcn. Exptl. trends can be explained under the assumption of significant σ-π interaction involving the satd. bridges. This interaction destabilizes low-energy excimer states, in contrast to the usual red shift obsd. for alkylbenzenes. The obsd. near-constancy of the onset of the absorption spectra can be explained by near-cancellation of through-bond and through-space contributions.
- 21Czuchajowski, L.; Wisor, A. K. Electronic Effects In Multibridged Cyclophanes As Viewed by the Indices of Excitation. J. Electron Spectrosc. Relat. Phenom. 1987, 43, 169– 181, DOI: 10.1016/0368-2048(87)80029-421https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2sXmsVGhtbk%253D&md5=6033e5669ca7e1c12d8784fb8b339385Electronic effects in multibridged cyclophanes as viewed by the indexes of excitationCzuchajowski, Leszek; Wisor, Antoni K.Journal of Electron Spectroscopy and Related Phenomena (1987), 43 (2), 169-81CODEN: JESRAW; ISSN:0368-2048.[2.2]Paracyclophane and its multibridged analogs contg. 3-6 bridges [3(1,2,3), 3(1,2,4), 3(1,3,5), 4(1,2,3,4), 4(1,2,3,5), 4(1,2,4,5), 5, and 6] were characterized by the indexes of excitation expressed as localization of excitation nos. and charge transfer nos. based on the anal. of the transition d. matrix. The MO theory, in supermol. approxn., was applied together with the PPP CI-1 method. The σ-π orbitals interactions between bridges and rings were considered. With regard to the 1st UV absorption band at 33000 ± 1000 cm-1, the relatively low transition energies for 3(1,3,5) and 4(1,2,4,5) resulted from the lowest degree of localization of excitation on the arom. rings and the highest transannular interaction. For 3(1,2,3) and 4(1,2,3,4), the opposite conclusion was reached. The 3(1,3,5) cyclophane was distinguished not only by neglecting the linear correlation between the transition energies E(S0 → S2) and the localization nos. that are valid for other cyclophanes, but also by the stronger transannular interaction appearing in the 21A' state connected with the 3rd absorption band.
- 22Meno, T.; Sako, K.; Suenaga, M.; Mouri, M.; Shinmyozu, T.; Inazu, T.; Takemura, H. Conformational analysis of [3.3.3](1,3,5)cyclophane systems. Can. J. Chem. 1990, 68, 440– 445, DOI: 10.1139/v90-067There is no corresponding record for this reference.
- 23Shinmyozu, T.; Hirakida, M.; Kusumoto, S.; Tomonou, M.; Inazu, T.; Rudziński, J. M. Synthesis of [35](1,2,3,4,5)Cyclophane. Chem. Lett. 1994, 23, 669– 672, DOI: 10.1246/cl.1994.669There is no corresponding record for this reference.
- 24Caramori, G. F.; Galembeck, S. E.; Laali, K. K. A Computational Study of [2.2]Cyclophanes. J. Org. Chem. 2005, 70, 3242– 3250, DOI: 10.1021/jo047864d24https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXisFOgt70%253D&md5=6a5e8e03d5c16465efcad7cad4c800cbA Computational Study of [2.2]CyclophanesCaramori, Giovanni F.; Galembeck, Sergio E.; Laali, Kenneth K.Journal of Organic Chemistry (2005), 70 (8), 3242-3250CODEN: JOCEAH; ISSN:0022-3263. (American Chemical Society)A computational study of isomeric [2.2]cyclophanes, [2.2]paracyclophane 1, [2.2]metacyclophane 2, and [2.2]metaparacyclophane 3, was carried out. For 1, geometry optimizations performed by various methods at different basis sets showed that MP2/6-31+G(d,p) and B3PW91/6-31+G(d,p) provide the best results in comparison to the x-ray data. Compd. 1 has D2 symmetry with distorted bridges. A conformational search was performed for [2.2]cyclophanes 2 and 3. Each cyclophane exists in two conformations which have different energies in the case of 3 but are degenerate in the case of 2. Relative energies and strain energies at the bridges follow the same order, indicating that the relief of bridge tension and repulsion between π clouds are detg. factors for the stability of [2.2]cyclophanes. Through a decompn. of strain energy, both the rings or the bridges can absorb strain, but it depends on the conformer of butane that is considered in the calcn. of SE(br). Changes in aromaticity of these compds. were evaluated by NICS and HOMA and were compared with benzene and xylenes dimers as models. Despite distortions from planarity and shortening and lengthening of the C-C bonds relative to the mean, the Ph rings are arom. NICS suggests a concn. of electronic d. between the rings as a result of bridging process. Computed MK, NPA, and GAPT charges were compared for the isomeric cyclophanes. The GIAO chem. shifts were calcd. and indicate that 1 has a larger diamagnetic anisotropy than the other isomers.
- 25Caramori, G. F.; Galembeck, S. E. Computational Study about Through-Bond and Through-Space Interactions in [2.2]Cyclophanes. J. Phys. Chem. A 2007, 111, 1705– 1712, DOI: 10.1021/jp066863h25https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXhsFOktbk%253D&md5=4b153e3e4894fe9356e5676d5a00ffb9Computational Study about Through-Bond and Through-Space Interactions in [2.2]CyclophanesCaramori, Giovanni F.; Galembeck, Sergio E.Journal of Physical Chemistry A (2007), 111 (9), 1705-1712CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)An anal. of the electron d., obtained by B3PW91/6-31+G(d,p), B3LYP/6-31+G(d,p), and MP2/6-31+G(d,p) for [2,2]cyclophane isomers, [2.2]paracyclophane, anti-[2.2]metacyclophane, syn-[2.2]metacyclophane, and [2.2]metaparacyclophane, was made through natural bond orbitals (NBO), natural steric anal. (NSA), and atoms in mols. (AIM) methods and through anal. of frontier MOs. NBO indicates that all compds. present through-bond interactions, but only the conformers of [2.2]metacyclophane present significant through-space interactions. The last interactions are obsd. in AIM anal. and by the plots of MOs. AIM indicates that these through-space interactions are closed-shell ones, and they stabilize the conformers. In contrast, all isomers present through-bond and through-space repulsive interactions. In addn., the at. properties, computed over the at. basins, showed that the position of the bridges and the relative displacement of the rings can affect the at. charges, the first at. moments, and the at. vols.
- 26Dodziuk, H.; Szymański, S.; Jaźwiński, J.; Ostrowski, M.; Demissie, T. B.; Ruud, K.; Kuś, P.; Hopf, H.; Lin, S.-T. Structure and NMR Spectra of Some [2.2]Paracyclophanes. The Dilemma of [2.2]Paracyclophane Symmetry. J. Phys. Chem. A 2011, 115, 10638– 10649, DOI: 10.1021/jp205693a26https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtFelu73F&md5=3cad57e454b879ffb27001f6fd27e90eStructure and NMR Spectra of Some [2.2]Paracyclophanes. The Dilemma of [2.2]Paracyclophane SymmetryDodziuk, Helena; Szymanski, Slawomir; Jazwinski, Jaroslaw; Ostrowski, Maciej; Demissie, Taye Beyene; Ruud, Kenneth; Kus, Piotr; Hopf, Henning; Lin, Shaw-TaoJournal of Physical Chemistry A (2011), 115 (38), 10638-10649CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)D. functional theory (DFT) quantum chem. calcns. of the structure and NMR parameters for highly strained hydrocarbon [2.2]paracyclophane 1 and its three derivs. are presented. The calcd. NMR parameters are compared with the exptl. ones. By least-squares fitting of the 1H spectra, almost all JHH coupling consts. could be obtained with high accuracy. Theor. vicinal JHH couplings in the aliph. bridges, calcd. using different basis sets (6-311G(d,p), and Huz-IV) reproduce the exptl. values with essentially the same root-mean-square error of ∼1.3 Hz, regardless of the basis set used. These discrepancies could be in part due to a considerable impact of rovibrational effects on the obsd. JHH couplings, since the latter show a measurable dependence on temp. Because of the lasting literature controversies concerning the symmetry of parent compd. 1, D2h vs. D2, a crit. anal. of the relevant literature data is carried out. The symmetry issue is prone to confusion because, according to some literature claims, the two hypothetical enantiomeric D2 structures of 1 could be sepd. by a very low energy barrier that would explain the occurrence of rovibrational effects on the obsd. vicinal JHH couplings. However, the D2h symmetry of 1 with a flat energy min. could also account for these effects.
- 27Fujitsuka, M.; Miyazaki, T.; Lu, C.; Shinmyozu, T.; Majima, T. Multistep Electron Transfer Systems Containing [2.2]- or [3.3]Paracyclophane. J. Phys. Chem. A 2016, 120, 1184– 1189, DOI: 10.1021/acs.jpca.5b1176627https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XitFeru7Y%253D&md5=f07abb306dd08911fed5ac60b90fbe10Multistep Electron Transfer Systems Containing [2.2]- or [3.3]ParacyclophaneFujitsuka, Mamoru; Miyazaki, Takaaki; Lu, Chao; Shinmyozu, Teruo; Majima, TetsuroJournal of Physical Chemistry A (2016), 120 (8), 1184-1189CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)Paracyclophanes (PCPs), which exhibit interesting properties due to their transannular interactions, have been employed as a spacer in various electron transfer (ET) systems. In the present work, we investigated ET processes in dyads and triads contg. [2.2]PCP or [3.3]PCP as donors to study their properties in multistep ET processes. The dyad mols. of PCP and 1,8-naphthalimide (NI) as a photosensitizing electron acceptor exhibited charge sepn. (CS) upon excitation of NI. In addn., triads of NI, PCP, and carbazole showed charge shift after an initial CS, thus confirming multistep ET. In this study, we demonstrated that use of [3.3]PCP in place of [2.2]PCP enhanced the initial CS rate. Lower oxidn. potentials and a smaller reorganization energy for [3.3]PCP are shown to be key factors for this enhanced CS rate. Both of these properties are closely related to the strained structure of PCP; hence, the present results demonstrate the importance of strain in ET chem.
- 28Matsuiwa, K.; Hayashi, S.; Nakanishi, W. Dynamic and Static Behavior of Intramolecular π–π Interactions in [2.2]- and [3.3]Cyclophanes, Elucidated by QTAIM Dual Functional Analysis with QC Calculations. ChemistrySelect 2017, 2, 1774– 1782, DOI: 10.1002/slct.201602047There is no corresponding record for this reference.
- 29Majerz, I.; Dziembowska, T. What Is the Main Feature Distinguishing the Through-Space Interactions in Cyclophanes from Their Aliphatic Analogues?. ACS Omega 2020, 5, 22314– 22324, DOI: 10.1021/acsomega.0c0267129https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhs1GgtbnO&md5=7df816f4787696b0c22447fc74b60547What Is the Main Feature Distinguishing the Through-Space Interactions in Cyclophanes from Their Aliphatic Analogues?Majerz, Irena; Dziembowska, TeresaACS Omega (2020), 5 (35), 22314-22324CODEN: ACSODF; ISSN:2470-1343. (American Chemical Society)Classical cyclophanes with two benzene rings have been compared with cyclophanes with one benzene ring replaced with an aliph. part and aliph. compds., which are cyclophane analogs. Anal. of geometry, at. charges, and arom. and steric energy and investigation of intramol. noncovalent interactions and charge mobility show that there is no special feature that distinguishes the classical cyclophanes from aliph. analogs, so the definition of cyclophanes can be extended to other compds.
- 30Zhang, X.-X.; Li, J.; Niu, Y.-Y. A Review of Crystalline Multibridged Cyclophane Cages: Synthesis, Their Conformational Behavior, and Properties. Molecules 2022, 27, 7083, DOI: 10.3390/molecules27207083There is no corresponding record for this reference.
- 31Nogita, R.; Matohara, K.; Yamaji, M.; Oda, T.; Sakamoto, Y.; Kumagai, T.; Lim, C.; Yasutake, M.; Shimo, T.; Jefford, C. W.; Shinmyozu, T. Photochemical Study of [33](1,3,5)Cyclophane and Emission Spectral Properties of [3n]Cyclophanes (n = 2–6). J. Am. Chem. Soc. 2004, 126, 13732– 13741, DOI: 10.1021/ja030032x31https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXnvFGgsL4%253D&md5=b1c761658dd686cf02d58a4736f7dd13Photochemical Study of [33](1,3,5)Cyclophane and Emission Spectral Properties of [3n]Cyclophanes (n = 2-6)Nogita, Rika; Matohara, Kumi; Yamaji, Minoru; Oda, Takuma; Sakamoto, Youichi; Kumagai, Tsutomu; Lim, Chultack; Yasutake, Mikio; Shimo, Tetsuro; Jefford, Charles W.; Shinmyozu, TeruoJournal of the American Chemical Society (2004), 126 (42), 13732-13741CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Photochem. reaction of [33](1,3,5)cyclophane 2, which is a photoprecursor for the formation of propella[33]prismane 18, was studied using a sterilizing lamp (254 nm). Upon photolysis in dry and wet CH2Cl2 or MeOH in the presence of 2 mol/L aq. HCl soln., the cyclophane 2 afforded novel cage compds. comprised of new skeletons, tetracyclo[6.3.1.0.2,704,11]dodeca-5,9-diene 43, hexacyclo[6.4.0.0.2,60.4,110.5,1009,12]dodecane 44, and pentacyclo[6.4.0.0.2,60.4,1105,10]dodecane 45. All of these products were confirmed by the x-ray structural analyses. A possible mechanism for the formation of these photoproducts via the hexaprismane deriv. 18 is proposed. The photophys. properties in the excited state of the [3n]cyclophanes ([3n]CP, n = 2-6) were investigated by measuring the emission spectra and detg. the quantum yields and lifetimes of the fluorescence. All [3n]CPs show excimeric fluorescence without a monomeric one. The lifetime of the excimer fluorescence becomes gradually longer with the increasing no. of the trimethylene bridges. The [3n]CPs also shows excimeric phosphorescence spectra without vibrational structures for n = 2, 4, and 5, while phosphorescence is absent for n = 3 and 6. With an increase in symmetry of the benzene skeleton in the [33]- and [36]CPs, the probability of the radiation (phosphorescence) process from the lowest triplet state may drastically decrease. Electronic supplementary information (ESI) is available at http://pubs.acs.org and contains alternative mechanism of single electron-transfer, crystal packing diagrams, and summary of crystallog. data and refinement details.
- 32Fujitsuka, M.; Tojo, S.; Shinmyozu, T.; Majima, T. Intramolecular dimer radical anions of [3n] cyclophanes: transannular distance dependent stabilization energy. Chem. Commun. 2009, 1553– 1555, DOI: 10.1039/b810122aThere is no corresponding record for this reference.
- 33Ghasemabadi, P. G.; Yao, T.; Bodwell, G. J. Cyclophanes containing large polycyclic aromatic hydrocarbons. Chem. Soc. Rev. 2015, 44, 6494– 6518, DOI: 10.1039/C5CS00274E33https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXptFOqs7g%253D&md5=134750980b78cb5345923017e39f55a0Cyclophanes containing large polycyclic aromatic hydrocarbonsGhasemabadi, Parisa Ghods; Yao, Tieguang; Bodwell, Graham J.Chemical Society Reviews (2015), 44 (18), 6494-6518CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)A review. Although a very large no. cyclophanes has been reported, only a very small proportion of them contain polycyclic arom. systems that can be thought of as 'large', i.e. with ≥4 rings. Such cyclophanes, illuminating both the chem. that was used to synthesize them and what was learned from studying them were highlighted. Context for the main body was provided by the careful consideration of the anatomy of a cyclophane and the classification of general synthetic approaches. The subsequent sections covered eleven different PAHs and are organized primarily according to increasing size of the arom. system, starting with pyrene (C16, the only large polycyclic arom. system to have been incorporated into numerous cyclophanes) and ending with hexabenzo[bc,ef,hi,kl,no,qr]coronene (C42).
- 34Jabłoński, M. Bond Paths Between Distant Atoms Do Not Necessarily Indicate Dominant Interactions. J. Comput. Chem. 2018, 39, 2183– 2195, DOI: 10.1002/jcc.2553234https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhvV2jsbfF&md5=72bd87bc238812e3840a9070a701dd62Bond paths between distant atoms do not necessarily indicate dominant interactionsJablonski, MiroslawJournal of Computational Chemistry (2018), 39 (26), 2183-2195CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)The goal of the article is to revive discussion on the interpretation of bond paths linking distant atoms, particularly tracing weak interactions in dimers. According to the Pendas' concept of privileged exchange channel, a bond path is formed between this pair of competing atoms, which is assocd. with larger value of the exchange energy. We point out that, due to the short-range nature of the exchange energy, bond paths linking distant atoms clearly become doubtful indicators of dominant intermol. interactions, particularly if some other characteristics (geometric, spectroscopic, based on electrostatic parameters, etc.) indicate other intermol. interactions as dominant. Several such cases are thoroughly investigated. We show that electrostatic parameters are much more reliable indicators of dominant intermol. interactions than bond paths. Then, we pay attention that the presence of ("unexpected", i.e., not necessarily indicating dominant intermol. interactions) bond paths between pairs of atoms featuring highly expanded charge distributions can be easily explained by visual exploration of isodensity contour plots. As always pointing in the direction of the steepest increase, the gradient vector of the electron d. favors areas of its high values gaining higher exchange energy, yet being blind to highly electron deficient areas nearby, which, however, can quite often be involved in dominant intermol. interactions as strongly suggested by many other bonding anal. We also suggest that an interat. component of Hellmann-Feynman force would most likely be the most reliable indicator of attractive or repulsive character of individual interat. interaction. © 2018 Wiley Periodicals, Inc.
- 35Jabłoński, M. On the Uselessness of Bond Paths Linking Distant Atoms and on the Violation of the Concept of Privileged Exchange Channels. ChemistryOpen 2019, 8, 497– 507, DOI: 10.1002/open.20190010935https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXosFKitr4%253D&md5=3c4c2268d8fc8a4e35bf6ef5e5900c5aOn the Uselessness of Bond Paths Linking Distant Atoms and on the Violation of the Concept of Privileged Exchange ChannelsJablonski, MiroslawChemistryOpen (2019), 8 (4), 497-507CODEN: CHOPCK; ISSN:2191-1363. (Wiley-VCH Verlag GmbH & Co. KGaA)We refer to frequently used determinants suggesting dominant interactions between distant atoms in various dimers. First of all, we show, against the still-prevailling opinion, that, in general, bond paths have nothing in common with dominant intermol. interactions and therefore they are useless in such cases. Quite the contrary, reliable information about dominant intermol. interactions can be obtained by means of electrostatic potential maps, which very convincingly explain mutual orientation of mols. in a dimer. For the first time, numerous examples of interactions that violate both the concept of privileged exchange channels proposed by Pendas and his collaborators as well as inequalities obtained by Tognetti and Joubert for the β parameter related to secondary interactions are presented. The possible cause of this violation is suggested. We also show that the so-called counterintuitive bond paths result from quite natural behavior of the electron d. gradient vector, i. e. searching for those areas of space that are characterized by large values of electron d. or the most expanded its distributions.
- 36Jabłoński, M. Counterintuitive bond paths: An intriguing case of the C(NO2)3– ion. Chem. Phys. Lett. 2020, 759, 137946, DOI: 10.1016/j.cplett.2020.137946There is no corresponding record for this reference.
- 37Jabłoński, M. The physical nature of the ultrashort spike–ring interaction in iron maiden molecules. J. Comput. Chem. 2022, 43, 1206– 1220, DOI: 10.1002/jcc.26879There is no corresponding record for this reference.
- 38Jabłoński, M. The Ultrashort Spike–Ring Interaction in Substituted Iron Maiden Molecules. Molecules 2023, 28, 2244, DOI: 10.3390/molecules28052244There is no corresponding record for this reference.
- 39Bader, R. F. W. Atoms in Molecules: A Quantum Theory; Oxford University Press: New York, USA, 1990.There is no corresponding record for this reference.
- 40Popelier, P. L. A. Atoms in Molecules: An Introduction; Longman: Singapore, 2000.There is no corresponding record for this reference.
- 41Matta, C. F.; Boyd, R. J. The Quantum Theory of Atoms in Molecules; Wiley VCH: Weinheim, Germany, 2007.There is no corresponding record for this reference.
- 42Li, A.; Xiong, S.; Zhou, W.; Zhai, H.; Liu, Y.; He, Q. Superphane: A new lantern-like receptor for encapsulation of a water dimer. Chem. Commun. 2021, 57, 4496– 4499, DOI: 10.1039/D1CC01158H42https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXos1elt7c%253D&md5=66490622fd05bbcaaa2ac7431976490eSuperphane: a new lantern-like receptor for encapsulation of a water dimerLi, Aimin; Xiong, Shenglun; Zhou, Wei; Zhai, Huijuan; Liu, Yuanchu; He, QingChemical Communications (Cambridge, United Kingdom) (2021), 57 (37), 4496-4499CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)A new superphane I, featuring an aesthetically pleasing structure, was successfully obtained via one-pot synthesis of a hexakis-amine and m-phthalaldehyde in a [2+6] manner. It proved capable of entrapping a water dimer within its cavity as inferred from the mass spectroscopy, crystallog. anal., NMR spectroscopy, and theor. calcns.
- 43Li, A.; Liu, Y.; Zhou, W.; Jiang, Y.; He, Q. Superphanes: Facile and efficient preparation, functionalization and unique properties. Tetrahedron Chem 2022, 1, 100006, DOI: 10.1016/j.tchem.2022.100006There is no corresponding record for this reference.
- 44Zhou, W.; Li, A.; Gale, P. A.; He, Q. A highly selective superphane for ReO4– recognition and extraction. Cell Rep. Phys. Sci. 2022, 3, 100875, DOI: 10.1016/j.xcrp.2022.100875There is no corresponding record for this reference.
- 45Zhou, W.; Wang, F.; Li, A.; Bai, S.; Feng, X.; He, Q. A Superphane-based carcerand for arsenic detoxification via imprisoning arsenate. Cell Rep. Phys. Sci. 2023, 4, 101295, DOI: 10.1016/j.xcrp.2023.10129545https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3sXktV2jsLg%253D&md5=9e98d5d1a63dfe7eb6353b10b66bdd80A Superphane-based carcerand for arsenic detoxification via imprisoning arsenateZhou, Wei; Wang, Fei; Li, Aimin; Bai, Silei; Feng, Xinxin; He, QingCell Reports Physical Science (2023), 4 (3), 101295CODEN: CRPSF5; ISSN:2666-3864. (Elsevier Inc.)Carcerands, special mol. constructs with enclosed interiors as a new phase of matter, have attracted immense interest because of their unique structures, physicochem. properties, and potential applications in many aspects, e.g., targeted drug delivery. However, carcerands for imprisoning, inter alia, anions of interest represent an unmet challenge. Herein, we report the design and synthesis of a superphane-based carcerand 1, featuring up to 18 anion binding sites and a fully enclosed interior space. Carcerand 1 is found capable of incarcerating H2PO4- anion, yielding an anion carceplex 5, as inferred from crystallog. anal., 1H NMR (NMR) spectroscopy, and diffusion-ordered NMR spectroscopy (DOSY), as well as mol. dynamics simulations. More importantly, highly toxic arsenate anion was also imprisoned within carcerand 1, offering the arsenate carceplex 6 that proved nontoxic compared with free arsenate or peripherally bound arsenate in the HEK293T cell line.
- 46Zhou, W.; Li, A.; Zhou, M.; Xu, Y.; Zhang, Y.; He, Q. Nonporous amorphous superadsorbents for highly effective and selective adsorption of iodine in water. Nat. Commun. 2023, 14, 5388, DOI: 10.1038/s41467-023-41056-546https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3sXhvVKhtrvM&md5=7ce0755635ae382a098365850447766eNonporous amorphous superadsorbents for highly effective and selective adsorption of iodine in waterZhou, Wei; Li, Aimin; Zhou, Min; Xu, Yiyao; Zhang, Yi; He, QingNature Communications (2023), 14 (1), 5388CODEN: NCAOBW; ISSN:2041-1723. (Nature Portfolio)Adsorbents widely utilized for environmental remediation, water purifn., and gas storage have been usually reported to be either porous or cryst. materials. In this contribution, we report the synthesis of two covalent org. superphane cages, that are utilized as the nonporous amorphous superadsorbents for aq. iodine adsorption with the record-breaking iodine adsorption capability and selectivity. In the static adsorption system, the cages exhibit iodine uptake capacity of up to 8.41 g g-1 in I2 aq. soln. and 9.01 g g-1 in I3- (KI/I2) aq. soln., resp., even in the presence of a large excess of competing anions. In the dynamic flow-through expt., the aq. iodine adsorption capability for I2 and I3- can reach up to 3.59 and 5.79 g g-1, resp. Moreover, these two superphane cages are able to remove trace iodine in aq. media from ppm level (5.0 ppm) down to ppb level concn. (as low as 11 ppb). Based on a binding-induced adsorption mechanism, such nonporous amorphous mol. materials prove superior to all existing porous adsorbents. This study can open up a new avenue for development of state-of-the-art adsorption materials for practical uses with conceptionally new nonporous amorphous superadsorbents (NAS).
- 47Xie, H.; Finnegan, T. J.; Liyana Gunawardana, V. W.; Pavlović, R. Z.; Moore, C. E.; Badjić, J. D. A Hexapodal Capsule for the Recognition of Anions. J. Am. Chem. Soc. 2021, 143, 3874– 3880, DOI: 10.1021/jacs.0c1232947https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXlsVCjtr4%253D&md5=ec3fafd54ea81865e9dd4b38d703f65bA Hexapodal Capsule for the Recognition of AnionsXie, Han; Finnegan, Tyler J.; Liyana Gunawardana, Vageesha W.; Pavlovic, Radoslav Z.; Moore, Curtis E.; Badjic, Jovica D.Journal of the American Chemical Society (2021), 143 (10), 3874-3880CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)We herein describe the prepn., characterization, and recognition characteristics of novel hexapodal capsule 1 composed of two benzenes joined by six hydrogen bonding (HB) groups to encircle space. This barrel-shaped host was obtained by reversible imine condensation of hexakis-aldehyde 2 and hexakis-amine 3 in the presence of oxyanions or halides acting as templates. Fascinatingly, capsule 1 includes 18 HB donating (Csp2-H and N-H) and 12 HB accepting groups (C=O and C=N) surrounding a binding pocket (78 Å3). In this regard, the complexation of fluoride, chloride, carbonate, sulfate, and hydrogen phosphate was probed by NMR spectroscopy (DMSO) and X-ray diffraction anal. to disclose the adaptive nature of 1 undergoing an adjustment of its conformation to complement each anionic guest. Furthermore, the rate by which encapsulated chloride was substituted by sulfate or hydrogen phosphate was slow (>7 days) while the stability of [SO4⊂1]2- was greatest in the series with Ka > 107 M-1 in highly competitive DMSO. With facile access to 1, the stage is set to probe this modular, polyvalent, and novel host to further improve the extn. of tetrahedral oxyanions from waste and the environment or control their chem. in living systems.
- 48Xie, H.; Gunawardana, V. W. L.; Finnegan, T. J.; Xie, W.; Badjić, J. D. Picking on Carbonate: Kinetic Selectivity in the Encapsulation of Anions. Angew. Chem., Int. Ed. 2022, 61, e202116518 DOI: 10.1002/anie.20211651848https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XisFKgtLo%253D&md5=0011dd70b5f35e0d91d23b2f4a8c29fbPicking on Carbonate: Kinetic Selectivity in the Encapsulation of AnionsXie, Han; Gunawardana, Vageesha W. Liyana; Finnegan, Tyler J.; Xie, William; Badjic, Jovica D.Angewandte Chemie, International Edition (2022), 61 (12), e202116518CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)Supramol. hosts bind to inorg. anions at a fast rate and select them in proportion with thermodn. stability of the corresponding [anion⊂host] complexes, forming in a reversible manner. In this study, we describe the action of hexapodal capsule 1 and its remarkable ability to select anions based on a large span of rates by which they enter this host. The thermodn. affinity of 1 toward eighteen anions extends over eight orders of magnitude (0<Ka<108 M-1; 1H NMR spectroscopy). The capsule would retain CO32- (Ka=107 M-1) for hours in the presence of eleven competing anions, including stronger binding SO42-, HAsO42- and HPO42- (Ka=107-108 M-1). The obsd. selection resulted from 1 possessing narrow apertures (ca. 3x6 S) comparable in size to anions (d=3.5-7.1 S) slowing down the encapsulation to last from seconds to days. The unorthodox mode of action of 1 sets the stage for creating hosts that pick anions by their ability to access the host.
- 49Oh, J. H.; Kim, J. H.; Kim, D. S.; Han, H. J.; Lynch, V. M.; Sessler, J. L.; Kim, S. K. Synthesis and Anion Recognition Features of a Molecular Cage Containing Both Hydrogen Bond Donors and Acceptors. Org. Lett. 2019, 21, 4336– 4339, DOI: 10.1021/acs.orglett.9b0151549https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhtVeit7rO&md5=a08603d33a84901f45f0716ecb438cffSynthesis and Anion Recognition Features of a Molecular Cage Containing Both Hydrogen Bond Donors and AcceptorsOh, Ju Hyun; Kim, Jeong Hyeon; Kim, Dong Sub; Han, Hye Jin; Lynch, Vincent M.; Sessler, Jonathan L.; Kim, Sung KukOrganic Letters (2019), 21 (11), 4336-4339CODEN: ORLEF7; ISSN:1523-7052. (American Chemical Society)A mol. cage, macrobicycle, contg. amide and pyrrole groups as hydrogen-bonding donors and imine groups as hydrogen-bonding acceptors has been synthesized. The macrobicycle was found to recognize tetrahedral oxyanions with high affinities, such as H2PO4-, HSO4-, SO42-, and HP2O73-, as well as the spherical halide anions, in chloroform. A single-crystal X-ray diffraction anal. revealed that the macrobicycle formed a 1:1 complex with H2PO4- in the solid state.
- 50Zhao, X.; Xiong, S.; Zhang, J.; Pu, J.; Ding, W.; Chen, X.; He, Q.; Zhang, Z. A hexapyrrolic molecular cage and the anion-binding studies in chloroform. J. Mol. Struct. 2023, 1293, 136232, DOI: 10.1016/j.molstruc.2023.136232There is no corresponding record for this reference.
- 51Li, A.; Liu, Y.; Luo, K.; He, Q. CO2 Capture in Liquid Phase and Room-Temperature Release and Concentration Using Mechanical Power. CCS Chem. 2024, DOI: 10.31635/ccschem.024.202404292There is no corresponding record for this reference.
Just Published.
- 52Jabłoński, M. Characteristics of Intermolecular Interactions between Encapsulated Molecules and the Lantern-Like Carcerand Superphanes. Molecules 2024, 29, 601, DOI: 10.3390/molecules29030601There is no corresponding record for this reference.
- 53Chai, J.-D.; Head-Gordon, M. Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections. Phys. Chem. Chem. Phys. 2008, 10, 6615– 6620, DOI: 10.1039/b810189b53https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhtlCksbfO&md5=c7848f8bf050e11972d438aaebd68fdfLong-range corrected hybrid density functionals with damped atom-atom dispersion correctionsChai, Jeng-Da; Head-Gordon, MartinPhysical Chemistry Chemical Physics (2008), 10 (44), 6615-6620CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)We report re-optimization of a recently proposed long-range cor. (LC) hybrid d. functional [J.-D. Chai and M. Head-Gordon, J. Chem. Phys., 2008, 128, 084106] to include empirical atom-atom dispersion corrections. The resulting functional, ωB97X-D yields satisfactory accuracy for thermochem., kinetics, and non-covalent interactions. Tests show that for non-covalent systems, ωB97X-D shows slight improvement over other empirical dispersion-cor. d. functionals, while for covalent systems and kinetics it performs noticeably better. Relative to our previous functionals, such as ωB97X, the new functional is significantly superior for non-bonded interactions, and very similar in performance for bonded interactions.
- 54Hohenberg, P.; Kohn, W. Inhomogeneous Electron Gas. Phys. Rev. 1964, 136, B864– B871, DOI: 10.1103/PhysRev.136.B864There is no corresponding record for this reference.
- 55Parr, R. G.; Yang, W. Density-Functional Theory of Atoms and Molecules; Oxford University Press: New York, NY, USA, 1989.There is no corresponding record for this reference.
- 56Jensen, F. Introduction to Computational Chemistry; John Wiley & Sons Ltd.: Chichester, UK, 2007.There is no corresponding record for this reference.
- 57Pritchard, B. P.; Altarawy, D.; Didier, B.; Gibson, T. D.; Windus, T. L. New Basis Set Exchange: An Open, Up-to-Date Resource for the Molecular Sciences Community. J. Chem. Inf. Model. 2019, 59, 4814– 4820, DOI: 10.1021/acs.jcim.9b0072557https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhvFCksrfJ&md5=fb809621ce47a29aad4b762c80365c22New Basis Set Exchange: An Open, Up-to-Date Resource for the Molecular Sciences CommunityPritchard, Benjamin P.; Altarawy, Doaa; Didier, Brett; Gibson, Tara D.; Windus, Theresa L.Journal of Chemical Information and Modeling (2019), 59 (11), 4814-4820CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)A review. The Basis Set Exchange (BSE) has been a prominent fixture in the quantum chem. community. First publicly available in 2007, it is recognized by both users and basis set creators as the de facto source for information related to basis sets. This popular resource has been rewritten, utilizing modern software design and best practices. The basis set data has been sepd. into a stand-alone library with an accessible API, and the Web site has been updated to use the current generation of web development libraries. The general layout and workflow of the Web site is preserved, while helpful features requested by the user community have been added. Overall, this design should increase adaptability and lend itself well into the future as a dependable resource for the computational chem. community. This article will discuss the decision to rewrite the BSE, the new architecture and design, and the new features that have been added.
- 58TeraChem. PetaChem. Version 1.9; LLC: Los Altos Hills, CA, USA, 2021.There is no corresponding record for this reference.
- 59Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. J. Am. Chem. Soc. 1996, 118, 11225– 11236, DOI: 10.1021/ja962176059https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XmtlOitrs%253D&md5=fef2924a69421881390282aa309ae91bDevelopment and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic LiquidsJorgensen, William L.; Maxwell, David S.; Tirado-Rives, JulianJournal of the American Chemical Society (1996), 118 (45), 11225-11236CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)The parametrization and testing of the OPLS all-atom force field for org. mols. and peptides are described. Parameters for both torsional and nonbonded energetics have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER all-atom force field. The torsional parameters were detd. by fitting to rotational energy profiles obtained from ab initio MO calcns. at the RHF/6-31G*//RHF/6-31G* level for more than 50 org. mols. and ions. The quality of the fits was high with av. errors for conformational energies of less than 0.2 kcal/mol. The force-field results for mol. structures are also demonstrated to closely match the ab initio predictions. The nonbonded parameters were developed in conjunction with Monte Carlo statistical mechanics simulations by computing thermodn. and structural properties for 34 pure org. liqs. including alkanes, alkenes, alcs., ethers, acetals, thiols, sulfides, disulfides, aldehydes, ketones, and amides. Av. errors in comparison with exptl. data are 2% for heats of vaporization and densities. The Monte Carlo simulations included sampling all internal and intermol. degrees of freedom. It is found that such non-polar and monofunctional systems do not show significant condensed-phase effects on internal energies in going from the gas phase to the pure liqs.
- 60Allinger, N. L.; Yuh, Y. H.; Lii, J. H. Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 1. J. Am. Chem. Soc. 1989, 111, 8551– 8566, DOI: 10.1021/ja00205a00160https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL1MXmtlWmsLo%253D&md5=e35207cdf829f8f78f2fdd6908887401Molecular mechanics. The MM3 force field for hydrocarbons. 1Allinger, Norman L.; Yuh, Young H.; Lii, Jenn HueiJournal of the American Chemical Society (1989), 111 (23), 8551-66CODEN: JACSAT; ISSN:0002-7863.A new mol. mechanics force field (called MM3) for the treatment of aliph. hydrocarbons has been developed and is presented here. This force field will enable one to calc. the structures and energies, including heats of formation, conformational energies, and rotational barriers, for hydrocarbons more accurately than was possible with earlier force fields. In addn. to simple mols., a great many highly strained mols. have been studied, and the results are almost always of exptl. accuracy.
- 61Frisch, M. J.; Gaussian 09. Revision D.01; Gaussian, Inc.: Wallingford, CT, USA, 2013.There is no corresponding record for this reference.
- 62Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 1983, 79, 926– 935, DOI: 10.1063/1.44586962https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL3sXksF2htL4%253D&md5=a1161334e381746be8c9b15a5e56f704Comparison of simple potential functions for simulating liquid waterJorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.; Impey, Roger W.; Klein, Michael L.Journal of Chemical Physics (1983), 79 (2), 926-35CODEN: JCPSA6; ISSN:0021-9606.Classical Monte Carlo simulations were carried out for liq. H2O in the NPT ensemble at 25° and 1 atm using 6 of the simpler intermol. potential functions for the dimer. Comparisons were made with exptl. thermodn. and structural data including the neutron diffraction results of Thiessen and Narten (1982). The computed densities and potential energies agree with expt. except for the original Bernal-Fowler model, which yields an 18% overest. of the d. and poor structural results. The discrepancy may be due to the correction terms needed in processing the neutron data or to an effect uniformly neglected in the computations. Comparisons were made for the self-diffusion coeffs. obtained from mol. dynamics simulations.
- 63Ponder, J. W. Tinker - Software Tools for Molecular Design . Version 7.1.3, 2015.There is no corresponding record for this reference.
- 64Bussi, G.; Donadio, D.; Parrinello, M. Canonical Sampling through Velocity Rescaling. J. Chem. Phys. 2007, 126, 014101, DOI: 10.1063/1.240842064https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXosVCltg%253D%253D&md5=9c182b57bfc65bca6be23c8c76b4be77Canonical sampling through velocity rescalingBussi, Giovanni; Donadio, Davide; Parrinello, MicheleJournal of Chemical Physics (2007), 126 (1), 014101/1-014101/7CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)The authors present a new mol. dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains const. during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. The authors illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liq. phases. Its performance is excellent and largely independent of the thermostat parameter also with regard to the dynamic properties.
Supporting Information
Supporting Information
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jcim.4c01040.
Figures showing evolution of conformations at the four initially inward pointing N atoms in H2O@n during the AIMD simulations, conformations at the nitrogen atoms in MD simulations for H2O encapsulated in 1–3, definitions of dN···H, dH-center and dO-center distances, and FF parameters and input structures (in the Tinker v7 format) for M@n (n = 1, 2, 3; M = H2O, HF, HCN, NH3, MeOH) (PDF)
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