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Exploring the Dynamical Nature of Intermolecular Hydrogen Bonds in Benzamide, Quinoline and Benzoic Acid Derivatives. Molecules 2022; 27:molecules27248847. [PMID: 36557978 PMCID: PMC9783803 DOI: 10.3390/molecules27248847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022] Open
Abstract
The hydrogen bonds properties of 2,6-difluorobenzamide, 5-hydroxyquinoline and 4-hydroxybenzoic acid were investigated by Car-Parrinello and path integral molecular dynamics (CPMD and PIMD), respectively. The computations were carried out in vacuo and in the crystalline phase. The studied complexes possess diverse networks of intermolecular hydrogen bonds (N-H…O, O-H…N and O-H…O). The time evolution of hydrogen bridges gave a deeper insight into bonds dynamics, showing that bridged protons are mostly localized on the donor side; however, the proton transfer phenomenon was registered as well. The vibrational features associated with O-H and N-H stretching were analyzed on the basis of the Fourier transform of the atomic velocity autocorrelation function. The spectroscopic effects of hydrogen bond formation were studied. The PIMD revealed quantum effects influencing the hydrogen bridges providing more accurate free energy sampling. It was found that the N…O or O…O interatomic distances decreased (reducing the length of the hydrogen bridge), while the O-H or N-H covalent bond was elongated, which led to the increase in the proton sharing. Furthermore, Quantum Theory of Atoms in Molecules (QTAIM) was used to give insight into electronic structure parameters. Finally, Symmetry-Adapted Perturbation Theory (SAPT) was employed to estimate the energy contributions to the interaction energy of the selected dimers.
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Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces. Molecules 2021; 26:molecules26185642. [PMID: 34577113 PMCID: PMC8468954 DOI: 10.3390/molecules26185642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/04/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022] Open
Abstract
Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds and substituent effects in these compounds were analyzed on the basis of Density Functional Theory (DFT), Møller-Plesset second-order perturbation theory (MP2), Coupled Clusters with Singles and Doubles (CCSD) and Car-Parrinello Molecular Dynamics (CPMD). The simulations were carried out in the gas and crystalline phases. The nuclear quantum effects were incorporated a posteriori using the snapshots taken from ab initio trajectories. Further, they were used to solve a vibrational Schrödinger equation. The proton reaction path was studied using B3LYP, ωB97XD and PBE functionals with a 6-311++G(2d,2p) basis set. Two energy minima (deep and shallow) were found, indicating that the proton transfer phenomena could occur in the electronic ground state. Next, the electronic structure and topology were examined in the molecular and proton transferred (PT) forms. The Atoms In Molecules (AIM) theory was employed for this purpose. It was found that the hydrogen bond is stronger in the proton transferred (PT) forms. In order to estimate the dimers' stabilization and forces responsible for it, the Symmetry-Adapted Perturbation Theory (SAPT) was applied. The energy decomposition revealed that dispersion is the primary factor stabilizing the dimeric forms and crystal structure of both compounds. The CPMD results showed that the proton transfer phenomena occurred in both studied compounds, as well as in both phases. In the case of compound 2, the proton transfer events are more frequent in the solid state, indicating an influence of the environmental effects on the bridged proton dynamics. Finally, the vibrational signatures were computed for both compounds using the CPMD trajectories. The Fourier transformation of the autocorrelation function of atomic velocity was applied to obtain the power spectra. The IR spectra show very broad absorption regions between 700 cm-1-1700 cm-1 and 2300 cm-1-3400 cm-1 in the gas phase and 600 cm-1-1800 cm-1 and 2200 cm-1-3400 cm-1 in the solid state for compound 1. The absorption regions for compound 2 were found as follows: 700 cm-1-1700 cm-1 and 2300 cm-1-3300 cm-1 for the gas phase and one broad absorption region in the solid state between 700 cm-1 and 3100 cm-1. The obtained spectroscopic features confirmed a strong mobility of the bridged protons. The inclusion of nuclear quantum effects showed a stronger delocalization of the bridged protons.
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Sensitivity of Intra- and Intermolecular Interactions of Benzo[h]quinoline from Car-Parrinello Molecular Dynamics and Electronic Structure Inspection. Int J Mol Sci 2021; 22:ijms22105220. [PMID: 34069244 PMCID: PMC8156133 DOI: 10.3390/ijms22105220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 01/29/2023] Open
Abstract
The O-H...N and O-H...O hydrogen bonds were investigated in 10-hydroxybenzo[h]quinoline (HBQ) and benzo[h]quinoline-2-methylresorcinol complex in vacuo, solvent and crystalline phases. The chosen systems contain analogous donor and acceptor moieties but differently coupled (intra- versus intermolecularly). Car–Parrinello molecular dynamics (CPMD) was employed to shed light onto principle components of interactions responsible for the self-assembly. It was applied to study the dynamics of the hydrogen bonds and vibrational features as well as to provide initial geometries for incorporation of quantum effects and electronic structure studies. The vibrational features were revealed using Fourier transformation of the autocorrelation function of atomic velocity and by inclusion of nuclear quantum effects on the O-H stretching solving vibrational Schrödinger equation a posteriori. The potential of mean force (Pmf) was computed for the whole trajectory to derive the probability density distribution and for the O-H stretching mode from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling and nuclear quantum effects. The electronic structure changes of the benzo[h]quinoline-2-methylresorcinol dimer and trimers were studied based on Constrained Density Functional Theory (CDFT) whereas the Electron Localization Function (ELF) method was applied for all systems. It was found that the bridged proton is localized on the donor side in both investigated systems in vacuo. The crystalline phase simulations indicated bridged proton-sharing and transfer events in HBQ. These effects are even more pronounced when nuclear quantization is taken into account, and the quantized Pmf allows the proton to sample the acceptor area more efficiently. The CDFT indicated the charge depletion at the bridged proton for the analyzed dimer and trimers in solvent. The ELF analysis showed the presence of the isolated proton (a signature of the strongest hydrogen bonds) only in some parts of the HBQ crystal simulation. The collected data underline the importance of the intramolecular coupling between the donor and acceptor moieties.
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Theoretical study of intramolecular hydrogen bond in selected symmetric "proton sponges" on the basis of DFT and CPMD methods. J Mol Model 2020; 26:37. [PMID: 31989276 DOI: 10.1007/s00894-020-4296-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/14/2020] [Indexed: 12/21/2022]
Abstract
"Proton sponges," derivatives of prototypic 1,8-bis(dimethylamino)naphthalene (DMAN), exhibit remarkable basicity, which made them interesting for various experimental and theoretical studies. The details of bridged proton dynamics in protonated DMAN and its derivative denoted as TMGN (1,8-bis(tetramethylguanidino)naphthalene) were investigated on the basis of density functional theory (DFT) and Car-Parrinello molecular dynamics (CPMD) methods. Special attention was paid to the effects of symmetry of the molecular skeleton and the type of substituent on the bridged proton neighborhood statistics and dynamics. The metric parameter analyses of hydrogen bridge provided us with a conclusion that proton migration events in TMGNH+ are less numerous than in DMANH+, which can be rationalized by noticing the slower dynamics of large substituents of TMGN with respect to the smaller -N(Me)2 groups of DMAN. The atomic velocity power spectra served as computational models of the vibrational signatures associated with the presence of the intramolecular hydrogen bond. A broad feature was registered for hydrogen bonds present in both compounds. The computations were verified by experimental data available.
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Brela MZ, Boczar M, Malec LM, Wójcik MJ, Nakajima T. Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 197:194-201. [PMID: 29395929 DOI: 10.1016/j.saa.2018.01.050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/11/2018] [Accepted: 01/16/2018] [Indexed: 06/07/2023]
Abstract
Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers.
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Affiliation(s)
- Mateusz Z Brela
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Marek Boczar
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Leszek M Malec
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Marek J Wójcik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan.
| | - Takahito Nakajima
- RIKEN, Advanced Institute for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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Sobczyk L, Chudoba D, Tolstoy PM, Filarowski A. Some Brief Notes on Theoretical and Experimental Investigations of Intramolecular Hydrogen Bonding. Molecules 2016; 21:E1657. [PMID: 27918442 PMCID: PMC6273268 DOI: 10.3390/molecules21121657] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 11/18/2016] [Accepted: 11/28/2016] [Indexed: 11/16/2022] Open
Abstract
A review of selected literature data related to intramolecular hydrogen bonding in ortho-hydroxyaryl Schiff bases, ortho-hydroxyaryl ketones, ortho-hydroxyaryl amides, proton sponges and ortho-hydroxyaryl Mannich bases is presented. The paper reports on the application of experimental spectroscopic measurements (IR and NMR) and quantum-mechanical calculations for investigations of the proton transfer processes, the potential energy curves, tautomeric equilibrium, aromaticity etc. Finally, the equilibrium between the intra- and inter-molecular hydrogen bonds in amides is discussed.
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Affiliation(s)
- Lucjan Sobczyk
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie Str., 50-383 Wrocław, Poland.
| | - Dorota Chudoba
- Faculty of Physics, A. Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland.
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia.
| | - Peter M Tolstoy
- Center for Magnetic Resonance, St. Petersburg State University, St. Petersburg 198504, Russia.
| | - Aleksander Filarowski
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie Str., 50-383 Wrocław, Poland.
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia.
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Tautomeric stability, molecular structure, NBO, electronic and NMR analyses of salicylideneimino-ethylimino-pentan-2-one. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.02.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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8
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Theoretical Modeling of Vibrational Spectra and Proton Tunneling in Hydrogen-Bonded Systems. ADVANCES IN CHEMICAL PHYSICS 2016. [DOI: 10.1002/9781119165156.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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9
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Głębocka A, Raczyńska ED, Chylewska A, Makowski M. Experimental (FT-IR) and theoretical (DFT) studies on prototropy and H-bond formation for pyrazine-2-amidoxime. J PHYS ORG CHEM 2016. [DOI: 10.1002/poc.3538] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Angelika Głębocka
- Laboratory of Intermolecular Interactions, Faculty of Chemistry; University of Gdańsk; Wita Stwosza 63 80-308 Gdańsk Poland
| | - Ewa D. Raczyńska
- Department of Chemistry; Warsaw University of Life Sciences; Nowoursynowska 159c 02-776 Warszawa Poland
| | - Agnieszka Chylewska
- Laboratory of Intermolecular Interactions, Faculty of Chemistry; University of Gdańsk; Wita Stwosza 63 80-308 Gdańsk Poland
| | - Mariusz Makowski
- Laboratory of Intermolecular Interactions, Faculty of Chemistry; University of Gdańsk; Wita Stwosza 63 80-308 Gdańsk Poland
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10
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Hydrogen bonds in quinoline N-oxide derivatives: first-principle molecular dynamics and metadynamics ground state study. Struct Chem 2015. [DOI: 10.1007/s11224-015-0720-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Jezierska A, Panek JJ. First-Principle Molecular Dynamics Study of Selected Schiff and Mannich Bases: Application of Two-Dimensional Potential of Mean Force to Systems with Strong Intramolecular Hydrogen Bonds. J Chem Theory Comput 2015; 4:375-84. [PMID: 26620779 DOI: 10.1021/ct7002644] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Car-Parrinello Molecular Dynamics simulations were performed for selected anharmonic systems, i.e., Schiff and Mannich base-type compounds, to investigate the vibrational properties associated with O-H stretching. All calculations were performed in the gas phase to compare them with available experimental data. First the vibrational properties of the two compounds were analyzed on the basis of well-established approaches: Fourier transformation of the autocorrelation function of both the atomic velocities and dipole moments. Then path integral molecular dynamics simulations were performed to demonstrate the influence of quantum effects on the proton's position in the hydrogen bridge. In addition, quantum effects were incorporated a posteriori into calculations of O-H stretching envelopes for the Schiff and Mannich bases. Proton potential snapshots were extracted from the ab initio molecular dynamics trajectory. Vibrational Schrödinger equations (one- and two-dimensional) were solved numerically for the snapshots, and the O-H stretching envelopes were calculated as a superposition of the 0→1 transitions. Subsequently, one- and two-dimensional potentials of mean force (1D and 2D pmf) were calculated for the proton stretching mode from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling and nuclear quantum effects. The results show that the applied methodologies are in good agreement with experimental infrared spectra. Additionally, it is demonstrated that the 2D pmf method could be applied in systems with strong anharmonicity to describe the properties of the O-H stretching mode more accurately. Future applications of the 2D pmf technique include, in principle, large biomolecular systems treated within the QM/MM framework.
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Affiliation(s)
- Aneta Jezierska
- University of Wrocław, Faculty of Chemistry, F. Joliot-Curie 14, 50-383 Wrocław, Poland, and National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Jarosław J Panek
- University of Wrocław, Faculty of Chemistry, F. Joliot-Curie 14, 50-383 Wrocław, Poland, and National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
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12
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Hydrogen bridges of polycyclic aromatic systems with O-H···O bonds--a gas-phase vs. solid-state Car-Parrinello study. J Mol Model 2015; 21:15. [PMID: 25617206 PMCID: PMC4305098 DOI: 10.1007/s00894-014-2550-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 11/30/2014] [Indexed: 11/26/2022]
Abstract
The current study belongs to a series of investigations of polycyclic aromatic compounds containing intramolecular hydrogen bonds. Close proximity of the coupled aromatic system and hydrogen bridges gives rise to resonance-assisted hydrogen bonding phenomena. Substituted naphthols are ideally suited for this kind of investigation. The parent compound, 1-hydroxy-8-methoxy-3-methylnaphthalene, and its derivative, 1-bromo-5-hydroxy-4-isopropoxy-7-methylnaphthalene, both with known crystal structure, are investigated. Car-Parrinello molecular dynamics (CPMD) is chosen as a theoretical background for this study. Gas phase and solid state simulations are carried out. The effect of Grimme’s dispersion corrections is also included. The report presents time evolution of structural parameters, spectroscopic signatures based on the CPMD simulations, and comparison with available experimental data. We show that the proton transfer phenomena do not occur within the simulations, which is consistent with evaluation based on the acidity of the donor and acceptor sites. The effects of the substitution in the aromatic system and change of the environment (gas vs. condensed phase) are of similar magnitude.
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Li X, Yan L, Yue B. Maleimide: a potential building block for the design of proton exchange membranes studied by ab initio molecular dynamics simulations. RSC Adv 2015. [DOI: 10.1039/c5ra14272e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Ab initio molecular dynamics (AIMD) simulations are applied to the study of proton transport in solid state maleimide.
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Affiliation(s)
- Xuejiao Li
- Department of Chemistry
- College of Sciences
- Shanghai University
- Shanghai 20044
- China
| | - Liuming Yan
- Department of Chemistry
- College of Sciences
- Shanghai University
- Shanghai 20044
- China
| | - Baohua Yue
- Department of Chemistry
- College of Sciences
- Shanghai University
- Shanghai 20044
- China
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15
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Wójcik MJ, Kwiendacz J, Boczar M, Boda Ł, Ozaki Y. Quantum-mechanical and Car–Parrinello molecular dynamics simulations of infrared spectra of crystalline imidazole. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2013.10.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Vener MV, Shishkina AV, Rykounov AA, Tsirelson VG. Cl···Cl interactions in molecular crystals: insights from the theoretical charge density analysis. J Phys Chem A 2013; 117:8459-67. [PMID: 23924151 DOI: 10.1021/jp405119x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The structure, IR harmonic frequencies and intensities of normal vibrations of 20 molecular crystals with the X-Cl···Cl-X contacts of different types, where X = C, Cl, and F and the Cl···Cl distance varying from ~3.0 to ~4.0 Å, are computed using the solid-state DFT method. The obtained crystalline wave functions have been further used to define and describe quantitatively the Cl···Cl interactions via the electron-density features at the Cl···Cl bond critical points. We found that the electron-density at the bond critical point is almost independent of the particular type of the contact or hybridization of the ipso carbon atom. The energy of Cl···Cl interactions, E(int), is evaluated from the linking E(int) and local electronic kinetic energy density at the Cl···Cl bond critical points. E(int) varies from 2 to 12 kJ/mol. The applicability of the geometrical criterion for the detection of the Cl···Cl interactions in crystals with two or more intermolecular Cl···Cl contacts for the unique chlorine atom is not straightforward. The detection of these interactions in such crystals may be done by the quantum-topological analysis of the periodic electron density.
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Affiliation(s)
- Mikhail V Vener
- Department of Quantum Chemistry, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia.
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Katsyuba SA, Vener MV, Zvereva EE, Fei Z, Scopelliti R, Laurenczy G, Yan N, Paunescu E, Dyson PJ. How strong is hydrogen bonding in ionic liquids? Combined X-ray crystallographic, infrared/Raman spectroscopic, and density functional theory study. J Phys Chem B 2013; 117:9094-105. [PMID: 23822750 DOI: 10.1021/jp405255w] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Hydrogen bonding in ionic liquids based on the 1-(2'-hydroxylethyl)-3-methylimidazolium cation ([C₂OHmim](+)) and various anions ([A](-)) of differing H-bond acceptor strength, viz. hexafluorophosphate [PF6](-), tetrafluoroborate [BF₄](-), bis(trifluoromethanesulfonimide) [Tf₂N](-), trifluoromethylsulfonate [OTf](-), and trifluoroacetate [TFA](-), was studied by a range of spectroscopic and computational techniques and, in the case of [C₂OHmim][PF6], by single crystal X-ray diffraction. The first quantitative estimates of the energy (E(HB)) and the enthalpy (-ΔH(HB)) of H-bonds in bulk ILs were obtained from a theoretical analysis of the solid-state electron-density map of crystalline [C₂OHmim][PF6] and an analysis of the IR spectra in crystal and liquid samples. E(HB) for OH···[PF6](-) H-bonds amounts to ~3.4-3.8 kcal·mol(-1), whereas weaker H-bonds (2.8-3.1 kcal·mol(-1)) are formed between aromatic C2H group of imidazolium ring and the [PF6](-) anion. The enthalpy of the OH···[A](-) H-bonds follows the order: [PF6] (2.4 kcal·mol(-1)) < [BF₄] (3.3 kcal·mol(-1)) < [Tf₂N] (3.4 kcal·mol(-1)) < [OTf] (4.7 kcal·mol(-1)l) < [TFA] (6.2 kcal·mol(-1)). The formation of aggregates of self-associated [C₂OHmim](+) cations is present in liquid [C₂OHmim][PF6], [C₂OHmim][BF₄], and [C₂OHmim][Tf₂N], with the energy of the OH···OH H-bonds amounting to ~6 kcal·mol(-1). Multiple secondary interactions in the bulk ILs influence their structure, vibrational spectra, and H-bond strength. In particular, these interactions can blue-shift the stretching frequencies of the CH groups of the imidazolium ring in spite of red-shifting CH···[A](-) H-bonds. They also weaken the H-bonding in the IL relative to the isolated ion pairs, with these anticooperative effects amounting to ca. 50% of the E(HB) value.
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Affiliation(s)
- Sergey A Katsyuba
- A. E. Arbuzov Institute of Organic and Physical Chemistry of Kazan Scientific Centre of the Russian Academy of Sciences, Arbuzov str. 8, 420088 Kazan, Russia.
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18
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Car–Parrinello simulation of the vibrational spectra of strong hydrogen bonds with isotopic substitution effects: Application to oxalic acid dihydrate. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2012.12.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Martyniak A, Panek J, Jezierska-Mazzarello A, Filarowski A. Triple hydrogen bonding in a circular arrangement: ab initio, DFT and first-principles MD studies of tris-hydroxyaryl enamines. J Comput Aided Mol Des 2012; 26:1045-53. [PMID: 22955961 PMCID: PMC3474916 DOI: 10.1007/s10822-012-9597-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Accepted: 08/29/2012] [Indexed: 11/17/2022]
Abstract
First-principles Car-Parrinello molecular dynamics, ab initio (MP2) and density functional schemes have been used to explore the tautomeric equilibrium in three tris(amino(R)methylidene)cyclohexane-1,3,5-triones (R = hydrogen, methyl or phenyl group). The dynamic nature of the cyclic hydrogen bonding has been studied by the first-principles MD method. The comparison of the results obtained by aforesaid methods has been accomplished on the basis of calculations of structural and spectroscopic characteristics of the compounds. The conformational analysis of the studied compounds has been carried out at the MP2/6-31+G(d,p) and B3LYP/6-31+G(d,p) levels of theory. The influence of steric and electronic effects on the cyclic hydrogen bonding has been analysed. The extent of the proton delocalization has been modified by the substituents according to the sequence: hydrogen < phenyl < methyl. This fact is verified by the spectroscopic and structural data as well as the energy potential curve. A prevalence of the keto-enamine tautomeric form has been observed in the static ab initio and DFT models, and confirmed by the first-principles MD.
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Affiliation(s)
- Agata Martyniak
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie str., 50-383 Wrocław, Poland
| | - Jarosław Panek
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie str., 50-383 Wrocław, Poland
| | | | - Aleksander Filarowski
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie str., 50-383 Wrocław, Poland
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Vener MV, Egorova AN, Churakov AV, Tsirelson VG. Intermolecular hydrogen bond energies in crystals evaluated using electron density properties: DFT computations with periodic boundary conditions. J Comput Chem 2012; 33:2303-9. [PMID: 22786749 DOI: 10.1002/jcc.23062] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 06/14/2012] [Accepted: 06/19/2012] [Indexed: 11/11/2022]
Abstract
The hydrogen bond (H-bond) energies are evaluated for 18 molecular crystals with 28 moderate and strong O-H···O bonds using the approaches based on the electron density properties, which are derived from the B3LYP/6-311G** calculations with periodic boundary conditions. The approaches considered explore linear relationships between the local electronic kinetic G(b) and potential V(b) densities at the H···O bond critical point and the H-bond energy E(HB). Comparison of the computed E(HB) values with the experimental data and enthalpies evaluated using the empirical correlation of spectral and thermodynamic parameters (Iogansen, Spectrochim. Acta Part A 1999, 55, 1585) enables to estimate the accuracy and applicability limits of the approaches used. The V(b)-E(HB) approach overestimates the energy of moderate H-bonds (E(HB) < 60 kJ/mol) by ~20% and gives unreliably high energies for crystals with strong H-bonds. On the other hand, the G(b)-E(HB) approach affords reliable results for the crystals under consideration. The linear relationship between G(b) and E(HB) is basis set superposition error (BSSE) free and allows to estimate the H-bond energy without computing it by means of the supramolecular approach. Therefore, for the evaluation of H-bond energies in molecular crystals, the G(b) value can be recommended to be obtained from both density functional theory (DFT) computations with periodic boundary conditions and precise X-ray diffraction experiments.
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Affiliation(s)
- M V Vener
- Department of Quantum Chemistry, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia.
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21
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Flakus HT, Rekik N, Jarczyk A. Polarized IR spectra of the hydrogen bond in 2-thiopheneacetic acid and 2-thiopheneacrylic acid crystals: H/D isotopic and temperature effects. J Phys Chem A 2012; 116:2117-30. [PMID: 22272930 DOI: 10.1021/jp210950n] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Polarized IR spectra of 2-thiopheneacetic acid and of 2-thiopheneacrylic acid crystals were measured at 293 and 77 K in the υ(O-H) and υ(O-D) band frequency ranges. The corresponding spectra of the two individual systems strongly differ, one from the other, by the corresponding band shapes as well as by the temperature effect characterizing the bands. The crystal spectral properties remain in close relation with the electronic structure of the two different molecular systems. We show that a vibronic coupling mechanism involving the hydrogen bond protons and the electrons on the π- electronic systems in the molecules determines the way in which the vibrational exciton coupling between the hydrogen bonds in the carboxylic acid dimers occurs. Strong coupling in 2-thiopheneacrylic acid dimers prefers a "tail-to-head"-type Davydov coupling widespread by the π- electrons. A weak through-space coupling in 2-thiopheneacetic acid dimers, of a van der Waals type, is responsible for a "side-to-side"-type coupling. The relative contribution of each exciton coupling mechanism in the dimer spectra generation is temperature and the molecular electronic structure dependent. This explains the observed difference in the temperature- induced evolution of the compared spectra.
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Affiliation(s)
- Henryk T Flakus
- Institute of Chemistry, University of Silesia, Katowice, Poland.
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22
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Begue D, Pouchan C, Guillemin JC, Benidar A. Anharmonic treatment of vibrational resonance polyads—the diborane: a critical case for numerical methods. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1122-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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23
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Meyer MP. New Applications of Isotope Effects in the Determination of Organic Reaction Mechanisms. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2012. [DOI: 10.1016/b978-0-12-398484-5.00002-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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24
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Markle TF, Rhile IJ, Mayer JM. Kinetic effects of increased proton transfer distance on proton-coupled oxidations of phenol-amines. J Am Chem Soc 2011; 133:17341-52. [PMID: 21919508 PMCID: PMC3228417 DOI: 10.1021/ja2056853] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To test the effect of varying the proton donor-acceptor distance in proton-coupled electron transfer (PCET) reactions, the oxidation of a bicyclic amino-indanol (2) is compared with that of a closely related phenol with an ortho CPh(2)NH(2) substituent (1). Spectroscopic, structural, thermochemical, and computational studies show that the two amino-phenols are very similar, except that the O···N distance (d(ON)) is >0.1 Å longer in 2 than in 1. The difference in d(ON) is 0.13 ± 0.03 Å from X-ray crystallography and 0.165 Å from DFT calculations. Oxidations of these phenols by outer-sphere oxidants yield distonic radical cations (•)OAr-NH(3)(+) by concerted proton-electron transfer (CPET). Simple tunneling and classical kinetic models both predict that the longer donor-acceptor distance in 2 should lead to slower reactions, by ca. 2 orders of magnitude, as well as larger H/D kinetic isotope effects (KIEs). However, kinetic studies show that the compound with the longer proton-transfer distance, 2, exhibits smaller KIEs and has rate constants that are quite close to those of 1. For example, the oxidation of 2 by the triarylamminium radical cation N(C(6)H(4)OMe)(3)(•+) (3a(+)) occurs at (1.4 ± 0.1) × 10(4) M(-1) s(-1), only a factor of 2 slower than the closely related reaction of 1 with N(C(6)H(4)OMe)(2)(C(6)H(4)Br)(•+) (3b(+)). This difference in rate constants is well accounted for by the slightly different free energies of reaction: ΔG° (2 + 3a(+)) = +0.078 V versus ΔG° (1 + 3b(+)) = +0.04 V. The two phenol-amines do display some subtle kinetic differences: for instance, compound 2 has a shallower dependence of CPET rate constants on driving force (Brønsted α, Δ ln(k)/Δ ln(K(eq))). These results show that the simple tunneling model is not a good predictor of the effect of proton donor-acceptor distance on concerted-electron transfer reactions involving strongly hydrogen-bonded systems. Computational analysis of the observed similarity of the two phenols emphasizes the importance of the highly anharmonic O···H···N potential energy surface and the influence of proton vibrational excited states.
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Affiliation(s)
- Todd F Markle
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA.
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25
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Yan YA, Kühn O. Unraveling the Correlated Dynamics of the Double Hydrogen Bonds of Nucleic Acid Base Pairs in Solution. J Phys Chem B 2011; 115:5254-9. [DOI: 10.1021/jp108521g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yun-an Yan
- Institut für Physik, Universität Rostock, D-18051 Rostock, Germany
| | - Oliver Kühn
- Institut für Physik, Universität Rostock, D-18051 Rostock, Germany
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26
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Kwiendacz J, Boczar M, Wójcik MJ. Car–Parrinello molecular dynamics simulations of infrared spectra of crystalline imidazole. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2010.12.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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27
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Gaigeot MP, Martinez M, Vuilleumier R. Infrared spectroscopy in the gas and liquid phase from first principle molecular dynamics simulations: application to small peptides. Mol Phys 2010. [DOI: 10.1080/00268970701724974] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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28
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Pirc G, Stare J, Mavri J. Car-Parrinello simulation of hydrogen bond dynamics in sodium hydrogen bissulfate. J Chem Phys 2010; 132:224506. [PMID: 20550407 DOI: 10.1063/1.3429251] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We studied proton dynamics of a short hydrogen bond of the crystalline sodium hydrogen bissulfate, a hydrogen-bonded ferroelectric system. Our approach was based on the established Car-Parrinello molecular dynamics (CPMD) methodology, followed by an a posteriori quantization of the OH stretching motion. The latter approach is based on snapshot structures taken from CPMD trajectory, calculation of proton potentials, and solving of the vibrational Schrodinger equation for each of the snapshot potentials. The so obtained contour of the OH stretching band has the center of gravity at about 1540 cm(-1) and a half width of about 700 cm(-1), which is in qualitative agreement with the experimental infrared spectrum. The corresponding values for the deuterated form are 1092 and 600 cm(-1), respectively. The hydrogen probability densities obtained by solving the vibrational Schrodinger equation allow for the evaluation of potential of mean force along the proton transfer coordinate. We demonstrate that for the present system the free energy profile is of the single-well type and features a broad and shallow minimum near the center of the hydrogen bond, allowing for frequent and barrierless proton (or deuteron) jumps. All the calculated time-averaged geometric parameters were in reasonable agreement with the experimental neutron diffraction data. As the present methodology for quantization of proton motion is applicable to a variety of hydrogen-bonded systems, it is promising for potential use in computational enzymology.
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Affiliation(s)
- Gordana Pirc
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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29
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Dega-Szafran Z, Katrusiak A, Szafran M. Very short OHO hydrogen bond in bis(2-quinuclidinium-propionate) hydrobromide. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.06.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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30
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Theoretical and spectroscopic study of hydrogen bond vibrations in imidazole and its deuterated derivative. Chem Phys 2010. [DOI: 10.1016/j.chemphys.2010.04.034] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Theoretical description of hydrogen bonding in oxalic acid dimer and trimer based on the combined extended-transition-state energy decomposition analysis and natural orbitals for chemical valence (ETS-NOCV). J Mol Model 2010; 16:1789-95. [PMID: 20505966 PMCID: PMC2949554 DOI: 10.1007/s00894-010-0740-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 05/03/2010] [Indexed: 10/27/2022]
Abstract
In the present study we have analyzed hydrogen bonding in dimer and trimer of oxalic acid, based on a recently proposed charge and energy decomposition scheme (ETS-NOCV). In the case of a dimer, two conformations, α and β, were considered. The deformation density contributions originating from NOCV's revealed that the formation of hydrogen bonding is associated with the electronic charge deformation in both the σ-(Δρ(σ)) and π-networks (Δρ(π)). It was demonstrated that σ-donation is realized by electron transfer from the lone pair of oxygen on one monomer into the empty P*(H-O) orbital of the second oxalic acid fragment. In addition, a covalent contribution is observed by the density transfer from hydrogen of H-O group in one oxalic acid monomer to the oxygen atom of the second fragment. The resonance assisted component (Δρ(π)), is based on the transfer of electron density from the π-orbital localized on the oxygen of OH on one oxalic acid monomer to the oxygen atom of the other fragment. ETS-NOCV allowed to conclude that the σ(O---HO) component is roughly eight times as important as π (RAHB) contribution in terms of energetic estimation. The electrostatic factor (ΔE(elstat)) is equally as important as orbital interaction term (ΔE(orb)). Finally, comparing β-dimer of oxalic acid with trimer we found practically no difference concerning each of the O---HO bonds, neither qualitative nor quantitative.
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32
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Yan YA, Petković M, Krishnan GM, Kühn O. IR spectrum of the O–H⋯O hydrogen bond of phthalic acid monomethylester in gas phase and in CCl4 solution. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2009.12.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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33
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Yan YA, Kühn O. Geometric correlations and infrared spectrum of adenine–uracil hydrogen bonds in CDCl3 solution. Phys Chem Chem Phys 2010; 12:15695-703. [DOI: 10.1039/c0cp00009d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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34
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Kwiatkowska E, Majerz I. Analysis of potential energy curve for proton motion in intermolecular hydrogen bond. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2009.11.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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35
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Ghalla H, Rekik N, Michta A, Oujia B, Flakus HT. Theoretical modeling of infrared spectra of the hydrogen and deuterium bond in aspirin crystal. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 75:37-47. [PMID: 19884041 DOI: 10.1016/j.saa.2009.09.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Revised: 09/06/2009] [Accepted: 09/13/2009] [Indexed: 05/28/2023]
Abstract
An extended quantum theoretical approach of the nu(X-H) IR lineshape of cyclic dimers of weakly H-bonded species is proposed. We have extended a previous approach [M.E.-A. Benmalti, P. Blaise, H.T. Flakus, O. Henri-Rousseau, Chem. Phys. 320 (2006) 267] by accounting for the anharmonicity of the slow mode which is described by a "Morse" potential in order to reproduce the polarized infrared spectra of the hydrogen and deuterium bond in acetylsalicylic acid (aspirin) crystals. From comparison of polarized IR spectra of isotopically neat and isotopically diluted aspirin crystals it resulted that centrosymmetric aspirin dimer was the bearer of the crystal main spectral properties. In this approach, the adiabatic approximation is performed for each separate H-bond bridge of the dimer and a strong non-adiabatic correction is introduced into the model via the resonant exchange between the fast mode excited states of the two moieties. Within the strong anharmonic coupling theory, according to which the X-H...Y high-frequency mode is anharmonically coupled to the H-bond bridge, this model incorporated the Davydov coupling between the excited states of the two moieties, the quantum direct and indirect dampings and the anharmonicity for the H-bond bridge. The spectral density is obtained within the linear response theory by Fourier transform of the damped autocorrelation functions. The evaluated spectra are in fairly good agreement with the experimental ones by using a minimum number of independent parameters. The effect of deuteration has been well reproduced by reducing simply the angular frequency of the fast mode and the anharmonic coupling parameter.
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Affiliation(s)
- Houcine Ghalla
- Laboratoire de Physique Quantique, Faculté des Sciences de Monastir, 5000 route de Kairouan, Tunisia
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36
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Jezierska-Mazzarello A, Vuilleumier R, Panek JJ, Ciccotti G. Molecular Property Investigations of an ortho-Hydroxy Schiff Base Type Compound with the First-Principle Molecular Dynamics Approach. J Phys Chem B 2009; 114:242-53. [DOI: 10.1021/jp903501m] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aneta Jezierska-Mazzarello
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland, National Institute of Chemistry, Hajdrihova 19, SI-1001, Ljubljana, Slovenia, Université Pierre et Marie Curie 4, Laboratoire de Physique Théorique de la Matière Condenseé, 4 Place Jussieu, 75005 Paris, France, and Dipartimento di Fisica, and CNISM unit 1, Università di Roma ‘La Sapienza’, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Rodolphe Vuilleumier
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland, National Institute of Chemistry, Hajdrihova 19, SI-1001, Ljubljana, Slovenia, Université Pierre et Marie Curie 4, Laboratoire de Physique Théorique de la Matière Condenseé, 4 Place Jussieu, 75005 Paris, France, and Dipartimento di Fisica, and CNISM unit 1, Università di Roma ‘La Sapienza’, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Jarosław J. Panek
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland, National Institute of Chemistry, Hajdrihova 19, SI-1001, Ljubljana, Slovenia, Université Pierre et Marie Curie 4, Laboratoire de Physique Théorique de la Matière Condenseé, 4 Place Jussieu, 75005 Paris, France, and Dipartimento di Fisica, and CNISM unit 1, Università di Roma ‘La Sapienza’, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Giovanni Ciccotti
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland, National Institute of Chemistry, Hajdrihova 19, SI-1001, Ljubljana, Slovenia, Université Pierre et Marie Curie 4, Laboratoire de Physique Théorique de la Matière Condenseé, 4 Place Jussieu, 75005 Paris, France, and Dipartimento di Fisica, and CNISM unit 1, Università di Roma ‘La Sapienza’, Piazzale Aldo Moro 5, 00185 Roma, Italy
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37
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Rekik N, Ghalla H, Flakus HT, JabÅonÌska M, Blaise P, Oujia B. Polarized Infrared Spectra of the H(D) Bond in 2-Thiophenic Acid Crystals: A Spectroscopic and Computational Study. Chemphyschem 2009; 10:3021-33. [DOI: 10.1002/cphc.200900376] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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38
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Jezierska A, Panek JJ, Żukowska GZ, Sporzyński A. A combined experimental and theoretical study of benzoxaborole derivatives by Raman and IR spectroscopy, static DFT, and first-principle molecular dynamics. J PHYS ORG CHEM 2009. [DOI: 10.1002/poc.1625] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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39
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Nedeltcheva D, Antonov L. Relative strength of the intramolecular hydrogen bonding in 1-phenylazo-naphthalen-2-ol and 1-phenyliminomethyl-naphtahlen-2-ol. J PHYS ORG CHEM 2009. [DOI: 10.1002/poc.1464] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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40
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Johannissen LO, Scrutton NS, Sutcliffe MJ. The enzyme aromatic amine dehydrogenase induces a substrate conformation crucial for promoting vibration that significantly reduces the effective potential energy barrier to proton transfer. J R Soc Interface 2009; 5 Suppl 3:S225-32. [PMID: 18495615 DOI: 10.1098/rsif.2008.0068.focus] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The role of promoting vibrations in enzymic reactions involving hydrogen tunnelling is contentious. While models incorporating such promoting vibrations have successfully reproduced and explained experimental observations, it has also been argued that such vibrations are not part of the catalytic effect. In this study, we have employed combined quantum mechanical/molecular mechanical methods with molecular dynamics and potential energy surface calculations to investigate how enzyme and substrate motion affects the energy barrier to proton transfer for the rate-limiting H-transfer step in aromatic amine dehydrogenase (AADH) with tryptamine as substrate. In particular, the conformation of the iminoquinone adduct induced by AADH was found to be essential for a promoting vibration identified previously-this lowers significantly the 'effective' potential energy barrier, that is the barrier which remains to be surmounted following collective, thermally equilibrated motion attaining a quantum degenerate state of reactants and products. When the substrate adopts a conformation similar to that in the free iminoquinone, this barrier was found to increase markedly. This is consistent with AADH facilitating the H-transfer event by holding the substrate in a conformation that induces a promoting vibration.
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Affiliation(s)
- Linus O Johannissen
- School of Chemical Engineering and Analytical Science and Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester, UK
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41
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Vener MV, Egorova AN, Fomin DP, Tsirelson VG. Hierarchy of the non-covalent interactions in the alanine-based secondary structures. DFT study of the frequency shifts and electron-density features. J PHYS ORG CHEM 2008. [DOI: 10.1002/poc.1445] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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42
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Yan YA, Krishnan GM, Kühn O. QM/MM lineshape simulation of the hydrogen-bonded uracil NH stretching vibration of the adenine:uracil base pair in CDCl3. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.09.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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43
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Rekik N, Oujia B, Wójcik MJ. Theoretical infrared spectral density of H-bonds in liquid and gas phases: Anharmonicities and dampings effects. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.05.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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44
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Jezierska A, Panek JJ, Koll A. Spectroscopic properties of a strongly anharmonic Mannich base N-oxide. Chemphyschem 2008; 9:839-46. [PMID: 18338342 DOI: 10.1002/cphc.200700769] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Car-Parrinello molecular dynamics simulations in vacuum and in the solid state are performed on a strongly anharmonic system, namely, 2-(N-diethylamino-N-oxymethyl)-4,6-dichlorophenol, to investigate its molecular and spectroscopic properties. The investigated compound contains two slightly different molecules in the crystal cell with very short intramolecular hydrogen bonds (of 2.400 and 2.423 A), as determined previously by neutron diffraction. The vibrational properties of the compound are studied on the basis of standard approaches, that is, Fourier transformation of the autocorrelation functions of the atomic velocities and dipole moments. Then, the trajectory obtained from ab initio molecular dynamics is sampled and the obtained snapshots are used to solve the vibrational Schrödinger equations and to calculate the O--H stretching envelope as a superposition of the 0-->1 transition. Using an envelope method, the a posteriori quantum effects are included in the O--H stretching. In addition, NMR spectra are calculated also using the obtained snapshots. One- and two-dimensional potentials of mean force (1D and 2D pmf) are derived to explain the details of the proton dynamics. The computational results are supported by NMR experimental data. In addition, the calculated results are compared with previously published X-ray, neutron diffraction, and spectroscopic descriptions. A detailed analysis of the bridged proton's dynamics is thus obtained. The application of 1D and 2D pmf in a system with a strong bridged-proton delocalization is also demonstrated.
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Affiliation(s)
- Aneta Jezierska
- University of Wrocław, Faculty of Chemistry, F. Joliot-Curie 14, 50-383 Wrocław, Poland.
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45
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Theoretical IR spectral density of H-bond in liquid phase: Combined effects of anharmonicities, Fermi resonances, direct and indirect relaxations. J Mol Liq 2008. [DOI: 10.1016/j.molliq.2007.10.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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46
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He N, Xie HB, Ding YH. Structures and stability of lithium monosilicide clusters SiLin (n = 4-16): What is the maximum number, magic number, and core number for lithium coordination to silicon? J Comput Chem 2008; 29:1850-8. [DOI: 10.1002/jcc.20959] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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47
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Polosan S, Chow TJ, Tsuboi T. Density functional theory analysis of a mixed-ligand iridium compound for multi-color organic light-emitting diodes. J PHYS ORG CHEM 2008. [DOI: 10.1002/poc.1329] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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48
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Stare J, Panek J, Eckert J, Grdadolnik J, Mavri J, Hadži D. Proton Dynamics in the Strong Chelate Hydrogen Bond of Crystalline Picolinic Acid N-Oxide. A New Computational Approach and Infrared, Raman and INS Study. J Phys Chem A 2008; 112:1576-86. [DOI: 10.1021/jp077107u] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jernej Stare
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
| | - Jarosław Panek
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
| | - Juergen Eckert
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
| | - Jože Grdadolnik
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
| | - Janez Mavri
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
| | - Dušan Hadži
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
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Xing D, Bu Y, Tan X. Characterizing the properties of the N7,N9-dimethylguaninium chloride ion pairs: prospecting for the design of a novel ionic liquid. J Phys Chem A 2008; 112:106-16. [PMID: 18076149 DOI: 10.1021/jp0760509] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structures, infrared spectra, and electronic properties of the N7,N9-dimethylguaninium chloride have been studied. The interaction of one cation with one to four Cl anions and one Cl anion with two cations were investigated. Fifteen stable conformers are obtained. It is found that there are four acidic regions in the vicinity of the guaninium cations. In these regions, the cation could H-bond with one to three Cl anions but no more than three nearest anions. One Cl anion could H-bond with two cations. Additionally, evidence of a Cl...pi interaction between the anion and cation is observed. Among these structures, one cation interaction with two anions and two cations interaction with one anion have the larger interaction energies than the other series. Natural bond orbital analyses and molecular orbitals reveal that the charge transfer from anion(s) to the cation(s) occurs mainly through either the Cllp --> sigma C-H, Cllp --> sigma N-H, or Cllp --> pi C8-N7 interactions. The interaction between Cl and sigma (C/N-H) or pi C-N produces a small bond order. This indicates that the Cl...H (Cl...pi) interaction exhibits a weak covalent character and suggests a strong ionic H-bond (Cl...pi bond). What's more, formation of Cl...H/Cl...pi bond decreases the bond order of the associated C/N-H bond or C8-N7 bond. In addition, examination of vibrational spectrum of each conformer explains the origin of H-bonding character.
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Affiliation(s)
- Dianxiang Xing
- Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, People's Republic of China. sdu.edu.cn
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