1
|
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.
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Brela M, Stare J, Pirc G, Sollner-Dolenc M, Boczar M, Wójcik MJ, Mavri J. Car-Parrinello simulation of the vibrational spectrum of a medium strong hydrogen bond by two-dimensional quantization of the nuclear motion: application to 2-hydroxy-5-nitrobenzamide. J Phys Chem B 2012; 116:4510-8. [PMID: 22429110 DOI: 10.1021/jp2094559] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The nature of medium strong intra- and intermolecular hydrogen bonding in 2-hydroxy-5-nitrobenzamide in the crystal phase was examined by infrared spectroscopy and Car-Parrinello molecular dynamics simulation. The focal point of our study was the part of the infrared spectra associated with the O-H and N-H stretching modes that are very sensitive to the strength of hydrogen bonding. For spectra calculations we used an isolated dimer and the fully periodic crystal environment. We calculated the spectra by using harmonic approximation, the time course of the dipole moment function as obtained from the Car-Parrinello simulation, and the quantization of the nuclear motion of the proton for an instantaneous snapshot of the structures in one and two dimensions. Although quantitative assessment of the agreement between the computed and experimental band contour is difficult due to the fact that the experimental band is very broad, we feel that the most reasonable qualitative agreement with the experiment is obtained from snapshot structures and two-dimensional quantization of the proton motion. We have also critically examined the methods of constructing the one-dimensional proton potential. Perspectives are given for the treatment of nuclear quantum effects in biocatalysis.
Collapse
Affiliation(s)
- Mateusz Brela
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Ljubljana, Slovenia
| | | | | | | | | | | | | |
Collapse
|
4
|
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.
Collapse
Affiliation(s)
- Henryk T Flakus
- Institute of Chemistry, University of Silesia, Katowice, Poland.
| | | | | |
Collapse
|
5
|
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]
|
6
|
Dopieralski P, Perrin CL, Latajka Z. On the Intramolecular Hydrogen Bond in Solution: Car-Parrinello and Path Integral Molecular Dynamics Perspective. J Chem Theory Comput 2011; 7:3505-13. [PMID: 26598249 DOI: 10.1021/ct200580c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The issue of the symmetry of short, low-barrier hydrogen bonds in solution is addressed here with advanced ab initio simulations of a hydrogen maleate anion in different environments, starting with the isolated anion, going through two crystal structures (sodium and potassium salts), then to an aqueous solution, and finally in the presence of counterions. By Car-Parrinello and path integral molecular dynamics simulations, it is demonstrated that the position of the proton in the intramolecular hydrogen bond of an aqueous hydrogen maleate anion is entirely related to the solvation pattern around the oxygen atoms of the intramolecular hydrogen bond. In particular, this anion has an asymmetric hydrogen bond, with the proton always located on the oxygen atom that is less solvated, owing to the instantaneous solvation environment. Simulations of water solutions of hydrogen maleate ion with two different counterions, K(+) and Na(+), surprisingly show that the intramolecular hydrogen-bond potential in the case of the Na(+) salt is always asymmetric, regardless of the hydrogen bonds to water, whereas for the K(+) salt, the potential for H motion depends on the location of the K(+). It is proposed that repulsion by the larger and more hydrated K(+) is weaker than that by Na(+) and competitive with solvation by water.
Collapse
Affiliation(s)
| | - Charles L Perrin
- Department of Chemistry and Biochemistry, University of California at San Diego , La Jolla, California 92093-0358, United States
| | - Zdzislaw Latajka
- Faculty of Chemistry, University of Wroclaw , Joliot-Curie 14, 50-383 Wroclaw, Poland
| |
Collapse
|
7
|
Stare J, Mavri J, Grdadolnik J, Zidar J, Maksić ZB, Vianello R. Hydrogen Bond Dynamics of Histamine Monocation in Aqueous Solution: Car–Parrinello Molecular Dynamics and Vibrational Spectroscopy Study. J Phys Chem B 2011; 115:5999-6010. [DOI: 10.1021/jp111175e] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jernej Stare
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Janez Mavri
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | - Jože Grdadolnik
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | - Jernej Zidar
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | | | - Robert Vianello
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| |
Collapse
|
8
|
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]
|
9
|
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.
Collapse
Affiliation(s)
- Houcine Ghalla
- Laboratoire de Physique Quantique, Faculté des Sciences de Monastir, 5000 route de Kairouan, Tunisia
| | | | | | | | | |
Collapse
|
10
|
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]
|
11
|
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]
|
12
|
Klähn M, Seduraman A, Wu P. A Model for Self-Diffusion of Guanidinium-Based Ionic Liquids: A Molecular Simulation Study. J Phys Chem B 2008; 112:13849-61. [DOI: 10.1021/jp8048845] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Marco Klähn
- Institute of High Performance Computing, 1 Fusionopolis Way #16-16, Connexis, Singapore 138632
| | - Abirami Seduraman
- Institute of High Performance Computing, 1 Fusionopolis Way #16-16, Connexis, Singapore 138632
| | - Ping Wu
- Institute of High Performance Computing, 1 Fusionopolis Way #16-16, Connexis, Singapore 138632
| |
Collapse
|
13
|
Mitchell-Koch KR, Thompson WH. Infrared spectra of a model phenol-amine proton transfer complex in nanoconfined CH3Cl. J Phys Chem B 2008; 112:7448-59. [PMID: 18517239 DOI: 10.1021/jp076714e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The vibrational spectra of a model phenol-amine proton transfer complex dissolved in CH3Cl solvent confined in a 12 A radius spherical hydrophobic cavity were calculated using mixed quantum-classical molecular dynamics simulations. The reaction free energy of the proton transfer complex was varied in order to explore the contributions to the vibrational absorption band from product and reactant species. The vibrational spectra of the model proton transfer complex resulted in motionally narrowed spectral linewidths with two distinct peaks for products and reactants in cases where the system undergoes chemical exchange. It was found that the n=1 and n=2 vibrational excited states combine to form diabatic states such that the spectra have contributions from both n=0 --> n=1 and n=0 --> n=2 transitions. A strong relationship between the instantaneous vibrational frequency and a collective solvent coordinate was found that assists in understanding the origin of the spectral features.
Collapse
|
14
|
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.
Collapse
Affiliation(s)
- Aneta Jezierska
- University of Wrocław, Faculty of Chemistry, F. Joliot-Curie 14, 50-383 Wrocław, Poland.
| | | | | |
Collapse
|
15
|
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
| |
Collapse
|
16
|
Thar J, Zahn S, Kirchner B. When is a molecule properly solvated by a continuum model or in a cluster ansatz? A first-principles simulation of alanine hydration. J Phys Chem B 2008; 112:1456-64. [PMID: 18193863 DOI: 10.1021/jp077341k] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In order to test the validity of the cluster ansatz approach as well as of the continuum model approach and to learn about the solvation shell, we carried out first-principles molecular dynamics simulations of the alanine hydration. Our calculations contained one alanine molecule dissolved in 60 water molecules. Dipole moments of individual molecules were derived by means of maximally localized Wannier functions. We observed an average dipole moment of about 16.0 D for alanine and of about 3.3 D for water. In particular, the average water dipole moment in proximity of alanine's COO(-) group decayed continously with increasing distance, while, surprisingly, close to the CH3 and NH3+ group, the dipole moment first rose before its value dropped. In a cluster ansatz approach, we considered snapshots of alanine surrounded by different water molecule shells. The dipole moments from the cluster approaches utilizing both maximally localized Wannier functions as well as natural population analysis served to approximate the dipole moments of the total trajectory. Sufficient convergence of the cluster ansatz approach is found for either of the two solvent shells around the polar groups and one solvent shell around the apolar groups or two solvent shells around the polar groups surrounded by a dieletric continuum.
Collapse
Affiliation(s)
- Jens Thar
- Lehrstuhl für Theoretische Chemie, Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstr. 2, D-04103 Leipzig, Germany
| | | | | |
Collapse
|