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Ellis AM, Davies JA, Yurtsever E, Calvo F. Dimerization dynamics of carboxylic acids in helium nanodroplets. J Chem Phys 2022; 156:174304. [PMID: 35525638 DOI: 10.1063/5.0087957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The dimerization of molecules in helium nanodroplets is known to preferentially yield structures of higher energy than the global energy minimum structure for a number of quite different monomers. Here, we explore dimerization in this environment using an atomistic model within statistically converged molecular dynamics (MD) trajectories, treating the solvent implicitly through the use of a thermostat, or more explicitly by embedding one monomer in a He100 cluster. The focus is on the two simplest carboxylic acids, formic and acetic, both of which have been studied experimentally. While the global minimum structure, which comprises two CO⋯HO hydrogen bonds, is predicted to be the most abundant dimer in the absence of the helium solvent, this is no longer the case once helium atoms are included. The simulations confirm the importance of kinetic trapping effects and also shed light on the occurrence of specific dynamical effects, leading to the occasional formation of high-energy structures away from minima, such as saddle configurations. Theoretically predicted infrared spectra, based on the MD statistics, are in good agreement with the experimental spectra.
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Affiliation(s)
- Andrew M Ellis
- School of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Julia A Davies
- School of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Ersin Yurtsever
- Department of Chemistry, Koç University, Rumelifeneri Yolu, Sariyer, 34450 Istanbul, Turkey
| | - Florent Calvo
- Université Grenoble Alpes, CNRS, LiPhy, F38000 Grenoble, France
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Socha O, Dračínský M. Dimerization of Acetic Acid in the Gas Phase-NMR Experiments and Quantum-Chemical Calculations. Molecules 2020; 25:molecules25092150. [PMID: 32375390 PMCID: PMC7248931 DOI: 10.3390/molecules25092150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 11/24/2022] Open
Abstract
Due to the nature of the carboxylic group, acetic acid can serve as both a donor and acceptor of a hydrogen bond. Gaseous acetic acid is known to form cyclic dimers with two strong hydrogen bonds. However, trimeric and various oligomeric structures have also been hypothesized to exist in both the gas and liquid phases of acetic acid. In this work, a combination of gas-phase NMR experiments and advanced computational approaches were employed in order to validate the basic dimerization model of gaseous acetic acid. The gas-phase experiments performed in a glass tube revealed interactions of acetic acid with the glass surface. On the other hand, variable-temperature and variable-pressure NMR parameters obtained for acetic acid in a polymer insert provided thermodynamic parameters that were in excellent agreement with the MP2 (the second order Møller–Plesset perturbation theory) and CCSD(T) (coupled cluster with single, double and perturbative triple excitation) calculations based on the basic dimerization model. A slight disparity between the theoretical dimerization model and the experimental data was revealed only at low temperatures. This observation might indicate the presence of other, entropically disfavored, supramolecular structures at low temperatures.
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Affiliation(s)
- Ondřej Socha
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic;
- Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 166 10 Prague, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic;
- Correspondence: ; Tel./Fax: +42-02-2018-3139
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Lengvinaitė D, Aidas K, Kimtys L. Molecular aggregation in liquid acetic acid: insight from molecular dynamics/quantum mechanics modelling of structural and NMR properties. Phys Chem Chem Phys 2019; 21:14811-14820. [PMID: 31225541 DOI: 10.1039/c9cp01892a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The 1H NMR signal of the acidic proton in acetic acid molecules shows a marked upfield shift in the neat liquid as compared to that in low-concentration acetic acid solution in inert solvents where acetic acid cyclic dimers predominate. The underlying reasons for this phenomenon are analyzed in this work by considering classical molecular dynamics simulations and combined quantum mechanics/molecular mechanics calculations of the 1H NMR chemical shift of the acidic proton in the neat liquid and in the cyclic dimer of acetic acid in cyclohexane solution. Recorded trajectories were quantitatively analyzed in terms of different types of molecular aggregates formed in the neat liquid by using a geometrical definition of the hydrogen bond. Both the geometrical analysis and the computational NMR results indicate that the cyclic dimer cannot be the dominating aggregation pattern for acetic acid molecules in the neat liquid. The applied computational approach reproduces the lowering of the 1H NMR chemical shift of the acidic proton in acetic acid when going from cyclohexane solution to the neat liquid very well. The presence of acetic acid aggregates with hydrogen bonding between hydroxyl moieties and of monomeric acetic acid molecules in the neat liquid is found to lead to the observed lowering of the chemical shift, with lesser contribution from the formation of open acetic acid aggregates.
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Affiliation(s)
- Dovilė Lengvinaitė
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio al. 3, LT-10257 Vilnius, Lithuania.
| | - Kęstutis Aidas
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio al. 3, LT-10257 Vilnius, Lithuania.
| | - Liudvikas Kimtys
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio al. 3, LT-10257 Vilnius, Lithuania.
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Grabska J, Beć KB, Ishigaki M, Wójcik MJ, Ozaki Y. Spectra-structure correlations of saturated and unsaturated medium-chain fatty acids. Near-infrared and anharmonic DFT study of hexanoic acid and sorbic acid. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 185:35-44. [PMID: 28535459 DOI: 10.1016/j.saa.2017.05.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 05/10/2017] [Accepted: 05/10/2017] [Indexed: 06/07/2023]
Abstract
Quantum chemical reproduction of entire NIR spectra is a new trend, enabled by contemporary advances in the anharmonic approaches. At the same time, recent increase of the importance of NIR spectroscopy of biological samples raises high demand for gaining deeper understanding of NIR spectra of biomolecules, i.e. fatty acids. In this work we investigate saturated and unsaturated medium-chain fatty acids, hexanoic acid and sorbic acid, in the near-infrared region. By employing fully anharmonic density functional theory (DFT) calculations we reproduce the experimental NIR spectra of these systems, including the highly specific spectral features corresponding to the dimerization of fatty acids. Broad range of concentration levels from 5·10-4M in CCl4 to pure samples are investigated. The major role of cyclic dimers can be evidenced for the vast majority of these samples. A highly specific NIR feature of fatty acids, the elevation of spectral baseline around 6500-4000cm-1, is being explained by the contributions of combination bands resulting from the vibrations of hydrogen-bonded OH groups in the cyclic dimers. Based on the high agreement between the calculated and experimental NIR spectra, a detailed NIR band assignments are proposed for hexanoic acid and sorbic acid. Subsequently, the correlations between the structure and NIR spectra are elucidated, emphasizing the regions in which clear and universal traces of specific bands corresponding to saturated and unsaturated alkyl chains can be established, thus demonstrating the wavenumber regions highly valuable for structural identifications.
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Affiliation(s)
- Justyna Grabska
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan; University of Wroclaw, F. Joliot-Curie 14, 50-383 Wrocław, Poland.
| | - Krzysztof B Beć
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan.
| | - Mika Ishigaki
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
| | - Marek J Wójcik
- Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland
| | - Yukihiro Ozaki
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
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Zhang M, Chen L, Yang H, Ma J. Theoretical Study of Acetic Acid Association Based on Hydrogen Bonding Mechanism. J Phys Chem A 2017; 121:4560-4568. [DOI: 10.1021/acs.jpca.7b03324] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Minhua Zhang
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical Technology and ‡Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Lihang Chen
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical Technology and ‡Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Huaming Yang
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical Technology and ‡Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jing Ma
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical Technology and ‡Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
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Grabska J, Ishigaki M, Beć KB, Wójcik MJ, Ozaki Y. Correlations between Structure and Near-Infrared Spectra of Saturated and Unsaturated Carboxylic Acids. Insight from Anharmonic Density Functional Theory Calculations. J Phys Chem A 2017; 121:3437-3451. [DOI: 10.1021/acs.jpca.7b02053] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Justyna Grabska
- Department
of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
- Faculty
of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Mika Ishigaki
- Department
of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
| | - Krzysztof B. Beć
- Department
of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
| | - Marek J. Wójcik
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland
| | - Yukihiro Ozaki
- Department
of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
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Beć KB, Futami Y, Wójcik MJ, Nakajima T, Ozaki Y. Spectroscopic and Computational Study of Acetic Acid and Its Cyclic Dimer in the Near-Infrared Region. J Phys Chem A 2016; 120:6170-83. [PMID: 27482762 DOI: 10.1021/acs.jpca.6b04470] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anharmonic vibrational analysis of near-infrared (NIR) spectra of acetic acid was carried out by anharmonic quantum chemical calculation in a wide concentration range of its CCl4 solution. By predicting vibrational spectra of acetic acid for the first time over a wide NIR region, it was possible to elucidate the influence of the formation of acetic acid cyclic dimer on its NIR spectrum. Quantum chemical simulations were based on coupled cluster and density functional theory quantum methods. Additionally, Møller-Plesset perturbation theory was employed for the additional calculation of hydrogen bonding stabilization energies. An anharmonic vibrational analysis was performed with the use of generalized second-order vibrational perturbation theory (GVPT2). A hybrid approach was assumed, in which monomeric species was treated by CCSD(T)/aug-cc-pVDZ (harmonic approximation) and B3LYP/SNSD (anharmonic approximation) methods. For the cyclic dimer, B3LYP and B2PLYP single and double hybrid functionals, paired with an SNSD basis set, were employed. DFT calculations were augmented with additional empirical dispersion correction. It was found that quantum chemically calculated vibrational modes in the NIR region are in a good agreement with experimental data. The results of anharmonic vibrational analysis were supported by a harmonic shift analysis, for elucidating the very strong anharmonic coupling observed between stretching modes of hydrogen bonded bridge in the cyclic dimer. However, the calculated wavenumbers for combination modes of double hydrogen bonded bridge in the cyclic dimer, which are very sensitive to the formation of hydrogen bonding, were found to be underestimated by quantum chemical methods. Therefore, by band fitting, the wavenumbers and shape parameters for these bands were found, and the modeled spectra were adjusted accordingly. A high accuracy of simulated spectra was achieved, and a detailed analysis of the experimental NIR spectra of acetic acid was possible, with successful identification of numerous experimental bands, including those which originate from concentration effects. It was also found that the main spectral features observed in the NIR spectra of carboxylic acid upon the formation of hydrogen bond should be accounted for combination modes of the stretching and bending vibrations of double hydrogen-bonded bridge in the cyclic dimers of acetic acid.
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Affiliation(s)
- Krzysztof B Beć
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University , Sanda, Hyogo 669-1337, Japan.,RIKEN , 519-1399 Aramaki-Aoba, Aoba-ku, Sendai, Miyagi 980-0845, Japan
| | - Yoshisuke Futami
- Department of Biological and Chemical Systems Engineering, National Institute of Technology, Kumamoto College , Yatsushiro, Kumamoto 866-8501, Japan
| | - Marek J Wójcik
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Kraków, Poland
| | - Takahito Nakajima
- RIKEN Advanced Institute for Computational Science , 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yukihiro Ozaki
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University , Sanda, Hyogo 669-1337, Japan
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Nagy PI. Competing intramolecular vs. intermolecular hydrogen bonds in solution. Int J Mol Sci 2014; 15:19562-633. [PMID: 25353178 PMCID: PMC4264129 DOI: 10.3390/ijms151119562] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/17/2014] [Accepted: 10/13/2014] [Indexed: 11/17/2022] Open
Abstract
A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed.
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Affiliation(s)
- Peter I Nagy
- Center for Drug Design and Development, the University of Toledo, Toledo, OH 43606-3390, USA.
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