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Feldman VI, Ryazantsev SV, Kameneva SV. Matrix isolation in laboratory astrochemistry: state-of-the-art, implications and perspective. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Wolf ME, Turney JM, Schaefer HF. High level ab initio investigation of the catalytic effect of water on formic acid decomposition and isomerization. Phys Chem Chem Phys 2020; 22:25638-25651. [PMID: 33146170 DOI: 10.1039/d0cp03796f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Formic acid (FA) is a ubiquitous molecule found in the atmosphere, and is relevant to many important processes. The FA molecule generally exists as the trans isomer, which can decompose into H2O and CO (dehydration). It can also exist in the less favorable cis isomer which can decompose into H2 and CO2 (decarboxylation). Our work examines the complexes formed between each isomer of FA with water. We present geometries and vibrational frequencies obtained at the reliable CCSD(T)/aug-cc-pVTZ level of theory for seven FAwater complexes. We utilize the focal point method to determine CCSDT(Q)/CBS plus corrections binding energies of 7.37, 3.36, and 2.02 kcal mol-1 plus 6.07, 3.79, 2.60, and 2.55 kcal mol-1 for the trans-FAwater and cis-FAwater complexes, respectively. Natural bond orbital analysis is used to further decompose the interactions in each complex and gain insight into their relative strengths. Furthermore, we examine the effect that a single water molecule has on the barrier heights to each decomposition pathway by optimizing the transition states and verifying their connectivity with intrinsic reaction coordinate computations as well as utilizing a kinetic model. Water lowers the barrier to dehydration by at most 15.78 kcal mol-1 and the barrier to decarboxylation by up to 15.90 kcal mol-1. Our research also examines for the first time the effect of one water molecule on the interconversion barrier and we find that the barrier from trans to cis is not catalyzed by water due to the strong FA and water interactions. Our results highlight some instances where different binary complexes result in different decomposition pathways and even a case where one binary complex can form the same decomposition products via two distinct mechanisms. Our results provide a reliable benchmark of the FAH2O system as well as provide insight into future studies of similar atmospheric systems.
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Affiliation(s)
- Mark E Wolf
- Center for Computational Quantum Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, USA.
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Gaines E, Di Tommaso D. Solvation and Aggregation of Meta-Aminobenzoic Acid in Water: Density Functional Theory and Molecular Dynamics Study. Pharmaceutics 2018; 10:pharmaceutics10010012. [PMID: 29360788 PMCID: PMC5874825 DOI: 10.3390/pharmaceutics10010012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 11/16/2022] Open
Abstract
Meta-aminobenzoic acid, an important model system in the study of polymorphism and crystallization of active pharmaceutical ingredients, exist in water in both the nonionic (mABA) and zwitterionic (mABA±) forms. However, the constituent molecules of the polymorph that crystallizes from aqueous solutions are zwitterionic. This study reports atomistic simulations of the events surrounding the early stage of crystal nucleation of meta-aminobenzoic acid from aqueous solutions. Ab initio molecular dynamics was used to simulate the hydration of mABA± and mABA and to quantify the interaction of these molecules with the surrounding water molecules. Density functional theory calculations were conducted to determine the low-lying energy conformers of meta-aminobenzoic acid dimers and to compute the Gibbs free energies in water of nonionic, (mABA)2, zwitterionic, (mABA±)2, and nonionic-zwitterionic, (mABA)(mABA±), species. Classical molecular dynamics simulations of mixed mABA–mABA± aqueous solutions were carried out to examine the aggregation of meta-aminobenzoic acid. According to these simulations, the selective crystallization of the polymorphs whose constituent molecules are zwitterionic is driven by the formation of zwitterionic dimers in solution, which are thermodynamically more stable than (mABA)2 and (mABA)(mABA±) pairs. This work represents a paradigm of the role of molecular processes during the early stages of crystal nucleation in affecting polymorph selection during crystallization from solution.
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Affiliation(s)
- Etienne Gaines
- School of Biological and Chemical Sciences, Materials Research Institute, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
| | - Devis Di Tommaso
- School of Biological and Chemical Sciences, Materials Research Institute, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
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Duarte L, Rekola I, Khriachtchev L. Complex between Formic Acid and Nitrous Oxide: A Matrix-Isolation and Computational Study. J Phys Chem A 2017; 121:8728-8737. [DOI: 10.1021/acs.jpca.7b09586] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luís Duarte
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Iiris Rekola
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Leonid Khriachtchev
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
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Di Tommaso D, Watson KL. Density functional theory study of the oligomerization of carboxylic acids. J Phys Chem A 2014; 118:11098-113. [PMID: 25357019 DOI: 10.1021/jp509100u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a density functional theory [M06-2X/6-31+G(d,p)] study of the structures and free energies of formation of oligomers of four carboxylic acids (formic acid, acetic acid, tetrolic acid, and benzoic acid) in water, chloroform, and carbon tetrachloride. Solvation effects were treated using the SMD continuum solvation model. The low-lying energy structures of molecular complexes were located by adopting an efficient search procedure to probe the potential energy surfaces of the oligomers of carboxylic acids (CA)n (n = 2-6). The free energies of the isomers of (CA)n in solution were determined as the sum of the electronic energy, vibrational-rotational-translational gas-phase contribution, and solvation free energy. The assessment of the computational protocol adopted in this study with respect to the dimerization of acetic acid, (AA)2, and formic acid, (FA)2, located new isomers of (AA)2 and (FA)2 and gave dimerization constants in good agreement with the experimental values. The calculation of the self-association of acetic acid, tetrolic acid, and benzoic acid shows the following: (i) Classic carboxylic dimers are the most stable isomer of (CA)2 in both the gas phase and solution. (ii) Trimers of carboxylic acid are stable in apolar aprotic solvents. (iii) Molecular clusters consisting of two interacting classic carboxylic dimers (CA)4,(D+D) are the most stable type of tetramers, but their formation from the self-association of classic carboxylic dimers is highly unfavorable. (iv) For acetic acid and tetrolic acid the reactions (CA)2 + 2CA → (CA)4,(D+D) and (CA)3 + CA → (CA)4,(D+D) are exoergonic, but these aggregation pathways go through unstable clusters that could hinder the formation of tetrameric species. (v) For tetrolic acid the prenucleation species that are more likely to form in solution are dimeric and trimeric structures that have encoded structural motifs resembling the α and β solid forms of tetrolic acid. (vi) Stable tetramers of benzoic acid could form in carbon tetrachloride from the aggregation of trimers and monomers. (vii) Higher order clusters such as acetic acid pentamers and tetrolic acid hexamers are highly unstable in all solvation environments.
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Affiliation(s)
- Devis Di Tommaso
- School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
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Rozenberg M, Loewenschuss A, Nielsen CJ. H-Bonded Clusters in the Trimethylamine/Water System: A Matrix Isolation and Computational Study. J Phys Chem A 2012; 116:4089-96. [DOI: 10.1021/jp3020035] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Mark Rozenberg
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904,
Israel
| | - Aharon Loewenschuss
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904,
Israel
| | - Claus J. Nielsen
- Centre for Theoretical and Computational Chemistry, Department of
Chemistry, University of Oslo, 1033 Blindern,
N-0315 Oslo, Norway
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Metzelthin A, Sánchez-García E, Birer Ö, Schwaab G, Thiel W, Sander W, Havenith M. Acetylene⋅⋅⋅Furan Trimer Formation at 0.37 K as a Model for Ultracold Aggregation of Non- and Weakly Polar Molecules. Chemphyschem 2011; 12:2009-17. [DOI: 10.1002/cphc.201001040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 03/11/2011] [Indexed: 11/06/2022]
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Rodríguez-Linares D, Codorniu-Hernández E, Velez-Ortíz E, Murillo-López JA, Villegas-Bolaños PA, Quijano-Tobón J. Theoretical study on the thermolysis of methyl-3-hydroxypropanoate in m-xylene solution. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Maçôas EMS, Myllyperkiö P, Kunttu H, Pettersson M. Vibrational Relaxation of Matrix-Isolated Carboxylic Acid Dimers and Monomers. J Phys Chem A 2009; 113:7227-34. [DOI: 10.1021/jp8099384] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ermelinda M. S. Maçôas
- Nanoscience Center, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 Finland
| | - Pasi Myllyperkiö
- Nanoscience Center, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 Finland
| | - Henrik Kunttu
- Nanoscience Center, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 Finland
| | - Mika Pettersson
- Nanoscience Center, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 Finland
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Mardyukov A, Sánchez-García E, Sander W. Matrix Isolation and Ab Initio Study of the Noncovalent Complexes between Formamide and Acetylene. J Phys Chem A 2009; 113:1086-95. [DOI: 10.1021/jp806675n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Artur Mardyukov
- Lehrstuhl für Organische Chemie II der Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Elsa Sánchez-García
- Lehrstuhl für Organische Chemie II der Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Wolfram Sander
- Lehrstuhl für Organische Chemie II der Ruhr-Universität Bochum, D-44780 Bochum, Germany
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Codorniu-Hernández E, Boese AD, Schauerte C, Rolo-Naranjo A, Miranda-Quintana R, Montero-Cabrera LA, Boese R. MMH-2 as a new approach for the prediction of intermolecular interactions: the crystal packing of acetamide. CrystEngComm 2009. [DOI: 10.1039/b905779j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Montero-Cabrera LA, Pérez-Badell Y, Mora-Fonz MJ. An Approach to Hydration of Model Silica Materials by Exploring Their Multiple Minima Hypersurfaces. The Role of Entropy of Association. J Phys Chem A 2008; 112:2880-7. [DOI: 10.1021/jp710583n] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Luis A. Montero-Cabrera
- Laboratorio de Química Computacional y Teórica, Facultad de Química, Universidad de La Habana, 10400 Havana, Cuba, and Centre for Theoretical and Computational Chemistry, Department of Chemistry, University College London, 20 Gordon Street, WH1H 0AJ London, U.K
| | - Y. Pérez-Badell
- Laboratorio de Química Computacional y Teórica, Facultad de Química, Universidad de La Habana, 10400 Havana, Cuba, and Centre for Theoretical and Computational Chemistry, Department of Chemistry, University College London, 20 Gordon Street, WH1H 0AJ London, U.K
| | - M. J. Mora-Fonz
- Laboratorio de Química Computacional y Teórica, Facultad de Química, Universidad de La Habana, 10400 Havana, Cuba, and Centre for Theoretical and Computational Chemistry, Department of Chemistry, University College London, 20 Gordon Street, WH1H 0AJ London, U.K
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Sánchez-García E, Mardyukov A, Tekin A, Crespo-Otero R, Montero LA, Sander W, Jansen G. Ab initio and matrix isolation study of the acetylene–furan dimer. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.09.053] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Mardyukov A, Sanchez-Garcia E, Rodziewicz P, Doltsinis NL, Sander W. Formamide Dimers: A Computational and Matrix Isolation Study. J Phys Chem A 2007; 111:10552-61. [PMID: 17887658 DOI: 10.1021/jp074927y] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dimerization of formamide (FMA) has been investigated by matrix isolation spectroscopy, static ab initio calculations, and ab initio molecular dynamics (AIMD) simulations. Comparison of the experimental matrix IR spectra with the ab initio calculations reveals that two types of dimers A and C are predominantly formed, with two and one strong NH...O hydrogen bonds, respectively. This is in accordance with previously published experiments. In addition, there is also experimental evidence for the formation of the thermally labile dimer B after deposition of high concentrations of FMA in solid xenon. The AIMD simulations of the aggregation process show that in all cases dimer C is initially formed, but rearrangement to the more stable doubly hydrogen-bonded structures A or B occurs for a fraction of collisions on the sub-picosecond time scale.
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Affiliation(s)
- Artur Mardyukov
- Lehrstuhl für Organische Chemie II and Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum
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Sánchez-García E, Mardyukov A, Studentkowski M, Montero LA, Sander W. Furan−Formic Acid Dimers: An ab Initio and Matrix Isolation Study. J Phys Chem A 2006; 110:13775-85. [PMID: 17181334 DOI: 10.1021/jp065064w] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The dimers formed by formic acid (FA) and furan are investigated by ab initio methods and matrix isolation spectroscopy. Nine complexes with binding energies between -3.91 and -0.82 kcal/mol (MP2/6-311++G(d,p) + ZPE + BSSE) are identified. Another five weaker bound complexes are localized at lower level of theory only. The binding in the furan-FA dimers can be described in terms of OH...O, C=O...H, HO...H, CH...O, OH...pi, and CH...pi interactions. Therefore, the furan-FA complexes are classified in two types: (1) the dimers where the OH hydrogen of formic acid interacts with the furan molecule and (2) the dimers where the main interactions of FA with the furan molecule are via the less acidic CH hydrogen. Duning's and Pople's triple and double basis sets were used to study the dependence of the geometries and energies of the complexes from the basis set. BSSE (basis set superposition error) counterpoise corrections (CP) were included during the geometry optimizations of all dimers at the MP2/6-31G(d,p) level of theory. Matrix isolation spectroscopy allowed us to record the IR spectrum of aggregates between FA and furan. By comparison of the experimental IR spectrum with calculated IR spectra of a variety of complexes, it was possible to identify the most stable furan-FA dimer as the major product of the aggregation.
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Affiliation(s)
- Elsa Sánchez-García
- Lehrstuhl für Organische Chemie II, Ruhr-Universität Bochum, D-44780 Bochum, Germany
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Sánchez-García E, Montero LA, Sander W. Computational Study of Noncovalent Complexes between Formamide and Formic Acid. J Phys Chem A 2006; 110:12613-22. [PMID: 17107112 DOI: 10.1021/jp0553636] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The geometries and binding energies of 1:1, 1:2, and 1:4 formic acid-formamide complexes (FA-FMA) are calculated by quantum chemical procedures. Vibrational spectra and intermolecular distances of the most stable FA-FMA dimers as well as the influence of the basis set superposition error (BSSE) on the geometries and energies of the dimers are also discussed. All FA-FMA dimers are optimized at the B3LYP/cc-pVTZ, the MP2/cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ levels of theory to study the influence of the level of theory on the calculated geometries and energies. CCSD(T)/cc-pVTZ single-point calculations at the MP2/aug-cc-pVTZ-optimized geometries were performed as reference for estimating the quality of lower level calculations. These calculations allow us to qualitatively describe the competition between different types of hydrogen-bonding interactions in FA-FMA complexes. FA-FMA dimers are compared to other formamide complexes and to the FA-FMA crystal structure.
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Affiliation(s)
- Elsa Sánchez-García
- Lehrstuhl für Organische Chemie II, Ruhr-Universität Bochum, D-44780 Bochum, Germany, and Laboratorio de Química Computacional y Teórica, Facultad de Química, Universidad de la Habana, 10400, Cuba
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