1
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Chen DP, Ma W, Yang CH, Li M, Zhou ZZ, Zhang Y, Quan ZJ. Interaction between hydroxymethanesulfonic acid and several organic compounds and its atmospheric significance. J Mol Graph Model 2024; 130:108782. [PMID: 38685182 DOI: 10.1016/j.jmgm.2024.108782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/14/2024] [Accepted: 04/23/2024] [Indexed: 05/02/2024]
Abstract
The interactions of the micro-mechanism of hydroxymethanesulfonic acid (HMSA) with the typical small organic molecule in atmospheric (X = methanol, formaldehyde, formic acid, methyl formate, dimethyl ether, acetone) has been investigated by density functional theory (DFT), quantum theory of atoms in molecules (QTAIM), Generalized Kohn-Sham Enery Decomposition Analysis (GKS-EDA) and the atmospheric clusters dynamic code (ACDC). The results of DFT show that the stable six- to eight-membered ring structures are easily formed in HMSA-X clusters. According to the topological analysis results of the AIM theory and the IRI method, a strong hydrogen bonding interaction is present in the complex. GKS-EDA results show that electrostatic energy is the main contributor to the interaction energy as it accounts for 51 %-55 % of the total attraction energy. The evaporation rates of HMSA-HMSA and HMSA-HCOOH clusters were much lower than those of the other HMSA complexes. In addition, the Gibbs energy of formation (ΔG) of HMSA-X dimers is investigated under atmosphere temperature T = 217-298 K and p = 0.19-1.0 atm, the ΔG decreased with decreasing of the atmosphere temperature and increased with the decrease of atmospheric pressure, indicating that the low temperature and high pressure may significantly facilitate to the formation of dimers.
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Affiliation(s)
- Dong-Ping Chen
- College of Chemistry and Chemical Engineering, Northwest Normal University, Gansu International Scientific and Technological Cooperation Base of Water-Retention Chemical Functional Materials, Lanzhou, Gansu, 730070, China.
| | - Wen Ma
- College of Chemistry and Chemical Engineering, Northwest Normal University, Gansu International Scientific and Technological Cooperation Base of Water-Retention Chemical Functional Materials, Lanzhou, Gansu, 730070, China
| | - Chun-Hong Yang
- College of Chemistry and Chemical Engineering, Northwest Normal University, Gansu International Scientific and Technological Cooperation Base of Water-Retention Chemical Functional Materials, Lanzhou, Gansu, 730070, China
| | - Ming Li
- College of Chemistry and Chemical Engineering, Northwest Normal University, Gansu International Scientific and Technological Cooperation Base of Water-Retention Chemical Functional Materials, Lanzhou, Gansu, 730070, China
| | - Zhao-Zhen Zhou
- College of Chemistry and Chemical Engineering, Northwest Normal University, Gansu International Scientific and Technological Cooperation Base of Water-Retention Chemical Functional Materials, Lanzhou, Gansu, 730070, China
| | - Yang Zhang
- College of Chemistry and Chemical Engineering, Northwest Normal University, Gansu International Scientific and Technological Cooperation Base of Water-Retention Chemical Functional Materials, Lanzhou, Gansu, 730070, China
| | - Zheng-Jun Quan
- College of Chemistry and Chemical Engineering, Northwest Normal University, Gansu International Scientific and Technological Cooperation Base of Water-Retention Chemical Functional Materials, Lanzhou, Gansu, 730070, China.
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2
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Abdelmouleh M, Amin M, Lalande M, Schlathölter T, Poully JC. Ionizing radiation induces cross-linking of two noncovalently bound collagen mimetic peptide triple helices in the absence of a molecular environment. Phys Chem Chem Phys 2023; 25:29249-29256. [PMID: 37874154 DOI: 10.1039/d3cp03264g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Cross-linking is a fundamental molecular process that is highly important for many applications, in particular, to tune the properties of collagen-based biomaterials. Chemical reagents, the action of enzymes or physical factors such as heat or radiation can facilitate collagen cross-linking. Ionizing radiation has the advantages of being fast, efficient and free from potentially toxic reagents. Collagen cross-linking by ionizing radiation is thought to occur via a water-mediated pathway. In the past, synthesized collagen mimetic peptides have proven to be of great value for understanding the influence of the amino acid sequence on the stability of tertiary (fibrous) as well as secondary (triple helical) structures of collagen. Cross-linking of synthetic collagen mimetic peptides is often used for modifying the properties of biomaterials. In this work, for the first time, we apply radiation-induced cross-linking to synthetic collagen mimetic peptides and present an experimental and theoretical study of peptide hexamers consisting of two noncovalently bound triple helices in the absence of a molecular environment, i.e. in the gas phase. Our results show that X-ray photoabsorption of the hydroxylated hexamer leads to ionization and cross-linking of the two triple helices: thus, we found evidence that cross-linking can be achieved by ionizing radiation, without the presence of any reagent or water. We propose a cross-linking mechanism involving the creation of two radicals on hydroxyproline side-chains and their recombination, ultimately leading to covalent bond formation between the triple helices.
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Affiliation(s)
- Marwa Abdelmouleh
- CIMAP UMR 6252 CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel 14070 Caen, France.
| | - Muhamed Amin
- University College Groningen, Hoendiep 23/24, 9718BG Groningen, The Netherlands
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mathieu Lalande
- CIMAP UMR 6252 CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel 14070 Caen, France.
| | - Thomas Schlathölter
- University College Groningen, Hoendiep 23/24, 9718BG Groningen, The Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Jean-Christophe Poully
- CIMAP UMR 6252 CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel 14070 Caen, France.
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3
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Kim JP, Go CY, Kang J, Choi Y, Kim JY, Kim J, Kwon O, Kim KC, Kim DW. Nanoporous multilayer graphene oxide membrane for forward osmosis metal ion recovery from spent Li-ion batteries. J Memb Sci 2023. [DOI: 10.1016/j.memsci.2023.121590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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4
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Jindal S, Hsu PJ, Phan HT, Tsou PK, Kuo JL. Capturing the potential energy landscape of large size molecular clusters from atomic interactions up to a 4-body system using deep learning. Phys Chem Chem Phys 2022; 24:27263-27276. [DOI: 10.1039/d2cp04441b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We propose a new method that utilizes the database of stable conformers and borrow the fragmentation concept of many-body-expansion (MBE) methods in ab initio methods to train a deep-learning machine learning (ML) model using SchNet.
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Affiliation(s)
- Shweta Jindal
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1 Roosevelt Road, Section 4, Daan District, Taipei City 10617, Taiwan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1 Roosevelt Road, Section 4, Daan District, Taipei City 10617, Taiwan
| | - Huu Trong Phan
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1 Roosevelt Road, Section 4, Daan District, Taipei City 10617, Taiwan
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Pei-Kang Tsou
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1 Roosevelt Road, Section 4, Daan District, Taipei City 10617, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1 Roosevelt Road, Section 4, Daan District, Taipei City 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
- Molecular Science and Technology, National Taiwan University, Section 4, Daan District, Taipei City 10617, Taiwan
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5
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Ananiadou A, Papamokos G, Steinhart M, Floudas G. Effect of confinement on the dynamics of 1-propanol and other monohydroxy alcohols. J Chem Phys 2021; 155:184504. [PMID: 34773957 DOI: 10.1063/5.0063967] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report the effect of confinement on the dynamics of three monohydroxy alcohols (1-propanol, 2-ethyl-1-hexanol, and 4-methyl-3-heptanol) differing in their chemical structure and, consequently, in the dielectric strength of the "Debye" process. Density functional theory calculations in bulk 1-propanol identified both linear and ring-like associations composed of up to five repeat units. The simulation results revealed that the ring structures, with a low dipole moment (∼2 D), are energetically preferred over the linear assemblies with a dipole moment of 2.18 D per repeat unit. Under confinement in nanoporous alumina (in templates with pore diameters ranging from 400 to 20 nm), all dynamic processes were found to speed up irrespective of the molecular architecture. The characteristic freezing temperatures of the α and the Debye-like processes followed the pore size dependence: Ta,D=Ta,D bulk-A/d1/2, where d is the pore diameter. The characteristic "freezing" temperatures for the Debye-like (the slow process for confined 1-propanol is non-Debye) and the α-processes decrease, respectively, by 6.5 and 13 K in confined 1-propanol, by 9.5 and 19 K in confined 2-ethyl-1-hexanol, and by 9 and 23 K in confined 4-methyl-3-heptanol within the same 25 nm pores. In 2-ethyl-1-hexanol, confinement reduced the number of linearly associated repeats from approximately heptamers in the bulk to dimers within 25 pores. In addition, the slower process in bulk 2-ethyl-1-hexanol and 4-methyl-3-heptanol, where the signal is dominated by ring-like supramolecular assemblies, is clearly non-Debye. The results suggest that the effect of confinement is dominant in the latter assemblies.
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Affiliation(s)
- Antonela Ananiadou
- Department of Physics, University of Ioannina, P.O. Box 1186, 45110 Ioannina, Greece
| | - George Papamokos
- Department of Physics, University of Ioannina, P.O. Box 1186, 45110 Ioannina, Greece
| | - Martin Steinhart
- Institut für Chemie neuer Materialien, Universität Osnabrück, D-49069 Osnabrück, Germany
| | - George Floudas
- Department of Physics, University of Ioannina, P.O. Box 1186, 45110 Ioannina, Greece
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6
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Anharmonicity modeling in hydrogen bonded solvent dimers. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Jukić I, Požar M, Lovrinčević B, Perera A. Universal features in the lifetime distribution of clusters in hydrogen-bonding liquids. Phys Chem Chem Phys 2021; 23:19537-19546. [PMID: 34524299 DOI: 10.1039/d1cp02027g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen-bonding liquids, typically water and alcohols, are known to form labile structures (network, chains, etc.); hence, the lifetime of these structures is an important microscopic parameter, which can be calculated via computer simulations. Since these cluster entities are mostly statistical in nature, one would expect that, in the short-timescale regime, their lifetime distribution would be a broad Gaussian-like function of time, with a single maximum representing their mean lifetime, and be weakly dependent on criteria such as the bonding distance and angle, much similar to non-hydrogen-bonding simple liquids, while the long-timescale regime is known to have some power law dependence. Unexpectedly, all the hydrogen-bonding liquids studied herein, namely water and alcohols, display three highly hierarchical specific lifetimes, in the sub-picosecond range 0-0.5 ps. The dominant lifetime depends very strongly on the bonding-distance criterion and is related to hydrogen-bonded pairs. This mode is absent in non-H-bonding simple liquids. The secondary and tertiary mean lifetimes are related to clusters and are nearly independent of the bonding criterion. Of these two lifetimes, only the first one can be related to that of simple liquids, which poses the question of the nature of the third lifetime. The study of alcohols reveals that this third lifetime is related to the topology of the H-bonded clusters and that its distribution may also be affected by the alkyl tail surrounding the "bath". This study shows that hydrogen-bonding liquids have a universal hierarchy of hydrogen-bonding lifetimes with a timescale regularity across very different types, and which depend on the topology of the cluster structures.
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Affiliation(s)
- Ivo Jukić
- Sorbonne Université, Laboratoire de Physique Théorique de la Matière Condensée (UMR CNRS 7600), 4 Place Jussieu, F75252, Paris cedex 05, France.
- University of Split, Faculty of Science, Ruđera Boškovića 33, 21000, Split, Croatia.
| | - Martina Požar
- University of Split, Faculty of Science, Ruđera Boškovića 33, 21000, Split, Croatia.
| | - Bernarda Lovrinčević
- University of Split, Faculty of Science, Ruđera Boškovića 33, 21000, Split, Croatia.
| | - Aurélien Perera
- Sorbonne Université, Laboratoire de Physique Théorique de la Matière Condensée (UMR CNRS 7600), 4 Place Jussieu, F75252, Paris cedex 05, France.
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8
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Temperature-dependent oxidation of BSCAPE molecule in methanol medium. J Mol Graph Model 2021; 105:107850. [PMID: 33592351 DOI: 10.1016/j.jmgm.2021.107850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 11/23/2022]
Abstract
Temperature-dependent solvation free energy and oxidation by free energy of ionization of 2-Phenylethyl (2E)-3-(1-benzenesulfonyl-4,5-dihydroxyphenyl) acrylate (BSCAPE) in methanol medium are the concerns of the present work. This molecule is a relevant phenolic acid enclosing multiple bioactivities. The explicit, implicit and discrete-continuum models of solvation were used. The methanol molecules were coordinated to this acid to form cluster complexes. The dual method M06-2X/6-31++G(d,p)//B3LYP/6-31G(d) was employed along with basis set superposition error correction. The results show that, the free energy of coordination and solvation are distant. Both quantities increase with temperature. From discrete-continuum treatment, there is non-spontaneity of solvation process, while coordination yielded spontaneity and non-spontaneity at cold and hot room temperatures, respectively. The ionization potential in gas phase, decreases with temperature. All the solvation models yielded lower ionization potential than that of gas phase. Thus, it follows that, the increase of temperature and methanol medium favours the oxidation of BSCAPE. Consequently, this favours its metabolism processes.
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9
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Infrared spectra of PEHA molecule and its resistance to oxidation in water and methanol media at 298.15 K: solvent cluster size dependency. J Mol Model 2020; 26:323. [PMID: 33123831 DOI: 10.1007/s00894-020-04584-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022]
Abstract
The present work investigates the infrared spectra and solvation free energies (SE) of PEHA ((E)-2-(Pyridin-2-yl) ethyl 3-(3,4-dihydroxyphenyl) acrylate) and their impact on the oxidation. The latter was examined through the ionization potential parameter (IP). These investigations were carried out by the DFT method at B3LYP/6-31G(d) for optimization and frequency calculations and corrected for BSSE. X3LYP/6-311++G(2d,2p) was employed for single-point energy calculations. Water and methanol cluster sizes were used for solvation through the explicit solvent model. Thus, the infrared spectra show that the overview frequencies of PEHA compare well with the experimental results. The intense infrared absorptions of complexes are due to the stretching of O-H bonds of solvent clusters in the range 2600-3850 cm-1. The binding energy per solvent molecule of complexes was calculated and shows that water and methanol clusters mimic the liquid state as from 5 to 10 solvent molecules. The SE of PEHA increases with the increase of the cluster size of water and methanol in the direction of the limit. The latter was censured by the solvation done using the combined explicit-implicit solvent model. As for IP parameter, the results are largely above the IP limit and lower than the IP from gas phase. Thus, water and methanol media have an effect of lowering the IP of PEHA compound. Consequently, both media favour the oxidation of PEHA molecule, which facilitates its metabolism in human organism.
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10
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Boda M, Patwari GN. Internal electric fields in methanol [MeOH] 2-6 clusters. Phys Chem Chem Phys 2020; 22:10917-10923. [PMID: 32373804 DOI: 10.1039/c9cp04571f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water and methanol are well known solvents showing cooperative hydrogen bonding, however the differences in the hydrogen bonding pattern in water and methanol are due to the presence of the methyl group in methanol. The presence of the methyl group leads to formation of C-HO hydrogen bonds apart from the usual O-HO hydrogen bonds. The electric fields evaluated along the hydrogen bonded donor OH and CH groups reveal that the C-HO hydrogen bonds can significantly influence the structure and energetics (by about 20%) of methanol clusters. A linear Stark effect was observed on the hydrogen bonded OH groups in methanol clusters with a Stark tuning rate of 3.1 cm-1 (MV cm-1)-1 as an average behaviour. Furthermore, the Stark tuning of the OH oscillators in methanol depends on their hydrogen bonding environment wherein molecules with the DAA motif show higher rates than the rest. The present work suggests that the OH group of methanol has higher sensitivity as a vibrational probe relative to the OH group of water.
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Affiliation(s)
- Manjusha Boda
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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11
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Malloum A, Fifen JJ, Conradie J. Exploration of the potential energy surfaces of small ethanol clusters. Phys Chem Chem Phys 2020; 22:13201-13213. [DOI: 10.1039/d0cp01393e] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The potential energy surfaces of small ethanol clusters, from dimer to pentamer, have been thoroughly explored using two different levels of theory. There is a clear relative energy gap between cyclic, linear and branched cyclic structures.
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Affiliation(s)
- Alhadji Malloum
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
- Department of Physics
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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12
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Kannan PP, Arivazhagan G, Sangeetha T, Karthick NK, Kumbharkhane AC. FTIR studies, DFT calculations and time domain reflectometry studies on tetrahydrofuran - methanol binary solutions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 222:117162. [PMID: 31176160 DOI: 10.1016/j.saa.2019.117162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/21/2019] [Accepted: 05/26/2019] [Indexed: 06/09/2023]
Abstract
FTIR signature of neat tetrahydrofuran (THF), methanol (MeOH) and their binary solutions at various molefractions (0.8:0.2 (THF:MeOH), 0.6:0.4, 0.4:0.6 and 0.2:0.8) have been recorded. Density Functional Theory (DFT) calculations have also been carried out on THF, MeOH multimers and possible THF-MeOH complex molecules. The results of FTIR studies and DFT calculations confirm the formation of 1:3 (THF:MeOH) and 1:4 complex structures with (MeOH)O - H⋯O(THF), (MeOH methyl)C - H⋯O(THF) and (THF methylene)C - H⋯O(MeOH) H-bond interactions. (MeOH)O - H⋯O(MeOH) homointeractions among the MeOH trimers and tetramers are stronger than the THF-MeOH heterointeractions in complexes. But, the stability of 1:4 complexes is more than that of the trimers and tetramers as inferred from the interaction energy values obtained by DFT calculations. Time Domain Reflectometry (TDR) study has also been carried out on the THF-MeOH binary solutions in the frequency range 10 MHz-30 GHz at 298 K. The results of dielectric studies have been correlated with that of FTIR studies and DFT calculations.
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Affiliation(s)
- P P Kannan
- Department of Physics, Thiagarajar College, Madurai 625009, Tamilnadu, India
| | - G Arivazhagan
- Department of Physics, Thiagarajar College, Madurai 625009, Tamilnadu, India.
| | - T Sangeetha
- Department of Physics, Thiagarajar College, Madurai 625009, Tamilnadu, India
| | - N K Karthick
- Department of Physics, Madura College, Madurai 625011, Tamilnadu, India
| | - A C Kumbharkhane
- School of Physical Sciences, S.R.T.M. University, Nanded 431606, MS, India
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13
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Kannan P, Karthick N, Mahendraprabu A, Kumbharkhane A, Joshi Y, Arivazhagan G. FTIR spectroscopy, quantum chemical calculations and time domain reflectometry studies on the behavior of methanol molecules in the environment of dibutyl ether. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.01.062] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Malloum A, Fifen JJ, Conradie J. Exploration of the potential energy surface of the ethanol hexamer. J Chem Phys 2019; 150:124308. [DOI: 10.1063/1.5085843] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Alhadji Malloum
- Department of Physics, Faculty of Science, University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon
| | - Jean Jules Fifen
- Department of Physics, Faculty of Science, University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
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15
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Sugawara N, Hsu PJ, Fujii A, Kuo JL. Competition between hydrogen bonds and van der Waals forces in intermolecular structure formation of protonated branched-chain alcohol clusters. Phys Chem Chem Phys 2018; 20:25482-25494. [PMID: 30276413 DOI: 10.1039/c8cp05222k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To investigate the influence of bulky alkyl groups on hydrogen-bonded (H-bonded) network structures of alcohols, infrared (IR) spectra of protonated clusters of 2-propanol (2-PrOH) and tert-butyl alcohol (t-BuOH) were observed in the OH and CH stretch regions. In addition, by varying the tag species, the temperature dependence profile of the isomer population of H+(t-BuOH)n was revealed. An extensive search for stable isomers was performed using dispersion-corrected density functional theory methods, and temperature-dependent IR spectral simulations were done on the basis of the harmonic superposition approximation. The computational results qualitatively agreed with the observed size and temperature dependence of the H-bonded network structures of these protonated bulky alcohol clusters. However, the difficulty in the quantitative evaluation of dispersion was also demonstrated. It was shown that H+(2-PrOH)n (n = 4-7) have essentially the same network structures as the protonated normal alcohol clusters studied so far. On the other hand, H+(t-BuOH)n (n = 4-8) showed a clear preference for the smaller-membered ring structures, that is very different from the preference of the protonated normal alcohol clusters. The origin of the different structure preferences was discussed in terms of the steric effect and dispersion.
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Affiliation(s)
- Natsuko Sugawara
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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16
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Lee HHL, Heo CE, Seo N, Yun SG, An HJ, Kim HI. Accurate Quantification of N-Glycolylneuraminic Acid in Therapeutic Proteins Using Supramolecular Mass Spectrometry. J Am Chem Soc 2018; 140:16528-16534. [PMID: 30153004 DOI: 10.1021/jacs.8b07864] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Practical applications of innovative host-guest systems are challenging because of unexpected guest competitors and/or subtle environmental differences. Herein, a supramolecular mass spectrometry (MS)-based method using a synthetic host, cucurbit[7]uril (CB[7]), was developed for identifying and quantifying N-glycolylneuraminic acid (Neu5Gc) in therapeutic glycoproteins, which critically reduces drug efficacy. The development of a reliable derivatization-free analytical method for Neu5Gc is highly challenging because of the interference by the abundant N-acetylneuraminic acid (Neu5Ac). CB[7] recognized the subtle structural differences between Neu5Gc and Neu5Ac. Distinct host-guest interactions between CB[7] and the two sialic acids produced a highly linear relationship between the complexation and concentration proportions of the two sialic acids in MS. Furthermore, the developed method had sub-picomolar quantification limits and a wide range of applicability for diverse glycoproteins, demonstrating the potential utility of this method as a reliable assay of Neu5Gc in therapeutic glycoproteins.
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Affiliation(s)
- Hyun Hee L Lee
- Department of Chemistry , Korea University , Seoul 02841 , Republic of Korea
| | - Chae Eun Heo
- Department of Chemistry , Korea University , Seoul 02841 , Republic of Korea
| | - Nari Seo
- Graduate School of Analytical Science & Technology , Chungnam National University , Daejon 34134 , Republic of Korea
| | - Seung Gyu Yun
- Department of Laboratory Medicine , Korea University College of Medicine , Seoul 02841 , Republic of Korea
| | - Hyun Joo An
- Graduate School of Analytical Science & Technology , Chungnam National University , Daejon 34134 , Republic of Korea
| | - Hugh I Kim
- Department of Chemistry , Korea University , Seoul 02841 , Republic of Korea
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17
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Malloum A, Fifen JJ, Conradie J. Solvation energies of the proton in methanol revisited and temperature effects. Phys Chem Chem Phys 2018; 20:29184-29206. [DOI: 10.1039/c8cp05823g] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Various functionals assessing solvation free energies and enthalpies of the proton in methanol.
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Affiliation(s)
- Alhadji Malloum
- Department of Physics, Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jean Jules Fifen
- Department of Physics, Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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18
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Pandey SK, Manogaran D, Manogaran S, Schaefer HF. Quantification of Hydrogen Bond Strength Based on Interaction Coordinates: A New Approach. J Phys Chem A 2017; 121:6090-6103. [DOI: 10.1021/acs.jpca.7b04752] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Dhivya Manogaran
- Department of Chemistry, Indian Institute of Technology, Kanpur 208 016, India
| | - Sadasivam Manogaran
- Department of Chemistry, Indian Institute of Technology, Kanpur 208 016, India
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
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19
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Abu-samha M, Ryding MJ, Uggerud E, Sæthre LJ, Børve KJ. Changing role of carrier gas in formation of ethanol clusters by adiabatic expansion. J Chem Phys 2017; 147:014301. [DOI: 10.1063/1.4989475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Mahmoud Abu-samha
- College of Sciences and Humanities, Fahad Bin Sultan University, P.O. Box 15700, 71454 Tabouk, Kingdom of Saudi Arabia
| | - Mauritz J. Ryding
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, NO-0315 Oslo, Norway
| | - Einar Uggerud
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, NO-0315 Oslo, Norway
| | - Leif J. Sæthre
- Department of Chemistry, University of Bergen, Allégaten 41, NO-5007 Bergen, Norway
| | - Knut J. Børve
- Department of Chemistry, University of Bergen, Allégaten 41, NO-5007 Bergen, Norway
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20
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Zhao H, Tang S, Du L. Hydrogen bond docking site competition in methyl esters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 181:122-130. [PMID: 28351818 DOI: 10.1016/j.saa.2017.03.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 03/07/2017] [Accepted: 03/17/2017] [Indexed: 06/06/2023]
Abstract
The OH⋯O hydrogen bonds in the 2,2,2-trifluoroethanol (TFE)-methyl ester complexes in the gas phase have been investigated by FTIR spectroscopy and DFT calculations. Methyl formate (MF), methyl acetate (MA), and methyl trifluoroacetate (MTFA) were chosen as the hydrogen bond acceptors. A dominant inter-molecular hydrogen bond was formed between the OH group of TFE and different docking sites in the methyl esters (carbonyl oxygen or ester oxygen). The competition of the two docking sites decides the structure and spectral properties of the complexes. On the basis of the observed red shifts of the OH-stretching transition with respect to the TFE monomer, the order of the hydrogen bond strength can be sorted as TFE-MA (119cm-1)>TFE-MF (93cm-1)>TFE-MTFA (44cm-1). Combining the experimental infrared spectra with the DFT calculations, the Gibbs free energies of formation were determined to be 1.5, 4.5 and 8.6kJmol-1 for TFE-MA, TFE-MF and TFE-MTFA, respectively. The hydrogen bonding in the MTFA complex is much weaker than those of the TFE-MA and TFE-MF complexes due to the effect of the CF3 substitution on MTFA, while the replacement of an H atom with a CH3 group in methyl ester only slightly increases the hydrogen bond strength. Topological analysis and localized molecular orbital energy decomposition analysis was also applied to compare the interactions in the complexes.
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Affiliation(s)
- Hailiang Zhao
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China
| | - Shanshan Tang
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China
| | - Lin Du
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China.
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21
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Zhao H, Jiang X, Du L. Contribution of methane sulfonic acid to new particle formation in the atmosphere. CHEMOSPHERE 2017; 174:689-699. [PMID: 28199945 DOI: 10.1016/j.chemosphere.2017.02.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 02/05/2017] [Accepted: 02/06/2017] [Indexed: 06/06/2023]
Abstract
Methane sulfonic acid (MSA) is present in substantial concentrations in the gas phase over oceans and coastal regions. We present an investigation into the contribution of MSA to new particle formation with the common atmospheric aerosol nucleation precursors including MSA, methanol, formic acid, acetone, dimethylether, formaldehyde, methyl formate, by making use a quantum chemical approach. Density functional theory calculations indicate that these bimolecular complexes are characterized by the presence of strong inter-molecular hydrogen bonds (SOH⋯O) with large binding energies and thermodynamic equilibrium constants. Topological analysis employing quantum theory of atoms in molecules shows that the charge density of the SOH⋯O hydrogen bonds of the MSA complexes falls in the range of hydrogen bonding criteria, but the Laplacian at bond critical points exceeds the range, which is due to the strong hydrogen bonding interactions. In all the studied complexes, the electrostatic interactions are found to be the main attractive force by localized molecular orbital energy decomposition analysis. All these indicate the environmental fate of MSA could play the role of nucleation centers in new particle formation. The effect of the atmospheric heights (0-12 km) was also considered. The Gibbs free energy of formation decreases with the increase of the atmospheric height owing to the decrease of the atmospheric temperature and pressure. The calculated Gibbs free energies of formation within the atmospheric temperature and pressure range could help to understand the atmospheric pollution.
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Affiliation(s)
- Hailiang Zhao
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100 Shandong, China
| | - Xiaotong Jiang
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100 Shandong, China
| | - Lin Du
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100 Shandong, China.
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22
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Lee YF, Kelterer AM, Matisz G, Kunsági-Máté S, Chung CY, Lee YP. Infrared absorption of methanol-water clusters (CH 3OH) n(H 2O), n = 1-4, recorded with the VUV-ionization/IR-depletion technique. J Chem Phys 2017; 146:144308. [PMID: 28411595 DOI: 10.1063/1.4979558] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We recorded infrared (IR) spectra in the CH- and OH-stretching regions of size-selected clusters of methanol (M) with one water molecule (W), represented as MnW, n = 1-4, in a pulsed supersonic jet using the photoionization/IR-depletion technique. Vacuum ultraviolet emission at 118 nm served as the source of ionization in a time-of-flight mass spectrometer to detect clusters MnW as protonated forms Mn-1WH+. The variations in intensities of Mn-1WH+ were monitored as the wavelength of the IR laser light was tuned across the range 2700-3800 cm-1. IR spectra of size-selected clusters were obtained on processing of the observed action spectra of the related cluster-ions according to a mechanism that takes into account the production and loss of each cluster due to IR photodissociation. Spectra of methanol-water clusters in the OH region show significant variations as the number of methanol molecules increases, whereas those in the CH region are similar for all clusters. Scaled harmonic vibrational wavenumbers and relative IR intensities predicted with the M06-2X/aug-cc-pVTZ method for the methanol-water clusters are consistent with our experimental results. For dimers, absorption bands of a structure WM with H2O as a hydrogen-bond donor were observed at 3570, 3682, and 3722 cm-1, whereas weak bands of MW with methanol as a hydrogen-bond donor were observed at 3611 and 3753 cm-1. For M2W, the free OH band of H2O was observed at 3721 cm-1, whereas a broad feature was deconvoluted to three bands near 3425, 3472, and 3536 cm-1, corresponding to the three hydrogen-bonded OH-stretching modes in a cyclic structure. For M3W, the free OH shifted to 3715 cm-1, and the hydrogen-bonded OH-stretching bands became much broader, with a weak feature near 3179 cm-1 corresponding to the symmetric OH-stretching mode of a cyclic structure. For M4W, the observed spectrum agrees unsatisfactorily with predictions for the most stable cyclic structure, indicating significant contributions from branched isomers, which is distinctly different from M5 of which the cyclic form dominates.
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Affiliation(s)
- Yu-Fang Lee
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Anne-Marie Kelterer
- Institute of Physical and Theoretical Chemistry, NAWI Graz, Graz University of Technology, Stremayrgasse 9/I, A-8010 Graz, Austria
| | - Gergely Matisz
- Department of General and Physical Chemistry, University of Pécs, Ifjúság 6, H-7624 Pécs, Hungary
| | - Sándor Kunsági-Máté
- Department of General and Physical Chemistry, University of Pécs, Ifjúság 6, H-7624 Pécs, Hungary
| | - Chao-Yu Chung
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Yuan-Pern Lee
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan
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23
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Sulaiman MI, Yang S, Ellis AM. Infrared Spectroscopy of Methanol and Methanol/Water Clusters in Helium Nanodroplets: The OH Stretching Region. J Phys Chem A 2017; 121:771-776. [DOI: 10.1021/acs.jpca.6b11170] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Media I. Sulaiman
- Department of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH, U.K
| | - Shengfu Yang
- Department of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH, U.K
| | - Andrew M. Ellis
- Department of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH, U.K
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24
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The DFT study of hydrogen bonding and thermodynamic parameters of (CH3OH)n(H2O)m (n, m=1–8) clusters at different temperatures. ARAB J CHEM 2016. [DOI: 10.1016/j.arabjc.2011.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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25
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Zhao H, Tang S, Li S, Ding L, Du L. Theoretical investigation of the hydrogen bond interactions of methanol and dimethylamine with hydrazone and its derivatives. Struct Chem 2016. [DOI: 10.1007/s11224-016-0749-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Zhao H, Zhang Q, Du L. Hydrogen bonding in cyclic complexes of carboxylic acid–sulfuric acid and their atmospheric implications. RSC Adv 2016. [DOI: 10.1039/c6ra16782a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Carboxylic acids form cyclic ring structures with sulfuric acid and they could potentially be important in new particle formation.
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Affiliation(s)
- Hailiang Zhao
- Environment Research Institute
- Shandong University
- China
| | - Qun Zhang
- Environment Research Institute
- Shandong University
- China
| | - Lin Du
- Environment Research Institute
- Shandong University
- China
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27
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28
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Braud I, Boulon J, Zamith S, L’Hermite JM. Attachment of Water and Alcohol Molecules onto Water and Alcohol Clusters. J Phys Chem A 2015; 119:6017-23. [DOI: 10.1021/jp511854r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Isabelle Braud
- Laboratoire Collisions Agrégats
Réactivité, IRSAMC, Université de Toulouse, UPS, F-31062 Toulouse, France
- CNRS, UMR 5589, F-31062 Toulouse, France
| | - Julien Boulon
- Laboratoire Collisions Agrégats
Réactivité, IRSAMC, Université de Toulouse, UPS, F-31062 Toulouse, France
- CNRS, UMR 5589, F-31062 Toulouse, France
| | - Sébastien Zamith
- Laboratoire Collisions Agrégats
Réactivité, IRSAMC, Université de Toulouse, UPS, F-31062 Toulouse, France
- CNRS, UMR 5589, F-31062 Toulouse, France
| | - Jean-Marc L’Hermite
- Laboratoire Collisions Agrégats
Réactivité, IRSAMC, Université de Toulouse, UPS, F-31062 Toulouse, France
- CNRS, UMR 5589, F-31062 Toulouse, France
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29
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Matisz G, Kelterer AM, Fabian WMF, Kunsági-Máté S. Structural properties of methanol–water binary mixtures within the quantum cluster equilibrium model. Phys Chem Chem Phys 2015; 17:8467-79. [DOI: 10.1039/c4cp05836d] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Quantum Cluster Equilibrium (QCE) method computes cluster distributions and thermodynamic properties of binary methanol–water mixtures in agreement with experiments.
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Affiliation(s)
- G. Matisz
- Department of General and Physical Chemistry
- University of Pécs
- 7624 Pécs
- Hungary
- János Szentágothai Research Center
| | - A.-M. Kelterer
- Institute of Physical and Theoretical Chemistry
- Graz University of Technology
- NAWI Graz
- 8010 Graz
- Austria
| | - W. M. F. Fabian
- Institute of Chemistry
- University of Graz
- NAWI Graz
- 8010 Graz
- Austria
| | - S. Kunsági-Máté
- Department of General and Physical Chemistry
- University of Pécs
- 7624 Pécs
- Hungary
- János Szentágothai Research Center
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30
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Gadre SR, Yeole SD, Sahu N. Quantum chemical investigations on molecular clusters. Chem Rev 2014; 114:12132-73. [PMID: 25341561 DOI: 10.1021/cr4006632] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Shridhar R Gadre
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208 016, India
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31
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Heger M, Suhm MA, Mata RA. Communication: Towards the binding energy and vibrational red shift of the simplest organic hydrogen bond: Harmonic constraints for methanol dimer. J Chem Phys 2014; 141:101105. [DOI: 10.1063/1.4895728] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Matthias Heger
- Georg-August-Universität Göttingen, Institut für Physikalische Chemie, Tammannstr. 6, 37077 Göttingen, Germany
| | - Martin A. Suhm
- Georg-August-Universität Göttingen, Institut für Physikalische Chemie, Tammannstr. 6, 37077 Göttingen, Germany
| | - Ricardo A. Mata
- Georg-August-Universität Göttingen, Institut für Physikalische Chemie, Tammannstr. 6, 37077 Göttingen, Germany
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32
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Nishimura Y, Lee YP, Irle S, Witek HA. Critical interpretation of CH– and OH– stretching regions for infrared spectra of methanol clusters (CH3OH)n (n = 2–5) using self-consistent-charge density functional tight-binding molecular dynamics simulations. J Chem Phys 2014; 141:094303. [DOI: 10.1063/1.4893952] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yoshifumi Nishimura
- Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan
| | - Yuan-Pern Lee
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Stephan Irle
- Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Henryk A. Witek
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan
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33
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Idrissi A, Polok K, Marekha B, De waele I, Bria M, Gadomski W. Inhomogeneous Distribution in Methanol/Acetone Mixture: Vibrational and NMR Spectroscopy Analysis. J Phys Chem B 2014; 118:1416-25. [DOI: 10.1021/jp412023g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Abdenacer Idrissi
- University Nord de France, Lille1,
LASIR (UMR CNRS A8516), 59655 Villeneuve d’Ascq Cedex, France
| | - Kamil Polok
- Laboratory of Physico-chemistry of Dielectrics and Magnetics, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Bogdan Marekha
- University Nord de France, Lille1,
LASIR (UMR CNRS A8516), 59655 Villeneuve d’Ascq Cedex, France
- Department
of Inorganic Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody sq., 61022, Kharkiv, Ukraine
| | - Isabelle De waele
- University Nord de France, Lille1,
LASIR (UMR CNRS A8516), 59655 Villeneuve d’Ascq Cedex, France
| | - Marc Bria
- University Nord de France, Lille1,
CCM RMN, Bât. C4, Villeneuve d’Ascq 59650, France
| | - Wojciek Gadomski
- Laboratory of Physico-chemistry of Dielectrics and Magnetics, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
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34
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Chang HC, Jiang JC, Chang HC, Wang LR, Lee YT. Hydrogen-Bond Rearrangement and Intermolecular Proton Transfer in Protonated Methanol Clusters. Isr J Chem 2013. [DOI: 10.1002/ijch.199900030] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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35
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Hu Y, Guan J, Bernstein ER. Mass-selected IR-VUV (118 nm) spectroscopic studies of radicals, aliphatic molecules, and their clusters. MASS SPECTROMETRY REVIEWS 2013; 32:484-501. [PMID: 24122973 DOI: 10.1002/mas.21387] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 04/25/2013] [Accepted: 04/25/2013] [Indexed: 06/02/2023]
Abstract
Mass-selected IR plus UV/VUV spectroscopy and mass spectrometry have been coupled into a powerful technique to investigate chemical, physical, structural, and electronic properties of radicals, molecules, and clusters. Advantages of the use of vacuum ultraviolet (VUV) radiation to create ions for mass spectrometry are its application to nearly all compounds with ionization potentials below the energy of a single VUV photon, its circumventing the requirement of UV chromophore group, its inability to ionize background gases, and its greatly reduced fragmenting capabilities. In this review, mass-selected IR plus VUV (118 nm) spectroscopy is introduced first in a general manner. Selected application examples of this spectroscopy are presented, which include the detections and structural analysis of radicals, molecules, and molecular clusters in a supersonic jet.
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Affiliation(s)
- Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
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36
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Lankau T, Yu CH. A Multi-Center Energy Analysis of the Tunable Proton Affinity of Hydrogen Bonded Cluster Ions. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200900012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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37
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Kazachenko S, Bulusu S, Thakkar AJ. Methanol clusters (CH3OH)n: Putative global minimum-energy structures from model potentials and dispersion-corrected density functional theory. J Chem Phys 2013; 138:224303. [DOI: 10.1063/1.4809528] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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38
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Fifen JJ, Nsangou M, Dhaouadi Z, Motapon O, Jaidane NE. Solvation Energies of the Proton in Methanol. J Chem Theory Comput 2013; 9:1173-81. [PMID: 26588760 DOI: 10.1021/ct300669v] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
pKa's, proton affinities, and proton dissociation free energies characterize numerous properties of drugs and the antioxidant activity of some chemical compounds. Even with a higher computational level of theory, the uncertainty in the proton solvation free energy limits the accuracy of these parameters. We investigated the thermochemistry of the solvation of the proton in methanol within the cluster-continuum model. The scheme used involves up to nine explicit methanol molecules, using the IEF-PCM and the strategy based on thermodynamic cycles. All computations were performed at B3LYP/6-31++G(dp) and M062X/6-31++G(dp) levels of theory. It comes out from our calculations that the functional M062X is better than B3LYP, on the evaluation of gas phase clustering energies of protonated methanol clusters, per methanol stabilization of neutral methanol clusters and solvation energies of the proton in methanol. The solvation free energy and enthalpy of the proton in methanol were obtained after converging the partial solvation free energy of the proton in methanol and the clustering free energy of protonated methanol clusters, as the cluster size increases. Finally, the recommended values for the solvation free energy and enthalpy of the proton in methanol are -257 and -252 kcal/mol, respectively.
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Affiliation(s)
- Jean Jules Fifen
- University of Ngaoundere, Faculty of Science, P.O. Box 454, Ngaoundere, Cameroon.,Fundamental Physics Lab, Graduate Training Unit in Physics and Engineering Sciences, Faculty of Science, University of Douala, P.O. Box 24157, Douala, Cameroon
| | - Mama Nsangou
- University of Ngaoundere, Faculty of Science, P.O. Box 454, Ngaoundere, Cameroon.,University of Maroua, P.O. Box 46, Maroua, Cameroon
| | - Zoubeida Dhaouadi
- Laboratoire de Spectroscopie Atomique et Moléculaire, Faculté des Sciences de Tunis, Université de Tunis El Manar, Campus Universitaire 1060, Tunis, Tunisia
| | - Ousmanou Motapon
- Fundamental Physics Lab, Graduate Training Unit in Physics and Engineering Sciences, Faculty of Science, University of Douala, P.O. Box 24157, Douala, Cameroon
| | - Nejm-Eddine Jaidane
- Laboratoire de Spectroscopie Atomique et Moléculaire, Faculté des Sciences de Tunis, Université de Tunis El Manar, Campus Universitaire 1060, Tunis, Tunisia
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39
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Kobayashi T, Shishido R, Mizuse K, Fujii A, Kuo JL. Structures of hydrogen bond networks formed by a few tens of methanol molecules in the gas phase: size-selective infrared spectroscopy of neutral and protonated methanol clusters. Phys Chem Chem Phys 2013; 15:9523-30. [DOI: 10.1039/c3cp50985k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Fu L, Han HL, Lee YP. Infrared absorption of methanethiol clusters (CH3SH)n, n = 2–5, recorded with a time-of-flight mass spectrometer using IR depletion and VUV ionization. J Chem Phys 2012; 137:234307. [DOI: 10.1063/1.4770227] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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41
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Do H, Besley NA. Structural optimization of molecular clusters with density functional theory combined with basin hopping. J Chem Phys 2012; 137:134106. [DOI: 10.1063/1.4755994] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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42
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Orestes E, Chaudhuri P, Canuto S. Effect of hydrogen bond formation on the elastic molecular scattering: a case study with methanol. Mol Phys 2012. [DOI: 10.1080/00268976.2011.646012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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43
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Chaiwongwattana S, Phonyiem M, Vchirawongkwin V, Prueksaaroon S, Sagarik K. Dynamics and mechanism of structural diffusion in linear hydrogen bond. J Comput Chem 2012; 33:175-88. [PMID: 22009491 DOI: 10.1002/jcc.21957] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Revised: 08/31/2011] [Accepted: 09/09/2011] [Indexed: 11/11/2022]
Abstract
Dynamics and mechanism of proton transfer in a protonated hydrogen bond (H-bond) chain were studied, using the CH(3)OH(2)(+)(CH(3)OH)(n) complexes, n = 1-4, as model systems. The present investigations used B3LYP/TZVP calculations and Born-Oppenheimer MD (BOMD) simulations at 350 K to obtain characteristic H-bond structures, energetic and IR spectra of the transferring protons in the gas phase and continuum liquid. The static and dynamic results were compared with the H(3)O(+)(H(2)O)(n) and CH(3)OH(2)(+)(H(2)O)(n) complexes, n = 1-4. It was found that the H-bond chains with n = 1 and 3 represent the most active intermediate states and the CH(3)OH(2)(+)(CH(3)OH)(n) complexes possess the lowest threshold frequency of proton transfer. The IR spectra obtained from BOMD simulations revealed that the thermal energy fluctuation and dynamics help promote proton transfer in the shared-proton structure with n = 3 by lowering the vibrational energy for the interconversion between the oscillatory shuttling and structural diffusion motions, leading to a higher population of the structural diffusion motion than in the shared-proton structure with n = 1. Additional explanation on the previously proposed mechanisms was introduced, with the emphases on the energetic of the transferring proton, the fluctuation of the number of the CH(3)OH molecules in the H-bond chain, and the quasi-dynamic equilibriums between the shared-proton structure (n = 3) and the close-contact structures (n ≥ 4). The latter prohibits proton transfer reaction in the H-bond chain from being concerted, since the rate of the structural diffusion depends upon the lifetime of the shared-proton intermediate state.
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Affiliation(s)
- Sermsiri Chaiwongwattana
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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Paul BK, Guchhait N. A computational investigation on the intramolecular hydrogen bonding interaction and excited state intramolecular proton transfer process in 2-quinolin-2-yl-phenol. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.09.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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LANKAU TIMM, WU YUCHUNG, ZOU JIANWEI, YU CHINHUI. THE COOPERATIVITY BETWEEN HYDROGEN AND HALOGEN BONDS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633608003563] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The cooperativity between hydrogen bonds and halogen bonds in X–HCN–Y ( X: C2H2, H2O, NH3, HCI, HCN, HF; Y: HF, BrF, Br2 is analyzed with MP2/6-311++G(d, p) and DFT/6-311++G(d, p) calculations using the B3LYP and mPW1PW91 hybrid functionals. The results from the quantum chemical calculations are typically clustered in groups according to the Y-ligand. By choosing the X–HCN–HF group as reference it is possible to describe the interaction between the hydrogen and the halogen bond with a two-parameter model. The value of the first parameter of the model describes the contribution of the X -ligand to the interbond cooperativity in the reference cluster. The second parameter of our model quantifies the changes in interbond cooperativity upon varying the Y -ligand. This simple model can be used to predict the cooperativity in X–HCN–Y trimers with reasonable accuracy and thereby to organize the results systematically. It is further shown that the conclusions drawn from this ordering scheme are independent from the computational method and thereby generally applicable.
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Affiliation(s)
- TIMM LANKAU
- Department of Chemistry, National Tsing Hua University, 101 Kuang Fu Road Sec. 2, Hsin Chu 30013, Taiwan
| | - YU-CHUNG WU
- Department of Chemistry, National Tsing Hua University, 101 Kuang Fu Road Sec. 2, Hsin Chu 30013, Taiwan
| | - JIAN-WEI ZOU
- Department of Chemistry, National Tsing Hua University, 101 Kuang Fu Road Sec. 2, Hsin Chu 30013, Taiwan
| | - CHIN-HUI YU
- Department of Chemistry, National Tsing Hua University, 101 Kuang Fu Road Sec. 2, Hsin Chu 30013, Taiwan
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Schildmann S, Reiser A, Gainaru R, Gainaru C, Böhmer R. Nuclear magnetic resonance and dielectric noise study of spectral densities and correlation functions in the glass forming monoalcohol 2-ethyl-1-hexanol. J Chem Phys 2011; 135:174511. [DOI: 10.1063/1.3647954] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Matisz G, Kelterer AM, Fabian WMF, Kunsági-Máté S. Coordination of Methanol Clusters to Benzene: A Computational Study. J Phys Chem A 2011; 115:10556-64. [DOI: 10.1021/jp206248w] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Gergely Matisz
- Department of General and Physical Chemistry, University of Pécs, Pécs, H-7624, Hungary
- Institute of Chemistry, Karl-Franzens University Graz, Heinrichstr. 28, Graz, A-8010, Austria
| | - Anne-Marie Kelterer
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9/I, A-8010 Graz, Austria
| | - Walter M. F. Fabian
- Institute of Chemistry, Karl-Franzens University Graz, Heinrichstr. 28, Graz, A-8010, Austria
| | - Sándor Kunsági-Máté
- Department of General and Physical Chemistry, University of Pécs, Pécs, H-7624, Hungary
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Rai D, Kulkarni AD, Gejji SP, Pathak RK. Methanol clusters (CH3OH)n, n = 3–6 in external electric fields: Density functional theory approach. J Chem Phys 2011; 135:024307. [DOI: 10.1063/1.3605630] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Han HL, Camacho C, Witek HA, Lee YP. Infrared absorption of methanol clusters (CH3OH)n with n = 2−6 recorded with a time-of-flight mass spectrometer using infrared depletion and vacuum-ultraviolet ionization. J Chem Phys 2011; 134:144309. [DOI: 10.1063/1.3572225] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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