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Belleflamme F, Hutter J. Radicals in aqueous solution: assessment of density-corrected SCAN functional. Phys Chem Chem Phys 2023; 25:20817-20836. [PMID: 37497572 DOI: 10.1039/d3cp02517a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
We study self-interaction effects in solvated and strongly-correlated cationic molecular clusters, with a focus on the solvated hydroxyl radical. To address the self-interaction issue, we apply the DC-r2SCAN method, with the auxiliary density matrix approach. Validating our method through simulations of bulk liquid water, we demonstrate that DC-r2SCAN maintains the structural accuracy of r2SCAN while effectively addressing spin density localization issues. Extending our analysis to solvated cationic molecular clusters, we find that the hemibonded motif in the [CH3S∴CH3SH]+ cluster is disrupted in the DC-r2SCAN simulation, in contrast to r2SCAN that preserves the (three-electron-two-center)-bonded motif. Similarly, for the [SH∴SH2]+ cluster, r2SCAN restores the hemibonded motif through spin leakage, while DC-r2SCAN predicts a weaker hemibond formation influenced by solvent-solute interactions. Our findings demonstrate the potential of DC-r2SCAN combined with the auxiliary density matrix method to improve electronic structure calculations, providing insights into the properties of solvated cationic molecular clusters. This work contributes to the advancement of self-interaction corrected electronic structure theory and offers a computational framework for modeling condensed phase systems with intricate correlation effects.
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Affiliation(s)
| | - Jürg Hutter
- Department of Chemistry, University of Zurich, Zurich, Switzerland.
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2
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Maşlakcı Z. Hydrogen bonding guest-water interactions in pinacolone, tert-butyl amine, and tert-butylmethyl ether: a theoretical study on energetics, structure, and topological + . J Mol Model 2023; 29:110. [PMID: 36964310 DOI: 10.1007/s00894-023-05519-2] [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: 01/27/2023] [Accepted: 03/16/2023] [Indexed: 03/26/2023]
Abstract
CONTEXT In guest-host interactions, guest molecules used for hydrogen bonding potential of clathrate hydrate cages are involved as "promoters" for hydrogen or methane storage. Among the promoter molecules, there are pinacolone and tert-butylmethyl ether containing oxygen atom, and tert-butyl amine among those containing nitrogen atom. The dimer and trimer interactions of these molecules with the water clusters were investigated. The cooperativity effect, which is a measure of the hydrogen bonding of these oxygen and nitrogen-containing complexes, was calculated and these complexes were analyzed. Moreover, molecular electrostatic potential (MEP) analysis was performed to determine intermolecular interactions. Clusters of several molecules may seem like a non-significant state of matter; however, in systematic studies with small clusters, important results can be obtained. Therefore, it is very useful to work with clusters to understand the properties of the dense phase, and this study aimed to examine the properties of structures, energies, infrared vibration frequencies, and topological parameters, which develop as a result of the interaction of structures in different clusters with water molecules. METHODS The MP2 level was performed using aug-cc-pVDZ basis set calculations for this study. Tight converting criteria were used in the optimization step. Harmonic vibrational modes were calculated at the MP2/aug-cc-pVDZ level. Each minima obtained from the MP2 level was subjected to single-point energy calculations using CCSD(T) levels with the aug-cc-pVDZ basis set by the Gaussian16 package program suite. The topological analyses were performed with non-covalent interaction (NCI). MEP surface of the complex was also composed by Gaussian program using the optimized geometry at a MP2/aug-cc-pvdz level.
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Affiliation(s)
- Zafer Maşlakcı
- Laboratory Technology Program, Department of Chemistry and Chemical Processing Technologies, Susurluk Vocational School, Bandırma Onyedi Eylul University, 10600, Balıkesir, Turkey.
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Computational examination on monomeric, dimeric, trimeric structural and vibrational interactions, AIM, Hirshfeld, IGM and oxygenated solvent effect on optical properties for pyridine N-oxide. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Bhattacharyya S, Ghosh S, Wategaonkar S. O-H stretching frequency red shifts do not correlate with the dissociation energies in the dimethylether and dimethylsulfide complexes of phenol derivatives. Phys Chem Chem Phys 2021; 23:5718-5739. [PMID: 33662068 DOI: 10.1039/d0cp01589j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this perspective, we present a comprehensive report on the spectroscopic and computational investigations of the hydrogen bonded (H-bonded) complexes of Me2O and Me2S with seven para-substituted H-bond donor phenols. The salient finding was that although the dissociation energies, D0, of the Me2O complexes were consistently higher than those of the analogous Me2S complexes, the red-shifts in phenolic O-H frequencies, Δν(O-H), showed the exactly opposite trend. This is in contravention of the general perception that the red shift in the X-H stretching frequency in the X-HY hydrogen bonded complexes is a reliable indicator of H-bond strength (D0), a concept popularly known as the Badger-Bauer rule. This is also in contrast to the trend reported for the H-bonded complexes of H2S/H2O with several para substituted phenols of different pKa values wherein the oxygen centered hydrogen bonded (OCHB) complexes consistently showed higher Δν(O-H) and D0 compared to those of the analogous sulfur centered hydrogen bonded (SCHB) complexes. Our effort was to understand these intriguing observations based on the spectroscopic investigations of 1 : 1 complexes in combination with a variety of high level quantum chemical calculations. Ab initio calculations at the MP2 level and the DFT calculations using various dispersion corrected density functionals (including DFT-D3) were performed on counterpoise corrected surfaces to compute the dissociation energy, D0, of the H-bonded complexes. The importance of anharmonic frequency computations is underscored as they were able to correctly reproduce the observed trend in the relative OH frequency shifts unlike the harmonic frequency computations. We have attempted to find a unified correlation that would globally fit the observed red shifts in the O-H frequency with the H-bonding strength for the four bases, namely, H2S, H2O, Me2O, and Me2S, in this set of H-bond donors. It was found that the proton affinity normalized Δν(O-H) values scale very well with the H-bond strength.
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Affiliation(s)
- Surjendu Bhattacharyya
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
| | - Sanat Ghosh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
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Abstract
The heavier chalcogen atoms S, Se, and Te can each participate in a range of different noncovalent interactions. They can serve as both proton donor and acceptor in H-bonds. Each atom can also act as electron acceptor in a chalcogen bond.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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6
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Tripathi MK, Ramanathan V. Conformational stability and structural analysis of methanethiol clusters: a revisit. RSC Adv 2021; 11:29207-29214. [PMID: 35479559 PMCID: PMC9040644 DOI: 10.1039/d1ra04900c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/18/2021] [Indexed: 01/12/2023] Open
Abstract
B3LYP/cc-pV(D/T/Q)Z and CCSD/cc-pVDZ levels of theory predict three minima for both dimers and trimers of methanethiol. Predictions at B3LYP/cc-pVDZ corroborates exceedingly well with the earlier reported experimental value but significantly differ from the previous computational predictions. Interaction energy between the molecules decreases with an increase in the size of the basis set for both the dimer and trimer. The dipole moment of methanethiol dimer gets reduced at the B3LYP/cc-pVDZ level of theory relative to all minima configurations, and the same is seen for trimer also. These new predictions are well supported by atoms in molecules (AIM), frontier molecular orbital (FMO), Mulliken charge (MC), and natural bond orbital (NBO) analysis. B3LYP/cc-pV(D/T/Q)Z and CCSD/cc-pVDZ levels of theory predict three minima for both dimers and trimers of methanethiol.![]()
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Affiliation(s)
- Manish Kumar Tripathi
- Department of Chemistry, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, India
| | - Venkatnarayan Ramanathan
- Department of Chemistry, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, India
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Biswal HS, Bhattacharyya S, Bhattacherjee A, Wategaonkar S. Nature and strength of sulfur-centred hydrogen bonds: laser spectroscopic investigations in the gas phase and quantum-chemical calculations. INT REV PHYS CHEM 2015. [DOI: 10.1080/0144235x.2015.1022946] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Hydrogen Bonds Involving Sulfur: New Insights from ab Initio Calculations and Gas Phase Laser Spectroscopy. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-14163-3_2] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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9
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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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Mó O, Yáñez M, Alkorta I, Elguero J. Modulating the Strength of Hydrogen Bonds through Beryllium Bonds. J Chem Theory Comput 2012; 8:2293-300. [PMID: 26588962 DOI: 10.1021/ct300243b] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mutual influence between beryllium bonds and inter- or intramolecular hydrogen bonds (HBs) has been investigated at the B3LYP/6-311++G(3df,2p) level of theory, using the complexes between imidazole dimer and malonaldehyde with BeH2 and BeF2 as suitable model systems. Imidazole and its dimer form very strong beryllium bonds with both BeH2 and BeF2, accompanied by a significant geometry distortion of the Lewis acid. More importantly, we have found a clear cooperativity between these two noncovalent interactions, since the intermolecular HB between the two imidazole molecules in the dimer-BeX2 complex becomes much stronger than in the isolated dimer, whereas the beryllium bond becomes also stronger in the dimer-BeX2 complex, with respect to that found in the imidazole-BeX2 complex. The effects of beryllium bonds are also dramatic on the strength of intramolecular HBs. Depending on to which center the BeX2 is attached, the intramolecular HB becomes much stronger or much weaker. The first situation is found when the beryllium derivative is attached to the HB donor, whereas the second occurs if it is attached to the HB acceptor. The first effect can be so strong as to produce a spontaneous proton transfer, as it is actually the case of the malonaldehyde-BeF2 complex.
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Affiliation(s)
- Otilia Mó
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Manuel Yáñez
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC) , Juan de la Cierva, 3, 28006-Madrid, Spain
| | - José Elguero
- Instituto de Química Médica (CSIC) , Juan de la Cierva, 3, 28006-Madrid, Spain
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12
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Angelova SE, Spassova MI, Deneva VV, Rogojerov MI, Antonov LM. Aggregation of 2-Aminobenzimidazole-A Combined Experimental and Theoretical Investigation. Chemphyschem 2011; 12:1747-55. [DOI: 10.1002/cphc.201100002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2011] [Revised: 03/27/2011] [Indexed: 11/09/2022]
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Canchaya JGS, Wang Y, Alcamí M, Martín F, Busnengo HF. Study of the interaction between short alkanethiols from ab initio calculations. Phys Chem Chem Phys 2010; 12:7555-65. [DOI: 10.1039/b923428d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Biswal HS, Chakraborty S, Wategaonkar S. Experimental evidence of O–H—S hydrogen bonding in supersonic jet. J Chem Phys 2008; 129:184311. [DOI: 10.1063/1.3012569] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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15
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Balci M, Boylu O, Uras-Aytemiz N. Nonadditive effects in the mixed trimers of HCl and methanethiol. J Chem Phys 2007; 126:244308. [PMID: 17614550 DOI: 10.1063/1.2747246] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Ab initio and density functional theory calculations with aug-cc-pVDZ and aug-cc-pVTZ basis sets have been performed on the HCl-CH3SH dimer and HCl-(CH3SH)2 and (HCl)2-CH3SH trimers. Structures, energetics, and infrared frequencies are calculated. The results are discussed in terms of the cooperativity effect which is a characteristic of H-bonded systems and compared to oxygen-containing analogs of the same trimers, HCl-(CH3OH)2 and (HCl)2-CH3OH, which have been published recently.
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Affiliation(s)
- Mine Balci
- Department of Chemistry, Süleyman Demirel University, 32260 Isparta, Turkey
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Morgado CA, McNamara JP, Hillier IH, Burton NA, Vincent MA. Density Functional and Semiempirical Molecular Orbital Methods Including Dispersion Corrections for the Accurate Description of Noncovalent Interactions Involving Sulfur-Containing Molecules. J Chem Theory Comput 2007; 3:1656-64. [DOI: 10.1021/ct700072a] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Claudio A. Morgado
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Jonathan P. McNamara
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Ian H. Hillier
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Neil A. Burton
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Mark A. Vincent
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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Garrison SL, Sandler SI. A potential from quantum chemistry for thermodynamic property predictions for methanethiol. J Chem Phys 2005; 123:054506. [PMID: 16108668 DOI: 10.1063/1.1991855] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An ab initio potential for methanethiol is determined by computing quantum-chemical interaction energies for a range of orientations and center-of-mass separation distances. These energies are initially fitted to a pairwise-additive, site-site Morse-C6 intermolecular potential. Additional interaction energies were then calculated at separation distances determined to be important from the angle-averaged Mayer f function calculated with the initial potential. This expanded set of interaction energies is then fitted using Boltzmann-type weighting to obtain the final intermolecular potential. Although there are some discrepancies in the fit for a particular type of orientation, the phase behavior calculated from Gibbs ensemble Monte Carlo simulations using this final potential is in very good agreement with experimental data. The prescription used here for obtaining the optimum potential from quantum-chemical methods should be applicable to other systems.
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Affiliation(s)
- Stephen L Garrison
- Department of Chemical Engineering, Center for Molecular and Engineering Thermodynamics, University of Delaware, Newark, Delaware 19716, USA
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Cabaleiro-Lago EM, Hermida-Ramón JM, Rodríguez-Otero J. Computational Study of the Interaction in (CH3)2X Dimer and Trimer (X = O, S). J Phys Chem A 2004. [DOI: 10.1021/jp0377679] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Enrique M. Cabaleiro-Lago
- Departamento de Química Física, Facultade de Ciencias, Universidade de Santiago de Compostela, Campus de Lugo, Avda Alfonso X El Sabio s/n, 27002 Lugo, Galicia, Spain
| | - Jose M. Hermida-Ramón
- Departamento de Química Física, Facultade de Ciencias, Universidade de Vigo, Campus Lagoas Marcosende, 36200 Vigo, Galicia, Spain
| | - Jesús Rodríguez-Otero
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Avda das Ciencias s/n, 15706 Santiago, Galicia, Spain
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