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Zeinalipour-Yazdi CD. A computational study of H-bonded networks in cyclic water clusters, (H 2O) n (n = 3-12). J Mol Model 2024; 30:58. [PMID: 38308065 DOI: 10.1007/s00894-024-05856-w] [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: 12/18/2023] [Accepted: 01/26/2024] [Indexed: 02/04/2024]
Abstract
CONTEXT We have performed a detailed MM and DFT investigation of neutral water clusters (H2O)n (n = 3-12). Our results show the trend of interaction energies in these clusters as a function of the size of the cluster. They show that the H-bond strength increases with cluster size and that the model of water is better described if two different partial charges are used on the hydrogen, depending on whether hydrogen is H-bonded or not. The average binding enthalpy change due to the formation of H-bonds between water molecules is found to be - 25.9 kJ mol-1 at B3LYP/aug-cc-pVDZ level of theory. We observe the formation of cyclic H-bonded networks through the analysis of frontier orbitals and IR vibrational frequencies spectra. For the water cluster with n = 11, we observe an unusual reduction of the bandgap indicative of a cyclic H-bonded network. METHODS Calculations were performed with the MMFF94 force field and the B3LYP method using various large basis sets. Molecular orbital diagrams and population analysis were done using standard tools in Gaussian.
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Affiliation(s)
- Constantinos D Zeinalipour-Yazdi
- Department of Computing, Mathematics, Engineering and Natural Sciences, Northeastern University London, London, E1W 1LP, UK.
- Department of Mechanical and Aerospaces, Brunel University London, Uxbridge, UB8 3PH, UK.
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2
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Yoshida D, Kita Y, Shimazaki T, Tachikawa M. A comprehensive theoretical study of positron binding and annihilation properties of hydrogen bonded binary molecular clusters. Phys Chem Chem Phys 2022; 24:26898-26907. [DOI: 10.1039/d2cp03813g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Small hydrogen inorganic molecules such as water have no positron binding ability. We revealed that their hydrogen bonded binary molecular clusters exhibit greater positron affinities due to the increased dipole moments and polarization effect.
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Affiliation(s)
- Daisuke Yoshida
- Nishina Center for Accelerator-Based Science, RIKEN, Hirosawa 2-1, Wako 351-0198, Japan
| | - Yukiumi Kita
- Quantum Chemistry Division, Yokohama City University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027, Japan
| | - Tomomi Shimazaki
- Quantum Chemistry Division, Yokohama City University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027, Japan
| | - Masanori Tachikawa
- Quantum Chemistry Division, Yokohama City University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027, Japan
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3
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Patkar D, Ahirwar MB, Shrivastava SP, Deshmukh MM. Assessment of hydrogen bond strengths and cooperativity in self- and cross-associating cyclic (HF)m(H2O)n (m + n = 2 to 8) clusters. NEW J CHEM 2022. [DOI: 10.1039/d1nj05431g] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In this work, we investigated the strengths of various self- and cross-associating hydrogen bonds (HBs) in mixed hydrogen fluoride–water cyclic (HF)m(H2O)n (m + n = 2 to 8) clusters, employing a molecular tailoring approach (MTA)-based method.
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Affiliation(s)
- Deepak Patkar
- Department of Chemistry, Dr Harisingh Gour Vishwavidyalaya (A Central University), Sagar, 470003, India
| | - Mini Bharati Ahirwar
- Department of Chemistry, Dr Harisingh Gour Vishwavidyalaya (A Central University), Sagar, 470003, India
| | - Satya Prakash Shrivastava
- Department of Chemistry, Dr Harisingh Gour Vishwavidyalaya (A Central University), Sagar, 470003, India
| | - Milind M. Deshmukh
- Department of Chemistry, Dr Harisingh Gour Vishwavidyalaya (A Central University), Sagar, 470003, India
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4
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Patkar D, Ahirwar MB, Gadre SR, Deshmukh MM. Unusually Large Hydrogen-Bond Cooperativity in Hydrogen Fluoride Clusters, (HF) n, n = 3 to 8, Revealed by the Molecular Tailoring Approach. J Phys Chem A 2021; 125:8836-8845. [PMID: 34612647 DOI: 10.1021/acs.jpca.1c06478] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, our recently proposed molecular tailoring approach (MTA)-based method is employed for the evaluation of individual hydrogen-bond (HB) energies in linear (L) and cyclic (C) hydrogen fluoride clusters, (HF)n (n = 3 to 8). The estimated individual HB energies calculated at the MP2(full)/aug-cc-pVTZ level for the L-(HF)n are between 6.2 to 9.5 kcal/mol and those in the C-(HF)n lie between 7.9 to 11.4 kcal/mol. The zero-point energy corrections and basis set superposition corrections are found to be very small (less than 0.6 and 1.2 kcal/mol, respectively). The cooperativity contribution toward individual HBs is seen to fall between 1.0 to 4.8 kcal/mol and 3.2 to 6.9 kcal/mol for linear and cyclic clusters, respectively. Interestingly, the HB energies in dimers, cleaved from these clusters, lie in a narrow range (4.4 to 5.2 kcal/mol) suggesting that the large HB strength in (HF)n clusters is mainly due to the large cooperativity contribution, especially for n ≥ 5 (50 to 62% of the HBs energy). Furthermore, the HB energies in these clusters show a good qualitative correlation with geometrical parameters (H···F distance and F-H···F angles), stretching frequencies of F-H bonds, and electron density values at the (3, -1) bond critical points.
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Affiliation(s)
- Deepak Patkar
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya, (A Central University), Sagar, 470003, India
| | - Mini Bharati Ahirwar
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya, (A Central University), Sagar, 470003, India
| | - Shridhar R Gadre
- Department of Scientific Computing, Modelling and Simulation, Savitribai Phule Pune University, Pune, 411 007, India
| | - Milind M Deshmukh
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya, (A Central University), Sagar, 470003, India
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5
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Malinowski J, Jacewicz D, Sikorski A, Urbaniak M, Rybiński P, Parnicka P, Zaleska-Medynska A, Gawdzik B, Drzeżdżon J. Cat-CrNP as new material with catalytic properties for 2-chloro-2-propen-1-ol and ethylene oligomerizations. Sci Rep 2021; 11:15212. [PMID: 34312412 PMCID: PMC8313536 DOI: 10.1038/s41598-021-94056-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/28/2021] [Indexed: 11/22/2022] Open
Abstract
The contemporary search for new catalysts for olefin oligomerization and polymerization is based on the study of coordinating compounds and/or organometallic compounds as post-metallocene catalysts. However known catalysts are suffered by many flaws, among others unsatisfactory activity, requirement of high pressure or instability at high temperatures. In this paper, we present a new catalyst i.e. the crystalline complex compound possesing high catalytic activity in the oligomerization of olefins, such as 2-chloro-2-propen-1-ol and ethylene under very mild conditions (room temperature, 0.12 bar for ethylene oligomerization, atmospheric pressure for 2-chloro-2-propen-1-ol oligomerization). New material—Cat-CrNP ([nitrilotriacetato-1,10-phenanthroline]chromium(III) tetrahydrate) has been obtained as crystalline form of the nitrilotriacetate complex compound of chromium(III) with 1,10-phenanthroline and characterized in terms of its crystal structure by the XRD method and by multi-analytical investigations towards its physicochemical propeties The yield of catalytic oligomerization over Cat-CrNP reached to 213.92 g · mmol−1 · h−1· bar−1 and 3232 g · mmol−1 · h−1 · bar−1 for the 2-chloro-2-propen-1-ol and ethylene, respectively. Furthemore, the synthesis of Cat-CrNP is cheap, easy to perform and solvents used during preparation are environmentally friendly.
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Affiliation(s)
- Jacek Malinowski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Dagmara Jacewicz
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Artur Sikorski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Mariusz Urbaniak
- Institute of Chemistry, Jan Kochanowski University, Swietokrzyska 15 G, 25-406, Kielce, Poland
| | - Przemysław Rybiński
- Institute of Chemistry, Jan Kochanowski University, Swietokrzyska 15 G, 25-406, Kielce, Poland
| | - Patrycja Parnicka
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | | | - Barbara Gawdzik
- Institute of Chemistry, Jan Kochanowski University, Swietokrzyska 15 G, 25-406, Kielce, Poland.
| | - Joanna Drzeżdżon
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
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Orabi EA, Faraldo-Gómez JD. New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology. J Chem Theory Comput 2020; 16:5105-5126. [PMID: 32615034 DOI: 10.1021/acs.jctc.0c00247] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hydrogen fluoride (HF) is the most polar diatomic molecule and one of the simplest molecules capable of hydrogen-bonding. HF deviates from ideality both in the gas phase and in solution and is thus of great interest from a fundamental standpoint. Pure and aqueous HF solutions are broadly used in chemical and industrial processes, despite their high toxicity. HF is a stable species also in some biological conditions, because it does not readily dissociate in water unlike other hydrogen halides; yet, little is known about how HF interacts with biomolecules. Here, we set out to develop a molecular-mechanics model to enable computer simulations of HF in chemical and biological applications. This model is based on a comprehensive high-level ab initio quantum chemical investigation of the structure and energetics of the HF monomer and dimer; (HF)n clusters, for n = 3-7; various clusters of HF and H2O; and complexes of HF with analogs of all 20 amino acids and of several commonly occurring lipids, both neutral and ionized. This systematic analysis explains the unique properties of this molecule: for example, that interacting HF molecules favor nonlinear geometries despite being diatomic and that HF is a strong H-bond donor but a poor acceptor. The ab initio data also enables us to calibrate a three-site molecular-mechanics model, with which we investigate the structure and thermodynamic properties of gaseous, liquid, and supercritical HF in a wide range of temperatures and pressures; the solvation structure of HF in water and of H2O in liquid HF; and the free diffusion of HF across a lipid bilayer, a key process underlying the high cytotoxicity of HF. Despite its inherent simplifications, the model presented significantly improves upon previous efforts to capture the properties of pure and aqueous HF fluids by molecular-mechanics methods and to our knowledge constitutes the first parameter set calibrated for biomolecular simulations.
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Affiliation(s)
- Esam A Orabi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
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Li D, Gao Z, Vasudevan NK, Li H, Gao X, Li X, Xi L. Molecular Mechanism for Azeotrope Formation in Ethanol/Benzene Binary Mixtures through Gibbs Ensemble Monte Carlo Simulation. J Phys Chem B 2020; 124:3371-3386. [PMID: 32250637 DOI: 10.1021/acs.jpcb.9b12013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Azeotropes have been studied for decades due to the challenges they impose on separation processes but fundamental understanding at the molecular level remains limited. Although molecular simulation has demonstrated its capability of predicting mixture vapor-liquid equilibrium (VLE) behaviors, including azeotropes, its potential for mechanistic investigation has not been fully exploited. In this study, we use the united atom transferable potentials for phase equilibria (TraPPE-UA) force field to model the ethanol/benzene mixture, which displays a positive azeotrope. Gibbs ensemble Monte Carlo (GEMC) simulation is performed to predict the VLE phase diagram, including an azeotrope point. The results accurately agree with experimental measurements. We argue that the molecular mechanism of azeotrope formation cannot be fully understood by studying the mixture liquid-state stability at the azeotrope point alone. Rather, azeotrope occurrence is only a reflection of the changing relative volatility between the two components over a much wider composition range. A thermodynamic criterion is thus proposed on the basis of the comparison of partial excess Gibbs energy between the components. In the ethanol/benzene system, molecular energetics shows that with increasing ethanol mole fraction, its volatility initially decreases but later plateaus, while benzene volatility is initially nearly constant and only starts to decrease when its mole fraction is low. Analysis of the mixture liquid structure, including a detailed investigation of ethanol hydrogen-bonding configurations at different composition levels, reveals the underlying molecular mechanism for the changing volatilities responsible for the azeotrope.
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Affiliation(s)
- Dongyang Li
- School of Chemical Engineering and Technology, National Engineering Research Center of Distillation Technology, and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China.,Department of Chemical Engineering, McMaster Universtiy, Hamilton, Ontario L8S 4L7, Canada
| | - Ziqi Gao
- Department of Chemical Engineering, McMaster Universtiy, Hamilton, Ontario L8S 4L7, Canada
| | - Naveen Kumar Vasudevan
- Department of Chemical Engineering, McMaster Universtiy, Hamilton, Ontario L8S 4L7, Canada
| | - Hong Li
- School of Chemical Engineering and Technology, National Engineering Research Center of Distillation Technology, and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Xin Gao
- School of Chemical Engineering and Technology, National Engineering Research Center of Distillation Technology, and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Xingang Li
- School of Chemical Engineering and Technology, National Engineering Research Center of Distillation Technology, and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Li Xi
- Department of Chemical Engineering, McMaster Universtiy, Hamilton, Ontario L8S 4L7, Canada
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8
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Nonempirically tuning range-separated functionals for dipole polarizabilities of nanostructures containing hydrogen bonds. Theor Chem Acc 2017. [DOI: 10.1007/s00214-016-2046-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Gulina LB, Schäfer M, Privalov AF, Tolstoy VP, Murin IV. Synthesis of LaF3 nanosheets with high fluorine mobility investigated by NMR relaxometry and diffusometry. J Chem Phys 2015; 143:234702. [PMID: 26696065 DOI: 10.1063/1.4937415] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ionically conducting lanthanum fluoride (LaF3), displaying a nanoscopic lamellar structure, has been synthesized at the surface of an aqueous solution of LaCl3 and HF. The structure and the chemical composition of the conductor have been analyzed by SEM, electron probe microanalysis, X-ray powder diffraction, FTIR, and (19)F magic angle spinning nuclear magnetic resonance (NMR) spectroscopy. The fluorine dynamics have been studied by NMR diffusometry and relaxometry in a temperature range from room temperature up to 875 K. The fluorine self-diffusion coefficient of the nanostructured LaF3 is about two orders of magnitude larger than that of bulk LaF3. This novel material is highly promising for many typical applications of fluorine ionic systems.
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Affiliation(s)
- L B Gulina
- Institute of Chemistry of St. Petersburg State University 198504, Universitetsky pr., 26 Peterhof, St. Petersburg, Russia
| | - M Schäfer
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - A F Privalov
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - V P Tolstoy
- Institute of Chemistry of St. Petersburg State University 198504, Universitetsky pr., 26 Peterhof, St. Petersburg, Russia
| | - I V Murin
- Institute of Chemistry of St. Petersburg State University 198504, Universitetsky pr., 26 Peterhof, St. Petersburg, Russia
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10
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Alipour M. Novel Recipe for Double-Hybrid Density Functional Computations of Linear and Nonlinear Polarizabilities of Molecules and Nanoclusters. J Phys Chem A 2014; 118:5333-42. [DOI: 10.1021/jp503959w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Mojtaba Alipour
- Department
of Chemistry,
College of Sciences, Shiraz University, Shiraz, Iran
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12
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Sophy KB, Kuo JL. Structure and vibrational spectra of H+(HF)n (n=2–9) clusters: An ab initio study. J Chem Phys 2009; 131:224307. [DOI: 10.1063/1.3268502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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13
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Luo Y, Maeda S, Ohno K. Automated exploration of stable isomers of H+(H2O)n(n= 5-7) viaab initiocalculations: An application of the anharmonic downward distortion following algorithm. J Comput Chem 2009; 30:952-61. [DOI: 10.1002/jcc.21117] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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14
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Maeda S, Ohno K. Microsolvation of Hydrogen Sulfide: Exploration of H2S·(H2O)n and SH-·H3O+·(H2O)n-1 (n = 5−7) Cluster Structures on Ab Initio Potential Energy Surfaces by the Scaled Hypersphere Search Method. J Phys Chem A 2008; 112:2962-8. [DOI: 10.1021/jp710494n] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Satoshi Maeda
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Koichi Ohno
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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