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Lukin VG, Khvostenko OG, Khatymova LZ, Tuymedov GM, Tseplin EE, Tseplina SN. Induced Charge and Dissociation of Negative Ions on a Conducting Surface. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2022. [DOI: 10.1134/s1990793121060063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Stocka J, Čeponkus J, Šablinskas V, Rodziewicz P. Conformational diversity of the THF molecule in N 2 matrix by means of FTIR matrix isolation experiment and Car-Parrinello molecular dynamics simulations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 238:118425. [PMID: 32413717 DOI: 10.1016/j.saa.2020.118425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 04/25/2020] [Accepted: 04/26/2020] [Indexed: 06/11/2023]
Abstract
Tetrahydrofuran (THF) is a widely used chemical compound, in particular as a solvent in organic and inorganic synthesis. The THF molecule has also an interesting property, namely, undergoes pseudorotation, similar to the case of the cyclopentane. Low energy difference between the envelope (Cs symmetry) and twisted (C2 symmetry) conformations of the THF molecule leads to the interconversion between the two conformers. We study the influence of the molecular environment (N2) on the Cs-C2 equilibrium of tetrahydrofuran in the THF@N2 system utilizing nitrogen matrix isolation infrared spectroscopy. We observe a different ratio between envelope (Cs) and twisted (C2) conformations with respect to a change of the temperature. FTIR experimental studies are supported by the results of the static density functional theory calculations and Car-Parrinello molecular dynamics simulations. We focus on the dynamics of the pseudorotation process, in particular, the lifetime of the THF conformations and their mutual rearrangements. On the basis of the THF@N2 matrix model, with explicit nitrogen molecules, the anharmonic infrared spectra are generated from the Fourier transformation of the dipole moment autocorrelation function.
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Affiliation(s)
- Joanna Stocka
- Departament of General Physics and Spectroscopy, Faculty of Physics, Vilnius University, Saultekio al. 9, Vilnius 10222, Lithuania
| | - Justinas Čeponkus
- Departament of General Physics and Spectroscopy, Faculty of Physics, Vilnius University, Saultekio al. 9, Vilnius 10222, Lithuania
| | - Valdas Šablinskas
- Departament of General Physics and Spectroscopy, Faculty of Physics, Vilnius University, Saultekio al. 9, Vilnius 10222, Lithuania
| | - Pawel Rodziewicz
- Institute of Chemistry, Jan Kochanowski University, Swietokrzyska 15G, 25-406 Kielce, Poland.
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Single-walled carbon nanotubes in tetrahydrofuran solution: microsolvation from first-principles calculations. J Mol Model 2019; 25:206. [PMID: 31256236 DOI: 10.1007/s00894-019-4050-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/24/2019] [Indexed: 10/26/2022]
Abstract
The molecular interactions between the commonly used solvent tetrahydrofuran (THF) and single-walled carbon nanotubes (SWCNT) are studied using density functional theory calculations and Car-Parrinello molecular dynamics simulations. The competitive interplay between THF-THF and THF-SWCNT interactions via C-H⋯O and C-H⋯π hydrogen bonds is analyzed in detail. The binding energies for different global and local energy minima configurations of THF monomers, dimers, trimers, and tetramers on SWCNT(10,0) were determined. The adsorbed species are analyzed in terms of their coordination to the surface via weak hydrogen bonds of the C-H⋯π type and in terms of their ability to form intermolecular C-H⋯O hydrogen bonds, which are responsible for the self-aggregation of THF molecules and a possible dimerization or tetramerization process. A special focus is put on the pseudorotation of the THF molecules at finite temperatures and on the formation of blue-shifting hydrogen bonds.
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Asfin RE, Melikova SM, Domanskaya AV, Rodziewicz P, Rutkowski KS. Degeneracy Lifting Effect in the FTIR Spectrum of Fluoroform Trapped in a Nitrogen Matrix. An Experimental and Car–Parrinello Molecular Dynamics Study. J Phys Chem A 2016; 120:3497-503. [DOI: 10.1021/acs.jpca.6b02039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ruslan E. Asfin
- Department
of Physics, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 Saint Petersburg, Russian Federation
| | - Sona M. Melikova
- Department
of Physics, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 Saint Petersburg, Russian Federation
| | | | - Paweł Rodziewicz
- Institute
of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-245 Bialystok, Poland
| | - Konstantin S. Rutkowski
- Department
of Physics, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 Saint Petersburg, Russian Federation
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Lach J, Goclon J, Rodziewicz P. Structural flexibility of the sulfur mustard molecule at finite temperature from Car-Parrinello molecular dynamics simulations. JOURNAL OF HAZARDOUS MATERIALS 2016; 306:269-277. [PMID: 26774981 DOI: 10.1016/j.jhazmat.2015.12.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/12/2015] [Accepted: 12/16/2015] [Indexed: 06/05/2023]
Abstract
Sulfur mustard (SM) is one of the most dangerous chemical compounds used against humans, mostly at war conditions but also in terrorist attacks. Even though the sulfur mustard has been synthesized over a hundred years ago, some of its molecular properties are not yet resolved. We investigate the structural flexibility of the SM molecule in the gas phase by Car-Parrinello molecular dynamics simulations. Thorough conformation analysis of 81 different SM configurations using density functional theory is performed to analyze the behavior of the system at finite temperature. The conformational diversity is analyzed with respect to the formation of intramolecular blue-shifting CH⋯S and CH⋯Cl hydrogen bonds. Molecular dynamics simulations indicate that all structural rearrangements between SM local minima are realized either in direct or non-direct way, including the intermediate structure in the last case. We study the lifetime of the SM conformers and perform the population analysis. Additionally, we provide the anharmonic dynamical finite temperature IR spectrum from the Fourier Transform of the dipole moment autocorrelation function to mimic the missing experimental IR spectrum.
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Affiliation(s)
- Joanna Lach
- Department of General Physics and Spectroscopy, Vilnius University, Sauletekio av. 3-9, Vilnius 10222, Lithuania
| | - Jakub Goclon
- Interdisciplinary Center for Molecular Materials (ICMM) and Computer-Chemistry-Center (CCC), Friedrich-Alexander-University Erlangen-Nürnberg, Nägelsbachstr. 25, 91052 Erlangen, Germany
| | - Pawel Rodziewicz
- Institute of Chemistry, University of Bialystok, Hurtowa 1, 15-399 Bialystok, Poland.
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Kozlowska M, Goclon J, Rodziewicz P. Intramolecular Hydrogen Bonds in Low-Molecular-Weight Polyethylene Glycol. Chemphyschem 2016; 17:1143-53. [DOI: 10.1002/cphc.201501182] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Mariana Kozlowska
- Institute of Chemistry; University of Bialystok; Ciolkowskiego Str. 1K 15-245 Bialystok Poland
| | - Jakub Goclon
- Institute of Chemistry; University of Bialystok; Ciolkowskiego Str. 1K 15-245 Bialystok Poland
- Interdisciplinary Center for Molecular Materials (ICMM) and Computer-Chemistry-Center (CCC); Friedrich-Alexander-University Erlangen-Nürnberg; Nägelsbachstr. 25 91052 Erlangen Germany
| | - Pawel Rodziewicz
- Institute of Chemistry; University of Bialystok; Ciolkowskiego Str. 1K 15-245 Bialystok Poland
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Reimers JR, Ford MJ, Goerigk L. Problems, successes and challenges for the application of dispersion-corrected density-functional theory combined with dispersion-based implicit solvent models to large-scale hydrophobic self-assembly and polymorphism. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1066504] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Reimers JR, Panduwinata D, Visser J, Chin Y, Tang C, Goerigk L, Ford MJ, Sintic M, Sum TJ, Coenen MJJ, Hendriksen BLM, Elemans JAAW, Hush NS, Crossley MJ. A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers. Proc Natl Acad Sci U S A 2015; 112:E6101-10. [PMID: 26512115 PMCID: PMC4653194 DOI: 10.1073/pnas.1516984112] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Modern quantum chemical electronic structure methods typically applied to localized chemical bonding are developed to predict atomic structures and free energies for meso-tetraalkylporphyrin self-assembled monolayer (SAM) polymorph formation from organic solution on highly ordered pyrolytic graphite surfaces. Large polymorph-dependent dispersion-induced substrate-molecule interactions (e.g., -100 kcal mol(-1) to -150 kcal mol(-1) for tetratrisdecylporphyrin) are found to drive SAM formation, opposed nearly completely by large polymorph-dependent dispersion-induced solvent interactions (70-110 kcal mol(-1)) and entropy effects (25-40 kcal mol(-1) at 298 K) favoring dissolution. Dielectric continuum models of the solvent are used, facilitating consideration of many possible SAM polymorphs, along with quantum mechanical/molecular mechanical and dispersion-corrected density functional theory calculations. These predict and interpret newly measured and existing high-resolution scanning tunnelling microscopy images of SAM structure, rationalizing polymorph formation conditions. A wide range of molecular condensed matter properties at room temperature now appear suitable for prediction and analysis using electronic structure calculations.
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Affiliation(s)
- Jeffrey R Reimers
- International Centre for Quantum and Molecular Structure, College of Sciences, Shanghai University, Shanghai 200444, China; School of Mathematical and Physical Sciences, The University of Technology Sydney, Sydney, NSW 2007, Australia;
| | - Dwi Panduwinata
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Johan Visser
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Yiing Chin
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chunguang Tang
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Lars Goerigk
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia; School of Chemistry, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Michael J Ford
- School of Mathematical and Physical Sciences, The University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Maxine Sintic
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Tze-Jing Sum
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Michiel J J Coenen
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Bas L M Hendriksen
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Johannes A A W Elemans
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Noel S Hush
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia; School of Biomolecular Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Maxwell J Crossley
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia;
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Kozlowska M, Goclon J, Rodziewicz P. A computational study of intramolecular hydrogen bonds breaking/formation: impact on the structural flexibility of the ranitidine molecule. J Mol Model 2015; 21:94. [PMID: 25791352 DOI: 10.1007/s00894-015-2591-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 01/26/2015] [Indexed: 11/25/2022]
Abstract
Ranitidine is a histamine H2-receptor antagonist that reduces gastric acid secretion. We studied the flexibility of the ranitidine molecule with the special focus on the network of diverse intramolecular hydrogen bonds: N-H⋯O, N-H⋯N, C-H⋯O, C-H⋯N and N-H⋯S. We performed static density functional theory calculations of global and local minima and analyzed their stability at finite temperature in the Car-Parrinello molecular dynamics simulations. We observed intramolecular H-bonds breaking/formation crucial for the structural rearrangements leading to the folding process. The lifetimes of the closed structures of ranitidine were also estimated. The existence of hydrogen bonds and their strength were confirmed on the basis of topological parameters in the bond critical points utilizing Quantum Theory of Atoms in Molecules.
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Affiliation(s)
- Mariana Kozlowska
- Institute of Chemistry, University of Bialystok, Hurtowa 1, 15-399, Bialystok, Poland,
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