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Yildirim A, Tekpinar M. Building Quantitative Bridges between Dynamics and Sequences of SARS-CoV-2 Main Protease and a Diverse Set of Thirty-Two Proteins. J Chem Inf Model 2023; 63:9-19. [PMID: 36513349 DOI: 10.1021/acs.jcim.2c01206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Proteases are major drug targets for many viral diseases. However, mutations can render several antiprotease drugs inefficient rapidly even though these mutations may not alter protein structures significantly. Understanding relations between quickly mutating residues, protease structures, and the dynamics of the proteases is crucial for designing potent drugs. Due to this reason, we studied relations between the evolutionary information on residues in the amino acid sequences and protein dynamics for SARS-CoV-2 main protease. More precisely, we analyzed three dynamical quantities (Schlitter entropy, root-mean-square fluctuations, and dynamical flexibility index) and their relation to the amino acid conservation extracted from multiple sequence alignments of the main protease. We showed that a quantifiable similarity can be built between a sequence-based quantity called Jensen-Shannon conservation and those three dynamical quantities. We validated this similarity for a diverse set of 32 different proteins, other than the SARS-CoV-2 main protease. We believe that establishing these kinds of quantitative bridges will have larger implications for all viral proteases as well as all proteins.
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Affiliation(s)
- Ahmet Yildirim
- Department of Biology, Siirt University, 56100Siirt, Turkey
| | - Mustafa Tekpinar
- CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, Sorbonne University, 75005Paris, France
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Tekpinar M, Yildirim A. Impact of dimerization and N3 binding on molecular dynamics of SARS-CoV and SARS-CoV-2 main proteases. J Biomol Struct Dyn 2021; 40:6243-6254. [PMID: 33525993 PMCID: PMC7869440 DOI: 10.1080/07391102.2021.1880481] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SARS-CoV-2 main protease is one of the major targets in drug development efforts against Covid-19. Even though several structures were reported to date, its dynamics is not understood well. In particular, impact of dimerization and ligand binding on the dynamics is an important issue to investigate. In this study, we performed molecular dynamics simulations of SARS-CoV and SARS-CoV-2 main proteases to investigate influence of dimerization on the dynamics by modeling monomeric and dimeric apo and holo forms. The dimerization causes an organization of the interdomain dynamics as well as some local structural changes. Moreover, we investigated impact of a peptide mimetic (N3) on the dynamics of SARS-CoV and SARS-CoV-2 Mpro. The ligand binding to the dimeric forms causes some key local changes at the dimer interface and it causes an allosteric interaction between the active sites of two protomers. Our results support the idea that only one protomer is active on SARS-CoV-2 due to this allosteric interaction. Additionally, we analyzed the molecular dynamics trajectories from graph theoretical perspective and found that the most influential residues – as measured by eigenvector centrality – are a group of residues in active site and dimeric interface of the protease. This study may form a bridge between what we know about the dynamics of SARS-CoV and SARS-CoV-2 Mpro. We think that enlightening allosteric communication of the active sites and the role of dimerization in SARS-CoV-2 Mpro can contribute to development of novel drugs against this global health problem as well as other similar proteases. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Mustafa Tekpinar
- Unit of Structural Dynamics of Biological Macromolecules, Pasteur Institute, UMR 3528 CNRS, Paris, France
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3
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León-Pimentel CI, Martínez-Jiménez M, Saint-Martin H. Study of the Elusive Hydration of Pb2+ from the Gas Phase to the Liquid Aqueous Solution: Modeling the Hemidirected Solvation with a Polarizable MCDHO Force-Field. J Phys Chem B 2019; 123:9155-9166. [DOI: 10.1021/acs.jpcb.9b04541] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C. I. León-Pimentel
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Apdo. Postal 48-3, Cuernavaca, Morelos 62251, Ḿexico
| | - M. Martínez-Jiménez
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Apdo. Postal 48-3, Cuernavaca, Morelos 62251, Ḿexico
| | - H. Saint-Martin
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Apdo. Postal 48-3, Cuernavaca, Morelos 62251, Ḿexico
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Kührová P, Otyepka M, Šponer J, Banáš P. Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations. J Chem Theory Comput 2015; 10:401-11. [PMID: 26579919 DOI: 10.1021/ct400663s] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Hydrating water molecules are believed to be an inherent part of the RNA structure and have a considerable impact on RNA conformation. However, the magnitude and mechanism of the interplay between water molecules and the RNA structure are still poorly understood. In principle, such hydration effects can be studied by molecular dynamics (MD) simulations. In our recent MD studies, we observed that the choice of water model has a visible impact on the predicted structure and structural dynamics of RNA and, in particular, has a larger effect than type, parametrization, and concentration of the ions. Furthermore, the water model effect is sequence dependent and modulates the sequence dependence of A-RNA helical parameters. Clearly, the sensitivity of A-RNA structural dynamics to the water model parametrization is a rather spurious effect that complicates MD studies of RNA molecules. These results nevertheless suggest that the sequence dependence of the A-RNA structure, usually attributed to base stacking, might be driven by the structural dynamics of specific hydration. Here, we present a systematic MD study that aimed to (i) clarify the atomistic mechanism of the water model sensitivity and (ii) discover whether and to what extent specific hydration modulates the A-RNA structural variability. We carried out an extended set of MD simulations of canonical A-RNA duplexes with TIP3P, TIP4P/2005, TIP5P, and SPC/E explicit water models and found that different water models provided a different extent of water bridging between 2'-OH groups across the minor groove, which in turn influences their distance and consequently also inclination, roll, and slide parameters. Minor groove hydration is also responsible for the sequence dependence of these helical parameters. Our simulations suggest that TIP5P is not optimal for RNA simulations.
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Affiliation(s)
- Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. Listopadu 12, 771 46, Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. Listopadu 12, 771 46, Olomouc, Czech Republic.,Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic.,CEITEC - Central European Institute of Technology , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. Listopadu 12, 771 46, Olomouc, Czech Republic.,Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic
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Galashev AE. Structure of water clusters with captured methane molecules. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2015. [DOI: 10.1134/s1990793114110049] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Galashev AE. Structural changes in water clusters during methane adsorption. COLLOID JOURNAL 2014. [DOI: 10.1134/s1061933x14030041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Galashev AY. Atomistic simulations of methane interactions with an atmospheric moisture. J Chem Phys 2013; 139:124303. [PMID: 24089763 DOI: 10.1063/1.4821192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Methane is an extremely effective absorber of radiation, i.e., it is a relatively potent greenhouse gas, and the increased concentration of methane in the atmosphere must influence earth's radiation balance. The adsorption of one to six methane molecules by water clusters is studied by the method of molecular dynamics under near-atmospheric conditions. The capture of methane molecules by water clusters produces an increase in the integrated intensity of IR absorbance and the reflection coefficient. The Raman spectrum of the system is considerably depleted due to the addition of methane molecules to the disperse water system. The observed emission power of a dispersed aqueous system with adsorbed methane molecules has appreciably increased relative to the analogous characteristics of the pure water cluster system. The Voronoi polyhedra and simplified ones constructed within the framework of molecular-dynamic model of clusters are used for the analysis of the structure changes occurring with increasing the number of adsorbed CH4 molecules.
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Affiliation(s)
- Alexander Y Galashev
- Institute of Industrial Ecology of the Ural Branch of the Russian Academy of Sciences, Sofia Kovalevskaya Str. 20, Yekaterinburg 620990, Russia
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Galashev AE. A computer study of ammonium adsorption on water clusters. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2013. [DOI: 10.1134/s1990793113050047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Galashev AE. Molecular dynamics investigation of the interaction between IR radiation and an ammonia-water medium. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2013. [DOI: 10.1134/s0036024413060095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Galashev AE. IR and Raman spectra of a water-methane disperse system. Computer experiment. COLLOID JOURNAL 2013. [DOI: 10.1134/s1061933x1303006x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Galashev AE. Adsorption of ammonia by water clusters. Computer experiment. COLLOID JOURNAL 2013. [DOI: 10.1134/s1061933x13020063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Galashev AE. Spectral characteristics of water clusters in the presence of nitrate ions. COLLOID JOURNAL 2012. [DOI: 10.1134/s1061933x12060075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Galashev AE, Polukhin VA. Computer-assisted study of silver absorption by porous silicon dioxide nanoparticles. COLLOID JOURNAL 2011. [DOI: 10.1134/s1061933x11050036] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Galashev AE, Rakhmanova OR, Novruzova OA, Galasheva AA, Novruzov AN. Computer simulation of oxygen and nitrate ion absorption by water clusters. COLLOID JOURNAL 2011. [DOI: 10.1134/s1061933x11050048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Galashev AE, Rakhmanova OR, Novruzova OA. Spectral characteristics of water clusters in the interaction with ozone molecules and bromide ions. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2011. [DOI: 10.1134/s1990793111030201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Galashev AE, Rakhmanova OR, Zemnukhova LA. Modeling the infrared and raman spectra of silicon dioxide clusters absorbing water. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2011. [DOI: 10.1134/s003602441106015x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Galashev AE, Rakhmanova OR. Interaction of chloride ions with water clusters absorbing ozone: A computer experiment. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2011. [DOI: 10.1134/s1990793111020321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Galashev AY. Computer study of absorption of oxygen and ozone molecules by water clusters with Cl– and Br–. CAN J CHEM 2011. [DOI: 10.1139/v10-174] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Infrared absorption and Raman spectra were calculated by using the molecular dynamics method for water clusters with chlorine and bromine ions in a medium of water and either ozone or oxygen molecules. The intensity of IR absorption spectra of clusters with absorbed oxygen increased and that of clusters with absorbed ozone decreased as the number of chlorine ions grew. When Br– were present in the system the inverse behaviour was observed. An increase in the number of ions weakened the intensity of the Raman spectra when either oxygen or ozone was absorbed; for ozone this weakening was more noticeable. A stronger reduction of the integrated intensity of the Raman spectrum with an increase in the number of Br– was observed in the presence of ozone molecules in the system. Cl– ions caused an amplification of the emission power of the IR radiation for both systems in the presence of oxygen and ozone, and Br– strengthened the emission of IR radiation for systems containing ozone, and weakened it for systems with oxygen molecules.
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Affiliation(s)
- Alexander Y. Galashev
- Institute of Industrial Ecology, Ural Division, Russian Academy of Sciences, Sofia Kovalevskaya Str, 20a, GSP-594, Yekaterinburg 620219, Russia (e-mail: )
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Muchová E, Gladich I, Picaud S, Hoang PNM, Roeselová M. The Ice−Vapor Interface and the Melting Point of Ice Ih for the Polarizable POL3 Water Model. J Phys Chem A 2011; 115:5973-82. [DOI: 10.1021/jp110391q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Eva Muchová
- Faculty of Science, Charles University Prague, Albertov 6, Prague, 128 43, Czech Republic
| | - Ivan Gladich
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, Prague, 166 10, Czech Republic
| | - Sylvain Picaud
- Institut UTINAM -UMR CNRS 6213, Université de Franche-Comté, 25030 Besançon Cedex, France
| | - Paul N. M. Hoang
- Institut UTINAM -UMR CNRS 6213, Université de Franche-Comté, 25030 Besançon Cedex, France
| | - Martina Roeselová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, Prague, 166 10, Czech Republic
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Galashev AE, Rakhmanova OR, Novruzova OA. Calculation of spectral characteristics of water clusters upon interaction with oxygen molecules and bromine ions. COLLOID JOURNAL 2010. [DOI: 10.1134/s1061933x10060086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Galashev AE, Rakhmanova OR, Borisikhin AA. IR absorption and Raman spectra of silicon dioxide nanoparticles in the presence of water: Computer experiment. COLLOID JOURNAL 2010. [DOI: 10.1134/s1061933x10060074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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González BS, Noya EG, Vega C, Sesé LM. Nuclear Quantum Effects in Water Clusters: The Role of the Molecular Flexibility. J Phys Chem B 2010; 114:2484-92. [DOI: 10.1021/jp910770y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Briesta S. González
- Departamento Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Eva G. Noya
- Departamento Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Carlos Vega
- Departamento Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Luis M. Sesé
- Departamento Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias, UNED, Paseo Senda del Rey 9, 28040 Madrid, Spain
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Galashev AE, Rakhmanova OR, Novrusova OA, Galasheva AA. Spectral characteristics of water clusters upon interaction with oxygen molecules and chlorine ions. COLLOID JOURNAL 2009. [DOI: 10.1134/s1061933x09060039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Galashev AE. The spectral characteristics of chlorine-containing water clusters in the presence of ozone and oxygen. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2009. [DOI: 10.1134/s0036024409130123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Novruzova OA, Rakhmanova OP, Galashev AE. The stability and structure of (N2)j(H2O)i and (Ar)j(H2O)i clusters. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2007. [DOI: 10.1134/s0036024407110180] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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Novruzova OA, Galasheva AA, Galashev AE. IR spectra of aqueous disperse systems adsorbing atmospheric gases: 2. Argon. COLLOID JOURNAL 2007. [DOI: 10.1134/s1061933x07040102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Novruzova OA, Galasheva AA, Galashev AE. IR spectra of aqueous disperse systems adsorbed atmospheric gases: 1. Nitrogen. COLLOID JOURNAL 2007. [DOI: 10.1134/s1061933x07040096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Novruzova OA. Spectral characteristics of aqueous dispersions enriched in oxygen. RUSS J GEN CHEM+ 2006. [DOI: 10.1134/s1070363206110035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Novruzova OA, Chukanov VN, Galashev AE. Computer-aided study of oxygen absorption by water clusters. IR spectra of heteroclusters. COLLOID JOURNAL 2006. [DOI: 10.1134/s1061933x06040107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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San-Román ML, Carrillo-Tripp M, Saint-Martin H, Hernández-Cobos J, Ortega-Blake I. A Theoretical Study of the Hydration of Li+ by Monte Carlo Simulations with Refined Ab Initio Based Model Potentials. Theor Chem Acc 2006. [DOI: 10.1007/s00214-005-0053-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Abascal JLF, Vega C. A general purpose model for the condensed phases of water: TIP4P/2005. J Chem Phys 2005; 123:234505. [PMID: 16392929 DOI: 10.1063/1.2121687] [Citation(s) in RCA: 2287] [Impact Index Per Article: 120.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A potential model intended to be a general purpose model for the condensed phases of water is presented. TIP4P/2005 is a rigid four site model which consists of three fixed point charges and one Lennard-Jones center. The parametrization has been based on a fit of the temperature of maximum density (indirectly estimated from the melting point of hexagonal ice), the stability of several ice polymorphs and other commonly used target quantities. The calculated properties include a variety of thermodynamic properties of the liquid and solid phases, the phase diagram involving condensed phases, properties at melting and vaporization, dielectric constant, pair distribution function, and self-diffusion coefficient. These properties cover a temperature range from 123 to 573 K and pressures up to 40,000 bar. The model gives an impressive performance for this variety of properties and thermodynamic conditions. For example, it gives excellent predictions for the densities at 1 bar with a maximum density at 278 K and an averaged difference with experiment of 7 x 10(-4) g/cm3.
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Affiliation(s)
- J L F Abascal
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain.
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Abstract
Polarizability is considered to be the single most significant development in the next generation of force fields for biomolecular simulations. However, the self-consistent computation of induced atomic dipoles in a polarizable force field is expensive due to the cost of solving a large dense linear system at each step of a simulation. This article introduces methods that reduce the cost of computing the electrostatic energy and force of a polarizable model from about 7.5 times the cost of computing those of a nonpolarizable model to less than twice the cost. This is probably sufficient for the routine use of polarizable forces in biomolecular simulations. The reduction in computing time is achieved by an efficient implementation of the particle-mesh Ewald method, an accurate and robust predictor based on least-squares fitting, and non-stationary iterative methods whose fast convergence is accelerated by a simple preconditioner. Furthermore, with these methods, the self-consistent approach with a larger timestep is shown to be faster than the extended Lagrangian approach. The use of dipole moments from previous timesteps to calculate an accurate initial guess for iterative methods leads to an energy drift, which can be made acceptably small. The use of a zero initial guess does not lead to perceptible energy drift if a reasonably strict convergence criterion for the iteration is imposed.
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Affiliation(s)
- Wei Wang
- Beckman Institute, University of Illinois, Urbana, Illinois 61801, USA.
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Vega C, Abascal JLF. Relation between the melting temperature and the temperature of maximum density for the most common models of water. J Chem Phys 2005; 123:144504. [PMID: 16238404 DOI: 10.1063/1.2056539] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Water exhibits a maximum in density at normal pressure at 4 degrees above its melting point. The reproduction of this maximum is a stringent test for potential models used commonly in simulations of water. The relation between the melting temperature and the temperature of maximum density for these potential models is unknown mainly due to our ignorance about the melting temperature of these models. Recently we have determined the melting temperature of ice I(h) for several commonly used models of water (SPC, SPC/E, TIP3P, TIP4P, TIP4P/Ew, and TIP5P). In this work we locate the temperature of maximum density for these models. In this way the relative location of the temperature of maximum density with respect to the melting temperature is established. For SPC, SPC/E, TIP3P, TIP4P, and TIP4P/Ew the maximum in density occurs at about 21-37 K above the melting temperature. In all these models the negative charge is located either on the oxygen itself or on a point along the H-O-H bisector. For the TIP5P and TIP5P-E models the maximum in density occurs at about 11 K above the melting temperature. The location of the negative charge appears as a geometrical crucial factor to the relative position of the temperature of maximum density with respect to the melting temperature.
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Affiliation(s)
- C Vega
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain.
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Hernández-Cobos J, Saint-Martin H, Mackie AD, Vega LF, Ortega-Blake I. Water liquid-vapor equilibria predicted by refined ab initio derived potentials. J Chem Phys 2005; 123:044506. [PMID: 16095368 DOI: 10.1063/1.1950627] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Coexistence properties for water near the critical point using several ab initio models were calculated using grand canonical Monte Carlo simulations with multiple histogram reweighting techniques. These models, that have proved to yield a good reproduction of the water properties at ambient conditions, perform rather well, improving the performance of a previous ab initio model. It is also shown that bulk geometry and dipole values, predicted by the simulation, can be used and a good approximation obtained with a polarizable rigid water model but not when polarization is excluded.
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Affiliation(s)
- Jorge Hernández-Cobos
- Centro de Ciencias Físicas, Universidad Nacional Autónoma de México, Apartado Postal 48-3, 62251 Cuernavaca, Morelos, Mexico.
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Abascal JLF, Sanz E, García Fernández R, Vega C. A potential model for the study of ices and amorphous water: TIP4P/Ice. J Chem Phys 2005; 122:234511. [PMID: 16008466 DOI: 10.1063/1.1931662] [Citation(s) in RCA: 662] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ability of several water models to predict the properties of ices is discussed. The emphasis is put on the results for the densities and the coexistence curves between the different ice forms. It is concluded that none of the most commonly used rigid models is satisfactory. A new model specifically designed to cope with solid-phase properties is proposed. The parameters have been obtained by fitting the equation of state and selected points of the melting lines and of the coexistence lines involving different ice forms. The phase diagram is then calculated for the new potential. The predicted melting temperature of hexagonal ice (Ih) at 1 bar is 272.2 K. This excellent value does not imply a deterioration of the rest of the properties. In fact, the predictions for both the densities and the coexistence curves are better than for TIP4P, which previously yielded the best estimations of the ice properties.
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Affiliation(s)
- J L F Abascal
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
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Saint-Martin H, Hernández-Cobos J, Ortega-Blake I. Water models based on a single potential energy surface and different molecular degrees of freedom. J Chem Phys 2005; 122:224509. [PMID: 15974693 DOI: 10.1063/1.1931567] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Up to now it has not been possible to neatly assess whether a deficient performance of a model is due to poor parametrization of the force field or the lack of inclusion of enough molecular properties. This work compares several molecular models in the framework of the same force field, which was designed to include many-body nonadditive effects: (a) a polarizable and flexible molecule with constraints that account for the quantal nature of the vibration [B. Hess, H. Saint-Martin, and H. J. C. Berendsen, J. Chem. Phys. 116, 9602 (2002), H. Saint-Martin, B. Hess, and H. J. C. Berendsen, J. Chem. Phys. 120, 11133 (2004)], (b) a polarizable and classically flexible molecule [H. Saint-Martin, J. Hernandez-Cobos, M. I. Bernal-Uruchurtu, I. Ortega-Blake, and H. J. C. Berendsen, J. Chem. Phys. 113, 10899 (2000)], (c) a polarizable and rigid molecule, and finally (d) a nonpolarizable and rigid molecule. The goal is to determine how significant the different molecular properties are. The results indicate that all factors--nonadditivity, polarizability, and intramolecular flexibility--are important. Still, approximations can be made in order to diminish the computational cost of the simulations with a small decrease in the accuracy of the predictions, provided that those approximations are counterbalanced by the proper inclusion of an effective molecular property, that is, an average molecular geometry or an average dipole. Hence instead of building an effective force field by parametrizing it in order to reproduce the properties of a specific phase, a building approach is proposed that is based on adequately restricting the molecular flexibility and/or polarizability of a model potential fitted to unimolecular properties, pair interactions, and many-body nonadditive contributions. In this manner, the same parental model can be used to simulate the same substance under a wide range of thermodynamic conditions. An additional advantage of this approach is that, as the force field improves by the quality of the molecular calculations, all levels of modeling can be improved.
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Affiliation(s)
- Humberto Saint-Martin
- Centro de Ciencias Físicas, Universidad Nacional Autónoma de México, Apartado Postal 48-3, 62251 Cuernavaca, Morelos, Mexico.
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Abstract
Computer simulations of ice Ih with different proton orientations are presented. Simulations of proton disordered ice are carried out using a Monte Carlo method which samples over proton degree of freedom, allowing for the calculation of the dielectric constant and for the examination of the degree of proton disorder. Simulations are also presented for two proton ordered structures of ice Ih, the ferroelectric Cmc2(1) structure or ice XI and the antiferroelectric Pna2(1) structure. These simulations indicate that a transition to a proton ordered phase occurs at low temperatures (below 80 K). The symmetry of the ordered phase is found to be dependent on the water potential. The stability of the two proton ordered structures is due to a balance of short-ranged interactions which tend to stabilize the Pna2(1) structure and longer-range interactions which stabilize the Cmc2(1) structure.
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Affiliation(s)
- Steven W Rick
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA.
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