151
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Hinteregger E, Pribil AB, Hofer TS, Randolf BR, Weiss AKH, Rode BM. Structure and Dynamics of the Chromate Ion in Aqueous Solution. An ab Initio QMCF-MD Simulation. Inorg Chem 2010; 49:7964-8. [DOI: 10.1021/ic101001e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ernst Hinteregger
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Andreas B. Pribil
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Bernhard R. Randolf
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Alexander K. H. Weiss
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Bernd M. Rode
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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152
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153
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Terrier C, Vitorge P, Gaigeot MP, Spezia R, Vuilleumier R. Density functional theory based molecular dynamics study of hydration and electronic properties of aqueous La3+. J Chem Phys 2010; 133:044509. [DOI: 10.1063/1.3460813] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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154
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Qaiser Fatmi M, Hofer TS, Rode BM. The stability of [Zn(NH(3))(4)](2+) in water: A quantum mechanical/molecular mechanical molecular dynamics study. Phys Chem Chem Phys 2010; 12:9713-8. [PMID: 20544098 DOI: 10.1039/c002021d] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To investigate the structural and dynamical properties of the tetraamminezinc(ii) complex (Zn-tetraamine) in aqueous solution, ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulation was performed for 50 ps at the Hartree-Fock (HF) level of theory. A predominant 4-coordinate solvation structure with a maximum probability of the Zn-N distance at approximately 2.1 A was observed, which seems to be involved in the associative mode of water exchange reactions to produce a short-lived, 5-coordinated trigonal bipyramidal structure. Several sets of structural and dynamical parameters such as radial distribution functions (RDF), coordination number distributions (CND), angular distributions (ADF), ligands' mean residence times (MRT) and ion-ligand stretching frequencies have been evaluated in order to get an in depth knowledge of the physical and chemical properties of the tetraamminezinc(ii) complex in aqueous solution. A comparative study of the tetraamminezinc(ii) complex with previously published mono-, di- and triamminezinc(ii) complexes has been also performed, which yielded significant insights into the complex properties as a function of an increasing number of first-shell ammonia ligands.
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Affiliation(s)
- M Qaiser Fatmi
- Department of Chemistry, University of California at Riverside, Riverside, CA-92507, USA.
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155
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156
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D’Angelo P, Migliorati V, Guidoni L. Hydration Properties of the Bromide Aqua Ion: the Interplay of First Principle and Classical Molecular Dynamics, and X-ray Absorption Spectroscopy. Inorg Chem 2010; 49:4224-31. [DOI: 10.1021/ic9025574] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Paola D’Angelo
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Valentina Migliorati
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Leonardo Guidoni
- Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università degli Studi dell’Aquila, via Campo di Pile, zona industriale di Pile, 67100, L’Aquila, Italy
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157
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Tongraar A, Hannongbua S, Rode BM. QM/MM MD Simulations of Iodide Ion (I−) in Aqueous Solution: A Delicate Balance between Ion−Water and Water−Water H-Bond Interactions. J Phys Chem A 2010; 114:4334-9. [DOI: 10.1021/jp910435d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anan Tongraar
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Supot Hannongbua
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Bernd Michael Rode
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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158
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Lim LHV, Bhattacharjee A, Asam SS, Hofer TS, Randolf BR, Rode BM. Structural and dynamical aspects of the unsymmetric hydration of Sb(III): an ab initio quantum mechanical charge field molecular dynamics simulation. Inorg Chem 2010; 49:2132-40. [PMID: 20121188 DOI: 10.1021/ic901737y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation was performed to investigate the behavior of the Sb(3+) ion in aqueous solution. The simulation reveals a significant influence of the residual valence shell electron density on the solvation structure and dynamics of Sb(3+). A strong hemidirectional behavior of the ligand binding pattern is observed for the first hydration shell extending up to the second hydration layer. The apparent domain partitioned structural behavior was probed by solvent reorientational kinetics and three-body distribution functions. The three-dimensional hydration space was conveniently segmented such that domains having different properties were properly resolved. The approach afforded a fair isolation of localized solvent structural and dynamical motifs that Sb(3+) seems to induce to a remarkable degree. Most intriguing is the apparent impact of the lone pair electrons on the second hydration shell, which offers insight into the mechanistic aspects of hydrogen bonding networks in water. Such electronic effects observed in the hydration of Sb(3+) can only be studied by applying a suitable quantum mechanical treatment including first and second hydration shell as provided by the QMCF ansatz.
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Affiliation(s)
- Len Herald V Lim
- Theoretical Chemistry Division, Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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159
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Bhattacharjee A, Pribil AB, Lim LHV, Hofer TS, Randolf BR, Rode BM. Structural and Dynamic Aspects of Hydration of HAsO4−2: An ab initio QMCF MD Simulation. J Phys Chem B 2010; 114:3921-6. [DOI: 10.1021/jp911860y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anirban Bhattacharjee
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Andreas B. Pribil
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Len Herald V. Lim
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Bernhard R. Randolf
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Bernd M. Rode
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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160
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Kritayakornupong C, Hannongbua S. Temperature effects on the structure and dynamics of the Jahn-Teller distorted Cr(2+) ion in aqueous solution: a hybrid QM/MM molecular dynamics simulation. Dalton Trans 2010; 39:1176-8. [PMID: 20104337 DOI: 10.1039/b918817g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The influences of an elevated temperature on the structure and dynamics of the Jahn-Teller distorted [Cr(H(2)O)(6)](2+) complex have been studied using an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation, showing that the increased temperature affects the lifetime distortions of the hydrated Cr(2+) ion by decreasing the inversion time to 0.5-2 ps.
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Affiliation(s)
- Chinapong Kritayakornupong
- Department of Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand.
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161
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Cooper TE, Armentrout P. Threshold collision-induced dissociation of hydrated cadmium (II): Experimental and theoretical investigation of the binding energies for Cd2+(H2O)n complexes (n=4–11). Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2009.12.053] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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162
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Hofer TS, Pribil AB, Randolf BR, Rode BM. Ab Initio Quantum Mechanical Charge Field Molecular Dynamics—A Nonparametrized First-Principle Approach to Liquids and Solutions. ADVANCES IN QUANTUM CHEMISTRY 2010. [DOI: 10.1016/s0065-3276(10)59007-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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163
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Frick RJ, Hofer TS, Pribil AB, Randolf BR, Rode BM. Structure and dynamics of the UO+2 ion in aqueous solution: an ab initio QMCF-MD study. Phys Chem Chem Phys 2010; 12:11736-43. [DOI: 10.1039/c003169k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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164
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Hofer TS, Rode BM, Pribil AB, Randolf BR. Simulations of Liquids and Solutions Based on Quantum Mechanical Forces. ADVANCES IN INORGANIC CHEMISTRY 2010. [DOI: 10.1016/s0898-8838(10)62004-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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165
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Duvail M, Ruas A, Venault L, Moisy P, Guilbaud P. Molecular Dynamics Studies of Concentrated Binary Aqueous Solutions of Lanthanide Salts: Structures and Exchange Dynamics. Inorg Chem 2009; 49:519-30. [DOI: 10.1021/ic9017085] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Magali Duvail
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, F-30207 Bagnols sur Cèze, France
| | - Alexandre Ruas
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, F-30207 Bagnols sur Cèze, France
| | - Laurent Venault
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, F-30207 Bagnols sur Cèze, France
| | - Philippe Moisy
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, F-30207 Bagnols sur Cèze, France
| | - Philippe Guilbaud
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, F-30207 Bagnols sur Cèze, France
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166
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Di Tommaso D, de Leeuw NH. Structure and dynamics of the hydrated magnesium ion and of the solvated magnesium carbonates: insights from first principles simulations. Phys Chem Chem Phys 2009; 12:894-901. [PMID: 20066374 DOI: 10.1039/b915329b] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report first principles molecular dynamics simulations based on the density functional theory and the Car-Parrinello method to study the structures and dynamics of the hydrated Mg(2+) ion and of the solvated MgHCO(3)(+) and MgCO(3) complexes in aqueous solution. According to these simulations, the first hydration shell of the hydrated magnesium ion consists of six water molecules, whereas in the solvated magnesium bicarbonate and magnesium carbonate complexes the Mg(2+) is mostly five-coordinated, which indicates that when coordinated to magnesium the HCO(3)(-) and CO(3)(2-) anions reduce its the coordination sphere. Our simulations show that the structures of the most stable monomers of magnesium bi-carbonate and magnesium carbonate in solution are Mg[eta(1)-HCO(3)](H(2)O)(4)(+) and Mg[eta(1)-CO(3)](H(2)O)(4), i.e. the preferred hydration number is four, while the (bi-)carbonate is coordinated to the magnesium in a monodentate mode. The analysis of the exchange processes of the water molecules in the first and second hydration shell of Mg(2+) shows that the HCO(3)(-) or CO(3)(2-) ligands affect the dynamics of the magnesium coordination spheres by making its hydration shell more "labile". Furthermore, molecular dynamics simulations of the non-associated Mg(2+)/Cl(-) pair in water suggest that, despite negligible differences in the coordination spheres of Mg(2+), the chloride anion has a significant influence on the water exchange rates in the second hydration shell of Mg(2+).
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Affiliation(s)
- Devis Di Tommaso
- Department of Chemistry, Christopher Ingold Laboratories, University College London, 20 Gordon Street, London, UKWC1H 0AJ.
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167
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Kritayakornupong C. Structural and dynamical properties of the V3+ion in dilute aqueous solution: Anab initioQM/MM molecular dynamics simulation. J Comput Chem 2009; 30:2777-83. [DOI: 10.1002/jcc.21278] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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168
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Kerisit S, Rosso KM. Transition path sampling of water exchange rates and mechanisms around aqueous ions. J Chem Phys 2009; 131:114512. [DOI: 10.1063/1.3224737] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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169
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Bhattacharjee A, Hofer TS, Pribil AB, Randolf BR, Lim LHV, Lichtenberger AF, Rode BM. Revisiting the Hydration of Pb(II): A QMCF MD Approach. J Phys Chem B 2009; 113:13007-13. [DOI: 10.1021/jp905848x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anirban Bhattacharjee
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria, and Technical College HTL Anichstrasse, Innsbruck Anichstrasse, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria, and Technical College HTL Anichstrasse, Innsbruck Anichstrasse, A-6020 Innsbruck, Austria
| | - Andreas B. Pribil
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria, and Technical College HTL Anichstrasse, Innsbruck Anichstrasse, A-6020 Innsbruck, Austria
| | - Bernhard R. Randolf
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria, and Technical College HTL Anichstrasse, Innsbruck Anichstrasse, A-6020 Innsbruck, Austria
| | - Len Herald V. Lim
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria, and Technical College HTL Anichstrasse, Innsbruck Anichstrasse, A-6020 Innsbruck, Austria
| | - Andreas F. Lichtenberger
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria, and Technical College HTL Anichstrasse, Innsbruck Anichstrasse, A-6020 Innsbruck, Austria
| | - Bernd M. Rode
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria, and Technical College HTL Anichstrasse, Innsbruck Anichstrasse, A-6020 Innsbruck, Austria
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170
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Frick RJ, Hofer TS, Pribil AB, Randolf BR, Rode BM. Structure and Dynamics of the UO22+ Ion in Aqueous Solution: An Ab Initio QMCF MD Study. J Phys Chem A 2009; 113:12496-503. [DOI: 10.1021/jp903750r] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert J. Frick
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Andreas B. Pribil
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Bernhard R. Randolf
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Bernd M. Rode
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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171
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Ibuki K, Bopp PA. Molecular dynamics simulations of aqueous LiCl solutions at room temperature through the entire concentration range. J Mol Liq 2009. [DOI: 10.1016/j.molliq.2008.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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172
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Frick RJ, Pribil AB, Hofer TS, Randolf BR, Bhattacharjee A, Rode BM. Structure and dynamics of the U4+ ion in aqueous solution: an ab initio quantum mechanical charge field molecular dynamics study. Inorg Chem 2009; 48:3993-4002. [PMID: 19338289 DOI: 10.1021/ic801554p] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure and dynamics of the stable four-times positively charged uranium(IV) cation in aqueous solution have been investigated by ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) simulation at the Hartree-Fock double-zeta quantum mechanical level. The QMCF-MD approach enables investigations with the accuracy of a quantum mechanics/molecular mechanics approach without the need for the construction of solute-solvent potentials. Angular distribution functions; radial distribution functions; coordination numbers of the first, second, and third shell (9, 19, and 44, respectively); coordination number distribution functions; tilt- and Theta-angle distribution functions; as well as local density corrected triangle distribution functions have been employed for the evaluation of the hydrated ion's structure. Special attention was paid to the determination of the geometry of the first hydration layer, and the results were compared to experimental large-angle X-ray scattering and extended X-ray absorption fine structure data. The solvent dynamics around the ion were also investigated using mean ligand residence times and related data and, resulting from the unavailability of any experimental data, were compared to ions with similar properties.
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Affiliation(s)
- Robert J Frick
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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173
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Duvail M, Vitorge P, Spezia R. Building a polarizable pair interaction potential for lanthanoids(III) in liquid water: A molecular dynamics study of structure and dynamics of the whole series. J Chem Phys 2009; 130:104501. [DOI: 10.1063/1.3081143] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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174
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Payaka A, Tongraar A, Rode BM. Combined QM/MM MD Study of HCOO−−Water Hydrogen Bonds in Aqueous Solution. J Phys Chem A 2009; 113:3291-8. [DOI: 10.1021/jp810341u] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Apirak Payaka
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Anan Tongraar
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Bernd Michael Rode
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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175
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Sikander Azam S, Hofer TS, Randolf BR, Rode BM. Germanium(II) in water: An unusual hydration structure results of a QMCF MD simulation. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.01.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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176
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Kritayakornupong C, Vchirawongkwin V, Rode BM. An ab initio quantum mechanical charge field molecular dynamics simulation of a dilute aqueous HCl solution. J Comput Chem 2009; 31:1785-92. [DOI: 10.1002/jcc.21469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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177
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Vchirawongkwin V, Pribil AB, Rode BM. Ab Initioquantum mechanical charge field study of hydrated bicarbonate ion: Structural and dynamical properties. J Comput Chem 2009; 31:249-57. [DOI: 10.1002/jcc.21308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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178
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Azam SS, Lim LHV, Hofer TS, Randolf BR, Rode BM. Hydrated germanium (II): Irregular structural and dynamical properties revealed by a quantum mechanical charge field molecular dynamics study. J Comput Chem 2009; 31:278-85. [DOI: 10.1002/jcc.21315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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179
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Li M, Duan Z, Zhang Z, Zhang C, Weare J. The structure, dynamics and solvation mechanisms of ions in water from long time molecular dynamics simulations: a case study of CaCl2(aq) aqueous solutions. Mol Phys 2008. [DOI: 10.1080/00268970802634981] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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180
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Pribil AB, Hofer TS, Randolf BR, Rode BM. Structure and dynamics of phosphate ion in aqueous solution: an ab initio QMCF MD study. J Comput Chem 2008; 29:2330-4. [PMID: 18473325 DOI: 10.1002/jcc.20968] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A simulation of phosphate in aqueous solution was carried out employing the new QMCF MD approach which offers the possibility to investigate composite systems with the accuracy of a QMMM method but without the time consuming creation of solute-solvent potential functions. The data of the simulations give a clear picture of the hydration shells of the phosphate anion. The first shell consists of 13 water molecules and each oxygen of the phosphate forms in average three hydrogens bonds to different solvent molecules. Several structural parameters such as radial distribution functions and coordination number distributions allow to fully characterize the embedding of the highly charged phosphate ion in the solvent water. The dynamics of the hydration structure of phosphate are described by mean residence times of the solvent molecules in the first hydration shell and the water exchange rate.
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Affiliation(s)
- Andreas B Pribil
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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181
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The role of second shell quantum effects on the preferential solvation of Li+ in aqueous ammonia: An extended ab initio QM/MM MD simulation with enlarged QM region. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.10.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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182
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Kritayakornupong C, Vchirawongkwin V, Hofer TS, Rode BM. Structural and dynamical properties of hydrogen fluoride in aqueous solution: an ab initio quantum mechanical charge field molecular dynamics simulation. J Phys Chem B 2008; 112:12032-7. [PMID: 18729507 DOI: 10.1021/jp805321c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The novel ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation at the Hartree-Fock level has been employed to investigate hydration structure and dynamics of hydrogen fluoride in aqueous solution. The average H-F bond length of 0.93 A obtained from the QMCF MD simulation is in good agreement with the experimental data. The HHF...Ow distance of 1.62 A was evaluated for the first hydration shell, and 2.00 A was observed for the FHF...Hw distance. The stability of hydrogen bonding is more pronounced in the hydrogen site of hydrogen fluoride, with a single water molecule in this part of the first hydration shell. A wide range of coordination numbers between 3 and 9 with an average value of 5.6 was obtained for the fluorine site. The force constants of 819.1 and 5.9 N/m were obtained for the HHF-FHF and HHF...Ow interactions, respectively, proving the stability of the nondissociated form of hydrogen fluoride in aqueous solution. The mean residence times of 2.1 and 2.5 ps were determined for ligand exchange processes in the neighborhood of fluorine and hydrogen atoms of hydrogen fluoride, respectively, indicating a weak structure-making effect of hydrogen fluoride in water. The corresponding H-bond lifetimes attribute this effect to the H atom site of HF.
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Affiliation(s)
- Chinapong Kritayakornupong
- Department of Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140 Thailand.
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183
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Hofer TS, Randolf BR, Rode BM. Al(III) hydration revisited. An ab initio quantum mechanical charge field molecular dynamics study. J Phys Chem B 2008; 112:11726-33. [PMID: 18729393 DOI: 10.1021/jp802663h] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To assess the novel quantum mechanical charge field (QMCF) molecular dynamics (MD) approach, two simulations of hydrated Al(III) have been carried out, as this system proved to be a well-suited test case for hybrid ab initio/molecular mechanics simulations. Two different population analysis schemes according to Mulliken and Lowdin have been applied to evaluate the atomic charges in the QM region. It is shown that the QMCF MD approach yields a substantially improved description of the system and that, due to the fact that solute-solvent potentials can be renounced, the QMCF MD framework is a more convenient approach to investigate solvated systems compared to conventional ab initio QM/MM MD approaches.
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Affiliation(s)
- Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, Innsbruck, Austria
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184
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185
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Hofer TS, Randolf BR, Rode BM. The hydration of the mercury(I)-dimer – A quantum mechanical charge field molecular dynamics study. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.12.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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186
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Laage D, Hynes JT. On the Residence Time for Water in a Solute Hydration Shell: Application to Aqueous Halide Solutions. J Phys Chem B 2008; 112:7697-701. [DOI: 10.1021/jp802033r] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Damien Laage
- Ecole Normale Supérieure, Département de Chimie, 24 rue Lhomond, F-75005 Paris, France, CNRS, UMR 8640 PASTEUR, F-75005 Paris, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309
| | - James T. Hynes
- Ecole Normale Supérieure, Département de Chimie, 24 rue Lhomond, F-75005 Paris, France, CNRS, UMR 8640 PASTEUR, F-75005 Paris, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309
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187
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188
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Fatmi MQ, Hofer TS, Randolf BR, Rode BM. Exploring Structure and Dynamics of the Diaquotriamminezinc(II) Complex by QM/MM MD Simulation. J Phys Chem B 2008; 112:5788-94. [DOI: 10.1021/jp710270z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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189
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Kritayakornupong C. The Jahn-Teller effect of the Ag2+ ion in aqueous solution: A hybrid ab initio quantum mechanical/molecular mechanical molecular dynamics simulation. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.02.103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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190
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HOFER THOMASS, RANDOLF BERNHARDR, RODE BERNDM. Molecular Dynamics Simulation Methods including Quantum Effects. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2008. [DOI: 10.1007/978-1-4020-8270-2_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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191
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Hofer TS, Pribil AB, Randolf BR. Capabilities of chemical simulation methods in the elucidation of structure and dynamics of solutions. PURE APPL CHEM 2008. [DOI: 10.1351/pac200880061195] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
As a result of recent methodological developments in connection with enhanced computational capacity, theoretical methods have become increasingly valuable and reliable tools for the investigation of solutions. Simulation techniques utilizing a quantum mechanical (QM) approach for the treatment of the chemically most relevant region so-called hybrid quantum mechanical/molecular mechanical (QM/MM) simulations have reached a level of accuracy that often equals or may even surpass experimental methods. The latter is true in particular whenever ultrafast (i.e., picosecond) dynamics prevail, such as in labile hydrates or structure-breaking systems. The recent development of an improved QM/MM framework, the quantum mechanical charge field (QMCF) ansatz, enables a broad spectrum of solute systems to be elucidated. As this novel methodology does not require any solute solvent potential functions, the applicability of the QMCF method is straightforward and universal. This advantage is bought, however, at the price of a substantial increase of the QM subregion, and an attendant increase in computational periods to levels of months, and even a year, despite parallelizing high-performance computing (HPC) clusters. Molecular dynamics (MD) simulations of chemical systems showing increasing complexity have been performed, and demonstrate the superiority of the QMCF ansatz over conventional QM/MM schemes. The systems studied include Pd2+, Pt2+, and Hg22+, as well as composite anions such as PO43- and ClO4-.
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Affiliation(s)
- Thomas S. Hofer
- 1Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Andreas B. Pribil
- 1Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Bernhard R. Randolf
- 1Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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192
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Tongraar A, Hannongbua S. Solvation Structure and Dynamics of Ammonium (NH4+) in Liquid Ammonia Studied by HF/MM and B3LYP/MM Molecular Dynamics Simulations. J Phys Chem B 2008; 112:885-91. [DOI: 10.1021/jp076173t] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anan Tongraar
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supot Hannongbua
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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193
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Hesske H, Gloe K. Hydration Behavior of Alkyl Amines and Their Corresponding Protonated Forms. 1. Ammonia and Methylamine. J Phys Chem A 2007; 111:9848-53. [PMID: 17803287 DOI: 10.1021/jp073154a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure and dynamics of hydration of ammonia/ammonium and methylamine/methylammonium systems have been studied by Car-Parrinello molecular dynamics simulation. While methylamine interacts weakly with the aqueous environment, the interaction of ammonia is found to be much stronger than expected. Both protonated species show a highly structured first solvation sphere. The solvent exchange mechanisms for all species were also investigated, along with the geometry of the hydration spheres. Comparison of these exchange mechanisms with that published for the ammonium ion shows only a minor difference. Analysis of the respective distribution functions has allowed insight into the thermodynamics of solvation for both systems. The calculated pKa values (9.23/10.65) correspond very closely with the published experimental values of 9.25 and 10.65.
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Affiliation(s)
- Holger Hesske
- TU Dresden, Department of Chemistry and Food Chemistry, 01062 Dresden, Germany.
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194
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Jiao D, King C, Grossfield A, Darden TA, Ren P. Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential. J Phys Chem B 2007; 110:18553-9. [PMID: 16970483 DOI: 10.1021/jp062230r] [Citation(s) in RCA: 194] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The alkaline earth metals calcium and magnesium are critically involved in many biomolecular processes. To understand the hydration thermodynamics of these ions, we have performed molecular dynamics simulations using a polarizable potential. Particle-mesh Ewald for point multipoles has been applied to the calculation of electrostatic interactions. The parameters in this model have been determined from an ab initio quantum mechanical calculation of dimer interactions between ions and water. Two methods for ion solvation free energy calculation, free energy perturbation, and the Bennett acceptance ratio have been compared. Both predict results consistent with other theoretical estimations while the Bennett approach leads to a much smaller statistical error. Based on the Born theory and the ion-oxygen radial distribution functions, we estimate the effective size of the ions in solution, concluding that K(+) > Na(+) congruent with Ca(2+) > Mg(2+). There appears to be much stronger perturbation in water structure, dynamics, and dipole moment around the divalent cations than the monovalent K(+) and Na(+). The average water coordination numbers for Ca(2+) and Mg(2+) are 7.3 and 6, respectively. The lifetime of water molecules in the first solvation shell of Mg(2+) is on the order of hundreds of picoseconds, in contrast to only few picoseconds for Ca(2+), K(+), or Na(+).
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Affiliation(s)
- Dian Jiao
- Department of Biomedical Engineering, The University of Texas-Austin, Austin, TX 78712, USA
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195
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Abstract
A molecular dynamics (MD) simulation based on a combined ab initio quantum mechanics/molecular mechanics (QM/MM) method has been performed to investigate the solvation structure and dynamics of H3O+ in water. The QM region is a sphere around the central H3O+ ion, and contains about 6-8 water molecules. It is treated at the Hartree-Fock (HF) level, while the rest of the system is described by means of classical pair potentials. The Eigen complex (H9O4+) is found to be the most prevalent species in the aqueous solution, partly due to the selection scheme of the center of the QM region. The QM/MM results show that the Eigen complex frequently converts back and forth into the Zundel (H5O2+) structure. Besides the three nearest-neighbor water molecules directly hydrogen-bonded to H3O+, other neighbor waters, such as a fourth water molecule which interacts preferentially with the oxygen atom of the hydronium ion, are found occasionally near the ion. Analyses of the water exchange processes and the mean residence times of water molecules in the ion's hydration shell indicate that such next-nearest neighbor water molecules participate in the rearrangement of the hydrogen bond network during fluctuative formation of the Zundel ion and, thus, contribute to the Grotthuss transport of the proton.
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Affiliation(s)
- Pathumwadee Intharathep
- School of Chemistry, Institute of Science, Suranaree University of Technology, 30000 Nakhon Ratchasima, Thailand
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196
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Duvail M, Souaille M, Spezia R, Cartailler T, Vitorge P. Pair interaction potentials with explicit polarization for molecular dynamics simulations of La3+ in bulk water. J Chem Phys 2007; 127:034503. [PMID: 17655444 DOI: 10.1063/1.2751503] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Pair interaction potentials (IPs) were defined to describe the La(3+)-OH(2) interaction for simulating the La(3+) hydration in aqueous solution. La(3+)-OH(2) IPs are taken from the literature or parametrized essentially to reproduce ab initio calculations at the second-order Moller-Plesset level of theory on La(H(2)O)(8) (3+). The IPs are compared and used with molecular dynamics (MD) including explicit polarization, periodic boundary conditions of La(H(2)O)(216) (3+) boxes, and TIP3P water model modified to include explicit polarization. As expected, explicit polarization is crucial for obtaining both correct La-O distances (r(La-O)) and La(3+) coordination number (CN). Including polarization also modifies hydration structure up to the second hydration shell and decreases the number of water exchanges between the La(3+) first and second hydration shells. r(La-O) ((1))=2.52 A and CN((1))=9.02 are obtained here for our best potential. These values are in good agreement with experimental data. The tested La-O IPs appear to essentially account for the La-O short distance repulsion. As a consequence, we propose that most of the multibody effects are correctly described by the explicit polarization contributions even in the first La(3+) hydration shell. The MD simulation results are slightly improved by adding a-typically negative 1r(6)-slightly attractive contribution to the-typically exponential-repulsive term of the La-O IP. Mean residence times are obtained from MD simulations for a water molecule in the first (1082 ps) and second (7.6 ps) hydration shells of La(3+). The corresponding water exchange is a concerted mechanism: a water molecule leaving La(H(2)O)(9) (3+) in the opposite direction to the incoming water molecule. La(H(2)O)(9) (3+) has a slightly distorded "6+3" tricapped trigonal prism D(3h) structure, and the weakest bonding is in the medium triangle, where water exchanges take place.
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Affiliation(s)
- Magali Duvail
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, CNRS UMR 8587, Université d'Evry Val d'Essonne, Boulevard F. Mitterrand, 91025 Evry Cedex, France
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197
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198
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Fatmi MQ, Hofer TS, Randolf BR, Rode BM. Stability of different zinc(II)-diamine complexes in aqueous solution with respect to structure and dynamics: a QM/MM MD study. J Phys Chem B 2007; 111:151-8. [PMID: 17201439 DOI: 10.1021/jp0654213] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the context of our detailed study of the chemical behavior of aquo- and ammine-Zn(II) complexes, ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations were performed at the Hartree-Fock (HF) level for the zinc(II)-diamine complexes in aqueous solution. The initial structures of cis and trans isomers of the tetraaquodiamminezinc(II) complex were found to transform into the triaquodiamminezinc(II) complex by releasing one water ligand after approximately 6 and approximately 22 ps of simulation time, respectively. The structural and dynamical properties of these three zinc complexes, i.e., cis-[Zn(NH3)2(H2O)4]2+, trans-[Zn(NH3)2(H2O)4]2+, and [Zn(NH3)2(H2O)3]2+, were analyzed in terms of radial distribution functions (RDF), coordination number distributions (CND), angular distribution functions (ADF), tilt and theta angle distributions, ligands' mean residence times (MRTs), and ion-ligand stretching frequencies. One considerably elongated Zn-O bond of 2.43 A was observed in the case of the cis isomer for one of the water ligands located in the trans position to an ammonia ligand. In the trans isomer the average Zn-O bond length was observed to be 2.23 A, while in the triaquodiamminezinc(II) complex two distinct Zn-O bonds, namely 2.12 A for the ligands in the trigonal plane and 2.26 A for axial water molecules, were observed. As both of the octahedral isomers are transformed into the pentacoordinated structure within the picosecond range, they might be regarded as "metastable species or intermediates", while the triaquodiamminezinc(II) complex is the most stable species of the zinc(II)-diamine complex in aqueous solution.
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Affiliation(s)
- M Qaiser Fatmi
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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199
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Vchirawongkwin V, Rode BM, Persson I. Structure and Dynamics of Sulfate Ion in Aqueous SolutionAn ab initio QMCF MD Simulation and Large Angle X-ray Scattering Study. J Phys Chem B 2007; 111:4150-5. [PMID: 17402778 DOI: 10.1021/jp0702402] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hydrated sulfate ion has been characterized in aqueous solution in structural and dynamic aspects using ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) simulation and large angle X-ray scattering (LAXS) methods. The LAXS data show an average coordination number of the sulfate ion of up to 12 water molecules bound through hydrogen bonding, while the QMCF MD simulation displays a wide range of coordination numbers between 8 and 14 with an average value of approximately 11. The Os...Ow distance cannot be distinguished from the Ow...Ow distance in the LAXS experiment; the weighted mean O...O distance is 2.880(10) A. In the simulation, the Os...Ow and Ow...Ow distances are found to be very similar, namely, 2.86 and 2.84 A, respectively. The S-Os bond and S...Ow distance have been determined by the LAXS experiment as 1.495(6) and 3.61(2) A, respectively, indicating an average nearly tetrahedral S-Os...Ow angle. The approximately 5% deviations of simulation distances (1.47 and 3.82 A) from the experimental ones can probably be ascribed to the neglect of correlation energy in the quantum mechanical method. The mean residence time of water ligands at O atoms, 2.57 ps, is longer than that in pure water, 1.7 ps, characterizing the sulfate ion as a weak structure maker.
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Affiliation(s)
- Viwat Vchirawongkwin
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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200
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Heyden A, Lin H, Truhlar DG. Adaptive Partitioning in Combined Quantum Mechanical and Molecular Mechanical Calculations of Potential Energy Functions for Multiscale Simulations. J Phys Chem B 2007; 111:2231-41. [PMID: 17288477 DOI: 10.1021/jp0673617] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In many applications of multilevel/multiscale methods, an active zone must be modeled by a high-level electronic structure method, while a larger environmental zone can be safely modeled by a lower-level electronic structure method, molecular mechanics, or an analytic potential energy function. In some cases though, the active zone must be redefined as a function of simulation time. Examples include a reactive moiety diffusing through a liquid or solid, a dislocation propagating through a material, or solvent molecules in a second coordination sphere (which is environmental) exchanging with solvent molecules in an active first coordination shell. In this article, we present a procedure for combining the levels smoothly and efficiently in such systems in which atoms or groups of atoms move between high-level and low-level zones. The method dynamically partitions the system into the high-level and low-level zones and, unlike previous algorithms, removes all discontinuities in the potential energy and force whenever atoms or groups of atoms cross boundaries and change zones. The new adaptive partitioning (AP) method is compared to Rode's "hot spot" method and Morokuma's "ONIOM-XS" method that were designed for multilevel molecular dynamics (MD) simulations. MD simulations in the microcanonical ensemble show that the AP method conserves both total energy and momentum, while the ONIOM-XS method fails to conserve total energy and the hot spot method fails to conserve both total energy and momentum. Two versions of the AP method are presented, one scaling as O(2N) and one with linear scaling in N, where N is the number of groups in a buffer zone separating the active high-level zone from the environmental low-level zone. The AP method is also extended to systems with multiple high-level zones to allow, for example, the study of ions and counterions in solution using the multilevel approach.
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Affiliation(s)
- Andreas Heyden
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA.
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