101
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Payaka A, Yotmanee P, Tongraar A. Characteristics of the “Hypercoordination” of hydroxide (OH−) in water: A comparative study of HF/MM and B3LYP/MM MD simulations. J Mol Liq 2013. [DOI: 10.1016/j.molliq.2013.09.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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102
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Canaval LR, Weiss AK, Rode BM. Structure and dynamics of the Th4+-ion in aqueous solution – An ab initio QMCF-MD study. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.08.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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103
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Moin ST, Hofer TS, Weiss AKH, Rode BM. Dynamics of ligand exchange mechanism at Cu(II) in water: An ab initio quantum mechanical charge field molecular dynamics study with extended quantum mechanical region. J Chem Phys 2013; 139:014503. [DOI: 10.1063/1.4811114] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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104
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Weiss AKH, Hofer TS. Urea in aqueous solution studied by quantum mechanical charge field-molecular dynamics (QMCF-MD). MOLECULAR BIOSYSTEMS 2013; 9:1864-76. [PMID: 23636218 DOI: 10.1039/c3mb25522k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work presents a quantum mechanical charge field-molecular dynamics (QMCF-MD) simulation of urea in dilute aqueous solution. Detailed data for structure and dynamics are provided and compared to previous works of other groups. Radial and angular distributions are employed, as well as higher degree spatial investigations, two-dimensional particle mapping, volume maps and the previously proposed SLICE formalism. Information on dynamical properties are presented in the form of hydrogen bond correlation functions and mean lifetime analysis based on weighted Voronoi decomposition. Dihedral and tilt/theta angle distributions substantiate the previous findings of other groups, that urea is far from being planar within aqueous solution. In addition to the analysis of the complete hydration shell, several specific regions of hydration have been identified, for which individual analysis has been performed in terms of hydrogen bond lifetime correlation functions and re-orientational times. A decomposition study based on Laguerre tessellation further investigates the structure and dynamics of the individual hydration layers. It is found that urea does not show properties found in the case of typical structure breaking agents, such as Rb(+) or Cs(+), which is in accordance with spectroscopic data of Rezus and Bakker.
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Affiliation(s)
- Alexander K H Weiss
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria.
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105
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Lutz OMD, Messner CB, Hofer TS, Glätzle M, Huck CW, Bonn GK, Rode BM. Combined Ab Initio Computational and Infrared Spectroscopic Study of the cis- and trans-Bis(glycinato)copper(II) Complexes in Aqueous Environment. J Phys Chem Lett 2013; 4:1502-1506. [PMID: 26282305 DOI: 10.1021/jz400288c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The cis- and trans-bis(glycinato)copper(II) complexes in aqueous solution have been investigated by means of a combined theoretical and experimental approach. The conducted quantum mechanical charge field molecular dynamics (QMCF-MD) studies, being the first quantum mechanical simulations of organometallic complexes by this method, yielded accurate structural details of the investigated isomers as well as novel dynamic data, which has successfully been confirmed and extended by subsequent mid-infrared measurements. The spectroscopic results, critically assessed by adjacent multivariate data analysis, indicate an isomeric stability at ambient conditions, vanishing at elevated temperatures.
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Affiliation(s)
- Oliver M D Lutz
- †Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, ‡Institute of Analytical Chemistry and Radiochemistry, and ⊥General and Inorganic Chemistry Divison, Institute of General, Inorganic and Theoretical Chemistry, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Christoph B Messner
- †Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, ‡Institute of Analytical Chemistry and Radiochemistry, and ⊥General and Inorganic Chemistry Divison, Institute of General, Inorganic and Theoretical Chemistry, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Thomas S Hofer
- †Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, ‡Institute of Analytical Chemistry and Radiochemistry, and ⊥General and Inorganic Chemistry Divison, Institute of General, Inorganic and Theoretical Chemistry, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Matthias Glätzle
- †Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, ‡Institute of Analytical Chemistry and Radiochemistry, and ⊥General and Inorganic Chemistry Divison, Institute of General, Inorganic and Theoretical Chemistry, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Christian W Huck
- †Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, ‡Institute of Analytical Chemistry and Radiochemistry, and ⊥General and Inorganic Chemistry Divison, Institute of General, Inorganic and Theoretical Chemistry, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Günther K Bonn
- †Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, ‡Institute of Analytical Chemistry and Radiochemistry, and ⊥General and Inorganic Chemistry Divison, Institute of General, Inorganic and Theoretical Chemistry, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Bernd M Rode
- †Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, ‡Institute of Analytical Chemistry and Radiochemistry, and ⊥General and Inorganic Chemistry Divison, Institute of General, Inorganic and Theoretical Chemistry, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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106
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Sripa P, Tongraar A, Kerdcharoen T. “Structure-Making” Ability of Na+ in Dilute Aqueous Solution: An ONIOM-XS MD Simulation Study. J Phys Chem A 2013; 117:1826-33. [DOI: 10.1021/jp312230g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pattrawan Sripa
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Anan Tongraar
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Teerakiat Kerdcharoen
- Department of Physics and NANOTEC Center
of Excellence, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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107
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Bogatko S, Cauët E, Bylaska E, Schenter G, Fulton J, Weare J. The aqueous Ca2+ system, in comparison with Zn2+, Fe3+, and Al3+: an ab initio molecular dynamics study. Chemistry 2013; 19:3047-60. [PMID: 23315704 DOI: 10.1002/chem.201202821] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Indexed: 11/08/2022]
Abstract
Herein, we report on the structure and dynamics of the aqueous Ca(2+) system studied by using ab initio molecular dynamics (AIMD) simulations. Our detailed study revealed the formation of well-formed hydration shells with characteristics that were significantly different to those of bulk water. To facilitate a robust comparison with state-of-the-art X-ray absorption fine structure (XAFS) data, we employ a 1st principles MD-XAFS procedure and directly compare simulated and experimental XAFS spectra. A comparison of the data for the aqueous Ca(2+) system with those of the recently reported Zn(2+), Fe(3+), and Al(3+) species showed that many of their structural characteristics correlated well with charge density on the cation. Some very important exceptions were found, which indicated a strong sensitivity of the solvent structure towards the cation's valence electronic structure. Average dipole moments for the 2nd shell of all cations were suppressed relative to bulk water.
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Affiliation(s)
- Stuart Bogatko
- Chemistry and Biochemistry Department, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA.
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108
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Wolthers M, Di Tommaso D, Du Z, de Leeuw NH. Variations in calcite growth kinetics with surface topography: molecular dynamics simulations and process-based growth kinetics modelling. CrystEngComm 2013. [DOI: 10.1039/c3ce40249e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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109
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Migliorati V, D'Angelo P. A quantum mechanics, molecular dynamics and EXAFS investigation into the Hg2+ ion solvation properties in methanol solution. RSC Adv 2013. [DOI: 10.1039/c3ra43412e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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110
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Trinapakul M, Kritayakornupong C, Tongraar A, Vchirawongkwin V. Active site of the solvated thiosulfate ion characterized by hydration structures and dynamics. Dalton Trans 2013; 42:10807-17. [PMID: 23783566 DOI: 10.1039/c3dt50329a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Montira Trinapakul
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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111
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Migliorati V, Mancini G, Tatoli S, Zitolo A, Filipponi A, De Panfilis S, Di Cicco A, D’Angelo P. Hydration Properties of the Zn2+ Ion in Water at High Pressure. Inorg Chem 2012; 52:1141-50. [DOI: 10.1021/ic302530k] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Valentina Migliorati
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le Aldo Moro 5, 00185 Roma, Italy
| | - Giordano Mancini
- CASPUR, Inter-University Consortium for Supercomputing in Research, via dei Tizii
6b, 00185 Roma, Italy
- Scuola Normale Superiore, Classe di Scienze, Pisa,
Italy
| | - Simone Tatoli
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le Aldo Moro 5, 00185 Roma, Italy
| | - Andrea Zitolo
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le Aldo Moro 5, 00185 Roma, Italy
| | - Adriano Filipponi
- Dipartimento di Scienze
Fisiche e Chimiche, Università degli Studi dell’Aquila, Via Vetoio, 67100 L’Aquila, Italy
| | - Simone De Panfilis
- Centre for Life Nano Science - IIT@Sapienza, Dipartimento
di Fisica, Università di Roma “La Sapienza”, P.le Aldo Moro 2, 00185 Roma, Italy
| | - Andrea Di Cicco
- CNISM, Sezione di Fisica, Scuola di Scienze e Tecnologie, Università di Camerino, 62032 Camerino (MC),
Italy
| | - Paola D’Angelo
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le Aldo Moro 5, 00185 Roma, Italy
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112
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Réal F, Trumm M, Schimmelpfennig B, Masella M, Vallet V. Further insights in the ability of classical nonadditive potentials to model actinide ion-water interactions. J Comput Chem 2012; 34:707-19. [DOI: 10.1002/jcc.23184] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 09/12/2012] [Accepted: 10/19/2012] [Indexed: 11/06/2022]
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113
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Vchirawongkwin V, Kritayakornupong C, Tongraar A, Rode BM. Characterization of structure and dynamics of an aqueous scandium(III) ion by an extended ab initio QM/MM molecular dynamics simulation. Dalton Trans 2012; 41:11889-97. [PMID: 22914797 DOI: 10.1039/c2dt31117h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydration structure and dynamics of an aqueous Sc(III) solution were characterized by means of an extended ab initio quantum mechanical/molecular dynamical (QM/MM) molecular dynamics simulation at Hartree-Fock level. A monocapped trigonal prismatic structure composed of seven water molecules surrounding scandium(III) ion was proposed by the QM/MM simulation including the quantum mechanical effects for the first and second hydration shells. The mean Sc(III)-O bond length of 2.14 Å was identified for six prism water molecules with one capping water located at around 2.26 Å, reproducing well the X-ray diffraction data. The Sc(III)-O stretching frequency of 432 cm(-1) corresponding to a force constant of 130 N m(-1), evaluated from the enlarged QM/MM simulation, is in good agreement with the experimentally determined value of 430 cm(-1) (128 N m(-1)). Various water exchange processes in the second hydration shell of the hydrated Sc(III) ion predict a mean ligand residence time of 7.3 ps.
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Affiliation(s)
- Viwat Vchirawongkwin
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
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114
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Thaomola S, Tongraar A, Kerdcharoen T. Insights into the structure and dynamics of liquid water: A comparative study of conventional QM/MM and ONIOM-XS MD simulations. J Mol Liq 2012. [DOI: 10.1016/j.molliq.2012.07.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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115
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Vchirawongkwin V, Pornpiganon C, Kritayakornupong C, Tongraar A, Rode BM. The Stability of Bisulfite and Sulfonate Ions in Aqueous Solution Characterized by Hydration Structure and Dynamics. J Phys Chem B 2012; 116:11498-507. [DOI: 10.1021/jp305648e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Viwat Vchirawongkwin
- Department
of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Chokchai Pornpiganon
- Department
of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Chinapong Kritayakornupong
- Department of Chemistry, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand
| | - Anan Tongraar
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - 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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116
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Analyzing coordination preferences of Mg2+ complexes: insights from computational and database study. Struct Chem 2012. [DOI: 10.1007/s11224-012-0113-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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117
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D'Angelo P, Spezia R. Hydration of Lanthanoids(III) and Actinoids(III): An Experimental/Theoretical Saga. Chemistry 2012; 18:11162-78. [DOI: 10.1002/chem.201200572] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Indexed: 11/06/2022]
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118
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Khan A, Weiss AKH, Uddin R, Randolf BR, Rode BM, Hofer TS. Ab Initio Quantum Mechanical Charge Field Molecular Dynamics Simulation (QMCF-MD) of Bi3+ in Water. J Phys Chem A 2012; 116:8008-14. [DOI: 10.1021/jp301569k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ajmal Khan
- Institute of General, Inorganic,
and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
- H. E. J. Research Institute
of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Alexander K. H. Weiss
- Institute of General, Inorganic,
and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Reaz Uddin
- Institute of General, Inorganic,
and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
- Dr. Panjwani Center for Molecular
Medicine and Drug Research, International Center for Chemical and
Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Bernhard R. Randolf
- Institute of General, Inorganic,
and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Bernd Michael Rode
- Institute of General, Inorganic,
and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Institute of General, Inorganic,
and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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119
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Lutz OMD, Hofer TS, Randolf BR, Weiss AKH, Rode BM. A QMCF-MD investigation of the structure and dynamics of Ce4+ in aqueous solution. Inorg Chem 2012; 51:6746-52. [PMID: 22651096 DOI: 10.1021/ic300385s] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A quantum-mechanical charge-field molecular dynamics simulation has been performed for a tetravalent Ce ion in aqueous solution. In this framework, the complete first and second hydration spheres are treated by ab initio quantum mechanics supplemented by an electrostatic embedding technique, making the construction of non-Coulombic solute-solvent potentials unnecessary. During the 10 ps of simulation time, the structural aspects of the solution were analyzed by various methods. Experimental results such as the mean Ce-O bond distance and the predicted first-shell coordination number were compared to the results obtained from the simulation resolving some ambiguities in the literature. The dynamics of the system were characterized by mean ligand residence times and frequency/force constant calculations. Furthermore, Ce-O and Ce-H angular radial distribution plots were employed, yielding deeper insight into the structural and dynamical aspects of the system.
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Affiliation(s)
- Oliver M D Lutz
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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120
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Spezia R, Beuchat C, Vuilleumier R, D’Angelo P, Gagliardi L. Unravelling the Hydration Structure of ThX4 (X = Br, Cl) Water Solutions by Molecular Dynamics Simulations and X-ray Absorption Spectroscopy. J Phys Chem B 2012; 116:6465-75. [DOI: 10.1021/jp210350b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Riccardo Spezia
- CNRS, Laboratoire Analyse et
Modélisation pour la Biologie et l’Environnement, UMR 8587 Université d’Evry Val d’Essonne, 91025 Evry Cedex, France
| | - Cesar Beuchat
- Department of Physical Chemistry, University of Geneva, 30 Quai Ernest Ansermet, CH-1211
Geneva, Switzerland
| | - Rodolphe Vuilleumier
- Ecole Normale Supérieure, Département
de Chimie, 24, rue Lhomond, 75005 Paris, France,
and UPMC Univ Paris 06, 4, Place Jussieu,
75005 Paris, UMR 8640 CNRS-ENS-UPMC, France
| | - Paola D’Angelo
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5,
00185 Roma, Italy
| | - Laura Gagliardi
- Department
of Chemistry and
Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United
States
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121
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Bhattacharjee A, Pribil AB, Randolf BR, Rode BM, Hofer TS. Hydration of Mg2+ and its influence on the water hydrogen bonding network via ab initio QMCF MD. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.03.049] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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122
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Mooney BL, Corrales LR, Clark AE. Novel Analysis of Cation Solvation Using a Graph Theoretic Approach. J Phys Chem B 2012; 116:4263-75. [DOI: 10.1021/jp300193j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Barbara Logan Mooney
- Department of Chemistry and
Biochemistry, University of Arizona, Tucson,
Arizona 87521, United States
| | - L. Rene Corrales
- Department of Chemistry and
Biochemistry, University of Arizona, Tucson,
Arizona 87521, United States
| | - Aurora E. Clark
- Department of Chemistry, Washington State University, Pullman, Washington 99164,
United States
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123
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Trumm M, Martínez YOG, Réal F, Masella M, Vallet V, Schimmelpfennig B. Modeling the hydration of mono-atomic anions from the gas phase to the bulk phase: The case of the halide ions F−, Cl−, and Br−. J Chem Phys 2012; 136:044509. [DOI: 10.1063/1.3678294] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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124
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Eklund L, Hofer TS, Pribil AB, Rode BM, Persson I. On the structure and dynamics of the hydrated sulfite ion in aqueous solution – an ab initio QMCF MD simulation and large angle X-ray scattering study. Dalton Trans 2012; 41:5209-16. [DOI: 10.1039/c2dt12467j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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125
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Pedevilla PA, Hofer TS, Randolf BR, Rode BM. Simulation of Ir(III) in Aqueous Solution: The Most Inert Ion Hydrate. Aust J Chem 2012. [DOI: 10.1071/ch12303] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) approach at Hartree-Fock level was used to simulate the tripositive iridium ion in aqueous solution, evaluating structure and dynamics of its hydrate complex. The Ir-OH2 force constant was of particular interest because of the observed high inertness of Ir(iii) in aqueous solution. Iridium forms three hydration shells. Six water molecules coordinate the ion in the first hydration shell in a well defined octahedral geometry, and no exchanges took place during the simulation time of 15 ps. The second hydration shell is very flexible, however, with a mean residence time of a water molecule of 3.6 ps. The third shell can be identified only by a slight ordering effect. This investigation classified the Ir-OH2 force constant as the strongest ion-OH2 bond known to date.
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126
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An ab initio quantum mechanical charge field molecular dynamics simulation of hydrogen peroxide in water. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2011.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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127
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Simulation of electronic excitation in the liquid state by quantum mechanical charge field molecular dynamics. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2011.11.066] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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128
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Wanprakhon S, Tongraar A, Kerdcharoen T. Hydration structure and dynamics of K+ and Ca2+ in aqueous solution: Comparison of conventional QM/MM and ONIOM-XS MD simulations. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.10.048] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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129
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Vchirawongkwin V, Kritayakornupong C, Tongraar A, Rode BM. Symmetry Breaking and Hydration Structure of Carbonate and Nitrate in Aqueous Solutions: A Study by Ab Initio Quantum Mechanical Charge Field Molecular Dynamics. J Phys Chem B 2011; 115:12527-36. [DOI: 10.1021/jp204809f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Viwat Vchirawongkwin
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Chinapong Kritayakornupong
- Department of Chemistry, Faculty of Science, King Mongkut's University of Technology, Thonburi, Bangkok 10140, Thailand
| | - Anan Tongraar
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - 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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130
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Vchirawongkwin V, Kritayakornupong C, Tongraar A. Characterization of the structure and dynamics of an aqueous Hg2+ solution by an ab initio molecular dynamics study. J Mol Liq 2011. [DOI: 10.1016/j.molliq.2011.08.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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131
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Boisson J, Stirnemann G, Laage D, Hynes JT. Water reorientation dynamics in the first hydration shells of F- and I-. Phys Chem Chem Phys 2011; 13:19895-901. [PMID: 21915404 DOI: 10.1039/c1cp21834d] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular dynamics and analytic theory results are presented for the reorientation dynamics of first hydration shell water molecules around fluoride and iodide anions. These ions represent the extremes of the (normal) halide series in terms of their size and conventional structure-making and -breaking categorizations. The simulated reorientation times are consistent with NMR and ultrafast IR experimental results. They are also in good agreement with the theoretical predictions of the analytic Extended Jump Model. Analysis through this model shows that while sudden, large amplitude jumps (in which the reorienting water exchanges hydrogen-bond partners) are the dominant reorientation pathway for the I(-) case, they are comparatively less important for the F(-) case. In particular, the diffusive reorientation of an intact F(-)···H(2)O hydrogen-bonded pair is found to be most important for the reorientation time, a feature related to the greater hydrogen-bond strength for the F(-)···H(2)O pair. The dominance of this effect for e.g. multiply charged ions is suggested.
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Affiliation(s)
- Jean Boisson
- Ecole Normale Supérieure, Chemistry Department, UMR CNRS-ENS-UPMC 8640, Paris, France
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132
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Somtua T, Tongraar A. Correlation effects on the structure and dynamics of the H3O+ hydrate: B3LYP/MM and MP2/MM MD simulations. Phys Chem Chem Phys 2011; 13:16190-6. [PMID: 21847469 DOI: 10.1039/c1cp20823c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations, namely B3LYP/MM and MP2/MM, have been performed to investigate the possible influence of electron correlation on the structure and dynamics of the H(3)O(+) hydrate. In comparison to the previously published HF/MM results, both B3LYP/MM and MP2/MM simulations clearly reveal stronger H(3)O(+)-water hydrogen bond interactions, which are reflected in a slightly greater compactness of the H(3)O(+) hydrate. However, the B3LYP/MM simulation, although providing structural details very close to the MP2/MM data, shows an artificially slow dynamic nature of some first shell water molecules as a consequence of the formation of a long-lived H(3)O(+)···H(2)O hydrogen bonding structure.
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Affiliation(s)
- Thanawat Somtua
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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133
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Lichtenberger PM, Ellmerer AE, Hofer TS, Randolf BR, Rode BM. Gold(I) and Mercury(II)—Isoelectronic Ions with Strongly Different Chemistry: Ab Initio QMCF Molecular Dynamics Simulations of Their Hydration Structure. J Phys Chem B 2011; 115:5993-8. [DOI: 10.1021/jp110736y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - T. S. Hofer
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - B. R. Randolf
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - B. 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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134
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Atta-Fynn R, Bylaska EJ, Schenter GK, de Jong WA. Hydration Shell Structure and Dynamics of Curium(III) in Aqueous Solution: First Principles and Empirical Studies. J Phys Chem A 2011; 115:4665-77. [DOI: 10.1021/jp201043f] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Raymond Atta-Fynn
- W. R. Wiley Environmental Molecular Sciences Laboratory and ‡Chemical and Material Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Eric J. Bylaska
- W. R. Wiley Environmental Molecular Sciences Laboratory and ‡Chemical and Material Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Gregory K. Schenter
- W. R. Wiley Environmental Molecular Sciences Laboratory and ‡Chemical and Material Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Wibe A. de Jong
- W. R. Wiley Environmental Molecular Sciences Laboratory and ‡Chemical and Material Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
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135
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Cooper TE, Armentrout PB. Sequential bond energies and barrier heights for the water loss and charge separation dissociation pathways of Cd2+(H2O)n, n = 3–11. J Chem Phys 2011; 134:114308. [DOI: 10.1063/1.3553813] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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136
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Moin ST, Lim LHV, Hofer TS, Randolf BR, Rode BM. Sulfur Dioxide in Water: Structure and Dynamics Studied by an Ab Initio Quantum Mechanical Charge Field Molecular Dynamics Simulation. Inorg Chem 2011; 50:3379-86. [DOI: 10.1021/ic102240p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Syed Tarique Moin
- 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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137
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138
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Messner CB, Hofer TS, Randolf BR, Rode BM. Structure and dynamics of the Zr4+ion in water. Phys Chem Chem Phys 2011; 13:224-9. [DOI: 10.1039/c0cp01330g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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139
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Tongraar A, Yotmanee P, Payaka A. Characteristics of CO32−–water hydrogen bonds in aqueous solution: insights from HF/MM and B3LYP/MM MD simulations. Phys Chem Chem Phys 2011; 13:16851-60. [DOI: 10.1039/c1cp21802f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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140
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Vchirawongkwin V, Kritayakornupong C, Rode BM. Structural and dynamical properties and vibrational spectra of bisulfate ion in water: a study by Ab initio quantum mechanical charge field molecular dynamics. J Phys Chem B 2010; 114:11561-9. [PMID: 20707370 DOI: 10.1021/jp105181n] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism was applied to simulate the bisulfate ion, HSO4-, in aqueous solution. The averaged geometry of bisulfate ion supports the separation of six normal modes of the O*-SO3 unit with C3v symmetry from three modes of the OH group in the evaluation of vibrational spectra obtained from the velocity autocorrelation functions (VACFs) with subsequent normal coordinate analyses. The calculated frequencies are in good agreement with the observations in Raman and IR experiments. The difference of the averaged coordination number obtained for the whole molecule (8.0) and the summation over coordinating sites (10.9) indicates some water molecules to be located in the overlapping volumes of individual hydration spheres. The averaged number of hydrogen bonds (H-bonds) during the simulation period (5.8) indicates that some water molecules are situated in the molecular hydration shell with an unsuitable orientation to form a hydrogen bond with the ion. The mean residence time in the surroundings of the bisulfate ion classify it generally as a weak structure-making ion, but the analysis of the individual sites reveals a more complex behavior of them, in particular a strong interaction with a water molecule at the hydrogen site.
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Affiliation(s)
- Viwat Vchirawongkwin
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
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141
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Structure and dynamics of hydrated Ag+: An ab initio quantum mechanical/charge field simulation. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.10.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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142
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The influence of the lone electron pair on structure and dynamics of divalent group IV metal ion hydrates. J Mol Liq 2010. [DOI: 10.1016/j.molliq.2010.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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143
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Azam SS, Hofer TS, Randolf BR, Rode BM. Hydration of sodium(I) and potassium(I) revisited: a comparative QM/MM and QMCF MD simulation study of weakly hydrated ions. J Phys Chem A 2010; 113:1827-34. [PMID: 19203258 DOI: 10.1021/jp8093462] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum mechanical/molecular mechanical (QM/MM) and quantum mechanical charge field (QMCF) molecular (MD) simulations have been performed to describe structural and dynamical properties of Na(I) and K(I) in water and to compare the two approaches. The first and second hydration shells were treated by ab initio quantum mechanics at the restricted Hartree-Fock (RHF) level. The structural data are in good agreement with previously published experimental and theoretical results. A considerable number of water exchange reactions were observed within the first shell during the simulation time of 12 ps. The number of exchange events in both shells is higher in the case of K(I) than Na(I) reflecting the weaker ion-ligand bond strength of K(I). Comparison of the "conventional" QM/MM framework with the QMCF method clearly indicates the latter to be advantageous, as ambiguities arising from the coupling of the subregions occurring in the QM/MM MD simulations did not evolve when the QMCF ansatz was applied.
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Affiliation(s)
- S Sikander Azam
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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144
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Iskrenova-Tchoukova E, Kalinichev AG, Kirkpatrick RJ. Metal cation complexation with natural organic matter in aqueous solutions: molecular dynamics simulations and potentials of mean force. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:15909-15919. [PMID: 20857966 DOI: 10.1021/la102535n] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Natural organic matter (NOM, or humic substance) has a known tendency to form colloidal aggregates in aqueous environments, with the composition and concentration of cationic species in solution, pH, temperature, and the composition of the NOM itself playing important roles. Strong interaction of carboxylic groups of NOM with dissolved metal cations is thought to be the leading chemical interaction in NOM supramolecular aggregation. Computational molecular dynamics (MD) study of the interactions of Na(+), Mg(2+), and Ca(2+) with the carboxylic groups of a model NOM fragment and acetate anions in aqueous solutions provides new quantitative insight into the structure, energetics, and dynamics of the interactions of carboxylic groups with metal cations, their association, and the effects of cations on the colloidal aggregation of NOM molecules. Potentials of mean force and the equilibrium constants describing overall ion association and the distribution of metal cations between contact ion pairs and solvent-separated ions pairs were computed from free MD simulations and restrained umbrella sampling calculations. The results provide insight into the local structural environments of metal-carboxylate association and the dynamics of exchange among these sites. All three cations prefer contact ion pair to solvent-separated ion pair coordination, and Na(+) and Ca(2+) show a strong preference for bidentate contact ion pair formation. The average residence time of a Ca(2+) ion in a contact ion pair with the carboxylic groups is of the order of 0.5 ns, whereas the corresponding residence time of a Na(+) ion is only between 0.02 and 0.05 ns. The average residence times of a Ca(2+) ion in a bidentate coordinated contact ion pair vs a monodentate coordinated contact ion pair are about 0.5 and 0.08 ns, respectively. On the 10 ns time scale of our simulations, aggregation of the NOM molecules occurs in the presence of Ca(2+) but not Na(+) or Mg(2+). These results agree with previous experimental observations and are explained by both Ca(2+) ion bridging between NOM molecules and decreased repulsion between the NOM molecules due to the reduced net charge of the NOM-metal complexes. Simulations on a larger scale are needed to further explore the relative importance of the different aggregation mechanisms and the stability of NOM aggregates.
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145
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Moin ST, Hofer TS, Randolf BR, Rode BM. Structure and dynamics of methanol in water: A quantum mechanical charge field molecular dynamics study. J Comput Chem 2010; 32:886-92. [DOI: 10.1002/jcc.21670] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 07/01/2010] [Accepted: 08/12/2010] [Indexed: 01/07/2023]
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146
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Kritayakornupong C, Vchirawongkwin V, Rode BM. Determination of Structure and Dynamics of the Solvated Bisulfide (HS−) Ion by ab Initio QMCF Molecular Dynamics. J Phys Chem B 2010; 114:12883-7. [DOI: 10.1021/jp104856q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chinapong Kritayakornupong
- Department of Chemistry, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok, 10140 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
| | - Viwat Vchirawongkwin
- Department of Chemistry, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok, 10140 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 M. Rode
- Department of Chemistry, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok, 10140 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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147
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Payaka A, Tongraar A, Rode BM. QM/MM Dynamics of CH3COO−−Water Hydrogen Bonds in Aqueous Solution. J Phys Chem A 2010; 114:10443-53. [DOI: 10.1021/jp105671f] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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148
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Moin ST, Hofer TS, Pribil AB, Randolf BR, Rode BM. A quantum mechanical charge field molecular dynamics study of Fe(2+) and Fe(3+) ions in aqueous solutions. Inorg Chem 2010; 49:5101-6. [PMID: 20441160 DOI: 10.1021/ic1002572] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulations have been performed for aqueous solutions of Fe(2+) and Fe(3+) ions at the Hartree-Fock level of theory to describe and compare their structural and dynamical behavior. The structural features of both hydrated ions are characterized by radial distribution functions that give the maximum probability of the ion-O distance for Fe(2+) and Fe(3+) ions at 2.15 and 2.03 A, respectively. The angular distribution functions of both ions prove the octahedral arrangement of six water ligands, whereas the second shells of these ions differ. Both ions show influence on the water molecules beyond the second shells. The structure-forming abilities of both ions are visible from the ligand mean residence times and ion-O stretching frequencies evaluated for both ions. The substantially improved data obtained from these QMCF-MD simulations show better correlation with available experimental results than the conventional quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) approaches with one hydration shell treated by quantum mechanics.
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Affiliation(s)
- Syed Tarique Moin
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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149
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150
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Cauët E, Bogatko S, Weare JH, Fulton JL, Schenter GK, Bylaska EJ. Structure and dynamics of the hydration shells of the Zn(2+) ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations. J Chem Phys 2010; 132:194502. [PMID: 20499974 DOI: 10.1063/1.3421542] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Results of ab initio molecular dynamics (AIMD) simulations (density functional theory+PBE96) of the dynamics of waters in the hydration shells surrounding the Zn(2+) ion (T approximately 300 K, rho approximately 1 gm/cm(3)) are compared to simulations using a combined quantum and classical molecular dynamics [AIMD/molecular mechanical (MM)] approach. Both classes of simulations were performed with 64 solvating water molecules ( approximately 15 ps) and used the same methods in the electronic structure calculation (plane-wave basis set, time steps, effective mass, etc.). In the AIMD/MM calculation, only six waters of hydration were included in the quantum mechanical (QM) region. The remaining 58 waters were treated with a published flexible water-water interaction potential. No reparametrization of the water-water potential was attempted. Additional AIMD/MM simulations were performed with 256 water molecules. The hydration structures predicted from the AIMD and AIMD/MM simulations are found to agree in detail with each other and with the structural results from x-ray data despite the very limited QM region in the AIMD/MM simulation. To further evaluate the agreement of these parameter-free simulations, predicted extended x-ray absorption fine structure (EXAFS) spectra were compared directly to the recently obtained EXAFS data and they agree in remarkable detail with the experimental observations. The first hydration shell contains six water molecules in a highly symmetric octahedral structure is (maximally located at 2.13-2.15 A versus 2.072 A EXAFS experiment). The widths of the peak of the simulated EXAFS spectra agree well with the data (8.4 A(2) versus 8.9 A(2) in experiment). Analysis of the H-bond structure of the hydration region shows that the second hydration shell is trigonally bound to the first shell water with a high degree of agreement between the AIMD and AIMD/MM calculations. Beyond the second shell, the bonding pattern returns to the tetrahedral structure of bulk water. The AIMD/MM results emphasize the importance of a quantum description of the first hydration shell to correctly describe the hydration region. In these calculations the full d(10) electronic structure of the valence shell of the Zn(2+) ion is retained. The simulations show substantial and complex charge relocation on both the Zn(2+) ion and the first hydration shell. The dipole moment of the waters in the first hydration shell is 3.4 D (3.3 D AIMD/MM) versus 2.73 D bulk. Little polarization is found for the waters in the second hydration shell (2.8 D). No exchanges were seen between the first and the second hydrations shells; however, many water transfers between the second hydration shell and the bulk were observed. For 64 waters, the AIMD and AIMD/MM simulations give nearly identical results for exchange dynamics. However, in the larger particle simulations (256 waters) there is a significant reduction in the second shell to bulk exchanges.
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Affiliation(s)
- Emilie Cauët
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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