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Petrov AI. Quantum chemical modeling of the thermodynamics of the formation of Au(III), Pd(II), and Pt(II) chloride complexes. J Mol Model 2022; 28:391. [DOI: 10.1007/s00894-022-05381-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
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2
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Migliorati V, Fazio G, Pollastri S, Gentili A, Tomai P, Tavani F, D'Angelo P. Solubilization properties and structural characterization of dissociated HgO and HgCl2 in deep eutectic solvents. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115505] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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3
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Theoretical insight on the solvation properties of Zn2+ in pure liquid ammonia: A quantum mechanical molecular charges field molecular dynamics (QMCF-MD) study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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4
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Saleh M, Zam ZZ, Hofer TS. Solvent influence on the presence of axial ligand coordination: A QMCF-MD study of the structural and dynamical properties of Pd(II) and Pd(II) tetra-ammine in aqueous solution. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Saputri WD, Wijaya K, Pranowo HD, Hofer TS. The Jahn-Teller effect in mixed aqueous solution: the solvation of Cu2+ in 18.6% aqueous ammonia obtained from ab initio quantum mechanical charge field molecular dynamics. PURE APPL CHEM 2019. [DOI: 10.1515/pac-2018-1115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
The solvation structure and dynamics of Cu2+ in 18.6 % aqueous ammonia have been investigated using an ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation approach at the Hartree–Fock (HF) level of theory applying the LANL2DZ ECP and Dunning DZP basis sets for Cu2+, ammonia and water, respectively. During a simulation time of 20 ps, only NH3 molecules are observed within the first solvation shell of Cu2+, resulting in the formation of an octahedral [Cu(NH3)6]2+ complex. While no exchange of these ligands with the second solvation shell are observed along the simulation, the monitoring of the associated N-Ntrans distances highlight the dynamics of the associated Jahn-Teller distortions, showing on average 2 elongated axial (2.19 Å) and 4 equatorial Cu–N bonds (2.39 Å). The observed structural properties are found in excellent agreement with experimental studies. In addition, an NBO analysis was carried out, confirming the strong electrostatic character of the Cu2+–NH3 interaction.
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Affiliation(s)
- Wahyu Dita Saputri
- Department of Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
- Austrian-Indonesian Centre for Computational Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
| | - Karna Wijaya
- Department of Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
| | - Harno Dwi Pranowo
- Department of Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
- Austrian-Indonesian Centre for Computational Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
| | - Thomas S. Hofer
- University of Innsbruck , Theoretical Chemistry Division , Innsbruck , Austria
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Prasetyo N, Hünenberger PH, Hofer TS. Single-Ion Thermodynamics from First Principles: Calculation of the Absolute Hydration Free Energy and Single-Electrode Potential of Aqueous Li + Using ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:6443-6459. [PMID: 30284829 DOI: 10.1021/acs.jctc.8b00729] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A recently proposed thermodynamic integration (TI) approach formulated in the framework of quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulations is applied to study the structure, dynamics, and absolute intrinsic hydration free energy Δs GM+,wat◦ of the Li+ ion at a correlated ab initio level of theory. Based on the results, standard values (298.15 K, ideal gas at 1 bar, ideal solute at 1 molal) for the absolute intrinsic hydration free energy [Formula: see text] of the proton, the surface electric potential jump χwat◦ upon entering bulk water, and the absolute single-electrode potential [Formula: see text] of the reference hydrogen electrode are calculated to be -1099.9 ± 4.2 kJ·mol-1, 0.13 ± 0.08 V, and 4.28 ± 0.04 V, respectively, in excellent agreement with the standard values recommended by Hünenberger and Reif on the basis of an extensive evaluation of the available experimental data (-1100 ± 5 kJ·mol-1, 0.13 ± 0.10 V, and 4.28 ± 0.13 V). The simulation results for Li+ are also compared to those for Na+ and K+ from a previous study in terms of relative hydration free energies ΔΔs GM+,wat◦ and relative electrode potentials [Formula: see text]. The calculated values are found to agree extremely well with the experimental differences in standard conventional hydration free energies ΔΔs GM+,wat• and redox potentials [Formula: see text]. The level of agreement between simulation and experiment, which is quantitative within error bars, underlines the substantial accuracy improvement achieved by applying a highly demanding QM/MM approach at the resolution-of-identity second-order Møller-Plesset perturbation (RIMP2) level over calculations relying on purely molecular mechanical or density functional theory (DFT) descriptions. A detailed analysis of the structural and dynamical properties of the Li+ hydrate indicates that a correct description of the solvation structure and dynamics is achieved as well at this level of theory. Consideration of the QM/MM potential-energy components also shows that the partitioning into QM and MM zones does not induce any significant energetic artifact for the system considered.
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Affiliation(s)
- Niko Prasetyo
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria.,Austria-Indonesia Centre (AIC) for Computational Chemistry , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia.,Department of Chemistry, Faculty of Mathematics and Natural Sciences , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie , ETH Zürich, ETH-Hönggerberg , HCI Building , CH-8093 Zürich , Switzerland
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria
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Saleh M, Hofer TS. Square planar or octahedral after all? The indistinct solvation of platinum(ii). Dalton Trans 2018; 47:13032-13045. [DOI: 10.1039/c8dt02169d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The solvation structures of Pd(ii) and Pt(ii) are typically reduced to the well-known square-planar structural motif, although it has been shown, in both experimental and theoretical investigations, that these solutes demonstrate the affinity to bind ligand molecules at elongated distance in axial coordination sites.
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Affiliation(s)
- Muhammad Saleh
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
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Moin ST, Hofer TS. Zinc- and copper-porphyrins in aqueous solution - two similar complexes with strongly contrasting hydration. MOLECULAR BIOSYSTEMS 2017; 12:2288-2295. [PMID: 27194391 DOI: 10.1039/c6mb00133e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We present detailed analysis of the hydration behavior of zinc and copper bound porphyrins treated via ab initio quantum mechanical charge field molecular dynamics which agrees well with available experimental data. The computed metal-water coordination in the case of zinc bound porphyrin demonstrates a strong association of water with zinc compared to the copper-water interaction which correlates well with the calculated free energy of binding. The H-bond dynamics in these hydrated systems yield weaker H-bond interactions as compared to that observed in the case of metal-free porphyrin; nevertheless, the effect of metal association with porphyrin resulted in shifts in the vibrational frequencies. These characteristic data suggest a contrasting behavior between these metalloporphyrins in solution which could also serve to correlate with the properties of biological systems.
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Affiliation(s)
- Syed Tarique Moin
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan.
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria.
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Saleh M, Hofer TS. Palladium(ii) in liquid ammonia: an investigation of structural and dynamical properties by applying quantum mechanical charge field molecular dynamics (QMCF-MD). Dalton Trans 2017; 46:9630-9638. [DOI: 10.1039/c7dt01548h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structural and dynamical properties of Pd2+ in liquid ammonia have been investigated via quantum mechanical charge field molecular dynamics.
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Affiliation(s)
- Muhammad Saleh
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
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Cvitkovic JP, Kaminski GA. Developing multisite empirical force field models for Pt(II) and cisplatin. J Comput Chem 2016; 38:161-168. [PMID: 27859392 DOI: 10.1002/jcc.24665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/12/2016] [Accepted: 10/26/2016] [Indexed: 12/15/2022]
Abstract
We have developed empirical force field parameters for Pt(II) and cisplatin. Two force field frameworks were used-modified OPLS-AA and our second-order polarizable POSSIM. A seven-site model was used for the Pt(II) ion. The goal was to create transferable parameter sets compatible with the force field models for proteins and general organic compounds. A number of properties of the Pt(II) ion and its coordination compounds have been considered, including geometries and energies of the complexes, hydration free energy, and radial distribution functions in water. Comparison has been made with experimental and quantum mechanical results. We have demonstrated that both versions are generally capable of reproducing key properties of the system, but the second-order polarizable POSSIM formalism permits more accurate quantitative results to be obtained. For example, the energy of formation of cisplatin as calculated with the modified OPLS-AA exhibited an error of 9.9%, while the POSSIM error for the same quantity was 6.2%. The produced parameter sets are transferable and suitable to be used in protein-metal binding simulations in which position or even coordination of the ion does not have to be constrained using preexisting knowledge. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- John P Cvitkovic
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Rd, Worcester, Massachusetts, 01609
| | - George A Kaminski
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Rd, Worcester, Massachusetts, 01609
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Melchior A, Tolazzi M, Martínez JM, Pappalardo RR, Sánchez Marcos E. Hydration of Two Cisplatin Aqua-Derivatives Studied by Quantum Mechanics and Molecular Dynamics Simulations. J Chem Theory Comput 2015; 11:1735-44. [DOI: 10.1021/ct500975a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Andrea Melchior
- Department
of Environmental and Physical Chemistry, University of Udine, 33100 Udine, Udine, Italy
| | - Marilena Tolazzi
- Department
of Environmental and Physical Chemistry, University of Udine, 33100 Udine, Udine, Italy
| | - José Manuel Martínez
- Department
of Physical Chemistry, University of Seville, 41012 Seville, Seville, Spain
| | - Rafael R. Pappalardo
- Department
of Physical Chemistry, University of Seville, 41012 Seville, Seville, Spain
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Hofer TS. Perspectives for hybrid ab initio/molecular mechanical simulations of solutions: from complex chemistry to proton-transfer reactions and interfaces. PURE APPL CHEM 2014. [DOI: 10.1515/pac-2014-5019] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
As a consequence of the ongoing development of enhanced computational resources, theoretical chemistry has become an increasingly valuable field for the investigation of a variety of chemical systems. Simulations employing a hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) technique have been shown to be a particularly promising approach, whenever ultrafast (i.e., picosecond) dynamical properties are to be studied, which are in many cases difficult to access via experimental techniques. Details of the quantum mechanical charge field (QMCF) ansatz, an advanced QM/MM protocol, are discussed and simulation results for various systems ranging from simple ionic hydrates to solvated organic molecules and coordination complexes in solution are presented. A particularly challenging application is the description of proton-transfer reactions in chemical simulations, which is a prerequisite to study acidified and basic systems. The methodical requirements for a combination of the QMCF methodology with a dissociative potential model for the description of the solvent are discussed. Furthermore, the possible extension of QM/MM approaches to solid/liquid interfaces is outlined.
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Melchior A, Martínez JM, Pappalardo RR, Sánchez Marcos E. Hydration of Cisplatin Studied by an Effective Ab Initio Pair Potential Including Solute–Solvent Polarization. J Chem Theory Comput 2013; 9:4562-73. [DOI: 10.1021/ct400433c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrea Melchior
- University of Udine, Department of Environmental and
Physical Chemistry, 33100 Udine, Italy
- University of Seville, Department of Physical Chemistry, 41012 Seville, Spain
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Torapava N, Elding LI, Mändar H, Roosalu K, Persson I. Structures of polynuclear complexes of palladium(ii) and platinum(ii) formed by slow hydrolysis in acidic aqueous solution. Dalton Trans 2013; 42:7755-60. [DOI: 10.1039/c3dt32859g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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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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Migliorati V, Zitolo A, Chillemi G, D'Angelo P. Influence of the Second Coordination Shell on the XANES Spectra of the Zn2+ Ion in Water and Methanol. Chempluschem 2012. [DOI: 10.1002/cplu.201100070] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Bowron DT, Beret EC, Martin-Zamora E, Soper AK, Sánchez Marcos E. Axial Structure of the Pd(II) Aqua Ion in Solution. J Am Chem Soc 2011; 134:962-7. [DOI: 10.1021/ja206422w] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel T. Bowron
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | | | | | - Alan K. Soper
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
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Abstract
Based on a series of ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulations, the broad spectrum of structural and dynamical properties of hydrates of trivalent and tetravalent ions is presented, ranging from extreme inertness to immediate hydrolysis. Main group and transition metal ions representative for different parts of the periodic system are treated, as are 2 threefold negatively charged anions. The results show that simple predictions of the properties of the hydrates appear impossible and that an accurate quantum mechanical simulation in cooperation with sophisticated experimental investigations seems the only way to obtain conclusive results.
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Affiliation(s)
| | | | | | - 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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Aullón G, Gómez K, González G, Jansat S, Martínez M, Poli R, Rodríguez-Zubiri M. Kinetico-Mechanistic Information about Alkene Hydroamination with Aniline in Bromide-Rich Ionic Media: Importance of Solvolysis. Inorg Chem 2011; 50:5628-36. [DOI: 10.1021/ic2003222] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gabriel Aullón
- Departament de Química Inorgànica, Universitat de Barcelona, Martí i Franquès 1-11, E-08028 Barcelona, Spain
| | - Kerman Gómez
- Institut Català d’Investigació Química, Avinguda dels Països Catalans 16, E-43007 Tarragona, Spain
| | - Gabriel González
- Institut Català d’Investigació Química, Avinguda dels Països Catalans 16, E-43007 Tarragona, Spain
| | - Susanna Jansat
- Departament de Química Inorgànica, Universitat de Barcelona, Martí i Franquès 1-11, E-08028 Barcelona, Spain
| | - Manuel Martínez
- Departament de Química Inorgànica, Universitat de Barcelona, Martí i Franquès 1-11, E-08028 Barcelona, Spain
| | - Rinaldo Poli
- CNRS, LCC (Laboratoire de Chimie de Coordination), Université de Toulouse, UPS, INP, 205 Route de Narbonne, F-31077 Toulouse, France
- Institut Universitaire de France, 103 Boulevard Saint Michel, 75005 Paris, France
| | - Mireia Rodríguez-Zubiri
- CNRS, LCC (Laboratoire de Chimie de Coordination), Université de Toulouse, UPS, INP, 205 Route de Narbonne, F-31077 Toulouse, France
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Vidossich P, Ortuño MÁ, Ujaque G, Lledós A. Do Metal⋅⋅⋅Water Hydrogen Bonds Hold in Solution? Insight from Ab Initio Molecular Dynamics Simulations. Chemphyschem 2011; 12:1666-8. [DOI: 10.1002/cphc.201100234] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Indexed: 11/11/2022]
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Truflandier LA, Autschbach J. Probing the Solvent Shell with 195Pt Chemical Shifts: Density Functional Theory Molecular Dynamics Study of PtII and PtIV Anionic Complexes in Aqueous Solution. J Am Chem Soc 2010; 132:3472-83. [DOI: 10.1021/ja9096863] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lionel A. Truflandier
- Department of Chemistry, 312 Natural Sciences Complex, State University of New York, Buffalo, New York 14260-3000
| | - Jochen Autschbach
- Department of Chemistry, 312 Natural Sciences Complex, State University of New York, Buffalo, New York 14260-3000
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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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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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25
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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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