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Simulation of Ligand Exchange Reactions

Simulation of Ligand Exchange Reactions

Bernd-Michael Rode (ORCID: )
  • Grant DOI 10.55776/P16221
  • Funding program Principal Investigator Projects
  • Status ended
  • Start March 1, 2003
  • End June 30, 2006
  • Funding amount € 242,256
  • Project website

Disciplines

Chemistry (100%)

Keywords

    Molecular Dynamics, Quantum Chemical Simulations, Ligand Exchange Reactions, Complex Chemistry, Solvation, Reaction Mechanisms

Abstract Final report

The development of intermolecular potentials including 3-body terms based on Hartree-Fock ab initio calculations and of a mixed quantum mechanical / molecular mechanical approach to molecular dynamics simulations for a larger number of ions has shown that it is possible through such simulations, to obtain very detailed information about the mechanism of very fast ligand exchange reactions in complexes. Numerous models have been proposed for such reactions, but due to the time-scale in the picosecond range, they can hardly be verified by experimental methods. The present project intends to systematically investigate such reactions by means of the aforementioned simulation technique, in order to obtain a solid basis for the interpretation of experimental data, and for the mechanism of these reactions. The systems envisaged for these investigations are solvate complexes of alkaline, alkaline earth and transition metal ions, plus a few selected monoatomic anions. Water, ammonia and complex-forming anions will be considered as ligands involved in the exchange reactions. In the case of transition metal ions with very stable first hydration shell, exchange reactions in the second solvation sphere and replacement of first-shell water by ligands of affinity higher than water will be investigated. Apart from " classical" publications, the results of these investigations will be presented in the form of video clips, with the help of a proprietary software (MOLVISION) recently developed by the applicant and coworkers. These video clips will be made available via the Internet and provide a most illustrative description of the chemical reactions investigated.

As most of the relevant chemical reactions proceed in the liquid state and almost all biochemical processes in aqueous medium, the detailed understanding of solvation is crucial for the understanding of chemistry and related disciplines. This is particularly true for solvated ions, which play manifold roles in chemistry and biology. Experimental investigations of structure and dynamics of liquid systems are highly complicated and expensive, and for numerous processes suitable experimental settings are not even available yet. Classical theoretical simulation methods for liquids on the other hand are mostly not accurate enough to correctly reveal all details of solvated ions and molecules. The target of the present project was, therefore, to develop further the methodology of hybrid quantum mechanical - molecular mechanical molecular dynamics simulations, which provide the required accuracy, albeit at the price of an almost hundred-fold computational effort. With this methodology a large number of chemically and biologically important ions was studied, focussing on the dynamics of ligand exchange, which is crucial for the reactivity of these ions in the liquid state and in the interaction with other compounds than the solvent itself. The 25 metal ions investigated in this project are representative for the most important parts of the periodic system, ranging from extremely stable solvates to the most labile structure-breakers. Besides water, ammonia and aqueous ammonia were included as solvents, and particular attention was paid to the influence of heteroligands in metal complexes on the dynamics of ligand exchange reactions. In addition, two halide anions were included in the studies, and an extensive investigation of liquid water by various levels of quantum mechanical simulation was performed, which proved the accuracy of the employed method by its full agreement with the most recent and sophisticated experimental techniques concerning hydrogen bonding and the ultrafast exchange rates. In the progress of the project work, ideas for a new, strongly inproved quantum mechanical ab initio simulation methodology (later on termed Quantum Mechanical Charge Field Molecular Dynamics, QMCF MD) were developed and successfully translated into a new program code. This new method provides the access to simulations of composite solutes without the need of analytical potentials and further improves the accuracy of the simulations for systems with strong charge-transfer and polarisation effects. The project resulted in 55 peer-reviewed publications, including 3 invited book contributions and 2 invited review articles. 3 of the other publications were also solicited articles. A number of invited lectures at international conferences document the broad interest in the project results.

Research institution(s)
  • Universität Innsbruck - 100%

Research Output

  • 1518 Citations
  • 41 Publications
Publications
  • 2019
    Title Ab initio QMM/MM Simulations: A Powerful Tool for the Study of Structure and Ultrafast Dynamics of Electrolyte Solutions
    DOI 10.1201/9780429081385-282
    Type Book Chapter
    Author Rode B
    Publisher Taylor & Francis
    Pages 1112-1114
  • 2007
    Title Quantum mechanical/molecular mechanical simulations of the Tl(III) ion in water
    DOI 10.1002/jcc.20486
    Type Journal Article
    Author Vchirawongkwin V
    Journal Journal of Computational Chemistry
    Pages 1057-1067
  • 2007
    Title Quantum mechanical charge field molecular dynamics simulation of the TiO2+ ion in aqueous solution
    DOI 10.1002/jcc.20659
    Type Journal Article
    Author Fatmi M
    Journal Journal of Computational Chemistry
    Pages 1704-1710
  • 2006
    Title Structure and dynamics of the [Zn(NH 3 )(H 2 O) 5 ] 2+ complex in aqueous solution obtained by an ab initio QM/MM molecular dynamics study
    DOI 10.1039/b518223a
    Type Journal Article
    Author Fatmi M
    Journal Physical Chemistry Chemical Physics
    Pages 1675-1681
  • 2006
    Title Be( ii ) in aqueous solution—an extended ab initio QM/MM MD study
    DOI 10.1039/b603222b
    Type Journal Article
    Author D’Incal A
    Journal Physical Chemistry Chemical Physics
    Pages 2841-2847
  • 2006
    Title A Combined QM/MM Molecular Dynamics Simulations Study of Nitrate Anion (NO3 -) in Aqueous Solution
    DOI 10.1021/jp064779w
    Type Journal Article
    Author Tongraar A
    Journal The Journal of Physical Chemistry A
    Pages 12918-12926
    Link Publication
  • 2006
    Title A QM/MM MD simulation study of hydrated Pd2+
    DOI 10.1016/j.cplett.2006.05.132
    Type Journal Article
    Author Shah S
    Journal Chemical Physics Letters
    Pages 301-305
  • 2006
    Title Structure and dynamics of La(III) in aqueous solution – An ab initio QM/MM MD approach
    DOI 10.1016/j.chemphys.2006.03.045
    Type Journal Article
    Author Hofer T
    Journal Chemical Physics
    Pages 31-42
  • 2006
    Title Hydrogen bonding in liquid water: An ab initio QM/MM MD simulation study
    DOI 10.1016/j.molliq.2005.06.002
    Type Journal Article
    Author Xenides D
    Journal Journal of Molecular Liquids
    Pages 61-67
  • 2006
    Title The dynamics of the solvation of Pb(II) in aqueous solution obtained by an ab initio QM/MM MD approach
    DOI 10.1016/j.chemphys.2005.10.041
    Type Journal Article
    Author Hofer T
    Journal Chemical Physics
    Pages 473-478
  • 2006
    Title The influence of quantum forces on molecular dynamics simulation results for hydrated aluminium(III)
    DOI 10.1016/j.cplett.2006.03.012
    Type Journal Article
    Author Hofer T
    Journal Chemical Physics Letters
    Pages 492-495
  • 2005
    Title Structural and dynamical properties of Bi3+ in water
    DOI 10.1016/j.cplett.2005.02.082
    Type Journal Article
    Author Durdagi S
    Journal Chemical Physics Letters
    Pages 20-23
  • 2005
    Title Structure-breaking effects of solvated Rb(I) in dilute aqueous solution—An ab initio QM/MM MD approach
    DOI 10.1002/jcc.20232
    Type Journal Article
    Author Hofer T
    Journal Journal of Computational Chemistry
    Pages 949-956
  • 2005
    Title An extended ab initio QM/MM MD approach to structure and dynamics of Zn(II) in aqueous solution
    DOI 10.1063/1.1996575
    Type Journal Article
    Author Fatmi M
    Journal The Journal of Chemical Physics
    Pages 054514
  • 2005
    Title Structure and Dynamics of Solvated Sn(II) in Aqueous Solution: An ab Initio QM/MM MD Approach
    DOI 10.1021/ja052700f
    Type Journal Article
    Author Hofer T
    Journal Journal of the American Chemical Society
    Pages 14231-14238
  • 2005
    Title Structure and dynamics of solvated Ba(II) in dilute aqueous solution – an ab initio QM/MM MD approach
    DOI 10.1016/j.chemphys.2004.11.023
    Type Journal Article
    Author Hofer T
    Journal Chemical Physics
    Pages 81-88
  • 2005
    Title The influence of heteroligands on the reactivity of Ni 2+ in solution
    DOI 10.1039/b419072f
    Type Journal Article
    Author Schwenk C
    Journal Physical Chemistry Chemical Physics
    Pages 1669-1673
  • 2005
    Title Influence of polarization and many body quantum effects on the solvation shell of Al( iii ) in dilute aqueous solution—extended ab initio QM/MM MD simulations
    DOI 10.1039/b417491g
    Type Journal Article
    Author Hofer T
    Journal Physical Chemistry Chemical Physics
    Pages 1382-1387
  • 2005
    Title Ab initio QM/MM dynamics of anion–water hydrogen bonds in aqueous solution
    DOI 10.1016/j.cplett.2005.01.017
    Type Journal Article
    Author Tongraar A
    Journal Chemical Physics Letters
    Pages 314-319
  • 2005
    Title Structure and ultrafast dynamics of liquid water: A quantum mechanics/molecular mechanics molecular dynamics simulations study
    DOI 10.1063/1.1888465
    Type Journal Article
    Author Xenides D
    Journal The Journal of Chemical Physics
    Pages 174506
  • 2005
    Title Ab Initio QM/MM Simulation of Ag+ in 18.6% Aqueous Ammonia Solution: Structure and Dynamics Investigations
    DOI 10.1021/jp0462916
    Type Journal Article
    Author Armunanto R
    Journal The Journal of Physical Chemistry A
    Pages 4437-4441
  • 2005
    Title Temperature Effects on the Structural and Dynamical Properties of the Zn(II)-Water Complex in Aqueous Solution: A QM/MM Molecular Dynamics Study
    DOI 10.1021/jp0546655
    Type Journal Article
    Author Fatmi M
    Journal The Journal of Physical Chemistry B
    Pages 616-621
  • 2005
    Title Structural arrangement and dynamics of the hydrated Mg2+: An ab initio QM/MM molecular dynamics simulation
    DOI 10.1016/j.cplett.2005.04.062
    Type Journal Article
    Author Tongraar A
    Journal Chemical Physics Letters
    Pages 304-309
  • 2004
    Title Structure and dynamics of the Cr(III) ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation
    DOI 10.1002/jcc.20085
    Type Journal Article
    Author Kritayakornupong C
    Journal Journal of Computational Chemistry
    Pages 1576-1583
  • 2004
    Title Structure and Dynamics of Au+ Ion in Aqueous Solution: Ab Initio QM/MM MD Simulations
    DOI 10.1021/ja037340f
    Type Journal Article
    Author Armunanto R
    Journal Journal of the American Chemical Society
    Pages 2582-2587
  • 2004
    Title Gold(I) in Liquid Ammonia: Ab Initio QM/MM Molecular Dynamics Simulation
    DOI 10.1021/ja031740l
    Type Journal Article
    Author Armunanto R
    Journal Journal of the American Chemical Society
    Pages 9934-9935
  • 2004
    Title Ag(I) ion in liquid ammonia
    DOI 10.1016/j.cplett.2004.03.035
    Type Journal Article
    Author Armunanto R
    Journal Chemical Physics Letters
    Pages 395-399
  • 2004
    Title The Jahn–Teller Effect of the TiIII Ion in Aqueous Solution: Extended Ab Initio QM/MM Molecular Dynamics Simulations
    DOI 10.1002/cphc.200400019
    Type Journal Article
    Author Kritayakornupong C
    Journal ChemPhysChem
    Pages 1499-1506
  • 2004
    Title Influence of Electron Correlation Effects on the Solvation of Cu2+
    DOI 10.1021/ja046784o
    Type Journal Article
    Author Schwenk C
    Journal Journal of the American Chemical Society
    Pages 12786-12787
  • 2004
    Title Cuii in Liquid Ammonia: An Approach by Hybrid Quantum-Mechanical/Molecular-Mechanical Molecular Dynamics Simulation
    DOI 10.1002/cphc.200300972
    Type Journal Article
    Author Schwenk C
    Journal ChemPhysChem
    Pages 342-348
  • 2004
    Title Structure and dynamics of hydrated ions—new insights through quantum mechanical simulations
    DOI 10.1016/j.molliq.2003.09.016
    Type Journal Article
    Author Rode B
    Journal Journal of Molecular Liquids
    Pages 105-122
  • 2004
    Title “Structure Breaking” Effect of Hydrated Cs+
    DOI 10.1021/jp037179v
    Type Journal Article
    Author Schwenk C
    Journal The Journal of Physical Chemistry A
    Pages 1509-1514
  • 2004
    Title Dynamical properties of water molecules in the hydration shells of Na+ and K+: ab initio QM/MM molecular dynamics simulations
    DOI 10.1016/j.cplett.2004.01.010
    Type Journal Article
    Author Tongraar A
    Journal Chemical Physics Letters
    Pages 378-383
  • 2004
    Title Ab initio QM/MM molecular dynamics simulation of preferential K + solvation in aqueous ammonia solution
    DOI 10.1039/b310825b
    Type Journal Article
    Author Tongraar A
    Journal Physical Chemistry Chemical Physics
    Pages 411-416
  • 2004
    Title Structure and dynamics of Co2+ in liquid ammonia: ab initio QM/MM molecular dynamics simulation
    DOI 10.1016/j.chemphys.2004.06.049
    Type Journal Article
    Author Armunanto R
    Journal Chemical Physics
    Pages 135-140
  • 2003
    Title Structure and Dynamics of Hydrated Ag (I): Ab Initio Quantum Mechanical-Molecular Mechanical Molecular Dynamics Simulation
    DOI 10.1021/jp027769d
    Type Journal Article
    Author Armunanto R
    Journal The Journal of Physical Chemistry A
    Pages 3132-3138
  • 2003
    Title QM/MM Molecular Dynamics Simulation of the Structure of Hydrated Fe(II) and Fe(III) Ions
    DOI 10.1021/jp027007i
    Type Journal Article
    Author Remsungnen T
    Journal The Journal of Physical Chemistry A
    Pages 2324-2328
  • 2003
    Title Structure and Dynamics of the Cd2+ Ion in Aqueous Solution: Ab Initio QM/MM Molecular Dynamics Simulation
    DOI 10.1021/jp0354548
    Type Journal Article
    Author Kritayakornupong C
    Journal The Journal of Physical Chemistry A
    Pages 10330-10334
  • 2003
    Title Ultrafast ligand exchange rates determined by ab initio QM/MM molecular dynamics
    DOI 10.1016/j.cplett.2003.10.043
    Type Journal Article
    Author Schwenk C
    Journal Chemical Physics Letters
    Pages 460-465
  • 2003
    Title Classical and QM/MM molecular dynamics simulations of Co2+ in water
    DOI 10.1016/j.chemphys.2003.08.006
    Type Journal Article
    Author Armunanto R
    Journal Chemical Physics
    Pages 63-70
  • 2003
    Title New Insights into the Jahn–Teller Effect through ab initio Quantum-Mechanical/Molecular-Mechanical Molecular Dynamics Simulations of CuII in Water
    DOI 10.1002/cphc.200300659
    Type Journal Article
    Author Schwenk C
    Journal ChemPhysChem
    Pages 931-943

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