Molecular Mechanics Force Field for Octahedral Organometallic Compounds with Inclusion of the Trans Influence

Tubert‐Brohman, Ivan; Schmid, Maurus; Meuwly, Markus

doi:10.1021/ct800392n

Cited by 41 publications

(63 citation statements)

References 43 publications

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“…31–33,63 The additional force field term not only describes the energetics around the energy minimum but also for very large angle distortions and helps to model hypervalent molecules and transition metal complexes. 34,64 …”

Section: Methodsmentioning

confidence: 99%

“…1b). All simulations are carried out using CHARMM 44 with provisions for the VALBOND 34 force field to describe the metal complex. 31–33 All bonds involving hydrogen atoms are constrained by applying SHAKE.…”

Section: Methodsmentioning

confidence: 99%

“…For the VALBOND 34 simulations, after 10 ns of NVT simulation, an NVE simulation is performed for 1 ns using starting coordinates and velocities obtained from the NVT simulation. From this 1 ns of NVE trajectory, coordinates and velocities at 100 frames separated by 10 ps are stored and used as initial conditions for the subsequent non-equilibrium simulations.…”

Section: Methodsmentioning

confidence: 99%

“…In this study, we focus on the VALBOND model, which was originally proposed by Landis and co-workers to treat large amplitude angular motions of transition metal ligands. 31–33 The model has been recently implemented in CHARMM by Meuwly and co-workers, 34 who showed promising applications in several organometallic systems. 35,36 Here we develop the VALBOND model for copper and compare its performance to DFTB3/MM for [Cu(NH 3 ) 4 ] +/2+ in water (Fig.…”

Section: Introductionmentioning

confidence: 99%

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Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations

et al. 2015

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We apply two recently developed computational methods, DFTB3 and VALBOND, to study copper oxidation/reduction processes in solution and protein. The properties of interest include the coordination structure of copper in different oxidation states in water or in a protein (plastocyanin) active site, the reduction potential of the copper ion in different environments, and the environmental response to copper oxidation. The DFTB3/MM and VALBOND simulation results are compared to DFT/MM simulations and experimental results whenever possible. For a solvated copper ion, DFTB3/MM results are generally close to B3LYP/MM with a medium basis, including both solvation structure and reduction potential for Cu(II); for Cu(I), however, DFTB3/MM finds a two-water coordination, similar to previous Born-Oppenheimer molecular dynamics simulations using BLYP and HSE, while B3LYP/MM leads to a tetrahedron coordination. For a tetra-ammonia copper complex in solution, VALBOND and DFTB3/MM are consistent in terms of both structural and dynamical properties of solvent near copper for both oxidation states. For copper reduction in plastocyanin, DFTB3/MM simulations capture the key properties of the active site, and the computed reduction potential and reorganization energy are in fair agreement with experiment, especially when periodic boundary condition is used. Overall, the study supports the value of VALBOND and DFTB3(/MM) to the analysis of fundamental copper redox chemistry in water and protein, and the results also help highlight areas where further improvements in these methods are desirable.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations

et al. 2015

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“…[50] Corresponding simulations for the Fe-complex, also using the VA L-BOND-Trans (VBT) force field, confirm this finding. [51] The simulations employ the VBT force field [52] which is an extension of the VA LBOND force field. VA LBOND, developed by Landis and coworkers, [53][54][55] is based on valence bond theory, where hybrid orbital strength functions are used for the molecular mechanics.…”

Section: Solvation Dynamicsmentioning

confidence: 99%

Quantitative Atomistic Simulations of Reactive and Non-Reactive Processes

Meuwly¹

2014

Chimia

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The interpretation of physico-chemical observables in terms of atomic motions is one of the primary objectives of atomistic simulations. Trajectories from a molecular simulation contain much valuable information about the relationship between motion of the atoms and physical observables related to them, provided that the interactions used to generate the trajectories are of sufficiently high quality. On the other hand, many experimental observables are averages over a large number of physical realizations of the system. Thus, a statistically large number of trajectories needs to be generated and analyzed in order to provide a meaningful basis for comparison with and interpretation of experiments. The preferred computational approach which allows such extensive averaging while retaining the quantitative aspects of the intermolecular interactions are accurate force field-based molecular dynamics simulations. This contribution provides an overview of our group's current technological improvements in force field technology and its application to fundamental physico-chemical questions.Keywords: Computational spectroscopy · Force fields · Molecular dynamics simulations · Multipoles · Reaction dynamicsIn the physical sciences simulations provide a third approach -next to experiment and theory -to characterize and understand a wide range of phenomena. For chemistry and chemical physics in particular, atomistic simulations are paramount in providing insights into the energetics and dynamics of complex systems, such as proteins, chemical reactivity, solvation dynamics or spectroscopy.The use of atomistic simulations in reaction dynamics has been established for almost 50 years when molecular dynamics (MD) simulations were used to better understand the H 2 + H reaction dynamics. [1] Since then, MD simulations have become an important complement to investigate complex systems at atomic resolution. The major driving forces behind this development are i) the increase in computational power, ii) the improvement of algorithms and energy functions and iii) the more direct interaction between experiment and simulation. It is the latter that will eventually let this field mature to a degree which allows quantitative and ideally predictive work to be carried out which must be the ultimate goal of atomistic simulations.In the present contribution I will summarize our efforts to item ii) above. More specifically, our group is concerned with improved and widely applicable energy functions for spectroscopic and thermodynamic applications and the development of computational methods to follow chemical reactions in the gas phase and in solution. Quantitative Intermolecular InteractionsWithin the framework of atomistic simulations, intermolecular interactions are described by an empirical energy function ('force field') which is based on a ball-andspring model for the bonded interactions (such as bonds, valence angles, dihedrals) and Coulomb and van der Waals interactions for the nonbonded interactions. [2] This is in contrast t...

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Unusual Structure, Fluxionality, and Reaction Mechanism of Carbonyl Hydrosilylation by Silyl Hydride Complex [(ArN)Mo(H)(SiH₂Ph)(PMe₃)₃]

Khalimon

Ignatov

Охапкин

et al. 2013

Chemistry A European J

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The reactions of bis(borohydride) complexes [(RN=)Mo(BH4)2(PMe3)2] (4: R = 2,6-Me2C6H3; 5: R = 2,6-iPr2C6H3) with hydrosilanes afford new silyl hydride derivatives [(RN=)Mo(H)(SiR'3)(PMe3)3] (3: R = Ar, R'3 = H2Ph; 8: R = Ar', R'3 = H2Ph; 9: R = Ar, R'3 = (OEt)3; 10: R = Ar, R'3 = HMePh). These compounds can also be conveniently prepared by reacting [(RN=)Mo(H)(Cl)(PMe3)3] with one equivalent of LiBH4 in the presence of a silane. Complex 3 undergoes intramolecular and intermolecular phosphine exchange, as well as exchange between the silyl ligand and the free silane. Kinetic and DFT studies show that the intermolecular phosphine exchange occurs through the predissociation of a PMe3 group, which, surprisingly, is facilitated by the silane. The intramolecular exchange proceeds through a new non-Bailar-twist pathway. The silyl/silane exchange proceeds through an unusual Mo(VI) intermediate, [(ArN=)Mo(H)2(SiH2Ph)2(PMe3)2] (19). Complex 3 was found to be the catalyst of a variety of hydrosilylation reactions of carbonyl compounds (aldehydes and ketones) and nitriles, as well as of silane alcoholysis. Stoichiometric mechanistic studies of the hydrosilylation of acetone, supported by DFT calculations, suggest the operation of an unexpected mechanism, in that the silyl ligand of compound 3 plays an unusual role as a spectator ligand. The addition of acetone to compound 3 leads to the formation of [trans-(ArN)Mo(OiPr)(SiH2Ph)(PMe3)2] (18). This latter species does not undergo the elimination of a Si-O group (which corresponds to the conventional Ojima's mechanism of hydrosilylation). Rather, complex 18 undergoes unusual reversible β-CH activation of the isopropoxy ligand. In the hydrosilylation of benzaldehyde, the reaction proceeds through the formation of a new intermediate bis(benzaldehyde) adduct, [(ArN=)Mo(η(2)-PhC(O)H)2(PMe3)], which reacts further with hydrosilane through a η(1)-silane complex, as studied by DFT calculations.

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Molecular Mechanics Force Field for Octahedral Organometallic Compounds with Inclusion of the Trans Influence

Cited by 41 publications

References 43 publications

Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations

Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations

Quantitative Atomistic Simulations of Reactive and Non-Reactive Processes

Unusual Structure, Fluxionality, and Reaction Mechanism of Carbonyl Hydrosilylation by Silyl Hydride Complex [(ArN)Mo(H)(SiH₂Ph)(PMe₃)₃]

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Molecular Mechanics Force Field for Octahedral Organometallic Compounds with Inclusion of the Trans Influence

Cited by 41 publications

References 43 publications

Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations

Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations

Quantitative Atomistic Simulations of Reactive and Non-Reactive Processes

Unusual Structure, Fluxionality, and Reaction Mechanism of Carbonyl Hydrosilylation by Silyl Hydride Complex [(ArN)Mo(H)(SiH2Ph)(PMe3)3]

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Unusual Structure, Fluxionality, and Reaction Mechanism of Carbonyl Hydrosilylation by Silyl Hydride Complex [(ArN)Mo(H)(SiH₂Ph)(PMe₃)₃]