Molecular Dynamics; Metal Force Fields; Multipolar Force Fields; Force Fields; Protein-Ligand Interactions; QM/MM Simulations; Reactive Dynamics
Hedin Florent, El Hage Krystel, Meuwly Markus (2016), A Toolkit to Fit Nonbonded Parameters from and for Condensed Phase Simulations, in JCIM
, 56(8), 1479-1489.
(2016), Computational Approaches for Studying Enzyme Mechanism
, Academic Press, NY.
Jin Haiyun, Goyal Puja, Das Akshaya Kumar, Gaus Michael, Meuwly Markus, Cui Qiang (2016), Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations, in JPCB
, 120(8), 1894-1910.
Das A. K., Meuwly M. (2016), Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins, in Voth GA (ed.), Springer, NY, 31-55.
El Hage Krystel, Bereau Tristan, Jakobsen Sofie, Meuwly Markus (2016), Impact of Quadrupolar Electrostatics on Atoms Adjacent to the Sigma-Hole in Condensed-Phase Simulations, in JCTC
, 12(7), 3008-3019.
Das Akshaya K., Solomon R. V., Hofmann Franziska, Meuwly Markus (2016), Inner-Shell Water Rearrangement Following Photoexcitation of Tris(2,2 `-bipyridine)iron(II), in JPCB
, 120(1), 206-216.
Gupta Prashant Kumar, Meuwly Markus (2016), Ligand and interfacial dynamics in a homodimeric hemoglobin, in Struct. Dyn.
, 3(1), 012003.
Mackeprang Kasper, Xu Zhen-Hao, Maroun Zeina, Meuwly Markus, Kjaergaard Henrik G. (2016), Spectroscopy and dynamics of double proton transfer in formic acid dimer, in PCCP
, 18(35), 24654-24662.
Soloviov Maksym, Das Akshaya K., Meuwly Markus (2016), Structural Interpretation of Metastable States in Myoglobin-NO, in Angewandte
, 55(34), 10126-10130.
Cazade Pierre-Andre, Zheng Wenwei, Prada-Gracia Diego, Berezovska Ganna, Rao Francesco, Clementi Cecilia, Meuwly Markus (2015), A comparative analysis of clustering algorithms: O-2 migration in truncated hemoglobin I from transition networks, in JCP
, 142(2), 025103.
Cazade Pierre-Andre, Berezovska Ganna, Meuwly Markus (2015), Coupled protein-ligand dynamics in truncated hemoglobin N from atomistic simulations and transition networks, in BBA
, 1850(5, SI), 996-1005.
Jakobsen Sofie, Bereau Tristan, Meuwly Markus (2015), Multipolar Force Fields and Their Effects on Solvent Dynamics around Simple Solutes, in JPCB
, 119(7), 3034-3045.
Soloviov Maksym, Meuwly Markus (2015), Reproducing kernel potential energy surfaces in biomolecular simulations: Nitric oxide binding to myoglobin, in JCP
, 143(10), 105103.
Cazade Pierre-Andre, Tran Halina, Bereau Tristan, Das Akshaya K., Klaesi Felix, Hamm Peter, Meuwly Markus (2015), Solvation of fluoro-acetonitrile in water by 2D-IR spectroscopy: A combined experimental-computational study, in JCP
, 142(21), 212415.
Cazade Pierre-Andre, Hedin Florent, Xu Zhen-Hao, Meuwly Markus (2015), Vibrational Relaxation and Energy Migration of N-Methylacetamide in Water: The Role of Non bonded Interactions, in JCP
, 119(7), 3112-3122.
Soloviov Maksym, Meuwly Markus (2014), CO-dynamics in the active site of cytochrome c oxidase, in JCP
, 140(14), 145101.
Cazade Pierre-Andre, Bereau Tristan, Meuwly Markus (2014), Computational Two-Dimensional Infrared Spectroscopy without Maps: N-Methylacetamide in Water, in JPCB
, 118(28), 8135-8147.
The overall goal of this project is to develop numerical methods andcomputational strategies to characterize, understand and eventuallypredict the energetics and dynamics of chemical reactions in complexenvironments and to apply them to chemically and biologically relevantsystems. To this end, a combination of reactive molecular dynamics andphysics-based/tailored force fields is employed to investigateprocesses including ligand-transport, ligand-binding and elementarysteps in metal-catalyzed reactions. At the methodological level, wewill implement energy-based switching in adiabatic reactive moleculardynamics (ARMD) to allow microcanonical sampling for small systems andcombine ARMD with VALBOND and VALBOND-TRANS to treat reactionsinvolving metal-containing complexes. Furthermore, distributedmultipoles (MTPs) based on local reference axis systems for MDsimulations of larger, pharmacologically relevant molecules will beimplemented. Many metal-based complexes in catalysis contain organicring-compounds which constitute important functional units and need tobe described with accurate force fields such as multipolarelectrostatics. These developments are applied to NO and N2Odiffusion in native and engineered Fe- and Cu-containing proteins. Toclarify the mode-of-action of metal-based catalysts, specifically aRu-catalyst suitable for converting methanol to molecular hydrogen,docking and crystallographic studies with host proteins includinglysozyme, ribonuclease A and ketosteroid isomerase will beundertaken. Furthermore, the combination of ARMD with VALBOND-TRANSwill be used to characterize individual reactive steps ofIr(III)-complexes involved in homogeneous water oxidation. For all thestudies involving Cu-, Ru- or Ir-containing species force fieldparametrizations based on VALBOND and MTPs will be developed based onexperimental and in silico data.