Enzymatic Reactions; Reactive Dynamics; Structure-Spectroscopy relationship; QM/MM simulations; Proton transfer; Molecular Dynamics; Force FieldsReactive dynamics; Computer Simulations; Catalysis; chemical reactions; Intermolecular Interactions; Computational Biophysics; fluctuating charges; proton transfer reactions
Lee Myung Won, Carr Joshua K., Goellner Michael, Hamm Peter, Meuwly Markus (2013), 2D IR spectra of cyanide in water investigated by molecular dynamics simulations, in JOURNAL OF CHEMICAL PHYSICS
, 139(5), 054506-054506.
Lee Myung Won, Carr Joshua K, Göllner Michael, Hamm Peter, Meuwly Markus (2013), 2D IR spectra of cyanide in water investigated by molecular dynamics simulations., in The Journal of chemical physics
, 139(5), 054506-054506.
Lee Myung Won, Meuwly Markus (2013), Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields., in Physical chemistry chemical physics : PCCP
, 15(46), 20303-12.
Huang Jing, Buchowiecki Marcin, Nagy Tibor, Vaníček Jiří, Meuwly Markus (2013), Kinetic isotope effect in malonaldehyde determined from path integral Monte Carlo simulations., in Physical chemistry chemical physics : PCCP
Kramer Christian, Gedeck Peter, Meuwly Markus (2012), Atomic multipoles: Electrostatic potential fit, local reference axis systems, and conformational dependence, in JOURNAL OF COMPUTATIONAL CHEMISTRY
, 33(20), 1673-1688.
Kramer C, Gedeck P, Meuwly M (2012), Atomic multipoles: Electrostatic potential fit, local reference axis systems, and conformational dependence, in JOURNAL OF COMPUTATIONAL CHEMISTRY
, 33(20), 1673-1688.
Kramer Christian, Gedeck Peter, Meuwly Markus (2012), Atomic multipoles: electrostatic potential fit, local reference axis systems, and conformational dependence., in Journal of computational chemistry
, 33(20), 1673-88.
Cazade PA, Huang J, Yosa J, Szymczak JJ, Meuwly M (2012), Atomistic simulations of reactive processes in the gas- and condensed-phase, in INTERNATIONAL REVIEWS IN PHYSICAL CHEMISTRY
, 31(2), 235-264.
Gupta PK, Meuwly M (2012), Dynamics of Water/Methanol Mixtures at Functionalized Chromatographic Interfaces, in JOURNAL OF PHYSICAL CHEMISTRY B
, 116(35), 10951-10959.
Huang J, Meuwly M (2012), Force field refinement from NMR scalar couplings, in CHEMICAL PHYSICS
, 396, 116-123.
Lee MW, Meuwly M (2012), Molecular Dynamics Simulation of Nitric Oxide in Myoglobin, in JOURNAL OF PHYSICAL CHEMISTRY B
, 116(14), 4154-4162.
Lutz S, Meuwly M (2012), Photodissociation Dynamics of ClCN at Different Wavelengths, in CHEMPHYSCHEM
, 13(1), 305-313.
Meuwly M, Cui Q (2012), Protein functional dynamics: From femtoseconds to milliseconds Preface, in CHEMICAL PHYSICS
, 396, 1-2.
Plattner N, Meuwly M (2012), Quantifying the Importance of Protein Conformation on Ligand Migration in Myoglobin, in BIOPHYSICAL JOURNAL
, 102(2), 333-341.
Meuwly M (2012), Reaction Dynamics: Rules Change with Molecular Size, in CHEMPHYSCHEM
, 13(3), 684-685.
Tong X, Nagy T, Reyes JY, Germann M, Meuwly M, Willitsch S (2012), State-selected ion-molecule reactions with Coulomb-crystallized molecular ions in traps, in CHEMICAL PHYSICS LETTERS
, 547, 1-8.
Helbing J, Devereux M, Nienhaus K, Nienhaus GU, Hamm P, Meuwly M (2012), Temperature Dependence of the Heat Diffusivity of Proteins, in JOURNAL OF PHYSICAL CHEMISTRY A
, 116(11), 2620-2628.
Gellrich U, Huang J, Seiche W, Keller M, Meuwly M, Breit B (2011), Ligand Self-Assembling through Complementary Hydrogen-Bonding in the Coordination Sphere of a Transition Metal Center: The 6-Diphenylphosphanylpyridin-2(1H)-one System, in JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
, 133(4), 964-975.
Lee MW, Meuwly M (2011), On the Role of Nonbonded Interactions in Vibrational Energy Relaxation of Cyanide in Water, in JOURNAL OF PHYSICAL CHEMISTRY A
, 115(20), 5053-5061.
Zhang LX, Meuwly M (2011), Stability and Dynamics of Cyclic Diguanylic Acid in Solution, in CHEMPHYSCHEM
, 12(2), 295-302.
Lutz S, Tubert-Brohman I, Yang YG, Meuwly M (2011), Water-assisted Proton Transfer in Ferredoxin I, in JOURNAL OF BIOLOGICAL CHEMISTRY
, 286(27), 23679-23687.
Buffa G, Tarrini O, Dore L, Meuwly M (2010), Experimental and Theoretical Study of the Broadening and Shifting of N2H+ Rotational Lines by Helium, in CHEMPHYSCHEM
, 11(14), 3141-3145.
Mishra Sabyashachi, Meuwly Markus (2010), Quantitative analysis of ligand migration from transition networks., in Biophysical journal
, 99(12), 3969-78.
Plattner Nuria, Lee Myung Won, Meuwly Markus (2010), Structural and spectroscopic characterization of mixed planetary ices., in Faraday discussions
, 147, 217-225.
Cazade PA, Lutz S, Lee MW, Meuwly M, Computational Spectroscopy and Reaction Dynamics, in CHIMIA
, 65(5), 326-329.
Huang J, Meuwly M, Force field refinement from NMR scalar couplings, in Chemical Physics
S. Lutz, M. Meuwly, Photodissociation Dynamics of ClCN at Different Wavelengths, in ChemPhysChem
Lutz S, Meuwly M, Structural characterization of spectroscopic substates in carbonmonoxy neuroglobin, in Faraday Discussions
, 150, 375-390.
The goal of the project is to develop numerical methods and computational strategies to understand the energetics and dynamics of chemical reactions in complex environments and to apply them to chemically and biologically relevant systems. Using a combination of adiabatic reactive molecular dynamics (ARMD), improved force fields, potential energy surface ``morphing'' procedures, and electronic structure calculations, reactions including hydrogen/proton-transfer, ligand-binding and ligand-transfer are investigated at a quantitative level. The ARMD method will be generalized to treat molecule-transfer, ligand exchange and vibrational-assisted dissociation reactions. Chemical and biochemical systems of particular interest include ligand exchange (Fe(II)--NO+O2->Fe(II)--O2+NO) in truncated Hemoglobin, ligand transfer in cytochrome c oxidase (Fe-CO+Cu -> Fe+Cu-CO), hydrogen transfer in malonaldehyde and acetylacetone, and the vibrationally assisted dissociation of sulfuric acid (SO4H2). For all systems detailed experimental data is available which allows to refine the interactions potentials required to describe the energetics, and to characterize the dynamics from extended atomistic simulations. Where possible and appropriate, interaction potentials will be derived from iteratively refined, dynamics-based potential energy functions which is an approach that was recently developed in our group. Given that ligands such as nitric oxide play a central role in our investigations, the distributed multipole (DM) approach will be extended to radicals to quantitatively describe O2 and NO interacting with the protein environment.