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Intermolecular Interactions and the Role of Dynamics for Chemical Reactions in Complex Systems

English title Intermolecular Interactions and the Role of Dynamics for Chemical Reactions in Complex Systems
Applicant Meuwly Markus
Number 132406
Funding scheme Project funding
Research institution Physikalische Chemie Departement Chemie Universität Basel
Institution of higher education University of Basel - BS
Main discipline Physical Chemistry
Start/End 01.10.2010 - 30.09.2013
Approved amount 426'198.00
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Keywords (14)

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

Lay Summary (English)

Lead
Lay summary
Over the past decade, "Computational Science" has emerged as a new discipline. In a broad sense, this subject includes all research areas of Science where computer simulation plays the leading role in the quest for new knowledge and understanding. The field bridges the gap between the two classical approaches to scientific research: theory and experiment. Paramount to the unprecedented rise of the importance of computer-based work is a dramatic increase in the power of computers. The main impetus for pursuing computational sciences is the desire to solve problems which are not accessible otherwise.The investigation of intermolecular interactions and the role of dynamics in enzymatic catalysis is paradigmatic for a computational approach to scientific questions. Experimental work alone can not unravel the physical, chemical and biological driving forces for enzymatic reactions. On the other hand, theoretical methods have their limitations due to the large number of degrees of freedom involved. This is why a carefully developed computational model, gauged with respect to experimental data, can give invaluable information about atomistic details involved in catalysis. Chemical reactions, in particular enzymatic reactions, are among the most important processes relevant to living organisms. Their understanding depends critically on an accurate description of the intermolecular interactions between the participating molecules and the nuclear dynamics of the atoms involved.For this project we develop numerical methods and computational strategies to understand the energetics and dynamics of chemical reactions in complex systems. Because many degrees of freedom are involved (often several 10000), a simplified energy expression based on a model that represents chemical bonds by harmonic springs is used. However, for more detailed investigations, such as the infrared spectroscopy of small molecules (a very powerful experimental method) in a protein environment, or the binding of pharmacologically relevant molecules still much work in improving the predictive power of force fields remains. With a combination of improved force fields and quantum chemical calculations we investigate chemical reactions including hydrogen/proton-transfer and ligand-binding at a quantitative level.Systems of particular interest for this research include myoglobin (responsible for storage and transport of oxygen), truncated Hemoglobin, Neuroglobin, and Hemoglobin. Some of the work is carried out in collaboration with experimental groups in Switzerland and abroad.
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
2D IR spectra of cyanide in water investigated by molecular dynamics simulations
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.
2D IR spectra of cyanide in water investigated by molecular dynamics simulations.
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.
Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields.
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.
Kinetic isotope effect in malonaldehyde determined from path integral Monte Carlo simulations.
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, 1111.
Atomic multipoles: Electrostatic potential fit, local reference axis systems, and conformational dependence
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.
Atomic multipoles: Electrostatic potential fit, local reference axis systems, and conformational dependence
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.
Atomic multipoles: electrostatic potential fit, local reference axis systems, and conformational dependence.
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.
Atomistic simulations of reactive processes in the gas- and condensed-phase
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.
Dynamics of Water/Methanol Mixtures at Functionalized Chromatographic Interfaces
Gupta PK, Meuwly M (2012), Dynamics of Water/Methanol Mixtures at Functionalized Chromatographic Interfaces, in JOURNAL OF PHYSICAL CHEMISTRY B, 116(35), 10951-10959.
Force field refinement from NMR scalar couplings
Huang J, Meuwly M (2012), Force field refinement from NMR scalar couplings, in CHEMICAL PHYSICS, 396, 116-123.
Molecular Dynamics Simulation of Nitric Oxide in Myoglobin
Lee MW, Meuwly M (2012), Molecular Dynamics Simulation of Nitric Oxide in Myoglobin, in JOURNAL OF PHYSICAL CHEMISTRY B, 116(14), 4154-4162.
Photodissociation Dynamics of ClCN at Different Wavelengths
Lutz S, Meuwly M (2012), Photodissociation Dynamics of ClCN at Different Wavelengths, in CHEMPHYSCHEM, 13(1), 305-313.
Protein functional dynamics: From femtoseconds to milliseconds Preface
Meuwly M, Cui Q (2012), Protein functional dynamics: From femtoseconds to milliseconds Preface, in CHEMICAL PHYSICS, 396, 1-2.
Quantifying the Importance of Protein Conformation on Ligand Migration in Myoglobin
Plattner N, Meuwly M (2012), Quantifying the Importance of Protein Conformation on Ligand Migration in Myoglobin, in BIOPHYSICAL JOURNAL, 102(2), 333-341.
Reaction Dynamics: Rules Change with Molecular Size
Meuwly M (2012), Reaction Dynamics: Rules Change with Molecular Size, in CHEMPHYSCHEM, 13(3), 684-685.
State-selected ion-molecule reactions with Coulomb-crystallized molecular ions in traps
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.
Temperature Dependence of the Heat Diffusivity of Proteins
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.
Ligand Self-Assembling through Complementary Hydrogen-Bonding in the Coordination Sphere of a Transition Metal Center: The 6-Diphenylphosphanylpyridin-2(1H)-one System
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.
On the Role of Nonbonded Interactions in Vibrational Energy Relaxation of Cyanide in Water
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.
Stability and Dynamics of Cyclic Diguanylic Acid in Solution
Zhang LX, Meuwly M (2011), Stability and Dynamics of Cyclic Diguanylic Acid in Solution, in CHEMPHYSCHEM, 12(2), 295-302.
Water-assisted Proton Transfer in Ferredoxin I
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.
Experimental and Theoretical Study of the Broadening and Shifting of N2H+ Rotational Lines by Helium
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.
Quantitative analysis of ligand migration from transition networks.
Mishra Sabyashachi, Meuwly Markus (2010), Quantitative analysis of ligand migration from transition networks., in Biophysical journal, 99(12), 3969-78.
Structural and spectroscopic characterization of mixed planetary ices.
Plattner Nuria, Lee Myung Won, Meuwly Markus (2010), Structural and spectroscopic characterization of mixed planetary ices., in Faraday discussions, 147, 217-225.
Computational Spectroscopy and Reaction Dynamics
Cazade PA, Lutz S, Lee MW, Meuwly M, Computational Spectroscopy and Reaction Dynamics, in CHIMIA, 65(5), 326-329.
Force field refinement from NMR scalar couplings
Huang J, Meuwly M, Force field refinement from NMR scalar couplings, in Chemical Physics.
Photodissociation Dynamics of ClCN at Different Wavelengths
S. Lutz, M. Meuwly, Photodissociation Dynamics of ClCN at Different Wavelengths, in ChemPhysChem.
Structural characterization of spectroscopic substates in carbonmonoxy neuroglobin
Lutz S, Meuwly M, Structural characterization of spectroscopic substates in carbonmonoxy neuroglobin, in Faraday Discussions, 150, 375-390.

Collaboration

Group / person Country
Types of collaboration
Brown University United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
University of Wisconsin United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Telluride Workshop 2013 Talk given at a conference 15.07.2013 Telluride, United States of America Meuwly Markus;
ICERM Workshop on Computational Biology Talk given at a conference 29.10.2012 Providence, RI, United States of America Meuwly Markus;
Charmm Meeting 2012 Talk given at a conference 09.07.2012 Washington, DC, United States of America Meuwly Markus;
Telluride Workshop Talk given at a conference 01.07.2012 Telluride, USA, United States of America Meuwly Markus;
Telluride Workshop Talk given at a conference 25.07.2011 Telluride, CO, USA, United States of America Meuwly Markus;
Charmm Meeting 2011 Talk given at a conference 15.07.2011 Madison, WI, USA, United States of America Meuwly Markus;


Associated projects

Number Title Start Funding scheme
117810 Intermolecular interactions and the role of dynamics for chemical reactions in complex systems 01.10.2007 Project funding
169079 Intermolecular Interactions and the Role of Dynamics for Chemical Reactions in Complex Systems 01.10.2016 Project funding
149439 Intermolecular Interactions and the Role of Dynamics for Chemical Reactions in Complex Systems 01.10.2013 Project funding
149439 Intermolecular Interactions and the Role of Dynamics for Chemical Reactions in Complex Systems 01.10.2013 Project funding

Abstract

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.
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