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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 188724
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 01.10.2019 - 30.09.2022
Approved amount 393'013.00
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Keywords (8)

Computational Vibrational Spectroscopy; Multipolar Force Fields; Force Fields; Reactive Dynamics; Protein-Ligand Interactions; Molecular Dynamics; QM/MM Simulations; Machine Learning

Lay Summary (German)

In diesem Projekt wird der Zusammenhang zwischen Struktur, nuklearer Dynamik,und der Spektroskopie von chemischen und biochemischen Systemen untersucht.
Lay summary
Die Dynamik komplexer chemischer und biochemischer Systeme wird durch
die zwischenmolekularen Wechselwirkungen bestimmt. Diese
Wechselwirkungen sind zum Beispiel für grundlegende physiologische
Prozesse wie die Atmung entscheidend. Computersimulationen können
dabei entscheidende Einblicke liefern, da mit ihnen sowohl der
zeitliche, als auch der räumliche Ablauf solcher Vorgänge untersucht
werden kann, was mit den momentan zur Verfügung stehenden
experimentellen Methoden nur unter grössten Schwierigkeiten
gelingt. Damit Computersimulationen in der Praxis anwendbar sind und
zu den erhofften Einsichten führen, benötigt man möglichst genaue und
effizient auszuwertende Modelle für die zwischenmolekularen
Wechselwirkungen. Im Rahmen diese Projektes werden solche
Energiefunktionen entwickelt und auf physikalisch, chemisch und
biologisch relevante Prozesse angewendet. Typische Probleme sind die
Umsetzung von kleinen Molekülen in der Atmosphaere oder die
Ligandbindung an Proteine. Ein wesentlicher Teil diese Projektes
beschäftigt sich mit der Interpretation von Experimenten und mit deren
Direct link to Lay Summary Last update: 16.10.2019

Responsible applicant and co-applicants


Associated projects

Number Title Start Funding scheme
169079 Intermolecular Interactions and the Role of Dynamics for Chemical Reactions in Complex Systems 01.10.2016 Project funding


The goal of this project is to develop, implement and apply computational strategies to characterize, understand and eventually predict properties of complex chemical and biochemical systems at a molecular level. To this end, techniques including multipolar force fields, (adiabatic) reactive molecular dynamics and neural network-based potential energy surfaces are further developed and used. Multipole force fields will be extended to treat general spectroscopic applications (1- and 2-dimensional infrared spectroscopy), using fluctuating multipoles and describing the energetics of the nuclear degrees of freedom with reproducing kernels. Applications include spectroscopic probes such as -CO, -NO and -N3 for which accurate, fully dimensional potential energy surfaces can be calculated. This will be used to characterize the site-specific dynamics and functional motions of proteins such as insulin, lysozyme, myoglobin and nitrophorin in solution. For insulin, analysis of motions at the dimerization interface will be used to quantify the physiologically relevant monomer/dimer equilibrium which is difficult to do with experimentally established, thermodynamic approaches. To account for vibrational coherences, partial linearized density matrix (PLDM) propagation will be generalized for vibrational dynamics (vPLDM). Nitrosylation of nitrophorin will investigate molecular determinants of NO-signaling in a protein. To study chemical reactions in the gas phase we will use machine learning within the PhysNet neural network architecture to generate fully-dimensional, reactive potential energy surfaces. Here, applications focus on systems relevant to atmospheric chemistry, including isomerization and decomposition reactions of acetaldehyde and pyruvic acid for which fragmentation patterns and final state distributions are important for subsequent reactions. In a next step, PhysNet will be used to investigate double proton transfer in the gas phase and in solution with the aim to characterize the role of solvent in chemical reactions at a molecular level. The present proposal involves two research themes: 1) reactive simulations in the gas- and condensed phase and 2) computational vibrational spectroscopy which both require accurate representations of the intermolecular interactions.