Department of

Computational Biological Chemistry

Research topics

We explore the chemical world by modeling large molecular systems on the computer and looking at their diverse properties such as structure, energies, dynamics and spectroscopic quantities.

We target systems that include, but are not limited to, proteins in solvated environments or complex electrolytes such as ionic liquids. Our investigations also encompass the study of micellar structures, both conventional and reversed, to elucidate their effects on the molecules located within the core and at the interfaces of these nanoscale entities. These systems, often comprising thousands of atoms, are studied to understand their behaviors over extended time scales of several hundred nanoseconds, relevant to experimental observables.

We are experts in molecular dynamics simulations, with a particular emphasis on advanced free energy calculations and the incorporation of polarizable force fields. Our proficiency in free energy calculations also includes quantum mechanics/molecular mechanics (QM/MM) and molecular mechanics/machine learning (MM/ML) hybrid approaches. Polarizable forces are essential to simulate systems containing large amounts of charged species. Furthermore, they enable to model charge and proton transfer. For both, simulation and analysis, we develop code for (highly parallel) computing on modern CPU and GPU architecture.

Free energy calculations

The change in free energy ΔA = A(β)-A(α) between two states α, β provides the single criterion for the spontaneity of a chemical or biological process. Computer simulations can not only determine free energy differences of interest, but they also make possible a microscopic (atomistic) explanation of the result obtained. Research interests concern both methodology, as well as application.

FWF P31024-N28: "Effects of tautomerization on computed binding affinities"

Grant holderS. Boresch
Funding period04/2018 - 04/2021

FWF P19100: "Towards more accurate and efficient free energy simulations"

Grant holderS. Boresch
Funding period09/2006 - 08/2010

Computational spectroscopy

To make spectroscopic calculations on nuclear motion feasible our molecular dynamics simulations usually are atom-resolved and based on classical mechanics. According to the requirements also hybrid (quantum mechanical), polarizable, coarse-grained, or multi-scale models are designed and implemented.

OeAD MK 06/2024: "Hybrid quantum and molecular dynamics for IR spectra in condensed phases"

Grant holderC. Schröder / L. Pejov
Funding period01/2024 - 12/2024

ÖAW DOC 24659: "Concepts of solvation dynamics in molecular dynamics simulation"

Awarded PhD studentE. Heid
SupervisorC. Schröder
Funding period08/2017 - 12/2019

FWF P28556-N34: "Computational solvation dynamics of oxyquinolines"

Grant holderC. Schröder
Funding period02/2016 - 08/2019

FP7 331932: "Simulation of dielectric spectra"

Grant holderC. Schröder
Principal investigatorM. Sega
Funding period03/2013 - 03/2015

Biomolecular interactions

Molecular dynamics simulations offer a powerful computational microscope that allows us to observe and analyze the dynamic behavior of biomolecules. They provide insights into the structural, functional, and thermodynamic properties of biological systems. In addition to classical protein-ligand binding of medical relevant proteins in cancer research, we are interested in ion channels, integral membrane proteins that facilitate the selective transport of ions across cell membranes, are of paramount interest due to their critical roles in cellular signaling, homeostasis, and physiology.
By leveraging the capabilities of MD simulations, we aim to bridge the gap between theoretical models and experimental observations, offering a comprehensive view of biomolecular dynamics. Our approach encompasses a wide range of methodologies, including classical MD simulations, free energy calculations, and the integration of polarizable force fields including proton transfer, to accurately capture the essence of biomolecular interactions.

ASEA UNINET 2023/UniWien/4: "Molecular dynamics simulations including explicit transfers reveal the conduction mechanism in the influenza M2 ion channel"

Grant holderC. Schröder / T. Rungrotmongkol
Funding period10/2023 - 09/2024

ASEA UNINET 2023/UniWien/2: "Computational and experimental binding studies on the epidermal growth factor receptor"

Grant holderC. Schröder / K. Choowongkomon
Funding period10/2023 - 09/2024

Ionic liquids

As a simple definition given by Paul Walden in 1914, ionic liquids are commonly recognized as salts with a melting point below 100° C. Popular cations are imidazoliums but other organic heterocyclic cations such as pyridinium or pyrrolidinium are also possible. In addition, ammonium, phosphonium and sulfonium cations with linear, branched or functionalized side chains have been used. Typical anorganic anions comprise halides, alkylsulfates, alkylsulfonates and in particular bis(trifluoromethyl-sulfonyl)imide. The plethora of cation/anion combinations allows for variation of the physico-chemical properties over a very broad range and can be further fine-tuned by side chain modifications of both, cations and anions.

FFG 57348110: "AI predicition of solvation parameters"

Principal investigatorC. Schröder
Funding period07/2024 - 08/2024

WTZ RS 04/2024: "Clean and Green Hydraulic Fluids: Ionic Liquids approach"

Principal investigatorC. Schröder, Milan Vranes
Funding period07/2024 - 06/2026

FWF I4383N: "Proton transfer in protic ionic liquids"

Principal investigatorC. Schröder
Funding period10/2020 - 09/2023

FWF 29146: "Ion-Aggregation of Chiral Ionic Liquids and its Impact for Asymmetric Synthesis"

Principal investigatorsK. Bica / C. Schröder
Funding period10/2016 - 08/2020

FWF P23494: "Polarization forces in molecular ionic liquids"

Principal investigatorsO. Steinhauser / C. Schröder
Funding period03/2012 - 07/2017

FWF P19807: "Simulation studies of ionic liquids"

Grant holderO. Steinhauser
Funding period06/2007 - 05/2012
Imprint: (as stipulated by Austrian law, MedienG 2005): S. Boresch / C. Schröder,
Institut für Computergestützte Biologische Chemie, Währinger Strasse 17, 1090 Wien, Austria