Publications by Manuel Dömer | EPFL Graph Search

Revealing the Structure of Tryptophan in Microhydrated Complexes by Cold Ion Spectroscopy

Natalia Nagornova, Oleg Boyarkine, Andrei Zviagin, Ruslan Yamaletdinov, Manuel Dömer

The geometry of biomolecules isolated in the gas phaseusuallydiffers substantially from their native structures in aqueous solution,which are the only ones truly relevant to life science. To connectthe high resolution of cold ion spectroscopy that can be a ...

2023

Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin

Ursula Röthlisberger, Ivano Tavernelli, Pablo Campomanes Ramos, Manuel Dömer

We extended a previously developed force matching approach to systems with covalent QM/MM boundaries and describe its user-friendly implementation in the publicly available software package CPMD. We applied this approach to the challenging case of the reti ...

2014

Solvent rearrangements during the transition from hydrophilic to hydrophobic solvation

Majed Chergui, Ursula Röthlisberger, Ivano Tavernelli, Thomas James Penfold, Manuel Dömer

We present an ab initio Born-Oppenheimer molecular dynamics study of the early time solvent dynamics after electron abstraction from aqueous iodide. An initial response occurs within ∼75 fs, corresponding to a water molecule sharing almost one electron wit ...

Elsevier2013

Intricacies of Describing Weak Interactions involving Halogen Atoms within Density Functional Theory

Ursula Röthlisberger, Ivano Tavernelli, Manuel Dömer

In this work we assess the performance of different dispersion-corrected DFT approaches (M06, M06-2X, DFT-D3 and DCACP) in reproducing high-level wave function based benchmark calculations on the weakly bound halogen dimers (X2)2 and X2-Ar (for X=F,Cl,Br,I ...

Amer Chemical Soc2013

In situ parameterisation of SCC-DFTB repulsive potentials by iterative Boltzmann inversion

Ursula Röthlisberger, Ivano Tavernelli, Elisa Liberatore, Manuel Dömer

The parameterisation of accurate and transferable repulsive potentials is a key ingredient for the self-consistent-charge density functional tight-binding method (SCC-DFTB). In the conventional parameterisation scheme the balanced description of different ...

Taylor & Francis2013

Assessing the performance of computational methods for the prediction of the ground state structure of a cyclic decapeptide

Ursula Röthlisberger, Thomas Rizzo, Ivano Tavernelli, Natalia Nagornova, Oleg Boyarkine, Matteo Guglielmi, Manuel Dömer

We benchmark the performance of various computational approaches, ranging from the classical nonpolarizable force fields AMBER FF96 and FF99SB, the polarizable force fields AMBER FF02polEP and AMOEBAbio09 to the semiempirical DFT method SCC-DFTB. The test ...

Wiley-Blackwell2013

Photodynamics of Lys+-Trp Protein Motifs: Hydrogen Bonds Ensure Photostability

Ursula Röthlisberger, Ivano Tavernelli, Matteo Guglielmi, Manuel Dömer

Cation-pi interactions such as Lys(+)-Trp, are highly abundant structural motifs in proteins. Both, experimental and theoretical studies of small prototypical gas phase systems, H(+)Trp, H(+)Trp center dot(H2O)(n) and H+ Gly-Trp, indicate such an arrangeme ...

Royal Soc Chemistry2013

Approaches to Increase the Accuracy of Molecular Dynamics Simulations : From Classical to Tight Binding and First Principles Methods

Manuel Dömer

EPFL2013

Cold Ion Spectroscopy Reveals the Intrinsic Structure of a Decapeptide

Ursula Röthlisberger, Thomas Rizzo, Ivano Tavernelli, Natalia Nagornova, Oleg Boyarkine, Matteo Guglielmi, Manuel Dömer

Wiley-VCH Verlag GmbH2011

Pushing the Frontiers of First-Principles Based Computer Simulations of Chemical and Biological Systems

Ursula Röthlisberger, Ivano Tavernelli, Polydefkis Diamantis, Basile Curchod, Thomas James Penfold, Pablo Campomanes Ramos, Giulia Palermo, Elizabeth Claire Brunk, Negar Ashari Astani, Marilisa Neri

The Laboratory of Computational Chemistry and Biochemistry is active in the development and application of first-principles based simulations of complex chemical and biochemical phenomena. Here, we review some of our recent efforts in extending these metho ...

2011