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Ursula Röthlisberger

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Related publications (291)

A wavelet analysis for the X-ray absorption spectra of molecules

Majed Chergui, Ursula Röthlisberger, Ivano Tavernelli, Amal El Nahhas, Marco Eli Reinhard, Thomas James Penfold

We present a Wavelet transform analysis for the X-ray absorption spectra of molecules. In contrast to the traditionally used Fourier transform approach, this analysis yields a 2D correlation plot in both R- and k-space. As a consequence, it is possible to ...

American Institute of Physics2013

Computational evidence that Vibrio vulnificus FrsA is not a cofactor-independent pyruvate decarboxylase

Ursula Röthlisberger, Elizabeth Claire Brunk

Amer Chemical Soc2013

Trajectory-Based Nonadiabatic Dynamics with Time-Dependent Density Functional Theory

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod

Understanding the fate of an electronically excited molecule constitutes an important task for theoretical chemistry, and practical implications range from the interpretation of atto- and femtosecond spectroscopy to the development of light-driven molecula ...

Wiley-Blackwell2013

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

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

Fatty acid amide hydrolase (FAAH) substrate specificity understood via molecular dynamics

Ursula Röthlisberger, Marilisa Neri, Pablo Campomanes Ramos, Giulia Palermo, Andrea Cavalli

Amer Chemical Soc2013

Molecular Engineering of a Fluorene Donor for Dye-Sensitized Solar Cells

Michael Graetzel, Jacques-Edouard Moser, Mohammad Khaja Nazeeruddin, Robin Humphry-Baker, Joël Teuscher, Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Negar Ashari Astani, Aswani Yella, Julien Edouard Frey, Simon Mathew, Lauren Elizabeth Polander

To improve their efficiency beyond the state-of-the-art, D-pi-A dyes must display increased spectral breadth and account for the physical limitations observed in the dye. sensitized solar cells. In particular, they should be designed to control the electro ...

Amer Chemical Soc2013

Computational design of biomimetic strategies for the production of chemical compounds

Ursula Röthlisberger, Elizabeth Claire Brunk

Amer Chemical Soc2013

Unravelling the Potential for Dithienopyrrole Sensitizers in Dye-Sensitized Solar Cells

Two D−π−A dyes based on the dithieno[3,2-b:2′,3′-d]pyrrole π-bridge (DTP) were synthesized, characterized using UV−vis absorption spectroscopy and electrochemistry, modeled using quantum chemical calculations, and used as sensitizers in dye-sensitized sola ...

Amer Chemical Soc2013

Excited State Dynamics with Quantum Trajectories

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod

Nuclear quantum dynamics beyond the Born-Oppenheimer approximation is performed using quantum trajectories. Within the adiabatic representation of the electronic states, NABDY (NonAdiabatic Bohmian DYnamics) is used in combination with DFT and LR-TDDFT to ...

Schweizerische Chemische Gesellschaft2012

Structure and dynamics of liquid water from ab initio molecular dynamics - Comparison of BLYP, PBE and revPBE density functionals with and without van der Waals corrections

Ursula Röthlisberger, Ivano Tavernelli, I-Chun Lin

We investigate the accuracy provided by different treatments of the exchange and correlation effects, in particular the London dispersion forces, on the properties of liquid water using ab initio molecular dynamics simulations with density functional theor ...

Amer Chemical Soc2012

Nanocomposites containing neutral blue emitting cyclometalated iridium(III) emitters for oxygen sensing

Michael Graetzel, Mohammad Khaja Nazeeruddin, Davide Di Censo, Rosario Scopelliti, Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Il Jung

The behavior toward oxygen sensing of nanocomposites made of the aluminum oxide-hydroxide nanostructured solid support (AP200/19) and neutral blue emitting cyclometalated iridium(III) complexes was studied. The results are compared with the same dyes immob ...

2012

Enhanced Sampling Molecular Dynamics Identifies PrPSc Structures Harboring a C-Terminal beta-Core

Ursula Röthlisberger, Ivano Tavernelli, Maria Carola Colombo

We perform a replica exchange molecular dynamics simulation corresponding to a 2.8 mu s total time for the extensive enhanced sampling of the conformational space of the C-terminal part (residues 124-226) of the mouse prion protein (PrP); 1.3% of the confo ...

Amer Chemical Soc2012

Ultrafast anisotropic x-ray scattering in the condensed phase

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

The advent of x-ray free electron lasers offers new opportunities for x-ray scattering (XRS) studies of ultrafast molecular dynamics in liquids, which have so far been limited to the 100 ps resolution of synchrotrons. In particular, anisotropic XRS induced ...

Institute of Physics (IoP) and Deutsche Physikalische Gesellschaft2012

Role of Environment for Catalysis of the DNA Repair Enzyme MutY

Ursula Röthlisberger, Jeremy Samuel Arey, Elizabeth Claire Brunk

Control of the N-glycosylase reaction by the DNA repair enzyme, MutY, entails the organization of solvent molecules. Classical molecular dynamics and QM/MM simulations were used to investigate the solvent and environment effects contributing to catalysis. ...

2012

Insights into Intrastrand Cross-Link Lesions of DNA from QM/MM Molecular Dynamics Simulations

Ursula Röthlisberger, Chandan Patel

DNA damages induced by oxidative intrastrand cross-links have been the subject of intense research during the past decade. Yet, the currently available experimental protocols used to isolate such lesions only allow to get structural information about linke ...

2012

Integrating computational methods to retrofit enzymes to synthetic pathways

Ursula Röthlisberger, Ivano Tavernelli, Vassily Hatzimanikatis, Marilisa Neri, Elizabeth Claire Brunk

Microbial production of desired compounds provides an efficient framework for the development of renewable energy resources. To be competitive to traditional chemistry, one requirement is to utilize the full capacity of the microorganism to produce target ...

Wiley-Blackwell2012

Acid-Induced Degradation of Phosphorescent Dopants for OLEDs and Its Application to the Synthesis of Tris-heteroleptic Iridium(III) Bis-cyclometalated Complexes

Michael Graetzel, Mohammad Khaja Nazeeruddin, Rosario Scopelliti, Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Julien Edouard Frey

Investigations of blue phosphorescent organic light emitting diodes (OLEDs) based on [Ir(2-(2,4-difluorophenyl)pyridine)(2)(picolinate)] (FIrPic) have pointed to the cleavage of the picolinate as a possible reason for device instability. We reproduced the ...

2012

A Simple Approach to Room Temperature Phosphorescent Allenylidene Complexes

Michael Graetzel, Mohammad Khaja Nazeeruddin, Davide Di Censo, Rosario Scopelliti, Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod

Wiley-Blackwell2012

Characterization of Molecular Determinants of the Conformational Stability of Macrophage Migration Inhibitory Factor: Leucine 46 Hydrophobic Pocket

Ursula Röthlisberger, Bruno Claude Daniel Fauvet, Hilal Lashuel, Hajer Ouertatani-Sakouhi, Michele Cascella, Farah El Turk, Marilisa Neri, Florence Pojer, Amer Ashrafi, Min Kyu Cho, Magdalena Zweckstetter

Macrophage Migration Inhibitory Factor (MIF) is a key mediator of inflammatory responses and innate immunity and has been implicated in the pathogenesis of several inflammatory and autoimmune diseases. The oligomerization of MIF, more specifically trimer f ...

Public Library of Science2012

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