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Ursula Röthlisberger

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Related publications (291)

Influence of Halogen Atoms on a Homologous Series of Bis-Cyclometalated Iridium(III) Complexes

Michael Graetzel, Mohammad Khaja Nazeeruddin, Rosario Scopelliti, Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Frédéric Steimer

A series of homologous bis-cyclometalated iridium(III) complexes Ir(2,4-di-X-phenyl-pyridine)2(picolinate) (X = H, F, Cl, Br) HIrPic, FIrPic, ClIrPic, and BrIrPic has been synthesized and characterized by NMR, X-ray crystallography, UV–vis absorption and e ...

2012

A Closer Look into G Protein Coupled Receptor Activation: X-Ray Crystallography and Long-Scale Molecular Dynamics Simulations

Ursula Röthlisberger, Stefano Vanni

G protein coupled receptors (GPCRs) are a large eukaryotic protein family of transmembrane receptors that react to a signal coming from the extracellular environment to generate an intracellular response through the activation of a signal transduction path ...

2012

Directed evolution of the suicide protein O⁶-alkylguanine-DNA alkyltransferase for increased reactivity results in an alkylated protein with exceptional stability

Kai Johnsson, Ursula Röthlisberger, Simone Schmitt, Florence Pojer, Birgit Mollwitz, Elizabeth Claire Brunk

Here we present a biophysical, structural, and computational analysis of the directed evolution of the human DNA repair protein O-6-alkylguanine-DNA alkyltransferase (hAGT) into SNAP-tag, a self-labeling protein tag. Evolution of hAGT led not only to incre ...

2012

Ion Binding and Internal Hydration in the Multidrug Resistance Secondary Active Transporter NorM Investigated by Molecular Dynamics Simulations

Ursula Röthlisberger, Pablo Campomanes Ramos, Stefano Vanni

Recently, a 3.65 angstrom resolution structure of the transporter, NorM from the multidrug and toxic compound extrusion family has been determined in the outward-facing conformation. This antiporter uses electrochemical gradients to drive substrate export ...

2012

Simulations of X-ray absorption spectra: the effect of the solvent

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

We perform quantum mechanics/molecular mechanics molecular dynamics simulations on the Pt-2(P2O5H2)(4) (abbreviated PtPOP) complex; in water, dimethylformamide and ethanol. These are used to calculate the ground state X-ray absorption spectrum of the ...

2012

Mixed Quantum Mechanical/Molecular Mechanical (QM/MM) simulations of Adiabatic and Nonadiabatic Ultrafast Phenomena

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Marilisa Neri, Pablo Campomanes Ramos, Stefano Vanni, Andrey Laktionov, Thomas James Penfold

A thorough theoretical description of ultrafast phenomena that occur in complex systems constitutes a formidable challenge. It not only necessitates the use of quantum mechanical methods that can describe ground and possibly even electronically excited sta ...

Schweizerische Chemische Gesellschaft2011

Local control theory in trajectory-based nonadiabatic dynamics

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Thomas James Penfold

In this paper, we extend the implementation of nonadiabatic molecular dynamics within the framework of time-dependent density-functional theory in an external field described in Tavernelli et al. [Phys. Rev. A 81, 052508 (2010)] by calculating on-the-fly p ...

2011

Cold Ion Spectroscopy Reveals the Intrinsic Structure of a Decapeptide

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

Wiley-VCH Verlag GmbH2011

Nonadiabatic Molecular Dynamics with Solvent Effects: a LR-TDDFT QM/MM Study of Ruthenium (II) Tris(bipyridine) in Water

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod

The previously derived trajectory-based nonadiabatic molecular dynamics scheme [E. Tapavicza, I. Tavernelli, U. Rothlisberger, Phys. Rev. Lett. 98 (2007) 023001] is extended to include the coupling of the quantum system with a classically described environ ...

Elsevier2011

Identification of clustering artifacts in photoactivated localization microscopy

Ursula Röthlisberger, Aleksandra Radenovic, Stefano Vanni, Paolo Annibale, Marco Scarselli

Nature Publishing Group2011

Predicting Novel Binding Modes of Agonists to β Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations

Ursula Röthlisberger, Ivano Tavernelli, Marilisa Neri, Stefano Vanni

Understanding the binding mode of agonists to adrenergic receptors is crucial to enabling improved rational design of new therapeutic agents. However, so far the high conformational flexibility of G protein-coupled receptors has been an obstacle to obtaini ...

Public Library of Science2011

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

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

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

Secondary Structure Assignment of Amyloid-β Peptide Using Chemical Shifts

Ursula Röthlisberger, Geoffrey Wood

The distinct conformational dependence of chemical shifts caused by R-helices and β-sheets renders NMR chemical shift analysis a powerful tool for the structural determination of proteins. However, the time scale of NMR experiments can make a secondary str ...

2011

Trajectory-based solution of the nonadiabatic quantum dynamics equations: an on-the-fly approach for molecular dynamics simulations

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod

The non-relativistic quantum dynamics of nuclei and electrons is solved within the framework of quantum hydrodynamics using the adiabatic representation of the electronic states. An on-the-fly trajectory-based nonadiabatic molecular dynamics algorithm is d ...

Royal Society of Chemistry2011

Studies of Glutathione Transferase P1-1 Bound to a Platinum(IV)-Based Anticancer Compound Reveal the Molecular Basis of Its Activation

Paul Joseph Dyson, Ursula Röthlisberger, Wee Han Ang, Pablo Campomanes Ramos

Platinum-based cancer drugs, such as cisplatin, are highly effective chemotherapeutic agents used extensively for the treatment of solid tumors. However, their effectiveness is limited by drug resistance, which, in some cancers, has been associated with an ...

Wiley-Blackwell2011

Low inhibiting power of N...CO based peptidomimetic compounds against HIV protease: Insights from a hybrid QM/MM study

Ursula Röthlisberger, Michele Cascella

Recently, Hasserodt et al. proposed new HIV-1 drug candidates based on a weak N center dot center dot center dot CO interaction, designed to be a close transition state analog (Gautier et al. Bioorg. Med. Chem. 2006, 14, 3835-3847; Waibel et al. J. Bioorg. ...

2010

Reactions of Alkynes with [RuCl(cyclopentadienyl)] Complexes: The Important First Steps

Kay Severin, Rosario Scopelliti, Euro Solari, Ursula Röthlisberger, Basile Curchod, Barnali Dutta, Pablo Campomanes Ramos

Cyclopentadienyl-ruthenium half-sandwich complexes with 2-bound alkyne ligands have been suggested as catalytic intermediates in the early stages of Ru-catalyzed reactions with alkynes. We show that electronically unsaturated complexes of the formula [RuCl ...

2010

Nonadiabatic coupling vectors for excited states within time-dependent density functional theory in the Tamm-Dancoff approximation and beyond

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Andrey Laktionov

Recently, we have proposed a scheme for the calculation of nonadiabatic couplings and nonadiabatic coupling vectors within linear response time-dependent density functional theory using a set of auxiliary many-electron wavefunctions [ I. Tavernelli, E. Tap ...

American Institute of Physics2010

Coordination Numbers of K+ and Na+ Ions Inside the Selectivity Filter of the KcsA Potassium Channel: Insights from First Principles Molecular Dynamics

Denis Bucher, Ursula Röthlisberger, Leonardo Guidoni, Paolo Carloni

Quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations were performed to estimate the coordination numbers of K+ and Na+ ions in the selectivity filter of the KcsA channel, and in water. At the DFT/BLYP level, K+ ions were found to displa ...

Elsevier2010

Mixed quantum-classical dynamics with time-dependent external fields: A time-dependent density-functional-theory approach

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod

A mixed quantum-classical method aimed at the study of nonadiabatic dynamics in the presence of external electromagnetic fields is developed within the framework of time-dependent density functional theory. To this end, we use a trajectory-based descriptio ...

2010

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