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Ursula Röthlisberger

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Related publications (291)

Molecular simulations of ion channels: a quantum chemist's perspective

Denis Bucher, Ursula Röthlisberger

Rockefeller University Press2010

Role of Aggregation in Rhodopsin Signal Transduction

Ursula Röthlisberger, Ivano Tavernelli, Marilisa Neri, Stefano Vanni

Many G protein-coupled receptors (GPCRs) are known to form dimers or even oligomers, and these aggregated states have been proposed as functional units responsible for signal transduction and G protein activation. However, the nature of their involvement h ...

2010

Electron Localization Dynamics in the Triplet Excited State of Ru(bpy)3]2+ in Aqueous Solution

Majed Chergui, Marc-Etienne Moret, Ursula Röthlisberger, Ivano Tavernelli

Hybrid DFT/classical molecular dynamics of the long-lived triplet excited state of [Ru(bpy)3]2+ (bpy=2,2-bipyridine) in aqueous solution is used to investigate the solvent-mediated electron localization and dynamics in the triplet metal-to-ligand charge-tr ...

2010

A conserved protonation-induced switch can trigger "ionic lock" formation in adrenergic receptors

Ursula Röthlisberger, Ivano Tavernelli, Marilisa Neri, Stefano Vanni

The mechanism of signal transduction in G-protein-coupled receptors (GPCRs) is a crucial step in cell signaling. However, the molecular details of this process are still largely undetermined. Carrying out submicrosecond molecular dynamics simulations of be ...

Elsevier2010

A combined QM/MM and Classical Molecular Dynamics Study of [Ru(bpy)3]2+ in Water

Marc-Etienne Moret, Ursula Röthlisberger, Ivano Tavernelli

The solvation of the Ru(bPy)(3) (bpy = 2,2'-bipyridyl) cation was studied by molecular dynamics simulations, using both a hybrid QM/MM Car-Parrinello scheme and a classical force field. The trajectory analysis reveals that the first solvation sphere ...

2009

Dispersion-Corrected Atom-Centered Potentials for Phosphorous

Ursula Röthlisberger, Ivano Tavernelli, Michele Cascella, I-Chun Lin

Dispersion-corrected atom-centered; potentials (DCACPs) for the element phosphorus were generated and tested for the BLYP, BP, and PBE generalized gradient approximations of the exchange-correlation functional. The accuracy and transferability of the DCACP ...

2009

Binding of Organometallic Ruthenium(II) Anticancer Compounds to Nucleobases: A Computational Study

Ursula Röthlisberger, Ivano Tavernelli, Christian Gossens

The reaction of the anticancer compound (eta(6)-benzene)Ru(en)(OH2) (1) toward the nucleobases guanine, adenine, and cytosine is studied computationally using DFT/BP86 calculations. The aqua leaving group of such compounds is known to undergo ligand ...

2009

Observation of Ionic Lock Formation in Molecular Dynamics Simulations of Wild-Type Beta1 and Beta2 Adrenergic Receptors

Ursula Röthlisberger, Ivano Tavernelli, Marilisa Neri, Stefano Vanni

2009

On the Proton Transfer Mechanism in Ammonia-Bridged 7-Hydroxyquinoline: a First-Principles TDDFT Molecular Dynamics Study

Ursula Röthlisberger, Ivano Tavernelli, Matteo Guglielmi

We have investigated the mechanism of proton transfer in the lowest photoexcited state of 7-hydroxyquinoline·(NH3)3 using TDDFT based molecular dynamics. We observe a concerted mechanism according to which all protons are transferred simultaneously in a fa ...

2009

Multicenter density functionals: revised expression of the standard approximations of exchange-correlation functional

Ursula Röthlisberger, Ivano Tavernelli, I-Chun Lin

We propose to express corrections to the standard approximations of the exchange-correlation functionals in the form of multiatom-centered functionals that can be related to the atoms-in-molecules theory of Bader and a multicenter density expansion. Unlike ...

2009

Hydrogen bonding described using dispersion-corrected density functional theory

Ursula Röthlisberger, I-Chun Lin, Jeremy Samuel Arey

In recent works, dispersion-corrected atom-centered potentials (DCACPs) were developed as a method to account for long-range dispersion forces between molecules in density functional theory calculations within the generalized gradient approximation (GGA). ...

2009

On nonadiabatic coupling vectors in time-dependent density functional theory

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod

In this note, we show that the development for the calculation of nonadiabatic coupling vectors in the framework of TDDFT introduced by the authors in the series of recent publications [E. Tapavicza , Phys. Rev. Lett.98, 023001 (2007); I. Tavernelli , J. C ...

American Institute of Physics2009

Tuning the efficacy of ruthenium(II)-arene (RAPTA) antitumour compounds with fluorinated arene ligands

Rosario Scopelliti, Paul Joseph Dyson, Ursula Röthlisberger, Enrico Marko Tapavicza, Andrew Douglas Phillips, Anna Katherine Renfrew

A series of compounds of general formula [Ru(eta(6)-fluoroarene)(pta)Cl-2] (fluoroarene = C6H5F, C6H5CF3, and 1,4-C6H4CH3F; pta = 1,3,5-triaza-7-phosphatricyclo[3.3.1.1]decane) have been prepared and characterized spectroscopically. Additionally, X-ray dif ...

American Chemical Society2009

Non-adiabatic coupling vectors within linear response time-dependent density functional theory

Ursula Röthlisberger, Ivano Tavernelli, Enrico Marko Tapavicza

A method is developed to compute the nonadiabatic coupling vectors (NACVs) between electronic ground and excited states as well as between any possible pair of excited states within the framework of linear response time-dependent density functional theory ...

2009

Importance of weak interactions in liquid water

Ursula Röthlisberger, Ivano Tavernelli, I-Chun Lin

We present ab initio molecular dynamics studies on liquid water using density functional theory in conjunction with either dispersion-corrected atom-centered potentials or empirical van der Waals corrections. Our results show that improving the description ...

2009

Accurate DFT descriptions for weak interactions of molecules containing sulfur

Ursula Röthlisberger, I-Chun Lin, Jeremy Samuel Arey

Dispersion corrected atom centered potentials (DCACPs) have been shown to significantly improve the density functional theory (DFT) description of weak interactions. In this work, we have calibrated a DCACP for sulfur in combination with the widely used Ge ...

2009

Ab Initio Excited State Properties and Dynamics of a Prototype sigma-Bridged-Donor-Acceptor Molecule

Ursula Röthlisberger, Ivano Tavernelli, Enrico Marko Tapavicza

2009

A QM/MM Investigation of Thymine Dimer Repair by DNA Photolyase

Ursula Röthlisberger

DNA photolyase is a highly efficient light-driven enzyme that repairs the UV-induced cyclobutane pyrimidine dimer in damaged DNA. Herein, we investigate the repair reaction of the thymine dimer by means of hybrid quantum mechanical/molecular mechanical QM/ ...

2009

New Paradigm in Molecular Engineering of Sensitizers for Solar Cell Applications

Michael Graetzel, Mohammad Khaja Nazeeruddin, Ursula Röthlisberger, Ivano Tavernelli, Matteo Guglielmi, Takeru Bessho

A novel thiocyanate-free cyclometalleted ruthenium sensitizer for solar cells is designed and developed. Upon anchoring to nanocrystalline TiO2 films, it exhibits a remarkable incident monochromatic photon-to-current conversion efficiency of 83%. The solar ...

2009

Developing Improved Charge Sets for the Modeling of the KcsA K+ Channel Using QM/MM Electrostatic Potentials

Denis Bucher, Ursula Röthlisberger, Leonardo Guidoni

The performance of popular molecular mechanics (MM) force fields in treating problems that involve ion-channel interactions is explored. We have used quantum mechanical/molecular mechanical (QM/MM) calculations to compute the electrostatic potential inside ...

2009

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