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Ursula Röthlisberger

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Publications associées (291)

CNDOL: A fast and reliable method for the calculation of electronic properties of very large systems. Applications to retinal binding pocket in rhodopsin and gas phase porphine

Majed Chergui, Ursula Röthlisberger

Very large mol. systems can be calcd. with the so called CNDOL approx. Hamiltonians that have been developed by avoiding oversimplifications and only using a priori parameters and formulas from the simpler NDO methods. A new diagonal monoelectronic term na ...

2007

Structural and energetic properties of organometallic ruthenium(II) diamine anticancer compounds and their interaction with nucleobases

Ursula Röthlisberger, Ivano Tavernelli, Christian Gossens

2007

Predicting noncovalent interactions between aromatic biomolecules with London-dispersion-corrected DFT

Ursula Röthlisberger, Ivano Tavernelli, Anatole von Lilienfeld, I-Chun Lin

2007

Protonation of the chromophore in the photoactive yellow protein

Ursula Röthlisberger, Leonardo Guidoni

2007

Optical Spectra of Cu(II)-Azurin by Hybrid TDDFT-Molecular Dynamics Simulations

Ursula Röthlisberger, Ivano Tavernelli, Michele Cascella

2007

Microsolvation effects on the excited state dynamics of protonated tryptophan

Oleg Boyarkine, Thomas Rizzo, Sébastien Mercier, Anthi Kamariotou, Ursula Röthlisberger, Ivano Tavernelli, Matteo Guglielmi, Michele Cascella

To better understand the complex photophysics of the amino acid tryptophan, which is widely used as a probe of protein structure and dynamics, we have measured electronic spectra of protonated, gas-phase tryptophan solvated with a controlled number of wate ...

2006

Influence of Long-range Electrostatic Treatments on the Folding of the N-terminal H4 Histone Tail Peptide

Ursula Röthlisberger

A series of ca. 20-ns molecular dynamics simulation runs of the N-terminal H4 histone tail in its un- and tetraacetylated forms were performed using three different long-range electrostatic treatments namely, spherical-cutoff, reaction field, and particle ...

2006

Influence of Hydrogen-Bonding Substituents on the Cytotoxicity of RAPTA Compounds

Sébastien Rochat, Paul Joseph Dyson, Ursula Röthlisberger, Ivano Tavernelli, Antoine Dorcier, Christian Gossens, Claudine Scolaro, Gianni Sava

A new series of organometallic ruthenium(II)-arene compounds of the type RuCl2(η6-arene)(phosphine) (phosphine = 1,3,5-triaza-7-phosphaadamantane, PTA, and 3,7-diacetly-1,3,7-triaza-5-phosphabicyclo[3.3.1]nonane, DAPTA) with different ...

2006

Role of protein frame and solvent for the redox properties of azurin from Pseudomonas Aeruginosa

Ursula Röthlisberger, Ivano Tavernelli, Michele Cascella, Paolo Carloni

National Academy of Sciences2006

Duocarmycins binding to DNA explored by Molecular Simulation

Ursula Röthlisberger, Paolo Carloni

2006

Mechanism of the bleomycin suicide: A Car-Parrinello molecular dynamics investigation

Ursula Röthlisberger, Christian Gossens

2006

A Comparative Theoretical Study of Dipeptide Solvation in Water

Ursula Röthlisberger

2006

Enantioselective Palladium-Catalyzed Hydrosilylation of Styrene: Influence of Electronic and Steric Effects on Enantioselectivity and Catayst Design via Hybrid QM/MM Molecular Dynamics Simulations

Ursula Röthlisberger

2006

Molecular dynamics in electronically excited states using time-dependent density functional theory

Ursula Röthlisberger, Ivano Tavernelli

The authors describe two different implementations of time-dependent d. functional theory (TDDFT) for use in excited state mol. dynamics simulations. One is based on the linear response formulation (LR-TDDFT), whereas the other uses a time propagation sche ...

Taylor & Francis2005

Solvent and protein effects on the structure and dynamics of the rhodopsin chromophore

Ursula Röthlisberger, Leonardo Guidoni

The structure and dynamics of the retinal chromophore of rhodopsin are investigated systematically in different environments (vacuum, methanol soln., and protein binding pocket) and with different computational approaches (classical, quantum, and hybrid qu ...

2005

Evolutionarily Conserved Functional Mechanics across Pepsin-like and Retroviral Aspartic Proteases

Ursula Röthlisberger, Michele Cascella, Paolo Carloni

The biol. function of the aspartic protease from HIV-1 has recently been related to the conformational flexibility of its structural scaffold. Here, we use a multistep strategy to investigate whether the same mechanism affects the functionality in the peps ...

2005

Electron transfer induced dissociation of chloro-cyano-benzene radical anion: driving chemical reactions via charge restraints

Ursula Röthlisberger

We introduce a new quantum mechanics/mol. mechanics based method to drive electron transfer reactions. Our approach uses the dynamically restrained electrostatic potential derived charges of the quantum atoms as a reaction coordinate, and allows an estn. o ...

2005

Folding pathways for initiator and effector procaspases from computer simulations

Ursula Röthlisberger

The folding pathways of procaspases 3, 7, and 8 were studied using a Go-like Hamiltonian and mol. dynamics simulations coupled with a parallel tempering scheme. The folding pathways and the overall structures of procaspases 3 and 7 were similar, and were c ...

2005

Core spin-polarization correction in pseudopotential-based electronic structure calculations

Lothar Helm, Ursula Röthlisberger, Ivano Tavernelli, Oleg Yazyev

A simple scheme for the evaluation of the core spin-polarization contribution within pseudopotential electronic structure methods is proposed. The method uses a reconstruction of the all-electron wave functions and the frozen valence spin-d. approxn. to so ...

2005

Duocarmycins binding to DNA explored by molecular simulation

Ursula Röthlisberger, Paolo Carloni

Duocarmycins are a potent class of antitumor agents. Their activity arises by their covalent binding to adenine nucleobases of DNA. We use classical mol. dynamics and hybrid (QM/MM) Car-Parrinello mol. dynamics simulations to study non-covalent and covalen ...

2005

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