Ursula Röthlisberger

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Author summary Adenylyl cyclases (ACs) are enzymes that can translate extracellular signals into the intracellular molecule cAMP, which is thus a 2nd messenger of extracellular events. The brain expresses nine membrane-bound AC variants, and AC5 is the dom ...

The redox properties of two large DNA fragments composed of 39 base pairs, differing only by an 8-oxoguanine (8oxoG) defect replacing a guanine (G), were investigated in physiological conditions using mixed quantum mechanical/molecular mechanical (QM/MM) m ...

Through millions of years of evolution, Nature has accomplished the development of highly efficient and sustainable processes and the idea to understand and copy natural strategies is therefore very appealing. However, in spite of intense experimental and ...

The photophysical and photochemical properties of 5-benzyluracil and 5,6-benzyluracil, the latter produced by photocyclization of the former through irradiation with femtosecond UV laser pulses, are investigated both experimentally and theoretically. The a ...

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 ...

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 ...

Second-order Moller-Plesset perturbation theory (MP2) is the most expedient wave function-based method for considering electron correlation in quantum chemical calculations and, as such, provides a cost-effective framework to assess the effects of basis se ...

The photo-driven charge transfer process of 4-(dimethylamino) benzonitrile (DMABN) in deep eutectic solvent (DES) is investigated through steady state and time resolved spectroscopy along with non -adiabatic molecular dynamic simulations. Simultaneous coex ...

The k(off) values of ligands unbinding to proteins are key parameters for drug discovery. Their predictions based on molecular simulation may under- or overestimate experiment in a system- and/or technique-dependent way. Here we use an established method-i ...

Rhodopsin is a photoactive G-protein-coupled receptor (GPCR) that converts dim light into a signal for the brain, leading to eyesight. Full activation of this GPCR is achieved after passing through several steps of the protein's photoactivation pathway. Ke ...

The transfer of charge at the molecular level plays a fundamental role in many areas of chemistry, physics, biology and materials science. Today, more than 60 years after the seminal work of R. A. Marcus, charge transfer is still a very active field of res ...

Horseradish peroxidase (HRP) is one of the most relevant peroxidase enzymes, used extensively in immunochemistry and biocatalysis applications. Unlike the closely related catalase enzymes, it exhibits a low activity to disproportionate hydrogen peroxide (H ...

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 ...

Ru(II) and Os(II) p-cymene dichloride complexes with either a pta (1,3,5-triaza-7-phosphatricyclo[3.3.1.1]decane) or [pta-Me]Cl ligand which exhibit anticancer activity were prepd. and characterized by 1H and 31P NMR spectroscopy and mass spectrometry. Thr ...

Effective masses are calculated for a large variety of perovskites of the form ABX(3) differing in chemical composition (A= Na, Li, Cs; B = Pb, Sn; X= Cl, Br, I) and crystal structure. In addition, the effects of some defects and dopants are assessed. We s ...

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). ...

Targeting defined histone protein sites in chromatin is an emerging therapeutic approach that can potentially be enhanced by allosteric effects within the nucleosome. Here we characterized a novel hetero-bimetallic compound with a design based on a nucleos ...

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/ ...

First-principles molecular dynamics (FPMD) and its quantum mechanical-molecular mechanical (QM/MM) extensions are powerful tools to follow the real-time dynamics of a broad variety of systems in their ground as well as electronically excited states. The co ...

Biomimicry is a strategy that makes practical use of evolution to find efficient and sustainable ways to produce chemical compounds or engineer products. Exploring the natural machinery of enzymes for the production of desired compounds is a highly profita ...

Ursula Röthlisberger

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Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals

Redox Properties of Native and Damaged DNA from Mixed Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations

Lessons from Nature: Computational Design of Biomimetic Compounds and Processes

Photophysics and Photochemistry of a DNA–Protein Cross-Linking Model: A Synergistic Approach Combining Experiments and Theory

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

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

Plane Waves Versus Correlation-Consistent Basis Sets: A Comparison of MP2 Non-Covalent Interaction Energies in the Complete Basis Set Limit

Control of excited state charge transfer dynamics of DMABN in deep eutectic solvent: Involvement of the partially twisted intermediate state

Accuracy of Molecular Simulation-Based Predictions of k(off) Values: A Metadynamics Study

How Rhodopsin Tunes the Equilibrium between Protonated and Deprotonated Forms of the Retinal Chromophore

Charge migration and charge transfer in molecular systems

The Molecular Mechanism of the Catalase-like Activity in Horseradish Peroxidase

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

Binding of Organometallic Ruthenium(II) and Osmium(II) Complexes to an Oligonucleotide: A Combined Mass Spectrometric and Theoretical Study

Computational Characterization of the Dependence of Halide Perovskite Effective Masses on Chemical Composition and Structure

Hydrogen bonding described using dispersion-corrected density functional theory

Crosslinking Allosteric Sites on the Nucleosome

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

Recent Advances in First-Principles Based Molecular Dynamics

Genetic-Algorithm-Based Optimization of a Peptidic Scaffold for Sequestration and Hydration of CO