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List of works by Ursula Röthlisberger

A QM/MM investigation of thymine dimer radical anion splitting catalyzed by DNA photolyase

scientific article

A Simple Approach to Room Temperature Phosphorescent Allenylidene Complexes

scientific article published on 29 June 2012

A Variational Definition of Electrostatic Potential Derived Charges

A Versatile Multiple Time Step Scheme for Efficient ab Initio Molecular Dynamics Simulations

scientific article published on 04 May 2018

A comparative theoretical study of dipeptide solvation in water.

scientific article published in April 2006

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

scientific article published on 2 February 2010

A genetic algorithm based design and experimental characterization of a highly thermostable metalloprotein

scientific article published on 16 January 2018

A mechanochemical switch to control radical intermediates

scientific article

A molecular spring for vision.

scientific article published in December 2004

A universal co-solvent dilution strategy enables facile and cost-effective fabrication of perovskite photovoltaics

scientific article published on 10 January 2022

Ab initio excited state properties and dynamics of a prototype sigma-bridged-donor-acceptor molecule

scientific article published on 01 September 2009

Accelerating rare reactive events by means of a finite electronic temperature

scientific article published on 01 July 2002

Accurate DFT Descriptions for Weak Interactions of Molecules Containing Sulfur

scientific article published in January 2009

Acid-induced degradation of phosphorescent dopants for OLEDs and its application to the synthesis of tris-heteroleptic iridium(III) bis-cyclometalated complexes

scientific article

All-atom simulations disentangle the functional dynamics underlying gene maturation in the intron lariat spliceosome

scientific article published on 11 June 2018

Allosteric cross-talk in chromatin can mediate drug-drug synergy

scientific article

An Organometallic Compound which Exhibits a DNA Topology-Dependent One-Stranded Intercalation Mode

scientific article

An Organometallic Compound which Exhibits a DNA Topology-Dependent One-Stranded Intercalation Mode

Anandamide hydrolysis in FAAH reveals a dual strategy for efficient enzyme-assisted amide bond cleavage via nitrogen inversion

scientific article published on 3 October 2014

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

Assigning the EPR Fine Structure Parameters of the Mn(II) Centers in Bacillus subtilis Oxalate Decarboxylase by Site-Directed Mutagenesis and DFT/MM Calculations

scientific article

Association of Both Inhibitory and Stimulatory Gα Subunits Implies Adenylyl Cyclase 5 Deactivation

scientific article published on 08 October 2019

Atomic-Level Microstructure of Efficient Formamidinium-Based Perovskite Solar Cells Stabilized by 5-Ammonium Valeric Acid Iodide Revealed by Multinuclear and Two-Dimensional Solid-State NMR

scientific article published on 23 October 2019

Automated Parametrization of Biomolecular Force Fields from Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations through Force Matching.

scientific article published in March 2007

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

scholarly article by Antoine Dorcier et al published April 2005 in Organometallics

Binding of organometallic ruthenium(II) anticancer compounds to nucleobases: a computational study

scientific article published in October 2009

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.

scientific article published in October 2007

Can Biomimetic Zinc Compounds Assist a (3 + 2) Cycloaddition Reaction? A Theoretical Perspective.

scientific article published on 26 October 2017

Chapter 9. First Principles Methods in Biology: From Continuum Models to Hybrid Ab initio Quantum Mechanics/Molecular Mechanics

scholarly article

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

scientific article

Charge migration and charge transfer in molecular systems.

scientific article published in November 2017

Charge separation and carrier dynamics in donor-acceptor heterojunction photovoltaic systems.

scientific article published in November 2017

Cold-Ion Spectroscopy Reveals the Intrinsic Structure of a Decapeptide

scientific article published on 06 May 2011

Combined QM/MM and classical molecular dynamics study of [Ru(bpy)3]2+ in water

scientific article published in June 2009

Computational insights into function and inhibition of fatty acid amide hydrolase

scientific article

Computational study of thymine dimer radical anion splitting in the self-repair process of duplex DNA.

scientific article

Computational, Structural, and Kinetic Evidence That Vibrio vulnificus FrsA Is Not a Cofactor-Independent Pyruvate Decarboxylase ⬇️

scientific article published on March 5, 2013

Coordination numbers of K(+) and Na(+) Ions inside the selectivity filter of the KcsA potassium channel: insights from first principles molecular dynamics

scientific article published on May 2010

Copper binding sites in the C-terminal domain of mouse prion protein: A hybrid (QM/MM) molecular dynamics study

scientific article published in February 2008

Crown Ether Modulation Enables over 23% Efficient Formamidinium-Based Perovskite Solar Cells

scientific article published on 10 November 2020

Cryogenic Spectroscopy and Quantum Molecular Dynamics Determine the Structure of Cyclic Intermediates Involved in Peptide Sequence Scrambling

scientific article published on 17 June 2015

DNA structural distortions induced by ruthenium-arene anticancer compounds.

scientific article

Describing weak interactions of biomolecules with dispersion-corrected density functional theory

scientific article published on 07 March 2008

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

scientific article

Development of Site-Specific Mg(2+)-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations.

scientific article

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

scientific article

Dispersion Corrected Atom-Centered Potentials for Phosphorus

scientific article published on November 2009

Does Proton Conduction in the Voltage-Gated H+ Channel hHv1 Involve Grotthuss-Like Hopping via Acidic Residues?

scientific article published in November 2016

Drug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations

scientific article published on October 2002

Duocarmycins binding to DNA investigated by molecular simulation

scientific article published on March 2006

Dye-sensitized solar cells with 13% efficiency achieved through the molecular engineering of porphyrin sensitizers.

scientific article published on 2 February 2014

Early steps of the intramolecular signal transduction in rhodopsin explored by molecular dynamics simulations

scientific article published in September 2002

Effect of N-Terminal Myristoylation on the Active Conformation of Gαi1-GTP.

scientific article

Effect of graphene oxide nanosheets on visible light-assisted antibacterial activity of vertically-aligned copper oxide nanowire arrays

scientific article published on 7 March 2018

Efficient treatment of correlation energies at the basis-set limit by Monte-Carlo summation of continuum states

scientific article published on 11 September 2020

Electron localization dynamics in the triplet excited state of [Ru(bpy)3]2+ in aqueous solution.

scientific article published in May 2010

Emergence of hidden phases of methylammonium lead iodide (CH3NH3PbI3) upon compression

Enhanced sampling molecular dynamics identifies PrP(Sc) structures harboring a C-terminal β-core.

scientific article published on 30 November 2012

Erratum: Local control theory in trajectory-based nonadiabatic dynamics [Phys. Rev. A84, 042507 (2011)]

scholarly article published in Physical Review A

Erratum: Publisher's Note: "Implications of short time scale dynamics on long time processes" (Struct. Dyn. 4, 061507 (2017)].

scientific article published on 12 January 2018

Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases

scientific article

Excited state dynamics with quantum trajectories

scientific article published on 01 January 2012

Exploiting Coordinate Scaling Relations To Accelerate Exact Exchange Calculations

scientific article published on 02 July 2018

Exploring the inhibition mechanism of adenylyl cyclase type 5 by n-terminal myristoylated Gαi1

scientific article published on 11 September 2017

Extended Intermolecular Interactions Governing Photocurrent–Voltage Relations in Ternary Organic Solar Cells

scientific article published on 22 September 2016

Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC

scientific article published on 25 September 2019

Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC

Fighting Cancer with Transition Metal Complexes: From Naked DNA to Protein and Chromatin Targeting Strategies

scientific article published on 04 December 2015

Folding pathways for initiator and effector procaspases from computer simulations

scientific article published on 01 June 2005

Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin

scientific article published on 18 November 2013

Genetic-Algorithm-Based Optimization of a Peptidic Scaffold for Sequestration and Hydration of CO2.

scientific article published on 5 October 2016

Guanine-Stabilized Formamidinium Lead Iodide Perovskites

scientific article published on 03 February 2020

Gαi1 inhibition mechanism of ATP-bound adenylyl cyclase type 5

scientific article published on 25 January 2021

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

scientific article published on 21 July 2017

Hydrogen Bonding Described Using Dispersion-Corrected Density Functional Theory

scientific article published on 01 April 2009

Identification of clustering artifacts in photoactivated localization microscopy

scientific article published on 12 June 2011

Implications of short time scale dynamics on long time processes.

scientific article published in November 2017

Importance of van der Waals interactions in liquid water

scientific article published on 01 January 2009

In Situ Mapping of the Molecular Arrangement of Amphiphilic Dye Molecules at the TiO2 Surface of Dye-Sensitized Solar Cells

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

Influence of halogen atoms on a homologous series of bis-cyclometalated iridium(III) complexes

scientific article

Insights into intrastrand cross-link lesions of DNA from QM/MM molecular dynamics simulations

scientific article published on 23 January 2012

Integrating computational methods to retrofit enzymes to synthetic pathways

scientific article published on 28 September 2011

Intricacies of Describing Weak Interactions Involving Halogen Atoms within Density Functional Theory

scientific article published on 27 December 2012

Ion binding and internal hydration in the multidrug resistance secondary active transporter NorM investigated by molecular dynamics simulations

scientific article published on 03 February 2012

Ionic polarization-induced current-voltage hysteresis in CH3NH3PbX3 perovskite solar cells

scientific article published on 8 February 2016

Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets

scientific article (publication date: June 2015)

Lessons from nature: computational design of biomimetic compounds and processes

scientific article

Ligand substitutions between ruthenium-cymene compounds can control protein versus DNA targeting and anticancer activity

scientific article

Local Control Theory in Trajectory Surface Hopping Dynamics Applied to the Excited-State Proton Transfer of 4-Hydroxyacridine

scientific article published on 3 June 2015

Local control theory in trajectory-based nonadiabatic dynamics

article

Local control theory using trajectory surface hopping and linear-response time-dependent density functional theory.

scientific article published on January 2013

Low Inhibiting Power of N···CO Based Peptidomimetic Compounds against HIV-1 Protease: Insights from a QM/MM Study

article

Mechanical (QM/MM) Simulations of Adiabatic and Nonadiabatic Ultrafast Phenomena

scientific article published on 01 January 2011

Mechanism to Trigger Unfolding in O6‐Alkylguanine‐DNA Alkyltransferase ⬇️

scientific article published on March 26, 2013

MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry.

scientific article published on 6 May 2019

MiMiC: Multiscale Modeling in Computational Chemistry

scientific article published on 20 March 2020

Microsolvation effects on the excited-state dynamics of protonated tryptophan.

scientific article

Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States

scientific article

Mixed time-dependent density-functional theory/classical trajectory surface hopping study of oxirane photochemistry.

scientific article

Molecular Basis of CLC Antiporter Inhibition by Fluoride

scientific article published on 09 April 2020

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

Molecular dynamics simulations of structural changes during procaspase 3 activation

scientific article

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

scientific article published on June 2010

Multidisciplinary Preclinical Investigations on Three Oxamniquine Analogues as Novel Drug Candidates for Schistosomiasis

scientific article published on 27 August 2020

Multiple Steering Molecular Dynamics Applied to Water Exchange at Alkali Ions

NMR solvent shifts of adenine in aqueous solution from hybrid QM/MM molecular dynamics simulations

scientific article

Nanocomposites Containing Neutral Blue Emitting Cyclometalated Iridium(III) Emitters for Oxygen Sensing

scholarly article by Marta Marín-Suárez et al published 6 June 2012 in Chemistry of Materials

New paradigm in molecular engineering of sensitizers for solar cell applications

scientific article published on 01 April 2009

Nonadiabatic ab initio molecular dynamics using linear-response time-dependent density functional theory

article

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

scientific article published on 01 November 2010

Nonadiabatic coupling vectors within linear response time-dependent density functional theory.

scientific article

Nonadiabatic effects in electronic and nuclear dynamics

scientific article published in November 2017

Observation of "ionic lock" formation in molecular dynamics simulations of wild-type beta 1 and beta 2 adrenergic receptors

scientific article published in June 2009

On nonadiabatic coupling vectors in time-dependent density functional theory

scientific article published in November 2009

On the Accuracy of Molecular Simulation-based Predictions of koff Values: A Metadynamics Study

scientific article published on 16 July 2020

On the proton transfer mechanism in ammonia-bridged 7-hydroxyquinoline: a TDDFT molecular dynamics study.

scientific article published on 21 April 2009

Optical spectra of Cu(II)-azurin by hybrid TDDFT-molecular dynamics simulations

scientific article published on 3 August 2007

Optimization of Effective Atom Centered Potentials for London Dispersion Forces in Density Functional Theory

scientific article

Origin of the spectral shifts among the early intermediates of the rhodopsin photocycle.

scientific article published on 25 February 2014

Origin of unusual bandgap shift and dual emission in organic-inorganic lead halide perovskites.

scientific article published on 28 October 2016

Parameterization of azole-bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure

scientific article published on 01 January 2008

Photodynamics of Lys+-Trp protein motifs: hydrogen bonds ensure photostability

scientific article published on 01 January 2013

Plane-wave implementation and performance of à-la-carte Coulomb-attenuated exchange-correlation functionals for predicting optical excitation energies in some notorious cases.

scientific article published on 16 April 2018

Polarization effects and charge transfer in the KcsA potassium channel

scientific article published on 26 April 2006

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

scientific article published on 5 December 2007

Predicting novel binding modes of agonists to β adrenergic receptors using all-atom molecular dynamics simulations

scientific article

Predictive Determination of Band Gaps of Inorganic Halide Perovskites.

scientific article

Prion versus doppel protein misfolding: new insights from replica-exchange molecular dynamics simulations.

scientific article published on 13 November 2013

Probing the electronic and geometric structure of ferric and ferrous myoglobins in physiological solutions by Fe K-edge absorption spectroscopy

scientific article published on 01 January 2014

Pushing the frontiers of first-principles based computer simulations of chemical and biological systems

scientific article published on January 2011

QM/MM Car-Parrinello molecular dynamics study of the solvent effects on the ground state and on the first excited singlet state of acetone in water

scientific article published on November 2003

Quantitative photo activated localization microscopy: unraveling the effects of photoblinking

scientific article

Reactions of alkynes with [RuCl(cyclopentadienyl)] complexes: the important first steps.

scientific article published in July 2010

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

scientific article published on 14 September 2020

Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls

scientific article published on 2 April 2013

Role of Environment for Catalysis of the DNA Repair Enzyme MutY ⬇️

scientific article published on May 11, 2012

Role of aggregation in rhodopsin signal transduction

scientific article published in June 2010

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

scientific article

Ruddlesden-Popper Phases of Methylammonium-Based Two-Dimensional Perovskites with 5-Ammonium Valeric Acid AVA2MA n-1Pb nI3 n+1 with n = 1, 2, and 3

scientific article published on 13 June 2019

Scanning Reactive Pathways with Orbital Biased Molecular Dynamics

scientific article published in July 2005

Secondary Structure Assignment of Amyloid-β Peptide Using Chemical Shifts

scientific article published on 22 April 2011

Shedding Light on the Basis Set Dependence of the Minnesota Functionals: Differences Between Plane Waves, Slater Functions, and Gaussians

scientific article published on 26 December 2018

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

scientific article published on 29 May 2012

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

scientific article published in September 2005

Stabilization of the Perovskite Phase of Formamidinium Lead Triiodide by Methylammonium, Cs, and/or Rb Doping

scientific article published on 23 February 2017

Structural and Energetic Properties of Organometallic Ruthenium(II) Diamine Anticancer Compounds and Their Interaction with Nucleobases.

scientific article published in May 2007

Structural and Photophysical Templating of Conjugated Polyelectrolytes with Single-Stranded DNA

scientific article published on 07 August 2020

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

scientific article published on 22 June 2012

Structure-based thermodynamic analysis of caspases reveals key residues for dimerization and activity

scientific article published in July 2003

Structure-property relationships based on Hammett constants in cyclometalated iridium(III) complexes: their application to the design of a fluorine-free FIrPic-like emitter

scientific article published on 18 December 2013

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

scientific article published on 16 June 2011

Study of the redox properties of singlet and triplet Tris(2,2'-bipyridine)ruthenium(II) ([Ru(bpy)3]2+) in aqueous solution by full quantum and mixed quantum/classical molecular dynamics simulations

scientific article published on 02 April 2014

Synthesis, characterization and ab initio investigation of a panchromatic ullazine–porphyrin photosensitizer for dye-sensitized solar cells

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

scientific article

The Structure of the Protonated Serine Octamer

scientific article published on 11 April 2018

The conformational flexibility of the carboxy terminal residues 105-114 is a key modulator of the catalytic activity and stability of macrophage migration inhibitory factor

scientific article

The mechanism of catalytic enantioselective fluorination: computational and experimental studies

scientific article published on 01 March 2002

The protonation state of the Glu-71/Asp-80 residues in the KcsA potassium channel: a first-principles QM/MM molecular dynamics study

scientific article published on 25 May 2007

The role and perspective of ab initio molecular dynamics in the study of biological systems

scientific article

Towards Compatibility between Ruthenium Sensitizers and Cobalt Electrolytes in Dye-Sensitized Solar Cells

scientific article published on 04 July 2013

Trajectory surface hopping within linear response time-dependent density-functional theory.

scientific article published on 8 January 2007

Trajectory-based nonadiabatic dynamics with time-dependent density functional theory.

scientific article published on May 2013

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

scientific article published on 25 January 2011

Tuning the Efficacy of Ruthenium(II)-Arene (RAPTA) Antitumor Compounds with Fluorinated Arene Ligands

Two misfolding routes for the prion protein around pH 4.5.

scientific article

Ultrafast Relaxation Dynamics of the Ethylene Cation C2H4+

article

Ultrafast anisotropic x-ray scattering in the condensed phase

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches.

scientific article published in November 2017

Ultrafast nuclear dynamics of the acetylene cation C2H2+ and its impact on the infrared probe pulse induced C-H bond breaking efficiency

scientific article published on 01 August 2019

Ultrafast pulse shaping modulates perceived visual brightness in living animals

scientific article published in 2021

Unusual Ar-H/Rh-H J(HH) NMR coupling in complexes of rhodium(III): experimental evidence and theoretical support for an eta1-arene structure

scientific article published in October 2004

Vapor-assisted deposition of highly efficient, stable black-phase FAPbI3 perovskite solar cells

scientific article

Variational optimization of effective atom centered potentials for molecular properties

scientific article published in January 2005

Variational particle number approach for rational compound design

scientific article published on 07 October 2005

Vertical Ionization Energies and Electron Affinities of Native and Damaged DNA Bases, Nucleotides, and Pairs from Density Functional Theory Calculations: Model Assessment and Implications for DNA Damage Recognition and Repair

scientific article published on 11 February 2019

Wagging the Tail: Essential Role of Substrate Flexibility in FAAH Catalysis

scientific article published on 15 January 2013

Water-assisted reaction mechanism of monozinc beta-lactamases

scientific article published in October 2004

Wavefunction-Based Electrostatic-Embedding QM/MM Using CFOUR through MiMiC

scientific article published on 14 December 2021

Weakly Bonded Complexes of Aliphatic and Aromatic Carbon Compounds Described with Dispersion Corrected Density Functional Theory

scientific article published on 01 September 2007

Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns

scientific article published on 16 June 2016

Why choosing the right partner is important: stabilization of ternary CsyGUAxFA(1-y-x)PbI3 perovskites

scientific article published on 11 September 2020

pKaEstimation of Ruthenium(II)−Arene PTA Complexes and their Hydrolysis Products via a DFT/Continuum Electrostatics Approach

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