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Ursula Röthlisberger

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Related publications (291)

Origin of the Spectral Shifts among the Early Intermediates of the Rhodopsin Photocycle

Ursula Röthlisberger, Ivano Tavernelli, Marilisa Neri, Pablo Campomanes Ramos, Stefano Vanni, Bruno Araujo Cautiero Horta

A combined strategy based on the computation of absorption energies, using the ZINDO/S semiempirical method, for a statistically relevant number of thermally sampled configurations extracted from QM/MM trajectories is used to establish a one-to-one corresp ...

2014

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

Ursula Röthlisberger, Ivano Tavernelli, Pablo Campomanes Ramos, Manuel Dömer

We extended a previously developed force matching approach to systems with covalent QM/MM boundaries and describe its user-friendly implementation in the publicly available software package CPMD. We applied this approach to the challenging case of the reti ...

2014

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

Michael Graetzel, Mohammad Khaja Nazeeruddin, Robin Humphry-Baker, Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Negar Ashari Astani, Aswani Yella, Peng Gao, Simon Mathew

Dye-sensitized solar cells have gained widespread attention in recent years because of their low production costs, ease of fabrication and tunable optical properties, such as colour and transparency. Here, we report a molecularly engineered porphyrin dye, ...

2014

Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase

Ursula Röthlisberger, Ivano Tavernelli, Pablo Lopez Tarifa

We use time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods to investigate the fragmentation of doubly ionized uracil in gas phase. Different initial electronic excited states of the dication are obtained by removing ele ...

2014

Molecular dynamics and mutagenesis studies indicate structural flexibility as a key factor for substrate specificity in FAAH catalysis

Ursula Röthlisberger, Pablo Campomanes Ramos, Giulia Palermo, Andrea Cavalli

Amer Chemical Soc2014

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

Paul Joseph Dyson, Ursula Röthlisberger, Wee Han Ang, Pablo Campomanes Ramos, Alexey Nazarov, Michael Groessl, Catherine Marie Amélie Clavel

Ruthenium compounds have become promising alternatives to platinum drugs by displaying specific activities against different cancers and favourable toxicity and clearance properties. Nonetheless, their molecular targeting and mechanism of action are poorly ...

Nature Research2014

A Quantum Dynamics Study of the Ultrafast Relaxation in a Prototypical Cu(I)-Phenanthroline

Majed Chergui, Ursula Röthlisberger, Ivano Tavernelli, Thomas James Penfold, Gloria Capano

The ultrafast nonadiabatic dynamics of a prototypical Cu(I)phenanthroline complex, Cu(dmp)(2) (dmp = 2,9-dimethyl-1,10-phenanthroline), initiated after photoexcitation into the optically bright metal-to-ligand charge-transfer (MLCT) state (S-3) is inv ...

2014

Lessons from Nature: Computational Design of Biomimetic Compounds and Processes

Ursula Röthlisberger, Pablo Campomanes Ramos, Elizabeth Claire Brunk, Negar Ashari Astani, Esra Bozkurt, Marta Andreia Da Silva Perez, Nicholas John Browning

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 ...

2014

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

Ursula Röthlisberger, Ivano Tavernelli, Jérôme Florian Gonthier, Polydefkis Diamantis

The oxidation of ground-state (singlet) and triplet Ru(bpy)(3) were studied by full quantum-mechanical (QM) and mixed quantum/classical (QM/MM) molecular dynamics simulations. Both approaches provide reliable results for the redox potentials of the t ...

2014

Hydrolysis of anandamide in FAAH shows that nitrogen inversion is key to efficient enzyme-assisted amide bond cleavage

Ursula Röthlisberger, Pablo Campomanes Ramos, Giulia Palermo, Andrea Cavalli

Amer Chemical Soc2014

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

Majed Chergui, Ursula Röthlisberger, Ivano Tavernelli, Frederico Alves Lima, Marco Eli Reinhard, Thomas James Penfold

We present an iron K-edge X-ray absorption study of carboxymyoglobin (MbCO), nitrosylmyoglobin (MbNO), oxymyoglobin (MbO(2)), cyanomyoglobin (MbCN), aquomet myoglobin (metMb) and unligated myoglobin (deoxyMb) in physiological media. The analysis of the XAN ...

2014

Structural determinants of the optical shifts of the early photointermediates of rhodopsin

Ursula Röthlisberger

Amer Chemical Soc2014

A Vibronic Coupling Hamiltonian to Describe the Ultrafast Excited State Dynamics of a Cu(I)-Phenanthroline Complex

Ursula Röthlisberger, Ivano Tavernelli, Thomas James Penfold, Gloria Capano

We present a model Hamiltonian to study the nonadiabatic dynamics of photoexcited Cu(dmp)(2), (dmp = 2,9-dimethyl-1,10-phenanthroline). The relevant normal modes, identified by the magnitude of the first order coupling constants, correspond closely to ...

2014

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

Ursula Röthlisberger, Ivano Tavernelli, Sara Bonella, Mohammadhassan Valadan

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 ...

2014

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

Ursula Röthlisberger, Pablo Campomanes Ramos

Oxalate decarboxylase (OxDC) catalyzes the Mn-dependent conversion of the oxalate monoanion into CO2 and formate. EPR-based strategies for investigating the catalytic mechanism of decarboxylation are complicated by the difficulty of assigning the signals a ...

2014

A Mechanochemical Switch to Control Radical Intermediates

Ursula Röthlisberger, Elizabeth Claire Brunk

B-12-dependent enzymes employ radical species with exceptional prowess to catalyze some of the most chemically challenging, thermodynamically unfavorable reactions. However, dealing with highly reactive intermediates is an extremely demanding task, requiri ...

2014

X-ray Spectroscopic Study of Solvent Effects on the Ferrous and Ferric Hexacyanide Anions

Majed Chergui, Ursula Röthlisberger, Ivano Tavernelli, Marco Eli Reinhard, Mercedes Hannelore Rittmann-Frank, Thomas James Penfold

We present an Fe K alpha resonant inelastic X-ray scattering (RIXS) and X-ray emission (XES) study of ferrous and ferric hexacyanide dissolved in water and ethylene glycol. We observe that transitions below the absorption edge show that the solvent has a d ...

2014

Classical and Mixed Quantum Mechanical/Molecular Mechanical (Qm/Mm) Simulations of G Protein Coupled Receptors

Ursula Röthlisberger

Cell Press2014

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

Ursula Röthlisberger, Marilisa Neri, Pablo Campomanes Ramos, Giulia Palermo, Andrea Cavalli

The serine hydrolase, fatty acid amide hydrolase (FAAH), is responsible for the intracellular degradation of anandamide and other bioactive fatty acid ethanolamides involved in the regulation of pain, inflammation, and other pathophysiological processes. T ...

Amer Chemical Soc2013

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

Ursula Röthlisberger, Elizabeth Claire Brunk

The fermentation-respiration switch (FrsA) protein in Vibrio vulnificus was recently reported to catalyze the cofactor-independent decarboxylation of pyruvate. We now report quantum mechanical/molecular mechenical calculations that examine the energetics o ...

Amer Chemical Soc2013

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