Publications

Journal Articles

2019

Ruddlesden–Popper Phases of Methylammonium-Based Two-Dimensional Perovskites with 5-Ammonium Valeric Acid AVA2MAn–1PbnI3n+1 with n = 1, 2, and 3

N. Ashari Astani; F. Jahanbakhshi; M. Mladenovic; A. Q. M. Alanazi; I. Ahmadabadi et al. 

Journal of Physical Chemistry Letters. 2019-06-10. Vol. 10, p. 3543-3549. DOI : 10.1021/acs.jpclett.9b01111.

Cu–Al Spinel as a Highly Active and Stable Catalyst for the Reverse Water Gas Shift Reaction

A. Bahmanpour; F. E. Héroguel; M. Kiliç; C. J. Baranowski; L. Artiglia et al. 

ACS Catalysis. 2019-06-03. DOI : 10.1021/acscatal.9b01822.

MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry

J. M. H. Olsen; V. Bolnykh; S. Meloni; E. Ippoliti; M. P. Bircher et al. 

Journal Of Chemical Theory And Computation. 2019-06-01. Vol. 15, num. 6, p. 3810-3823. DOI : 10.1021/acs.jctc.9b00093.

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

P. Diamantis; I. Tavernelli; U. Rothlisberger 

Journal Of Chemical Theory And Computation. 2019-03-01. Vol. 15, num. 3, p. 2042-2052. DOI : 10.1021/acs.jctc.8b00645.

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

M. P. Bircher; P. Lopez-Tarifa; U. Rothlisberger 

Journal Of Chemical Theory And Computation. 2019-01-01. Vol. 15, num. 1, p. 557-571. DOI : 10.1021/acs.jctc.8b00897.

2018

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

F. Kiani; N. Ashari Astani; R. Rahighi; A. Tayyebi; M. Tayebi et al. 

Journal of Colloid and Interface Science. 2018-07-01. Vol. 521, p. 119-131. DOI : 10.1016/j.jcis.2018.03.013.

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

L. Casalino; G. Palermo; A. Spinello; U. Röthlisberger; A. Magistrato 

Proceedings of the National Academy of Sciences of the United States of America. 2018-06-26. Vol. 115, num. 26, p. 6584-6589. DOI : 10.1073/pnas.1802963115.

Exploiting Coordinate Scaling Relations To Accelerate Exact Exchange Calculations

M. P. Bircher; U. Röthlisberger 

Journal of Physical Chemistry Letters. 2018-06-25. Vol. 9, num. 14, p. 3886-3890. DOI : 10.1021/acs.jpclett.8b01620.

Plane-Wave Implementation and Performance of à-la-Carte Coulomb-Attenuated Exchange-Correlation Functionals for Predicting Optical Excitation Energies in Some Notorious Cases

M. P. Bircher; U. Röthlisberger 

J Chem Theory Comput. 2018-05-04. Vol. 14, num. 6, p. 3184-3195. DOI : 10.1021/acs.jctc.8b00069.

The Structure of the Protonated Serine Octamer

V. Scutelnic; M. A. S. Perez; M. Marianski; S. Warnke; A. Gregor et al. 

Journal of the American Chemical Society. 2018-04-11. Vol. 120, num. 24, p. 7554-7560. DOI : 10.1021/jacs.8b02118.

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

E. Liberatore; R. Meli; U. Röthlisberger 

Journal of Chemical Theory and Computation. 2018-04-06. Vol. 14, num. 6, p. 2834-2842. DOI : 10.1021/acs.jctc.7b01189.

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

K. El Hage; S. Brickel; S. Hermelin; G. Gaulier; C. Schmidt et al. 

Structural Dynamics. 2018-01-01. Vol. 5, num. 1, p. 019901. DOI : 10.1063/1.5020803.

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

E. Bozkurt; M. A. S. Perez; R. Hovius; N. J. Browning; U. Rothlisberger 

Journal of the American Chemical Society. 2018. Vol. 140, num. 13, p. 4517-4521. DOI : 10.1021/jacs.7b10660.

2017

Implications of short time scale dynamics on long time processes

K. El Hage; S. Brickel; S. Hermelin; G. Gaulier; C. Schmidt et al. 

Structural Dynamics. 2017. Vol. 4, num. 6, p. 061507. DOI : 10.1063/1.4996448.

Nonadiabatic effects in electronic and nuclear dynamics

M. P. Bircher; E. Liberatore; N. J. Browning; S. Brickel; C. Hofmann et al. 

Structural Dynamics. 2017. Vol. 4, num. 6, p. 061510. DOI : 10.1063/1.4996816.

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

S. Antipov; S. Bhattacharyya; K. El Hage; Z-H. Xu; M. Meuwly et al. 

Structural Dynamics. 2017. Vol. 4, num. 6, p. 061509. DOI : 10.1063/1.4996559.

Charge migration and charge transfer in molecular systems

H. J. Wörner; C. A. Arrell; N. Banerji; A. Cannizzo; M. Chergui et al. 

Structural Dynamics. 2017. Vol. 4, num. 6, p. 061508. DOI : 10.1063/1.4996505.

Photoemission and photoionization time delays and rates

L. Gallmann; I. Jordan; H. J. Wörner; L. Castiglioni; M. Hengsberger et al. 

Structural Dynamics. 2017. Vol. 4, num. 6, p. 061502. DOI : 10.1063/1.4997175.

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

J. Teuscher; J. C. Brauer; A. Stepanov; A. Solano; A. Boziki et al. 

Structural Dynamics. 2017. Vol. 4, num. 6, p. 061503. DOI : 10.1063/1.4996409.

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

E. Bozkurt; T. A. Soares; U. Rothlisberger 

Journal of Chemical Theory and Computation. 2017. Vol. 13, num. 12, p. 6382-6390. DOI : 10.1021/acs.jctc.7b00819.

Predictive Determination of Band Gaps of Inorganic Halide Perovskites

J. Wiktor; U. Rothlisberger; A. Pasquarello 

The Journal of Physical Chemistry Letters. 2017. Vol. 8, num. 22, p. 5507-5512. DOI : 10.1021/acs.jpclett.7b02648.

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

N. Ashari-Astani; S. Meloni; A. H. Salavati; G. Palermo; M. Gratzel et al. 

Journal Of Physical Chemistry C. 2017. Vol. 121, num. 43, p. 23886-23895. DOI : 10.1021/acs.jpcc.7b04898.

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

S. C. Van Keulen; U. Rothlisberger 

PLoS Computational Biology. 2017. Vol. 13, num. 9, p. e1005673. DOI : 10.1371/journal.pcbi.1005673.

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

S. C. Van Keulen; A. Solano; U. Rothlisberger 

Journal of Chemical Theory and Computation. 2017. Vol. 13, num. 9, p. 4524-4534. DOI : 10.1021/acs.jctc.7b00229.

Characterization of the Photochemical Properties of 5-Benzyluracil via Time-Dependent Density Functional Theory

M. Micciarelli; B. F. E. Curchod; S. Bonella; C. Altucci; M. Valadan et al. 

Journal Of Physical Chemistry A. 2017. Vol. 121, num. 20, p. 3909-3917. DOI : 10.1021/acs.jpca.6b12799.

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

O. A. Syzgantseva; M. Saliba; M. Grätzel; U. Rothlisberger 

The Journal of Physical Chemistry Letters. 2017. Vol. 8, num. 6, p. 1191-1196. DOI : 10.1021/acs.jpclett.6b03014.

Genetic Optimization of Training Sets for Improved Machine Learning Models of Molecular Properties

N. J. Browning; R. Ramakrishnan; O. A. Von Lilienfeld; U. Roethlisberger 

Journal Of Physical Chemistry Letters. 2017. Vol. 8, num. 7, p. 1351-1359. DOI : 10.1021/acs.jpclett.7b00038.

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

Z. Adhireksan; G. Palermo; T. Riedel; Z. Ma; R. Muhammad et al. 

Nature Communications. 2017. Vol. 8, p. 14860. DOI : 10.1038/ncomms14860.

Development of Site-Specific Mg2+-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations

L. Casalino; G. Palermo; N. Abdurakhmonova; U. Rothlisberger; A. Magistrato 

Journal Of Chemical Theory And Computation. 2017. Vol. 13, num. 1, p. 340-352. DOI : 10.1021/acs.jctc.6b00905.

Effect of N-Terminal Myristoylation on the Active Conformation of Gα

S. C. Van Keulen; U. Rothlisberger 

Biochemistry. 2017. Vol. 56, num. 1, p. 271-280. DOI : 10.1021/acs.biochem.6b00388.

2016

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

M. I. Dar; G. Jacopin; S. Meloni; A. Mattoni; N. Arora et al. 

Science Advances. 2016. Vol. 2, num. 10, p. e1601156-e1601156. DOI : 10.1126/sciadv.1601156.

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

W. Tress; B. Beyer; N. A. Astani; F. Gao; S. Meloni et al. 

Journal of Physical Chemistry Letters. 2016. Vol. 7, num. 19, p. 3936-3944. DOI : 10.1021/acs.jpclett.6b01962.

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

S. C. Van Keulen; E. Gianti; V. Carnevale; M. L. Klein; U. Rothlisberger et al. 

The Journal of Physical Chemistry B. 2016. Vol. 121, num. 15, p. 3340-3351. DOI : 10.1021/acs.jpcb.6b08339.

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

E. Brunk; M. A. S. Perez; P. Athri; U. Rothlisberger 

ChemPhysChem. 2016. Vol. 17, num. 23, p. 3831-3835. DOI : 10.1002/cphc.201601034.

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

Z. Ma; G. Palermo; Z. Adhireksan; B. S. Murray; T. Von Erlach et al. 

Angewandte Chemie-International Edition. 2016. Vol. 55, num. 26, p. 7441-7444. DOI : 10.1002/anie.201602145.

Valence and conduction band tuning in halide perovskites for solar cell applications

S. Meloni; G. Palermo; N. Ashari-Astani; M. Grätzel; U. Rothlisberger 

Journal of Materials Chemistry A. 2016. Vol. 4, p. 15997-16002. DOI : 10.1039/C6TA04949D.

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

L. Casalino; G. Palermo; U. Rothlisberger; A. Magistrato 

Journal of the American Chemical Society. 2016. Vol. 138, num. 33, p. 10374-10377. DOI : 10.1021/jacs.6b01363.

Ultrafast Relaxation Dynamics of the Ethylene Cation C

A. Ludwig; E. Liberatore; J. Herrmann; L. Kasmi; P. López-Tarifa et al. 

The Journal of Physical Chemistry Letters. 2016. Vol. 7, num. 10, p. 1901-1906. DOI : 10.1021/acs.jpclett.6b00646.

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

S. Mathew; N. A. Astani; B. F. E. Curchod; J. H. Delcamp; M. Marszalek et al. 

Journal of Materials Chemistry A. 2016. Vol. 4, num. 6, p. 2332-2339. DOI : 10.1039/C5TA08728G.

Entropic stabilization of mixed A-cation ABX3 metal halide perovskites for high performance perovskite solar cells

C. Yi; J. Luo; S. Meloni; A. Boziki; N. Ashari-Astani et al. 

Energy & Environmental Science. 2016. Vol. 9, num. 2, p. 656-662. DOI : 10.1039/C5EE03255E.

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

S. Meloni; T. Moehl; W. Tress; M. Franckevičius; M. Saliba et al. 

Nature Communications. 2016. Vol. 7, p. 10334. DOI : 10.1038/ncomms10334.

2015

Probing wavepacket dynamics using ultrafast x-ray spectroscopy

G. Capano; C. J. Milne; M. Chergui; U. Rothlisberger; I. Tavernelli et al. 

Journal of Physics B: Atomic, Molecular and Optical Physics. 2015. Vol. 48, num. 21, p. 214001. DOI : 10.1088/0953-4075/48/21/214001.

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

P. Campomanes; U. Rothlisberger; M. Alfonso-Prieto; C. Rovira 

Journal of the American Chemical Society. 2015. Vol. 137, num. 34, p. 11170-11178. DOI : 10.1021/jacs.5b06796.

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

G. Palermo; I. Bauer; P. Campomanes; A. Cavalli; A. Armirotti et al. 

PLOS Computational Biology. 2015. Vol. 11, num. 6, p. e1004231. DOI : 10.1371/journal.pcbi.1004231.

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

O. Aseev; M. A. S. Perez; U. Röthlisberger; T. R. Rizzo 

Journal of Physical Chemistry Letters. 2015. Vol. 6, p. 2524-2529. DOI : 10.1021/acs.jpclett.5b01088.

A Theoretical Rationalisation of the Emission Properties of Prototypical Cu(I)-Phenanthroline Complexes

G. Capano; U. Rothlisberger; I. Tavernelli; T. J. Penfold 

The Journal of Physical Chemistry A. 2015.  p. 150611163653007. DOI : 10.1021/acs.jpca.5b03842.

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

B. F. E. Curchod; T. J. Penfold; U. Rothlisberger; I. Tavernelli 

ChemPhysChem. 2015.  p. 2127-2133. DOI : 10.1002/cphc.201500190.

Anandamide Hydrolysis in FAAH Reveals a Dual Strategy for Efficient Enzyme-Assisted Amide Bond Cleavage via Nitrogen Inversion

G. Palermo; P. Campomanes; A. Cavalli; U. Rothlisberger; M. De Vivo 

Journal Of Physical Chemistry B. 2015. Vol. 119, num. 3, p. 789-801. DOI : 10.1021/jp5052276.

Infrared Spectroscopy of Mobility-Selected H+-Gly-Pro-Gly-Gly (GPGG)

A. Masson; M. K. Kamrath; M. A. S. Perez; M. S. Glover; U. Röthlisberger et al. 

Journal of the American Society for Mass Spectrometry. 2015. Vol. 26, p. 1444. DOI : 10.1007/s13361-015-1172-4.

In-situ mapping of the molecular arrangement of amphiphilic dye molecules at the TiO2 surface of dye sensitized solar cells

K. Voitchovsky; N. Ashari Astani; I. Tavernelli; N. Tetreault; U. Rothlisberger et al. 

ACS Applied Materials & Interfaces. 2015.  p. 150504082314007. DOI : 10.1021/acsami.5b01638.

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

E. Brunk; U. Rothlisberger 

Chemical Reviews. 2015.  p. 150423092647007. DOI : 10.1021/cr500628b.

2014

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

G. Capano; M. Chergui; U. Rothlisberger; I. Tavernelli; T. J. Penfold 

Journal of Physical Chemistry A. 2014. Vol. 118, num. 42, p. 9861-9869. DOI : 10.1021/jp509728m.

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

T. J. Penfold; M. Reinhard; M. H. Rittmann-Frank; I. Tavernelli; U. Rothlisberger et al. 

Journal Of Physical Chemistry A. 2014. Vol. 118, num. 40, p. 9411-9418. DOI : 10.1021/jp5055588.

Lessons from Nature: Computational Design of Biomimetic Compounds and Processes

E. Bozkurt; N. Ashari; N. Browning; E. Brunk; P. Campomanes et al. 

Chimia. 2014. Vol. 68, num. 9, p. 642-647. DOI : 10.2533/chimia.2014.642.

A Mechanochemical Switch to Control Radical Intermediates

E. Brunk; W. F. Kellett; N. G. J. Richards; U. Rothlisberger 

Biochemistry. 2014. Vol. 53, num. 23, p. 3830-3838. DOI : 10.1021/bi500050k.

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

M. Micciarelli; M. Valadan; B. Della Ventura; G. Di Fabio; L. De Napoli et al. 

The Journal of Physical Chemistry B. 2014. Vol. 118, num. 19, p. 4983-4992. DOI : 10.1021/jp4115018.

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

G. Capano; T. J. Penfold; U. Roethlisberger; I. Tavernelli 

Chimia. 2014. Vol. 68, num. 4, p. 227-230. DOI : 10.2533/chimia.2014.227.

Derivation of spin-orbit couplings in collinear linear-response TDDFT: A rigorous formulation

F. F. De Carvalho; B. F. E. Curchod; T. J. Penfold; I. Tavernelli 

Journal Of Chemical Physics. 2014. Vol. 140, num. 14, p. 144103. DOI : 10.1063/1.4870010.

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

Z. Adhireksan; G. E. Davey; P. Campomanes; M. Groessl; C. M. Clavel et al. 

Nature Communications. 2014. Vol. 5, p. 3462. DOI : 10.1038/ncomms4462.

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

P. Diamantis; J. F. Gonthier; I. Tavernelli; U. Rothlisberger 

Journal Of Physical Chemistry B. 2014. Vol. 118, num. 14, p. 3950-3959. DOI : 10.1021/jp412395x.

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

P. Campomanes; M. Neri; B. A. C. Horta; U. F. Roehrig; S. Vanni et al. 

Journal Of The American Chemical Society. 2014. Vol. 136, num. 10, p. 3842-3851. DOI : 10.1021/ja411303v.

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

J. Frey; B. F. E. Curchod; R. Scopelliti; I. Tavernelli; U. Rothlisberger et al. 

Dalton Transactions. 2014. Vol. 43, num. 15, p. 5667-5679. DOI : 10.1039/c3dt52739e.

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

P. Lopez-Tarifa; D. Penhoat; M-A. Herve; R. Vuilleumier; M-P. Gaigeot et al. 

Central European Journal Of Physics. 2014. Vol. 12, num. 2, p. 97-102. DOI : 10.2478/s11534-014-0428-0.

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

P. Campomanes; W. R. Kellett; L. M. Easthon; A. Ozarowski; K. N. Allen et al. 

Journal Of The American Chemical Society. 2014. Vol. 136, num. 6, p. 2313-2323. DOI : 10.1021/ja408138f.

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

S. Mathew; A. Yella; P. Gao; R. Humphry-Baker; B. F. E. Curchod et al. 

Nature Chemistry. 2014. Vol. 6, p. 242-247. DOI : 10.1038/nchem.1861.

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

M. Doemer; P. Maurer; P. Campomanes; I. Tavernelli; U. Rothlisberger 

Journal of Chemical Theory and Computation. 2014. Vol. 10, num. 1, p. 412-422. DOI : 10.1021/ct400697n.

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

F. A. Lima; T. J. Penfold; V. D. Veen; M. Renske; M. Reinhard et al. 

Physical Chemistry Chemical Physics. 2014. Vol. 16, num. 4, p. 1617. DOI : 10.1039/c3cp53683a.

2013

Prion versus Doppel Protein Misfolding: New Insights from Replica-Exchange Molecular Dynamics Simulations

P. Baillod; J. Garrec; I. Tavernelli; U. Rothlisberger 

Biochemistry. 2013. Vol. 52, num. 47, p. 8518-8526. DOI : 10.1021/bi400884e.

In situ parameterisation of SCC-DFTB repulsive potentials by iterative Boltzmann inversion

M. Doemer; E. Liberatore; J. M. Knaup; I. Tavernelli; U. Rothlisberger 

Molecular Physics. 2013. Vol. 111, num. 22-23, p. 3595-3607. DOI : 10.1080/00268976.2013.842011.

The Charge Transfer Problem in Density Functional Theory Calculations of Aqueously Solvated Molecules

C. M. Isborn; B. D. Mar; B. F. E. Curchod; I. Tavernelli; T. J. Martinez 

Journal Of Physical Chemistry B. 2013. Vol. 117, num. 40, p. 12189-12201. DOI : 10.1021/jp4058274.

The role of Hartree-Fock exchange in the simulation of X-ray absorption spectra: A study of photoexcited [Fe(bpy)(3)](2+)

G. Capano; T. J. Penfold; N. A. Besley; C. J. Milne; M. Reinhard et al. 

Chemical Physics Letters. 2013. Vol. 580, p. 179-184. DOI : 10.1016/j.cplett.2013.06.060.

Unravelling the Potential for Dithienopyrrole Sensitizers in Dye-Sensitized Solar Cells

L. E. Polander; A. Yella; J. Teuscher; R. Humphry-Baker; B. F. E. Curchod et al. 

Chemistry of Materials. 2013. Vol. 25, num. 13, p. 2642-2648. DOI : 10.1021/cm401144j.

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

L. E. Polander; A. Yella; B. F. E. Curchod; N. Ashari Astani; J. Teuscher et al. 

Angewandte Chemie International Edition. 2013. Vol. 52, num. 333, p. 8731-8735. DOI : 10.1002/anie.201304608.

Two Misfolding Routes for the Prion Protein around pH 4.5

J. Garrec; I. Tavernelli; U. Rothlisberger 

PLoS Computational Biology. 2013. Vol. 9, num. 5, p. e1003057. DOI : 10.1371/journal.pcbi.1003057.

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

A. Yella; R. Humphry-Baker; B. F. E. Curchod; N. Ashari Astani; J. Teuscher et al. 

Chemistry of Materials. 2013. Vol. 25, num. 13, p. 2733-2739. DOI : 10.1021/cm401593b.

Ab initio-driven trajectory-based nuclear quantum dynamics in phase space

I. Tavernelli 

Physical Review A. 2013. Vol. 87, num. 4. DOI : 10.1103/PhysRevA.87.042501.

Solvent Induced Luminescence Quenching: Static and Time-Resolved X-Ray Absorption Spectroscopy of a Copper(I) Phenanthroline Complex

T. J. Penfold; S. Karlsson; G. Capano; F. A. Lima; J. Rittmann et al. 

The Journal of Physical Chemistry A. 2013. Vol. 117, p. 4591-4601. DOI : 10.1021/jp403751m.

Photodynamics of Lys+-Trp Protein Motifs: Hydrogen Bonds Ensure Photostability

M. Guglielmi; M. Doemer; I. Tavernelli; U. Rothlisberger 

Faraday Discussions. 2013. Vol. 163, p. 189-203. DOI : 10.1039/c3fd00037k.

Local Control Theory using Trajectory Surface Hopping and Linear-Response Time-Dependent Density Functional Theory

B. F. E. Curchod; T. J. Penfold; U. Rothlisberger; I. Tavernelli 

CHIMIA International Journal for Chemistry. 2013. Vol. 67, num. 4, p. 218-221. DOI : 10.2533/chimia.2013.218.

Trajectory-Based Nonadiabatic Dynamics with Time-Dependent Density Functional Theory

B. F. E. Curchod; U. Rothlisberger; I. Tavernelli 

ChemPhysChem. 2013. Vol. 14, num. 7, p. 1314-1340. DOI : 10.1002/cphc.201200941.

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

W. F. Kellett; E. Brunk; B. J. Desai; A. A. Fedorov; S. C. Almo et al. 

Biochemistry. 2013. Vol. 52, num. 11, p. 1842-1844. DOI : 10.1021/bi400093y.

Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls

O. Valsson; P. Campomanes; I. Tavernelli; U. Rothlisberger; C. Filippi 

Journal of Chemical Theory and Computation. 2013. Vol. 9, p. 2441-2454. DOI : 10.1021/ct3010408.

Mechanism to Trigger Unfolding in O6--Alkylguanine-DNA Alkyltransferase

E. Brunk; B. Mollwitz; U. Rothlisberger 

ChemBioChem. 2013. Vol. 14, p. 703-710. DOI : 10.1002/cbic.201200566.

Charge transfer relaxation in donor–acceptor type conjugated materials

M. Scarongella; A. Laktionov; U. Rothlisberger; N. Banerji 

Journal of Materials Chemistry C. 2013. Vol. 1, num. 12, p. 2308-2319. DOI : 10.1039/c3tc00829k.

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

G. Palermo; P. Campomanes; M. Neri; D. Piomelli; A. Cavalli et al. 

Journal of Chemical Theory and Computation. 2013. Vol. 9, p. 1202-1213. DOI : 10.1021/ct300611q.

A wavelet analysis for the X-ray absorption spectra of molecules

T. J. Penfold; I. Tavernelli; C. J. Milne; M. Reinhard; A. E. Nahhas et al. 

The Journal of Chemical Physics. 2013. Vol. 138, num. 1, p. 014104. DOI : 10.1063/1.4772766.

X-ray Absorption Spectroscopy of Ground and Excited Rhenium–Carbonyl–Diimine Complexes: Evidence for a Two-Center Electron Transfer

A. El Nahhas; R. M. Van Der Veen; T. J. Penfold; V. T. Pham; F. A. Lima et al. 

The Journal of Physical Chemistry A. 2013. Vol. 117, p. 361. DOI : 10.1021/jp3106502.

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

M. Doemer; I. Tavernelli; U. Rothlisberger 

Journal of Chemical Theory and Computation. 2013. Vol. 9, p. 955-964. DOI : 10.1021/ct3007524.

Solvent rearrangements during the transition from hydrophilic to hydrophobic solvation

T. J. Penfold; I. Tavernelli; M. Doemer; R. Abela; U. Rothlisberger et al. 

Chemical Physics. 2013. Vol. 410, p. 25-30. DOI : 10.1016/j.chemphys.2012.10.008.

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

M. Doemer; M. Guglielmi; P. Athri; N. S. Nagornova; T. R. Rizzo et al. 

International Journal of Quantum Chemistry. 2013. Vol. 113, p. 808. DOI : 10.1002/qua.24085.

2012

Enhanced Sampling Molecular Dynamics Identifies PrPSc Structures Harboring a C-Terminal beta-Core

P. Baillod; J. Garrec; M-C. Colombo; I. Tavernelli; U. Rothlisberger 

Biochemistry. 2012. Vol. 51, num. 49, p. 9891-9899. DOI : 10.1021/bi301091x.

Ultrafast anisotropic x-ray scattering in the condensed phase

T. J. Penfold; I. Tavernelli; R. Abela; M. Chergui; U. Rothlisberger 

New Journal Of Physics. 2012. Vol. 14, p. 113002. DOI : 10.1088/1367-2630/14/11/113002.

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

F. El-Turk; B. Fauvet; A. Ashrafi; H. Ouertatani-Sakouhi; M-K. Cho et al. 

PLoS ONE. 2012. Vol. 7, num. 9, p. e45024. DOI : 10.1371/journal.pone.0045024.

A Simple Approach to Room Temperature Phosphorescent Allenylidene Complexes

F. Kessler; B. F. E. Curchod; I. Tavernelli; U. Rothlisberger; R. Scopelliti et al. 

Angewandte Chemie International Edition. 2012. Vol. 51, p. 8030-8033. DOI : 10.1002/anie.201203329.

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

T. J. Penfold; B. F. E. Curchod; I. Tavernelli; R. Abela; U. Rothlisberger et al. 

Physical Chemistry Chemical Physics. 2012. Vol. 14, p. 9444. DOI : 10.1039/c2cp24080g.

Nanocomposites containing neutral blue emitting cyclometalated iridium(III) emitters for oxygen sensing

M. Marín-Suárez; B. F. E. Curchod; I. Tavernelli; U. Rothlisberger; R. Scopelliti et al. 

Chemistry of Materials. 2012. Vol. 24, p. 2330. DOI : 10.1021/cm300575z.

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

I-C. Lin; A. P. Seitsonen; I. Tavernelli; U. Rothlisberger 

Journal of Chemical Theory and Computation. 2012. Vol. 8, p. 3902-3910. DOI : 10.1021/ct3001848.

Role of Environment for Catalysis of the DNA Repair Enzyme MutY

E. Brunk; J. S. Arey; U. Rothlisberger 

Journal of the American Chemical Society. 2012. Vol. 134, num. 20, p. 8608-8616. DOI : 10.1021/ja301714j.

Excited State Dynamics with Quantum Trajectories

B. F. E. Curchod; U. Rothlisberger; I. Tavernelli 

Chimia. 2012. Vol. 66, num. 4, p. 174-177. DOI : 10.2533/chimia.2012.174.

Insights into Intrastrand Cross-Link Lesions of DNA from QM/MM Molecular Dynamics Simulations

J. Garrec; C. Patel; U. Rothlisberger; E. Dumont 

Journal Of The American Chemical Society. 2012. Vol. 134, p. 2111-2119. DOI : 10.1021/ja2084042.

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

B. Mollwitz; E. Brunk; S. Schmitt; F. Pojer; M. Bannwarth et al. 

Biochemistry. 2012. Vol. 51, num. 5, p. 986-994. DOI : 10.1021/bi2016537.

Ion Binding and Internal Hydration in the Multidrug Resistance Secondary Active Transporter NorM Investigated by Molecular Dynamics Simulations

S. Vanni; P. Campomanes; M. Marcia; U. Rothlisberger 

Biochemistry. 2012. Vol. 51, num. 6, p. 1281-1287. DOI : 10.1021/bi2015184.

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

E. Baranoff; B. F. E. Curchod; F. Monti; F. Steimer; G. Accorsi et al. 

Inorganic Chemistry. 2012. Vol. 51, num. 2, p. 799-811. DOI : 10.1021/ic2011474.

Acid-Induced Degradation of Phosphorescent Dopants for OLEDs and Its Application to the Synthesis of Tris-heteroleptic Iridium(III) Bis-cyclometalated Complexes

E. Baranoff; B. F. E. Curchod; J. Frey; R. Scopelliti; F. Kessler et al. 

Inorganic chemistry. 2012. Vol. 51, p. 215-224. DOI : 10.1021/ic202162q.

Integrating computational methods to retrofit enzymes to synthetic pathways

E. Brunk; M. Neri; I. Tavernelli; V. Hatzimanikatis; U. Rothlisberger 

Biotechnology and Bioengineering. 2012. Vol. 109, p. 572-582. DOI : 10.1002/bit.23334.

2011

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

L. J. Parker; L. C. Italiano; C. J. Morton; N. C. Hancock; D. B. Ascher et al. 

Chemistry - A European Journal. 2011. Vol. 17, num. 28, p. 7806-7816. DOI : 10.1002/chem.201100586.

Ultrafast Nonadiabatic Fragmentation Dynamics of Doubly Charged Uracil in a Gas Phase

P. Lopez-Tarifa; M-A. H. du Penhoat; R. Vuilleumier; M-P. Gaigeot; I. Tavernelli et al. 

Physical Review Letters. 2011. Vol. 107, p. 023202. DOI : 10.1103/PhysRevLett.107.023202.

Probing the Transition from Hydrophilic to Hydrophobic Solvation with Atomic Scale Resolution

V. T. Pham; T. J. Penfold; R. M. van der Veen; F. Lima; A. El Nahhas et al. 

Journal Of The American Chemical Society. 2011. Vol. 133, p. 12740-12748. DOI : 10.1021/ja203882y.

Local control theory in trajectory-based nonadiabatic dynamics

B. F. E. Curchod; T. J. Penfold; U. Rothlisberger; I. Tavernelli 

Physical Review A. 2011. Vol. 84, p. 042507. DOI : 10.1103/PhysRevA.84.042507.

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

E. Brunk; N. Ashari; P. Athri; P. Campomanes; F. F. de Carvalho et al. 

Chimia. 2011. Vol. 65, p. 667-671. DOI : 10.2533/chimia.2011.667.

Quantitative Photo Activated Localization Microscopy: Unraveling the Effects of Photoblinking

P. Annibale; S. Vanni; M. Scarselli; U. Rothlisberger; A. Radenovic 

PLoS ONE. 2011. Vol. 6, num. 7, p. e22678. DOI : 10.1371/journal.pone.0022678.

Identification of clustering artifacts in photoactivated localization microscopy

P. Annibale; S. Vanni; M. Scarselli; U. Röthlisberger; A. Radenovic 

Nature Methods. 2011. Vol. 8, p. 527-528. DOI : 10.1038/nmeth.1627.

Secondary Structure Assignment of Amyloid-β Peptide Using Chemical Shifts

G. P. F. Wood; U. Rothlisberger 

Journal of Chemical Theory and Computation. 2011. Vol. 7, p. 1552. DOI : 10.1021/ct200156e.

Mixed Quantum Mechanical/Molecular Mechanical (QM/MM) simulations of Adiabatic and Nonadiabatic Ultrafast Phenomena

B. F. E. Curchod; P. Campomanes; A. Laktionov; M. Neri; T. J. Penfold et al. 

Chimia. 2011. Vol. 65, num. 5, p. 330-333. DOI : 10.2533/chimia.2011.330.

Nonadiabatic Molecular Dynamics with Solvent Effects: a LR-TDDFT QM/MM Study of Ruthenium (II) Tris(bipyridine) in Water

I. Tavernelli; B. F. E. Curchod; U. Rothlisberger 

Chemical Physics. 2011. Vol. 391, p. 101. DOI : 10.1016/j.chemphys.2011.03.021.

Cold Ion Spectroscopy Reveals the Intrinsic Structure of a Decapeptide

N. S. Nagornova; M. Guglielmi; M. Doemer; I. Tavernelli; U. Rothlisberger et al. 

Angewandte Chemie, International Edition. 2011. Vol. 50, p. 5383. DOI : 10.1002/anie.201100702.

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

B. F. E. Curchod; I. Tavernelli; U. Rothlisberger 

Physical Chemistry Chemical Physics. 2011. Vol. 13, p. 3231-3236. DOI : 10.1039/c0cp02175j.

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

S. Vanni; M. Neri; I. Tavernelli; U. Rothlisberger 

PLoS Computational Biology. 2011. Vol. 7, num. 1, p. e1001053. DOI : 10.1371/journal.pcbi.1001053.

2010

Coordination Numbers of K+ and Na+ Ions Inside the Selectivity Filter of the KcsA Potassium Channel: Insights from First Principles Molecular Dynamics

D. Bucher; L. Guidoni; P. Carloni; U. Rothlisberger 

Biophysical Journal. 2010. Vol. 98, p. L47-L49. DOI : 10.1016/j.bpj.2010.01.064.

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

I. Tavernelli; B. F. E. Curchod; A. Laktionov; U. Röthlisberger 

Journal of Chemical Physics. 2010. Vol. 133, num. 19, p. 194104. DOI : 10.1063/1.3503765.

The solvent shell structure of aqueous iodide: X-ray absorption spectroscopy and classical, hybrid QM/MM and full quantum molecular dynamics simulations

V. T. Pham; I. Tavernelli; C. J. Milne; R. M. van der Veen; P. D'Angelo et al. 

Chemical Physics. 2010. Vol. 371, p. 24-29. DOI : 10.1016/j.chemphys.2010.03.023.

Role of Aggregation in Rhodopsin Signal Transduction

M. Neri; S. Vanni; I. Tavernelli; U. Rothlisberger 

Biochemistry. 2010. Vol. 49, p. 4827-4832. DOI : 10.1021/bi100478j.

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

D. Bucher; U. Rothlisberger 

Journal Of General Physiology. 2010. Vol. 135, p. 549-554. DOI : 10.1085/jgp.201010404.

Mixed quantum-classical dynamics with time-dependent external fields: A time-dependent density-functional-theory approach

I. Tavernelli; B. F. E. Curchod; U. Rothlisberger 

Physical Review A. 2010. Vol. 81, p. 052508. DOI : 10.1103/PhysRevA.81.052508.

Reactions of Alkynes with [RuCl(cyclopentadienyl)] Complexes: The Important First Steps

B. Dutta; B. Curchod; P. Campomanes; E. Solari; R. Scopelliti et al. 

CHEMISTRY - A EUROPEAN JOURNAL. 2010. Vol. 16, p. 8400-8409. DOI : 10.1002/chem.201000855.

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

M-E. Moret; I. Tavernelli; M. Chergui; U. Röthlisberger 

Chemistry-A European Journal. 2010. Vol. 16, p. 5889-5894. DOI : 10.1002/chem.201000184.

Low inhibiting power of N...CO based peptidomimetic compounds against HIV protease: Insights from a hybrid QM/MM study

J. Garrrec; P. Fleurat Lessard; M. Cascella; U. Röthlisberger 

Journal of Chemical Theory and Computation. 2010. Vol. 6, p. 1369-1379. DOI : 10.1021/ct9004728.

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

S. Vanni; M. Neri; I. Tavernelli; U. Röthlisberger 

Journal of Molecular Biology. 2010. Vol. 397, p. 1339-1349. DOI : 10.1016/j.jmb.2010.01.060.

2009

On nonadiabatic coupling vectors in time-dependent density functional theory

I. Tavernelli; B. F. E. Curchod; U. Rothlisberger 

Journal of Chemical Physics. 2009. num. 131, p. 196101. DOI : 10.1063/1.3265858.

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

C. Gossens; I. Tavernelli; U. Rothlisberger 

Journal of Physical Chemistry A. 2009. Vol. 113, p. 11888-11897. DOI : 10.1021/jp903237w.

Non-adiabatic Dynamics Using Time-Dependent Density Functional Theory: assessing the Coupling Strengths

I. Tavernelli; E. Tapavicza; U. Rothlisberger 

Journal of Molecular Structure-TheoChem. 2009. Vol. 914, p. 22-29. DOI : 10.1016/j.theochem.2009.04.020.

Dispersion-Corrected Atom-Centered Potentials for Phosphorous

M. Cascella; I. Lin; I. Tavernelli; U. Rothlisberger 

Journal of Chemical Theory and Computation. 2009. Vol. 5, p. 2930-2934. DOI : 10.1021/ct9003756.

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

I. Tavernelli; E. Tapavicza; U. Rothlisberger 

Journal of Physical Chemistry A. 2009. Vol. 113, p. 9595-9602. DOI : 10.1021/jp901356k.

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

D. Bucher; L. Guidoni; P. Maurer; U. Rothlisberger 

Journal of Chemical Theory and Computation. 2009. Vol. 5, p. 2173-2179. DOI : 10.1021/ct9001619.

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

E. Tapavicza; A. K. Renfrew; A. D. Phillips; R. Scopelliti; U. Rothlisberger et al. 

Organometallics. 2009. Vol. 28, num. 17, p. 5061-5071. DOI : 10.1021/om900345n.

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

M. Moret; I. Tavernelli; U. Rothlisberger 

Journal of Physical Chemistry B. 2009. Vol. 113, num. 22, p. 7737-7744. DOI : 10.1021/jp900147r.

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

M. Guglielmi; I. Tavernelli; U. Rothlisberger 

Phys Chem Chem Phys. 2009. Vol. 11, p. 4549-4555. DOI : 10.1039/b903136g.

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

S. Vanni; M. Neri; I. Tavernelli; U. Rothlisberger 

Biochemistry. 2009. Vol. 48, num. 22, p. 4789-4797. DOI : 10.1021/bi900299f.

New Paradigm in Molecular Engineering of Sensitizers for Solar Cell Applications

T. Bessho; E. Yoneda; J. Yum; M. Guglielmi; I. Tavernelli et al. 

Journal of the American Chemical Society. 2009. Vol. 131, p. 5930-5934. DOI : 10.1021/ja9002684.

Hydrogen bonding described using dispersion-corrected density functional theory

J. S. Arey; P. C. Aeberhard; I-C. Lin; U. Rothlisberger 

Journal of Physical Chemistry B. 2009. Vol. 113, num. 14, p. 4726-4732. DOI : 10.1021/jp810323m.

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

I. Tavernelli; E. Tapavicza; U. Rothlisberger 

Journal of Chemical Physics. 2009. Vol. 130, p. 124107. DOI : 10.1063/1.3097192.

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

F. Masson; T. Laino; U. Rothlisberger; J. Hutter 

ChemPhysChem. 2009. Vol. 10, p. 400-410. DOI : 10.1002/cphc.200800624.

Importance of weak interactions in liquid water

I. Lin; A. Seitsonen; M. Coutinho-Neto; I. Tavernelli; U. Rothlisberger 

Journal of Physical Chemistry B. 2009. Vol. 113, p. 1127-1131. DOI : 10.1021/jp806376e.

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

I. Tavernelli; I. Lin; U. Rothlisberger 

Phys. Rev. B. 2009. Vol. 79, p. 045106. DOI : 10.1103/PhysRevB.79.045106.

Accurate DFT descriptions for weak interactions of molecules containing sulfur

P. C. Aeberhard; J. S. Arey; I-C. Lin; U. Rothlisberger 

Journal of Chemical Theory and Computation. 2009. Vol. 5, num. 1, p. 23-28. DOI : 10.1021/ct800299y.

2008

Mixed Time-Dependent Density-Functional/Classical Trajectory Study of Oxirane Photochemistry

E. Tapavicza; I. Tavernelli; U. Rothlisberger; C. Filippi; M. E. Casida 

Journal of Chemical Physics. 2008. Vol. 129, p. 124108. DOI : 10.1063/1.2978380.

DNA structural distortions induced by ruthenium-arene anticancer compounds

C. Gossens; I. Tavernelli; U. Rothlisberger 

Journal of the American Chemical Society. 2008. Vol. 130, p. 10921-10928. DOI : 10.1021/ja800194a.

Computational Study of Thymine Dimer Radical Anion Splitting in the Self-Repair Process of Duplex DNA

F. Masson; T. Laino; I. Tavernelli; U. Rothlisberger; J. Hutter 

Chimia. 2008. Vol. 62, p. 439. DOI : 10.2533/chimia.2008.439.

Atom-centered potentials for describing dispersion forces in density functional theory

-C. Lin; U. Rothlisberger 

Chimia. 2008. Vol. 62, p. 231-234. DOI : 10.2533/chimia.2008.231.

Computational Study of Thymine Dimer Radical Anion Splitting in the Self-Repair Process of Duplex DNA

F. Masson; T. Laino; I. Tavernelli; U. Rothlisberger; J. Hutter 

Journal of the American Chemical Society. 2008. Vol. 130, num. 11, p. 3443-3450. DOI : 10.1021/ja076081h.

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

I. C. Lin; U. Rothlisberger 

Physical Chemistry Chemical Physics. 2008. Vol. 10, p. 1-5. DOI : 10.1039/b718594d.

Hybrid QM/MM molecular dynamics study of copper binding sites in the C-terminal domain of mouse prion protein

M. Colombo; J. VandeVondele; A. Laio; L. Guidoni; U. Rothlisberger 

Proteins-Structure, Function, and Bioinformatics. 2008. Vol. 70, p. 1084-1098. DOI : 10.1002/prot.21604.

Parameterization of novel azole-bridged diplatinum anticancer drugs via a QM/MM force matching procedure

K. Spiegel; A. Magistrato; P. Maurer; P. Ruggerone; U. Rothlisberger et al. 

Journal of Computational Chemistry. 2008. Vol. 29, p. 38-49. DOI : 10.1002/jcc.20739.

2007

Self-interaction corrected density functional theory for the study of intramolecular electron transfer dynamics in radical carbocations

I. Tavernelli 

Journal Of Physical Chemistry A. 2007. Vol. 111, p. 13528-13536. DOI : 10.1021/jp0767056.

Formation of Boronate Ester Polymers with Efficient Intrastrand Charge Transfer Transitions by Three-Component Reactions

N. Christinat; E. Croisier; R. Scopelliti; M. Cascella; U. Rothlisberger et al. 

European Journal of Inorganic Chemistry. 2007. Vol. 33, p. 5177-5181. DOI : 10.1002/ejic.200700723.

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

-C. Lin; O. A. von Lilienfeld; M. D. Coutinho-Neto; I. Tavernelli; U. Rothlisberger 

Journal of Physical Chemistry B. 2007. Vol. 111, num. 51, p. 14346-14354. DOI : 10.1021/jp0750102.

pKa Estimation of Ruthenium(II)-Arene PTA Complexes and their Hydrolysis Products via a DFT/Continuum Electrostatics Approach

C. Gossens; A. Dorcier; P. J. Dyson; U. Rothlisberger 

Organometallics. 2007. Vol. 26, num. 16, p. 3969-3975. DOI : 10.1021/om700364s.

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

M. Cascella; M. L. Cuendet; I. Tavernelli; U. Rothlisberger 

Journal of Physical Chemistry B. 2007. Vol. 111, num. 34, p. 10239-10247. DOI : 10.1021/jp071938i.

Library of dispersion-corrected atom-centered potentials for generalized gradient approximation functionals: Elements H, C, N, O, He, Ne, Ar, and Kr

-C. Lin; M. D. Coutinho-Neto; C. Felsenheimer; O. A. von Lilienfeld; I. Tavernelli et al. 

Physical Review B. 2007. Vol. 75, p. 205131. DOI : 10.1103/PhysRevB.75.205131.

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

S. Komin; C. Gossens; U. Rothlisberger; D. Sebastiani 

Journal of Physical Chemistry B. 2007. Vol. 111, num. 19, p. 5225-5232. DOI : 10.1021/jp067263l.

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

C. Gossens; I. Tavernelli; U. Rothlisberger 

Journal of Chemical Theory and Computation. 2007. Vol. 3, num. 3, p. 1212-1222. DOI : 10.1021/ct6003577.

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

D. Bucher; L. Guidoni; U. Rothlisberger 

Biophysical Journal. 2007. Vol. 93, num. 7, p. 2315-2324. DOI : 10.1529/biophysj.106.102509.

Study of weakly bonded carbon compounds using dispersion corrected density functional theory

E. Tapavicza; I. Lin; O. vonLilienfeld; I. Tavernelli; M. Coutinho et al. 

Journal of Chemical Theory and Computation. 2007. Vol. 3, num. 5, p. 1673-1679. DOI : 10.1021/ct700049s.

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

E. Tapavicza; I. Tavernelli; U. Rothlisberger 

Physical Review Letters. 2007. Vol. 98, num. 2, p. Art. No. 023001. DOI : 10.1103/PhysRevLett.98.023001.

Automated parameterization of biomolecular force fields from QM/MM simulations through force matching

P. Maurer; A. Laio; U. Rothlisberger 

Journal of Chemical Theory and Computation. 2007. Vol. 3, num. 2, p. 628-639. DOI : 10.1021/ct600284f.

Protonation of the chromophore in the photoactive yellow protein

E. Leenders; L. Guidoni; U. Rothlisberger; P. Bolhuis; E. Meijer 

Journal of Physical Chemistry B. 2007. Vol. 111, num. 14, p. 3765-3773. DOI : 10.1021/jp067158b.

Early stages of radiation damage in graphite and carbon nanostructures: A first-principles molecular dynamics study

O. V. Yazyev; I. Tavernelli; U. Rothlisberger; L. Helm 

Physical Review B. 2007. Vol. 75, p. 115418/1-5. DOI : 10.1103/PhysRevB.75.115418.

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

L. A. Montero-Cabrera; U. Rohrig; J. A. Padron-Garcia; R. Crespo-Otero; A. L. Montero-Alejo et al. 

Journal of Chemical Physics. 2007. Vol. 127, num. 14, p. 145102/1-145102/7. DOI : 10.1063/1.2761869.

2006

Polarization effects and charge transfer in the KcsA potassium channel

D. Bucher; S. Raugei; L. Guidoni; M. Dal Peraro; U. Rothlisberger et al. 

Biophysical Chemistry. 2006. Vol. 124, num. 3, p. 292-301. DOI : 10.1016/j.bpc.2006.04.008.

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

M. Cascella; A. Magistrato; I. Tavernelli; P. Carloni; U. Rothlisberger 

Proceedings of the National Academy of Sciences of the United States of America. 2006. Vol. 103, num. 52, p. 19641-19646. DOI : 10.1073/pnas.0607890103.

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

A. Karawajczyk; C. Gossens; U. Rothlisberger; F. Buda 

Journal of Physical Chemistry B. 2006. Vol. 110, num. 42, p. 21245-21250. DOI : 10.1021/jp061673s.

Microsolvation effects on the excited state dynamics of protonated tryptophan

S. R. Mercier; O. V. Boyarkin; A. Kamariotis; M. Guglielmi; I. Tavernelli et al. 

Journal of the American Chemical Society. 2006. Vol. 128, p. 16938-16943. DOI : 10.1021/ja065980n.

A Comparative Theoretical Study of Dipeptide Solvation in Water

H. Hugosson; A. Laio; P. Maurer; U. Rothlisberger 

Journal of Computational Chemistry. 2006. Vol. 27, p. 672-684.

Duocarmycins binding to DNA explored by Molecular Simulation

K. Spiegel; U. Rothlisberger; P. Carloni 

Journal of Physical Chemistry B. 2006. Vol. 110, num. 8, p. 3647-3660. DOI : 10.1021/jp0548265.

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

R. Lins; U. Rothlisberger 

Journal of Chemical Theory and Computation. 2006. Vol. 2, p. 246-250.

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

A. Magistrato; A. Togni; U. Rothlisberger 

Organometallics. 2006. Vol. 25, num. 5, p. 1151-1157. DOI : 10.1021/om050246i.

Diabatic free energy curves and coordination fluctuations for the aqueous Ag(+)Ag(2+) redox couple: A biased Born-Oppenheimer molecular dynamics investigation

J. Blumberger; I. Tavernelli; L. Klein Michael; M. Sprik 

Journal of chemical physics. 2006. Vol. 124, num. 6, p. 64507. DOI : 10.1063/1.2162881.

A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein Conformational Space Sampling

R. Affentranger; I. Tavernelli; E. E. Di Iorio 

Journal of Chemical Theory and Computation. 2006. Vol. 2, num. 2, p. 217-228. DOI : 10.1021/ct050250b.

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

C. Scolaro; T. J. Geldbach; S. Rochat; A. Dorcier; C. Gossens et al. 

Organometallics. 2006. Vol. 25, num. 3, p. 756-765. DOI : 10.1021/om0508841.

2005

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

A. Dorcier; P. J. Dyson; C. Gossens; U. Rothlisberger; R. Scopelliti et al. 

Organometallics. 2005. Vol. 24, num. 9, p. 2114-2123. DOI : 10.1021/om049022a.

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

O. V. Yazyev; I. Tavernelli; L. Helm; U. Rothlisberger 

Physical Review B. 2005. Vol. 71, num. 11, p. 115110/1-115110/5.

Density-functional molecular-dynamics study of the redox reactions of two anionic, aqueous transition-metal complexes

Y. Tateyama; J. Blumberger; M. Sprik; I. Tavernelli 

Journal of Chemical Physics. 2005. Vol. 122, num. 23, p. 234505/1-234505/17. DOI : 10.1063/1.1938192.

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

M. Sulpizi; U. Rothlisberger; A. Laio 

Journal of Theoretical and Computational Chemistry. 2005. Vol. 4, num. 4, p. 985-999. DOI : 10.1142/S0219633605001957.

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

M. Cascella; C. Micheletti; U. Rothlisberger; P. Carloni 

Journal of the American Chemical Society. 2005. Vol. 127, num. 11, p. 3734-3742. DOI : 10.1021/ja044608+.

Folding pathways for initiator and effector procaspases from computer simulations

S. Piana; Z. Taylor; U. Rothlisberger 

Proteins-Structure Function and Bioinformatics. 2005. Vol. 59, num. 4, p. 765-772. DOI : 10.1002/prot.20451.

Hydroxide and proton migration in aquaporins

M. O. Jensen; U. Rothlisberger; C. Rovira 

Biophysical Journal. 2005. Vol. 89, num. 3, p. 1744-1759. DOI : 10.1529/biophysj.104.058206.

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

I. Tavernelli; U. F. Roehrig; U. Rothlisberger 

Molecular Physics. 2005. Vol. 103, num. 6-8, p. 963-981.

Optical properties of molecules in solution via hybrid TDDFT/MM simulations

M. Sulpizi; U. F. Roehrig; J. Hutter; U. Rothlisberger 

International Journal of Quantum Chemistry. 2005. Vol. 101, num. 6, p. 671-682. DOI : 10.1002/qua.20325.

Performance of optimized atom-centered potentials for weakly bonded systems using density functional theory

O. A. von Lilienfeld; I. Tavernelli; U. Rothlisberger; D. Sebastiani 

Physical Review B. 2005. Vol. 71, num. 19, p. 195119/1-195119/7.

Quantum mechanical/molecular mechanical (QM/MM) car-parrinello simulations in excited states

M-E. Moret; E. Tapavicza; L. Guidoni; U. F. Rohrig; M. Sulpizi et al. 

Chimia. 2005. Vol. 59, num. 7-8, p. 493-498.

Rational design of organo-ruthenium anticancer compounds

C. Gossens; I. Tavernelli; U. Rothlisberger 

Chimia. 2005. Vol. 59, num. 3, p. 81-84.

Scanning Reactive Pathways with Orbital Biased Molecular Dynamics

L. Guidoni; U. Rothlisberger 

Journal of Chemical Theory and Computation. 2005. Vol. 1, num. 4, p. 554-560. DOI : 10.1021/ct050081v.

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

U. F. Rohrig; L. Guidoni; U. Rothlisberger 

ChemPhysChem. 2005. Vol. 6, num. 9, p. 1836-1847.

Variational optimization of effective atom centered potentials for molecular properties

O. A. von Lilienfeld; I. Tavernelli; U. Rothlisberger; D. Sebastiani 

Journal of Chemical Physics. 2005. Vol. 122, num. 1, p. 014113/1-014113/6. DOI : 10.1063/1.1829051.

Variational Particle Number Approach for Rational Compound Design

O. A. von Lilienfeld; R. D. Lins; U. Rothlisberger 

Physical Review Letters. 2005. Vol. 95, num. 15, p. 153002/1-153002/4. DOI : 10.1103/PhysRevLett.95.153002.

Experimental and theoretical study of intramolecular exchange in Ir2Rh2(CO)(12) and Ir-4(CO)(11)(mu-SO2)

Z. Beni; L. Guidoni; G. Laurenczy; U. Roethlisberger; R. Roulet 

Dalton Transactions. 2005. num. 2, p. 310-314. DOI : 10.1039/b415147j.

2004

Electronic Structure and Solvation of Copper and Silver Ions: A Theoretical Picture of a Model Aqueous Redox Reaction

J. Blumberger; L. Bernasconi; I. Tavernelli; R. Vuilleumier; M. Sprik 

Journal of the American Chemical Society. 2004. Vol. 126, num. 12, p. 3928-3938. DOI : 10.1021/ja0390754.

Enantioselective Palladium-Catalyzed Hydrosilylation of Styrene: Detailed Reaction Mechanism from First-Principles and Hybrid QM/MM Molecular Dynamics Simulations

A. Magistrato; T. K. Woo; A. Togni; U. Rothlisberger 

Organometallics. 2004. Vol. 23, num. 13, p. 3218-3227. DOI : 10.1021/om049969c.

First-Principles Simulations of C-S Bond Cleavage in Rhenium Thioether Complexes

A. Magistrato; P. Maurer; T. Faessler; U. Rothlisberger 

Journal of Physical Chemistry A. 2004. Vol. 108, num. 11, p. 2008-2013. DOI : 10.1021/jp037932k.

Green oxidation catalysts: computational design of high-efficiency models of galactose oxidase

L. Guidoni; K. Spiegel; M. Zumstein; U. Roethlisberger 

Angewandte Chemie, International Edition. 2004. Vol. 43, num. 25, p. 3286-3289. DOI : 10.1002/anie.200454081.

Molecular dynamics simulations of structural changes during procaspase 3 activation

S. Piana; U. Rothlisberger 

Proteins-Structure Function and Bioinformatics. 2004. Vol. 55, num. 4, p. 932-941. DOI : 10.1002/prot.20046.

A Molecular Spring for Vision

U. F. Roehrig; L. Guidoni; A. Laio; I. Frank; U. Rothlisberger 

Journal of the American Chemical Society. 2004. Vol. 126, num. 47, p. 15328-15329.

Nuclear Magnetic Resonance Chemical Shifts from Hybrid DFT QM/MM Calculations

D. Sebastiani; U. Rothlisberger 

Journal of Physical Chemistry B. 2004. Vol. 108, num. 9, p. 2807-2815. DOI : 10.1021/jp0364304.

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

O. A. Von Lilienfeld; I. Tavernelli; U. Rothlisberger; D. Sebastiani 

Physical Review Letters. 2004. Vol. 93, num. 15, p. 153004/1-153004/4. DOI : 10.1103/PhysRevLett.93.153004.

Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations

S. Piana; D. Bucher; P. Carloni; U. Rothlisberger 

Journal of Physical Chemistry B. 2004. Vol. 108, num. 30, p. 11139-11149. DOI : 10.1021/jp037651c.

Theoretical Studies of the Reductive C-S Bond Cleavage in Complexes of the Form [M(9S3)2]2+ (M = Re, Tc, and Ru; 9S3 = 1,4,7-Trithiacyclononane)

P. Maurer; A. Magistrato; U. Rothlisberger 

Journal of Physical Chemistry A. 2004. Vol. 108, num. 52, p. 11494-11499. DOI : 10.1021/jp045615n.

Unusual Ar-H/Rh-H JHH NMR Coupling in Complexes of Rhodium(III): Experimental Evidence and Theoretical Support for an h1-Arene Structure

J. R. Krumper; M. Gerisch; A. Magistrato; U. Rothlisberger; R. G. Bergman et al. 

Journal of the American Chemical Society. 2004. Vol. 126, num. 39, p. 12492-12502.

A Variational Definition of Electrostatic Potential Derived Charges

A. Laio; F. L. Gervasio; J. VandeVondele; M. Sulpizi; U. Rothlisberger 

Journal of Physical Chemistry B. 2004. Vol. 108, num. 23, p. 7963-7968. DOI : 10.1021/jp0496405.

Water-Assisted Reaction Mechanism of Monozinc b-Lactamases

M. Dal Peraro; L. I. Llarrull; U. Rothlisberger; A. J. Vila; P. Carloni 

Journal of the American Chemical Society. 2004. Vol. 126, num. 39, p. 12661-12668. DOI : 10.1021/ja048071b.

2003

Characterization of the Dizinc Analogue of the Synthetic Diiron Protein DF1 Using ab Initio and Hybrid Quantum/Classical Molecular Dynamics Simulations

A. Magistrato; W. F. DeGrado; A. Laio; U. Rothlisberger; J. VandeVondele et al. 

Journal of Physical Chemistry B. 2003. Vol. 107, num. 17, p. 4182-4188. DOI : 10.1021/jp027032o.

Direct observation of an equilibrium between two anion-cation orientations in olefin Pt(II) complex ion pairs by HOESY NMR spectroscopy

A. Macchioni; A. Magistrato; I. Orabona; F. Ruffo; U. Rothlisberger et al. 

New Journal of Chemistry. 2003. Vol. 27, num. 3, p. 455-458. DOI : 10.1039/b212088g.

Dynamics of RNase-A and S-protein: A molecular dynamics simulation of the transition toward a folding intermediate

S. Cotesta; I. Tavernelli; E. E. Di Iorio 

Biophysical Journal. 2003. Vol. 85, num. 4, p. 2633-2640.

A hybrid TDDFT/MM investigation of the optical properties of aminocoumarins in water and acetonitrile solution

M. Sulpizi; P. Carloni; J. Hutter; U. Rothlisberger 

Physical Chemistry Chemical Physics. 2003. Vol. 5, num. 21, p. 4798-4805. DOI : 10.1039/b305846h.

Molecular dynamics studies of caspase-3

M. Sulpizi; U. Rothlisberger; P. Carloni 

Biophysical Journal. 2003. Vol. 84, num. 4, p. 2207-2215.

Oxidation of Nitrite by Peroxynitrous Acid

P. Maurer; C. F. Thomas; R. Kissner; H. Rueegger; O. Greter et al. 

Journal of Physical Chemistry A. 2003. Vol. 107, num. 11, p. 1763-1769. DOI : 10.1021/jp0269064.

Protein dynamics, thermal stability, and free-energy landscapes: A molecular dynamics investigation

I. Tavernelli; S. Cotesta; E. E. Di Iorio 

Biophysical Journal. 2003. Vol. 85, num. 4, p. 2641-2649.

Protonation states of methionine aminopeptidase and their relevance for inhibitor binding and catalytic activity

C. D. P. Klein; R. Schiffmann; G. Folkers; S. Piana; U. Roethlisberger 

Journal of Biological Chemistry. 2003. Vol. 278, num. 48, p. 47862-47867.

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

U. F. Roehrig; I. Frank; J. Hutter; A. Laio; J. VandeVondele et al. 

ChemPhysChem. 2003. Vol. 4, num. 11, p. 1177-1182.

Reaction mechanism of caspases: Insights from QM/MM Car-Parrinello simulations

M. Sulpizi; A. Laio; J. VandeVondele; A. Cattaneo; U. Rothlisberger et al. 

Proteins: Structure, Function, and Genetics. 2003. Vol. 52, num. 2, p. 212-224. DOI : 10.1002/prot.10275.

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

S. Piana; M. Sulpizi; U. Rothlisberger 

Biochemistry. 2003. Vol. 42, num. 29, p. 8720-8728. DOI : 10.1021/bi034032l.

2002

Ab Initio Molecular Dynamics for Molecules with Variable Numbers of Electrons

I. Tavernelli; R. Vuilleumier; M. Sprik 

Physical Review Letters. 2002. Vol. 88, num. 21, p. 213002/1-213002/4. DOI : 10.1103/PhysRevLett.88.213002.

Accelerating Rare Reactive Events by Means of a Finite Electronic Temperature

J. VandeVondele; U. Rothlisberger 

Journal of the American Chemical Society. 2002. Vol. 124, num. 27, p. 8163-8171. DOI : 10.1021/ja0126733.

Applications of density functional theory-based methods in medicinal chemistry

M. Sulpizi; G. Folkers; U. Rothlisberger; P. Carloni; L. Scapozza 

Quantitative Structure-Activity Relationships. 2002. Vol. 21, num. 2, p. 173-181. DOI : 10.1002/1521-3838(200207)21:2<173::AID-QSAR173>3.0.CO;2-B.

Canonical Adiabatic Free Energy Sampling (CAFES): A Novel Method for the Exploration of Free Energy Surfaces

J. VandeVondele; U. Rothlisberger 

Journal of Physical Chemistry B. 2002. Vol. 106, num. 1, p. 203-208. DOI : 10.1021/jp013346k.

Dialkyl Effect on Enantioselectivity: p-Stacking as a Structural Feature in P,N Complexes of Palladium(II)

P. Dotta; A. Magistrato; U. Rothlisberger; P. S. Pregosin; A. Albinati 

Organometallics. 2002. Vol. 21, num. 14, p. 3033-3041. DOI : 10.1021/om020314q.

D-RESP: Dynamically Generated Electrostatic Potential Derived Charges from Quantum Mechanics/Molecular Mechanics Simulations

A. Laio; J. VandeVondele; U. Rothlisberger 

Journal of Physical Chemistry B. 2002. Vol. 106, num. 29, p. 7300-7307. DOI : 10.1021/jp0143138.

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

S. Piana; P. Carloni; U. Rothlisberger 

Protein Science. 2002. Vol. 11, num. 10, p. 2393-2402. DOI : 10.1110/ps.0206702.

Early Steps of the Intramolecular Signal Transduction in Rhodopsin Explored by Molecular Dynamics Simulations

U. F. Roehrig; L. Guidoni; U. Rothlisberger 

Biochemistry. 2002. Vol. 41, num. 35, p. 10799-10809.

A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations

A. Laio; J. VandeVondele; U. Rothlisberger 

Journal of Chemical Physics. 2002. Vol. 116, num. 16, p. 6941-6947. DOI : 10.1063/1.1462041.

Hybrid Car-Parrinello/molecular mechanics modelling of transition metal complexes: Structure, dynamics and reactivity

L. Guidoni; P. Maurer; S. Piana; U. Rothlisberger 

Quantitative Structure-Activity Relationships. 2002. Vol. 21, num. 2, p. 119-127. DOI : 10.1002/1521-3838(200207)21:2<119::AID-QSAR119>3.0.CO;2-B.

Hybrid QM/MM Car-Parrinello simulations of catalytic and enzymatic reactions

M. C. Colombo; L. Guidoni; A. Laio; A. Magistrato; P. Maurer et al. 

Chimia. 2002. Vol. 56, num. 1-2, p. 13-19.

The mechanism of catalytic enantioselective fluorination: Computational and experimental studies

S. Piana; I. Devillers; A. Togni; U. Rothlisberger 

Angewandte Chemie, International Edition. 2002. Vol. 41, num. 6, p. 979-982. DOI : 10.1002/1521-3773(20020315)41:6<979::AID-ANIE979>3.0.CO;2-E.

Multiple Steering Molecular Dynamics Applied to Water Exchange at Alkali Ions

M. Cascella; L. Guidoni; A. Maritan; U. Rothlisberger; P. Carloni 

Journal of Physical Chemistry B. 2002. Vol. 106, num. 50, p. 13027-13032. DOI : 10.1021/jp026209b.

The Role and Perspective of Ab Initio Molecular Dynamics in the Study of Biological Systems

P. Carloni; U. Rothlisberger; M. Parrinello 

Accounts of Chemical Research. 2002. Vol. 35, num. 6, p. 455-464. DOI : 10.1021/ar010018u.

2001

Cis-Trans Isomerization in Triply-Bonded Ditungsten Complexes: A Multitude of Possible Pathways

J. VandeVondele; A. Magistrato; U. Rothlisberger 

Inorganic Chemistry. 2001. Vol. 40, num. 23, p. 5780-5786. DOI : 10.1021/ic010470+.

Estimating equilibrium properties from non-Hamiltonian dynamics

J. VandeVondele; U. Rothlisberger 

Journal of Chemical Physics. 2001. Vol. 115, num. 17, p. 7859-7864. DOI : 10.1063/1.1403689.

The fetlock tunnel syndrome in horses: literature review and retrospective study

U. Rothlisberger; B. Kaegi; H. Geyer; J. A. Auer 

Schweizer Archiv fur Tierheilkunde. 2001. Vol. 143, num. 6, p. 285-93.

The interplay between protein dynamics and frustration of non-bonded interactions as revealed by molecular dynamics simulations

I. Tavernelli; E. E. Di Iorio 

Chemical Physics Letters. 2001. Vol. 345, num. 3,4, p. 287-294. DOI : 10.1016/S0009-2614(01)00859-4.

Isolation of a highly persistent diphosphanyl radical: the phosphorus analogue of a hydrazyl

S. Loss; A. Magistrato; L. Cataldo; S. Hoffmann; M. Geoffroy et al. 

Angewandte Chemie, International Edition. 2001. Vol. 40, num. 4, p. 723-726.

The Role of p-p Stacking Interactions in Square Planar Palladium Complexes. Combined Quantum Mechanics/Molecular Mechanics QM/MM Studies

A. Magistrato; P. S. Pregosin; A. Albinati; U. Rothlisberger 

Organometallics. 2001. Vol. 20, num. 20, p. 4178-4184. DOI : 10.1021/om010485f.

2000

Chiral Palladium(II)-Bis(trichlorosilyl) Complexes. Synthesis, Structure, and Combined QM/MM Computational Studies

T. K. Woo; G. Pioda; U. Rothlisberger; A. Togni 

Organometallics. 2000. Vol. 19, num. 11, p. 2144-2152. DOI : 10.1021/om000130g.

A comparative study of galactose oxidase and active site analogs based on QM/MM Car-Parrinello simulations

U. Rothlisberger; P. Carloni; K. Doclo; M. Parrinello 

Journal of Biological Inorganic Chemistry. 2000. Vol. 5, num. 2, p. 236-250.

Conformational Equilibria of Peroxynitrous Acid in Water: A First-Principles Molecular Dynamics Study

K. Doclo; U. Rothlisberger 

Journal of Physical Chemistry A. 2000. Vol. 104, num. 27, p. 6464-6469. DOI : 10.1021/jp0012193.

Ditantalum Hydride Complexes with Bridging (2,6-iPr2C6H3)NSiHPh Silanimine Ligands Resulting from PhSiH3-Imido Ligand Coupling. A Combined Spectroscopic and Theoretical Investigation

U. Burckhardt; G. L. Casty; T. D. Tilley; T. K. Woo; U. Rothlisberger 

Organometallics. 2000. Vol. 19, num. 19, p. 3830-3841. DOI : 10.1021/om000455x.

Efficient multidimensional free energy calculations for ab initio molecular dynamics using classical bias potentials

J. VandeVondele; U. Rothlisberger 

Journal of Chemical Physics. 2000. Vol. 113, num. 12, p. 4863-4868. DOI : 10.1063/1.1289527.

Electronically and Sterically Induced Structural Distortions in Square-Planar d8 Complexes

A. Magistrato; M. Merlin; P. S. Pregosin; U. Rothlisberger; A. Albinati 

Organometallics. 2000. Vol. 19, num. 18, p. 3591-3596. DOI : 10.1021/om000466q.

Peroxynitrite does not decompose to singlet oxygen ((1)Delta (g)O(2)) and nitroxyl (NO(-))

G. R. Martinez; P. Di Mascio; M. G. Bonini; O. Augusto; K. Briviba et al. 

Proceedings of the National Academy of Sciences of the United States of America. 2000. Vol. 97, num. 19, p. 10307-12. DOI : 10.1073/pnas.190256897.

Three- and Four-Center Trans Effects in Triply Bonded Ditungsten Complexes: An ab Initio Molecular Dynamics Study of Compounds with Stoichiometry W2Cl4(NHEt)2(PMe3)2

A. Magistrato; J. VandeVondele; U. Rothlisberger 

Inorganic Chemistry. 2000. Vol. 39, num. 24, p. 5553-5560. DOI : 10.1021/ic000754e.

1999

Ab initio molecular dynamics studies of a synthetic biomimetic model of galactose oxidase

U. Rothlisberger; P. Carloni 

International Journal of Quantum Chemistry. 1999. Vol. 73, num. 2, p. 209-218. DOI : 10.1002/(SICI)1097-461X(1999)73:2<209::AID-QUA14>3.0.CO;2-B.

Conformational and orientational order and disorder in solid polytetrafluoroethylene

M. Sprik; U. Rothlisberger; M. L. Klein 

Molecular Physics. 1999. Vol. 97, num. 3, p. 355-373.

1998

Ab initio molecular dynamics simulations of the gas-phase reaction of hydroxyl radical with nitrogen dioxide radical

K. Doclo; U. Rothlisberger 

Chemical Physics Letters. 1998. Vol. 297, num. 3,4, p. 205-210. DOI : 10.1016/S0009-2614(98)01102-6.

Living polymers Ab initio molecular dynamics study of the initiation step in the polymerization of isoprene induced by ethyl lithium

U. Rothlisberger; M. Sprik; M. L. Klein 

Journal of the Chemical Society, Faraday Transactions. 1998. Vol. 94, num. 4, p. 501-508.

1997

Ab initio molecular dynamics simulation of liquid hydrogen fluoride

U. Roethlisberger; M. Parrinello 

Journal of Chemical Physics. 1997. Vol. 106, num. 11, p. 4658-4664.

Dynamic properties of monomeric insect erythrocruorin III from Chironomus thummi-thummi: relationships between structural flexibility and functional complexity

E. E. Di Iorio; I. Tavernelli; W. Yu 

Biophysical Journal. 1997. Vol. 73, num. 5, p. 2742-2751.

Inhibition of bovine nasal cartilage degradation by selective matrix metalloproteinase inhibitors

K. M. Bottomley; N. Borkakoti; D. Bradshaw; P. A. Brown; M. J. Broadhurst et al. 

Biochemical journal. 1997. Vol. 323, num. 2, p. 483-488. DOI : 10.1042/bj3230483.

Structure of solid poly(tetrafluoroethylene): a computer simulation study of chain orientational, translational, and conformational disorder

M. Sprik; U. Roethlisberger; M. L. Klein 

Journal of Physical Chemistry B. 1997. Vol. 101, num. 15, p. 2745-2749. DOI : 10.1021/jp963333k.

1996

Investigation on the structure of the active site of monoamine oxidase-B by affinity labeling with the selective inhibitor lazabemide and by site-directed mutagenesis

A. M. Cesura; J. Gottowik; H. W. Lahm; G. Lang; R. Imhof et al. 

European journal of biochemistry. 1996. Vol. 236, num. 3, p. 996-1002.

The torsional potential of perfluoro n-alkanes: a density functional study

U. Rothlisberger; K. Laasonen; M. L. Klein; M. Sprik 

Journal of Chemical Physics. 1996. Vol. 104, num. 10, p. 3692-700.

1995

Ab Initio Molecular Dynamics Investigation of Singlet C2H2Li2: Determination of the Ground State Structure and Observation of LiH Intermediates

U. Roethlisberger; M. L. Klein 

Journal of the American Chemical Society. 1995. Vol. 117, num. 1, p. 42-8. DOI : 10.1021/ja00106a005.

Na6Pb: a bimetallic cluster of striking stability

C. Yeretzian; U. Roethlisberger; E. Schumacher 

Chemical Physics Letters. 1995. Vol. 237, num. 3,4, p. 334-8. DOI : 10.1016/0009-2614(95)00310-Z.

1994

Competing interactions in self-assembled monolayers containing peptide groups: molecular dynamics studies of long-chain perfluoro mercaptans on Au(111)

U. Rothlisberger; M. L. Klein; M. Sprik 

Journal of Materials Chemistry. 1994. Vol. 4, num. 6, p. 793-803.

The performance of density functional methods for the description of weak interaction potentials. The torsional potential of butane

U. Roethlisberger; M. L. Klein 

Chemical Physics Letters. 1994. Vol. 227, num. 4-5, p. 390-5.

Structure of Hydrophilic Self-Assembled Monolayers: A Combined Scanning Tunneling Microscopy and Computer Simulation Study

M. Sprik; E. Delamarche; B. Michel; U. Roethlisberger; M. L. Klein et al. 

Langmuir. 1994. Vol. 10, num. 11, p. 4116-30. DOI : 10.1021/la00023a035.

Structure of nanoscale silicon clusters

U. Roethlisberger; W. Andreoni; M. Parrinello 

Physical Review Letters. 1994. Vol. 72, num. 5, p. 665-8.

1992

Ab-initio molecular dynamics studies of magnesium-doped sodium clusters

U. Roethlisberger; W. Andreoni 

International Journal of Modern Physics B. 1992. Vol. 6, num. 23-24, p. 3675-9.

Metal clusters with impurities: NanMg (n = 6-9, 18)

U. Roethlisberger; W. Andreoni 

Chemical Physics Letters. 1992. Vol. 198, num. 5, p. 478-82.

Thirteen-atom clusters: equilibrium geometries, structural transformations, and trends in sodium, magnesium, aluminum, and silicon

U. Roethlisberger; W. Andreoni; P. Giannozzi 

Journal of Chemical Physics. 1992. Vol. 96, num. 2, p. 1248-56.

1991

Structural and electronic properties of sodium microclusters (n = 2-20) at low and high temperatures: new insights from ab-initio molecular-dynamics studies

U. Roethlisberger 

Journal of Chemical Physics. 1991. Vol. 94, num. 12, Pt. 1, p. 8129-51.

Temperature-induced structural transitions and vibrational properties of microclusters: ab-initio molecular dynamics studies

U. Roethlisberger; W. Andreoni 

Zeitschrift für Physik D : Atoms, Molecules and Clusters. 1991. Vol. 20, num. 1-4, p. 243-6.

1990

Metal-metal coordination chemistry: free clusters of Group 12 elements with sodium

U. Heiz; U. Roethlisberger; A. Vayloyan; E. Schumacher 

Israel Journal of Chemistry. 1990. Vol. 30, num. 1-2, p. 147-55.

1989

Internal temperatures of neutral sodium clusters: a PIE-thermometer

U. Roethlisberger; M. Schaer; E. Schumacher 

Zeitschrift für Physik D : Atoms, Molecules and Clusters. 1989. Vol. 13, num. 2, p. 171-8.

1988

Metal clusters: Between atom and bulk

E. Schumacher; F. Blatter; M. Frey; U. Heiz; U. Roethlisberger et al. 

Chimia. 1988. Vol. 42, num. 11, p. 357-76.

Sodium cluster ionization potentials revised: higher-resolution measurements for Nax (x < 23) and their relation to bonding models

M. M. Kappes; M. Schaer; U. Roethlisberger; C. Yeretzian; E. Schumacher 

Chemical Physics Letters. 1988. Vol. 143, num. 3, p. 251-8. DOI : 10.1016/0009-2614(88)87376-7.

Conference Papers

2019

Pre-mRNA Splicing: The Gene Maturation Symphony of the Intron Lariat Spliceosome Revealed by Molecular Dynamics Simulations

L. Casalino; G. Palermo; A. Spinello; U. Roethlisberger; A. Magistrato 

2019-02-15. 63rd Annual Meeting of the Biophysical-Society, Baltimore, MD, Mar 02-06, 2019. p. 299A-299A. DOI : 10.1016/j.bpj.2018.11.1619.

2017

Does Proton Conduction in the Voltage-Gated Proton Channel hH(V)1 Involve Grotthus Hopping via Acidic Residues?

L. Delemotte; S. Van Keulen; U. Roethlisberger; E. Gianti; V. Carnevale et al. 

2017. 61st Annual Meeting of the Biophysical-Society, New Orleans, LA, FEB 11-15, 2017. p. 163A-164A.

2016

Molecular Simulations Integrated with Experiments Unravel the Key Factors of Lipid Selection in Fatty Acid Amide Hydrolase and Suggest A General Mechanism of Lipid-Processing in the Parent Enzymes

G. Palermo; I. Bauer; P. Campomanes; A. Cavalli; A. Armirotti et al. 

2016. 60th Annual Meeting of the Biophysical-Society, Los Angeles, CA, FEB 27-MAR 02, 2016. p. 202A-203A.

Molecular Mechanism of Chromatin Targeting by a Potent Anticancer Agent Acting at the Nucleosome Core Particle

G. Palermo; Z. Ma; B. S. Murray; P. J. Dyson; C. A. Davey et al. 

2016. 60th Annual Meeting of the Biophysical-Society, Los Angeles, CA, FEB 27-MAR 02, 2016. p. 68A-69A.

2015

Biomimetic Sequestration of CO2: reprogramming the B1 domain of protein g through a combined computational and experimental approach

E. Bozkurt; R. Hovius; T. A. Soares; U. Rothlisberger 

2015. 29th Annual Symposium of the Protein Society, July 22-25, 2015, Barcelona, Spain. p. 178. DOI : 10.1002/pro.2823.

2014

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

U. Rothlisberger 

2014. 247th National Spring Meeting of the American-Chemical-Society (ACS), Dallas, TX, MAR 16-20, 2014.

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

M. De Vivo; G. Palermo; I. Bauer; P. Campomanes; A. Cavalli et al. 

2014. 248th National Meeting of the American-Chemical-Society (ACS), San Francisco, CA, AUG 10-14, 2014.

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

M. De Vivo; G. Palermo; P. Campomanes; A. Cavalli; U. Rothlisberger 

2014. 248th National Meeting of the American-Chemical-Society (ACS), San Francisco, CA, AUG 10-14, 2014.

Nucleation of Silicon Nanoparticles in Amorphous Silicon Dioxide Matrices

S. Meloni 

2014. 10th International Symposium on SiO2, Advanced Dielectrics and Related Devices, Cagliari, ITALY, JUN 16-18, 2014. p. 95-103. DOI : 10.1063/1.4900463.

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

U. Rothlisberger 

2014. 58th Annual Meeting of the Biophysical-Society, San Francisco, CA, FEB 15-19, 2014. p. 446A-446A.

2013

Computational evidence that Vibrio vulnificus FrsA is not a cofactor-independent pyruvate decarboxylase

W. F. Kellett; E. Brunk; B. Desai; A. A. Fedorov; S. C. Almo et al. 

2013. 246th National Meeting of the American-Chemical-Society (ACS).

Structural element that controls the redox preferences of the active site manganese in oxalate decarboxylase

W. F. Kellett; P. Campomanes; L. Easton; A. Angerhofer; K. N. Allen et al. 

2013. 246th National Meeting of the American-Chemical-Society (ACS).

Computational assignment of EPR fine structure parameters for the Mn(II) centers in Bacillus subtilis oxalate decarboxylase

P. Campomanes; W. F. Kellett; A. Ozarowski; A. Angerhofer; U. Rothlisberger et al. 

2013. 246th National Meeting of the American-Chemical-Society (ACS).

Fatty acid amide hydrolase (FAAH) substrate specificity understood via molecular dynamics

G. Palermo; P. Campomanes; M. Neri; D. Piomelli; A. Cavalli et al. 

2013. 245th National Meeting of the American-Chemical-Society (ACS).

Mechano-chemical switch to control reactive intermediates by negative enzyme catalysis

E. Brunk; U. Rothlisberger 

2013. 245th National Meeting of the American-Chemical-Society (ACS).

Computational design of biomimetic strategies for the production of chemical compounds

E. Brunk; U. Roethlisberger 

2013. 245th National Meeting of the American-Chemical-Society (ACS).

Role of environment in the catalysis of the MutY DNA repair enzyme

E. Brunk; J. S. Arey; U. Rothlisberger 

2013. 245th National Meeting of the American-Chemical-Society (ACS).

Mechanism to trigger unfolding in alkylguanine alkyltransferase

E. Brunk; B. Mollwitz; U. Rothlisberger 

2013. 245th National Meeting of the American-Chemical-Society (ACS).

Nonadiabatic dynamics of complex molecular systems based on time-dependent density fucntional theory

I. Tavernelli; B. F. E. Curchod; U. Rothlisberger 

2013. 245th National Spring Meeting of the American-Chemical-Society (ACS).

2008

QMMM study of the thymine dimer radical anion splitting reaction: A comparison between the self-repair and the photolyase catalyzed process

F. Masson; T. Laino; J. Hutter; U. Rothlisberger 

2008. 236th National Meeting of the American-Chemical-Society, Philadelphia, PA, Aug 17-21, 2008. p. 386-COMP.

2005

Ab initio molecular dynamics simulation of redox reactions of transition metal ions in aqueous solution and proteins

J. Blumberger; I. Tavernelli; M. L. Klein; M. Sprik 

2005.  p. PHYS-234.

Binding of organoruthenium anticancer drugs to DNA

U. Rothlisberger; C. Gossens; I. Tavernelli 

2005.  p. COMP-333.

Duocarmycins binding to DNA explored by molecular simulation

K. Spiegel; U. Rothlisberger; P. Carloni 

2005.  p. COMP-321.

2004

Cisplatin binding to DNA oligomers from hybrid Car-Parrinello/molecular dynamics simulations

K. Spiegel; U. Rothlisberger; P. Carloni 

2004.  p. INOR-908.

Inclusion of dispersion into DFT by optimization of analytic pseudopotentials

O. A. von Lilienfeld-Toal; I. Tavernelli; U. Rothlisberger; D. Sebastiani 

2004.  p. PHYS-372.

QM and QM/MM studies of the phosphoryl transfer reaction catalyzed by a cyclin-dependent kinase (CDKs)

M. De Vivo; A. Cavalli; M. Recanatini; U. Roethlisberger; P. Carloni 

2004.  p. INOR-667.

QM/MM boundary atoms by variational optimization of analytic pseudopotentials

O. A. von Lilienfeld-Toal; I. Tavernelli; U. Rothlisberger; D. Sebastiani 

2004.  p. PHYS-410.

QM/MM Car-Parrinello molecular dynamics study of selectivity in a potassium channel

D. Bucher; U. Rothlisberger; L. Guidoni; P. Carloni 

2004.  p. PHYS-309.

Structure and stability of copper-prion protein

M. C. Colombo; J. H. B. VandeVondele; A. Laio; L. Guidoni; U. Rothlisberger 

2004.  p. PHYS-661.

2003

Mixed quantum mechanical/molecular mechanical simulation of biological systems

U. Rothlisberger 

2003.  p. COMP-088.

2002

Study of the structural and dynamical properties of a biomimetic compound of diiron proteins via ab initio and hybrid (QM/MM) molecular dynamics simulations

A. Magistrato; U. Rothlisberger; M. L. Klein 

2002.  p. COMP-138.

Study of the structural and dynamical properties of a biomimetic compound of diiron proteins via ab initio and hybrid molecular dynamics simulations

A. Magistrato; U. Rothlisberger; M. L. Klein 

2002.  p. INOR-045.

2000

Accelerating rare events in ab initio molecular dynamics simulations

U. Rothlisberger; J. H. B. VandeVondele 

2000.  p. PHYS-314.

Rational design of biomimetics with QM/MM Car-Parrinello simulations

U. Rothlisberger 

2000.  p. PHYS-334.

1997

Ab initio and hybrid molecular dynamics simulations of catalytic and enzymic reactions

U. Rothlisberger; W. F. Van Gunsteren 

1997.  p. COMP-096.

Reviews

2016

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

G. Palermo; A. Magistrato; T. Riedel; T. Von Erlach; C. A. Davey et al. 

ChemMedChem. 2016. Vol. 11, num. 12, p. 1199-1210. DOI : 10.1002/cmdc.201500478.

2015

Computational insights into function and inhibition of fatty acid amide hydrolase

G. Palermo; U. Rothlisberger; A. Cavalli; M. De Vivo 

European Journal Of Medicinal Chemistry. 2015. Vol. 91, p. 15-26. DOI : 10.1016/j.ejmech.2014.09.037.

2013

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

B. F. E. Curchod; T. J. Penfold; U. Rothlisberger; I. Tavernelli 

Central European Journal Of Physics. 2013. Vol. 11, num. 9, p. 1059-1065. DOI : 10.2478/s11534-013-0321-2.

2012

A Closer Look into G Protein Coupled Receptor Activation: X-Ray Crystallography and Long-Scale Molecular Dynamics Simulations

S. Vanni; U. Rothlisberger 

Current Medicinal Chemistry. 2012. Vol. 19, p. 1135-1145.

Theses

2019

Applications of Artificial Intelligence to Computational Chemistry

N. J. Browning / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2019. DOI : 10.5075/epfl-thesis-9645.

2018

Improving Performance and Accuracy of Hybrid-Functional Based Molecular Dynamics in Plane Waves

M. P. Bircher / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2018. DOI : 10.5075/epfl-thesis-9041.

Reprogramming the B1 Domain of Streptococcal Protein G (GB1)

E. Bozkurt / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2018. DOI : 10.5075/epfl-thesis-8029.

2017

Computational Investigation of Intracellular Signalling Cascades

S. C. van Keulen / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2017. DOI : 10.5075/epfl-thesis-7563.

2015

Computational studies for the characterization and design of dye sensitized solar cells (DSSCs) with improved efficiencies

N. Ashari Astani / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2015. DOI : 10.5075/epfl-thesis-6800.

2014

Capturing Non-local Effects in Kohn-Sham Density Functional Theory

A. Laktionov / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2014. DOI : 10.5075/epfl-thesis-6317.

Computational Studies of Redox-Active Chemical and Biological Systems

P. Diamantis / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2014. DOI : 10.5075/epfl-thesis-6247.

2013

A Classical and Quantum Trajectory Description of Nonadiabatic Dynamics within Time-Dependent Density Functional Theory

B. Curchod / I. Tavernelli; U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2013. DOI : 10.5075/epfl-thesis-5923.

Approaches to Increase the Accuracy of Molecular Dynamics Simulations

M. Dömer / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2013. DOI : 10.5075/epfl-thesis-5833.

Understanding Evolutionary Strategies of Enzymes and Exploiting them for Biomimetic Purposes

E. C. Brunk / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2013. DOI : 10.5075/epfl-thesis-5801.

2011

Exploring G-Protein Coupled Receptor Activation with Multiscale Molecular Simulations

S. Vanni / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2011. DOI : 10.5075/epfl-thesis-5005.

2010

Photophysics and Photochemistry from First Principles

M. Guglielmi / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2010. DOI : 10.5075/epfl-thesis-4740.

2008

Molecular Dynamics Simulations of a Lesion in DNA: Autocatalytic or Enzymatic Repair and Formation of Thymine Dimer

F. Masson / J. Hutter; U. Rothlisberger (Dir.)  

University of Zurich & EPFL, 2008. 

Development of a non-adiabatic ab initio molecular dynamics method and its application to photodynamical processes

E. M. Tapavicza / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2008. DOI : 10.5075/epfl-thesis-4115.

Solute energy based REMD

P. Baillod / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2008. DOI : 10.5075/epfl-thesis-4103.

Atom-centered potentials for describing London dispersion forces in density functional theory

-C. Lin / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2008. DOI : 10.5075/epfl-thesis-4058.

2007

In silico DNA-binding and rational design of ruthenium-arene anticancer drugs

C. Gossens / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2007. DOI : 10.5075/epfl-thesis-3723.

2006

Tools to study molecules in high electric fields

D. Bucher / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2006. DOI : 10.5075/epfl-thesis-3677.

On the structural stability of the free and metal-loaded c-terminal domain of the prion protein

M. C. Colombo / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2006. DOI : 10.5075/epfl-thesis-3592.

2005

Atom centered potentials for the description and the design of chemical compounds within density functional theory

O. A. v. Lilienfeld-Toal / U. Röthlisberger (Dir.)  

Lausanne: EPFL, 2005. DOI : 10.5075/epfl-thesis-3240.

Book Chapters

2012

Hybrid Car-Parrinello Molecular Dynamics/Molecular Mechanics Simulations: a Powerful Tool for the Investigation of Biological Systems

E. Ippoliti; J. Dreyer; P. Carloni; U. Röthlisberger 

Hierarchical Methods for Dynamics in Complex Molecular Systems; Forschungszentrum Jülich GmbH, 2012-03-09. p. 556.

2010

Hybrid QM/MM simulations of enzyme-catalyzed DNA repair reactions

D. Bucher; F. Masson; J. S. Arey; U. Rothlisberger 

Quantum Biochemistry; Wiley, 2010.

2006

Drug-target binding investigated by quantum mechanics/molecular mechanics methods

U. Rothlisberger; P. Carloni 

Computer simulations in condensed matter systems : from materials to chemical biology; Berlin: Springer, 2006. p. 447-476.

2003

Advances in density-functional-based modeling techniques - Recent extensions of the Car-Parrinello approach

D. Sebastiani; U. Roethlisberger 

Methods and Principles in Medicinal Chemistry; Weinheim: Wiley-VCH, 2003. p. 5-39.

2002

Time and length scales in ab initio molecular dynamics

U. Röthlisberger; M. Sprik; J. Hutter 

Bridging time scales : molecular simulations for the next decade; Berlin: Springer, 2002. p. 413-442.

Enantioselective hydrosilylation by chiral Pd based homogeneous catalysts with first-principles and combined QM/MM molecular dynamics simulations

A. Magistrato; A. Togni; U. Roethlisberger; T. K. Woo 

Computational modeling of homogeneous catalysis; Dordrecht: Kluwer, 2002. p. 213-252.

Magic and mysteries of modern molecular dynamics simulations: A basic introduction

U. Rothlisberger 

Strength from Weakness: Structural Consequences of Weak Interactions in Molecules, Supermolecules, and Crystals; Berlin: Springer, 2002. p. 121-141.

2001

Simulations of enzymatic systems: Perspectives from Car-Parrinello molecular dynamics simulations

P. Carloni; U. Rothlisberger 

Theoretical Biochemistry: Processes and Properties of Biological Systems; Amsterdam: Elsevier, 2001. p. 215-251.

15 years of Car-Parrinello simulations in physics, chemistry and biology

U. Rothlisberger 

Computational Chemistry: Reviews of Current Trends; Singapore: World Scientific, 2001. p. 33-68.

1998

Ab initio and hybrid molecular dynamics simulations of the active site of human carbonic anhydrase II: a test case study

U. Rothlisberger 

ACS Symposium Series; 1998. p. 264-274.

1994

Simulation of self-assembled monolayers:microscopic structure of amino alkylthiols

U. Rothlisberger; M. L. Klein; M. Sprik 

Computational Approaches in Supramolecular Chemistry; Dordrecht: Kluwer, 1994. p. 399-409.

1992

Some considerations on "isoarithmic" and isoelectronic clusters

W. Andreoni; U. Roethlisberger 

Nuclear physics concepts in the study of atomic cluster physics; Berlin: Springer, 1992. p. 352-357.