Publications

On this page, you will find all articles and letters published by LCBC. For lab’s different publication outputs please refer to:

2024

MiMiC: A high-performance framework for multiscale molecular dynamics simulations

A. Antalik; A. Levy; S. Kvedaravičiūtė; D. Carrasco-Busturia; S. K. Johnson et al. 

The Journal of Chemical Physics. 2024. Vol. 161, num. 2, p. 022501. DOI : 10.1063/5.0211053.

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From Chalcogen Bonding to S-π Interactions in Hybrid Perovskite Photovoltaics

W. Luo; S. Kim; N. Lempesis; L. Merten; E. Kneschaurek et al. 

ADVANCED SCIENCE. 2024. DOI : 10.1002/advs.202405622.

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Carbazole Treated Waterproof Perovskite Films with Improved Solar Cell Performance

J. Jeong; T. Chawanpunyawat; M. Kim; V. Slama; N. Lempesis et al. 

Advanced Energy Materials. 2024. DOI : 10.1002/aenm.202401965.

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Multiscale biomolecular simulations in the exascale era

D. Carrasco-Busturia; E. Ippoliti; S. Meloni; U. Rothlisberger; J. M. H. Olsen 

Current Opinion In Structural Biology. 2024. Vol. 86, p. 102821. DOI : 10.1016/j.sbi.2024.102821.

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Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach

S. Johnson; U. Rothlisberger 

Chimia. 2024. Vol. 78, num. 4, p. 243 – 250. DOI : 10.2533/chimia.2024.243.

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Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder

J. Villard; M. P. Bircher; U. Rothlisberger 

Chemical Science. 2024. DOI : 10.1039/d3sc05828j.

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2023

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

J. Villard; M. P. Bircher; U. Rothlisberger 

Journal Of Chemical Theory And Computation. 2023. Vol. 19, num. 24, p. 9211 – 9227. DOI : 10.1021/acs.jctc.3c00952.

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Redox-Based Defect Detection in Packed DNA: Insights from Hybrid Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations

M. Kilic; P. Diamantis; S. K. Johnson; O. Toth; U. Rothlisberger 

Journal Of Chemical Theory And Computation. 2023. Vol. 19, num. 22, p. 8434 – 8445. DOI : 10.1021/acs.jctc.3c01013.

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Low-loss contacts on textured substrates for inverted perovskite solar cells

S. M. Park; M. Wei; N. Lempesis; W. Yu; T. Hossain et al. 

Nature. 2023. Vol. 624, p. 289 – 294. DOI : 10.1038/s41586-023-06745-7.

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Buried Interface Engineering Enables Efficient and 1,960‐hour Isos‐L‐2i Stable Inverted Perovskite Solar Cells

L. Li; M. Wei; V. Carnevali; H. Zeng; m. Zeng et al. 

Advanced Materials. 2023. DOI : 10.1002/adma.202303869.

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Tautomeric mixture coordination enables efficient lead-free perovskite LEDs

D. Han; J. Wang; L. Agosta; Z. Zang; B. Zhao et al. 

Nature. 2023. Vol. 622, p. 493 – 498. DOI : 10.1038/s41586-023-06514-6.

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Mitigating the Heterointerface Driven Instability in Perovskite Photovoltaics

A. Krishna; V. Skorjanc; M. Dankl; J. Hieulle; H. Phirke et al. 

Acs Energy Letters. 2023. Vol. 8, num. 8, p. 3604 – 3613. DOI : 10.1021/acsenergylett.3c01029.

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Metal3D: a general deep learning framework for accurate metal ion location prediction in proteins

S. L. Durr; A. Levy; U. Rothlisberger 

Nature Communications. 2023. Vol. 14, num. 1, p. 2713. DOI : 10.1038/s41467-023-37870-6.

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MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations

B. Raghavan; F. K. Schackert; A. Levy; S. K. Johnson; E. Ippoliti et al. 

Journal Of Chemical Information And Modeling. 2023. Vol. 63, num. 5, p. 1406 – 1412. DOI : 10.1021/acs.jcim.2c01620.

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

A. Das; S. Bhattacharyya; E. J. Rohwer; M. Gazzetto; A. Cannizzo et al. 

Journal Of Molecular Liquids. 2023. Vol. 377, p. 121551. DOI : 10.1016/j.molliq.2023.121551.

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Surrogate Based Genetic Algorithm Method for Efficient Identification of Low-Energy Peptide Structures

J. Villard; M. Kilic; U. Rothlisberger 

Journal Of Chemical Theory And Computation. 2023. Vol. 19, num. 3, p. 1080 – 1097. DOI : 10.1021/acs.jctc.2c01078.

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Cooperative passivation of perovskite solar cells by alkyldimethylammonium halide amphiphiles

E. A. R. Alharbi; A. Krishna; N. Lempesis; M. Dankl; I. Mosquera-Lois et al. 

Joule. 2023. Vol. 7, num. 1, p. 183 – 200. DOI : 10.1016/j.joule.2022.11.013.

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2022

Hydration dynamics and IR spectroscopy of 4-fluorophenol

S. M. Salehi; S. Kaeser; K. Toepfer; P. Diamantis; R. Pfister et al. 

Physical Chemistry Chemical Physics. 2022. Vol. 24, num. 42, p. 26046 – 26060. DOI : 10.1039/d2cp02857c.

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Enhanced hydrogen evolution by using ternary nanocomposites of mesoporous carbon nitride/black phosphorous/transition metal nanoparticles (m-gCN/BP-M; M = Co, Ni, and Cu) as photocatalysts under visible light: A comparative experimental and theoretical study

S. Yilmaz; E. G. Acar; G. Yanalak; E. Aslan; M. Kilic et al. 

Applied Surface Science. 2022. Vol. 593, p. 153398. DOI : 10.1016/j.apsusc.2022.153398.

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Interplay of Kinetic and Thermodynamic Reaction Control Explains Incorporation of Dimethylammonium Iodide into CsPbI3

A. Mishra; D. J. Kubicki; A. Boziki; R. D. Chavan; M. Dankl et al. 

Acs Energy Letters. 2022. Vol. 7, num. 8, p. 2745 – 2752. DOI : 10.1021/acsenergylett.2c00877.

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Multiscale molecular simulations to investigate adenylyl cyclase-based signaling in the brain

S. C. van Keulen; J. Martin; F. Colizzi; E. Frezza; D. Trpevski et al. 

Wiley Interdisciplinary Reviews-Computational Molecular Science. 2022.  p. e1623. DOI : 10.1002/wcms.1623.

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Photo De-Mixing in Dion-Jacobson 2D Mixed Halide Perovskites

Y-R. Wang; A. Senocrate; M. Mladenovic; A. Ducinskas; G. Y. Kim et al. 

Advanced Energy Materials. 2022.  p. 2200768. DOI : 10.1002/aenm.202200768.

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Bismuthene as a versatile photocatalyst operating under variable conditions for the photoredox C-H bond functionalization

M. S. Ozer; Z. Eroglu; A. S. Yalin; M. Kilic; U. Rothlisberger et al. 

Applied Catalysis B-Environmental. 2022. Vol. 304, p. 120957. DOI : 10.1016/j.apcatb.2021.120957.

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Kinetics and energetics of metal halide perovskite conversion reactions at the nanoscale

N. Arora; A. Greco; S. Meloni; A. Hinderhofer; A. Mattoni et al. 

Communications Materials. 2022. Vol. 3, num. 1, p. 22. DOI : 10.1038/s43246-022-00239-1.

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Atom-by-Atom Synthesis of Multiatom-Supported Catalytic Clusters by Liquid-Phase Atomic Layer Deposition

B. P. Le Monnier; L. Savereide; M. Kilic; R. Schnyder; M. D. Mensi et al. 

Acs Sustainable Chemistry & Engineering. 2022. Vol. 10, num. 11, p. 3455 – 3465. DOI : 10.1021/acssuschemeng.1c07056.

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Reversible Pressure-Dependent Mechanochromism of Dion-Jacobson and Ruddlesden-Popper Layered Hybrid Perovskites

L. A. Muscarella; A. Ducinskas; M. Dankl; M. Andrzejewski; N. P. M. Casati et al. 

Advanced Materials. 2022.  p. 2108720. DOI : 10.1002/adma.202108720.

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A theoretical perspective of the ultrafast transient absorption dynamics of CsPbBr3

A. Boziki; P. Baudin; E. Liberatore; N. A. Astani; U. Rothlisberger 

Journal Of Computational Chemistry. 2022. Vol. 43, num. 8, p. 577 – 582. DOI : 10.1002/jcc.26815.

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A multiple time step algorithm for trajectory surface hopping simulations

P. Baudin; F. Mouvet; U. Rothlisberger 

Journal Of Chemical Physics. 2022. Vol. 156, num. 3, p. 034107. DOI : 10.1063/5.0065728.

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

H. Zhang; K. Darabi; N. Y. Nia; A. Krishna; P. Ahlawat et al. 

Nature Communications. 2022. Vol. 13, p. 89. DOI : 10.1038/s41467-021-27740-4.

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

T. Kirsch; J. M. H. Olsen; V. Bolnykh; S. Meloni; E. Ippoliti et al. 

Journal Of Chemical Theory And Computation. 2022. Vol. 18, num. 1, p. 13 – 24. DOI : 10.1021/acs.jctc.1c00878.

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2021

Methylammonium Triiodide for Defect Engineering of High-Efficiency Perovskite Solar Cells

E. A. Alharbi; A. Krishna; T. P. Baumeler; M. Dankl; G. C. Fish et al. 

ACS Energy Letters. 2021. Vol. 6, p. 3650 – 3660. DOI : 10.1021/acsenergylett.1c01754.

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Nanoscale interfacial engineering enables highly stable and efficient perovskite photovoltaics

A. Krishna; H. Zhang; Z. Zhou; T. Gallet; M. Dankl et al. 

Energy & Environmental Science. 2021. Vol. 14, p. 5552 – 5562. DOI : 10.1039/d1ee02454j.

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Naphthalenediimide/Formamidinium-Based Low-Dimensional Perovskites

A. Mishra; P. Ahlawat; G. C. Fish; F. Jahanbakhshi; M. Mladenovic et al. 

Chemistry of Materials. 2021. Vol. 33, num. 16, p. 6412 – 6420. DOI : 10.1021/acs.chemmater.1c01635.

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Multimodal host–guest complexation for efficient and stable perovskite photovoltaics

H. Zhang; F. T. Eickemeyer; Z. Zhou; M. Mladenović; F. Jahanbakhshi et al. 

Nature Communications. 2021. Vol. 12, num. 1, p. 3383. DOI : 10.1038/s41467-021-23566-2.

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A combined molecular dynamics and experimental study of two-step process enabling low-temperature formation of phase-pure α-FAPbI3

P. Ahlawat; A. Hinderhofer; E. A. R. Alharbi; H. Lu; A. Ummadisingu et al. 

Science Advances. 2021. Vol. 7, num. 17, p. eabe3326. DOI : 10.1126/sciadv.abe3326.

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Pseudo-halide anion engineering for α-FAPbI3 perovskite solar cells

J. Jeong; M. Kim; J. Seo; H. Lu; P. Ahlawat et al. 

Nature. 2021. Vol. 592, num. 7854, p. 381 – 385. DOI : 10.1038/s41586-021-03406-5.

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Ultrafast pulse shaping modulates perceived visual brightness in living animals

G. Gaulier; Q. Dietschi; S. Bhattacharyya; C. Schmidt; M. Montagnese et al. 

Science Advances. 2021. Vol. 7, num. 18, p. eabe1911. DOI : 10.1126/sciadv.abe1911.

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Molecular Origin of the Asymmetric Photoluminescence Spectra of CsPbBr3 at Low Temperature

A. Boziki; M. I. Dar; G. Jacopin; M. Gratzel; U. Rothlisberger 

Journal Of Physical Chemistry Letters. 2021. Vol. 12, num. 10, p. 2699 – 2704. DOI : 10.1021/acs.jpclett.1c00263.

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Gαi1 inhibition mechanism of ATP-bound adenylyl cyclase type 5

D. Narzi; S. C. van Keulen; U. Röthlisberger 

PLOS ONE. 2021. Vol. 16, num. 1, p. e0245197. DOI : 10.1371/journal.pone.0245197.

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Nanoscale Phase Segregation in Supramolecular π-Templating for Hybrid Perovskite Photovoltaics from NMR Crystallography

M. A. Hope; T. Nakamura; P. Ahlawat; A. Mishra; M. Cordova et al. 

Journal of the American Chemical Society. 2021. Vol. 143, num. 3, p. 1529 – 1538. DOI : 10.1021/jacs.0c11563.

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2020

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

T-S. Su; F. T. Eickemeyer; M. A. Hope; F. Jahanbakhshi; M. Mladenovic et al. 

Journal Of The American Chemical Society. 2020. Vol. 142, num. 47, p. 19980 – 19991. DOI : 10.1021/jacs.0c08592.

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

V. Buchter; Y. C. Ong; F. Mouvet; A. Ladaycia; E. Lepeltier et al. 

Chemistry-A European Journal. 2020. Vol. 26, num. 66, p. 15232 – 15241. DOI : 10.1002/chem.202002856.

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Efficient Treatment of Correlation Energies at the Basis-Set Limit by Monte Carlo Summation of Continuum States

M. P. Bircher; J. Villard; U. Rothlisberger 

Journal Of Chemical Theory And Computation. 2020. Vol. 16, num. 10, p. 6550 – 6559. DOI : 10.1021/acs.jctc.0c00724.

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

P. Diamantis; I. Tavernelli; U. Rothlisberger 

Journal Of Chemical Theory And Computation. 2020. Vol. 16, num. 10, p. 6690 – 6701. DOI : 10.1021/acs.jctc.0c00568.

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Vapor-assisted deposition of highly efficient, stable black-phase FAPbI(3) perovskite solar cells

H. Lu; Y. Liu; P. Ahlawat; A. Mishra; W. R. Tress et al. 

Science. 2020. Vol. 370, num. 6512, p. eabb898574. DOI : 10.1126/science.abb8985.

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Why choosing the right partner is important: stabilization of ternary Cs(y)GUA(x)FA((1-y-x))PbI(3)perovskites

A. Boziki; M. Mladenovic; M. Gratzel; U. Rothlisberger 

Physical Chemistry Chemical Physics. 2020. Vol. 22, num. 36, p. 20880 – 20890. DOI : 10.1039/d0cp03882b.

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Unravelling the structural complexity and photophysical properties of adamantyl-based layered hybrid perovskites

F. Jahanbakhshi; M. Mladenovic; E. Kneschaurek; L. Merten; M. C. Gelvez-Rueda et al. 

Journal Of Materials Chemistry A. 2020. Vol. 8, num. 34, p. 17732 – 17740. DOI : 10.1039/d0ta05022a.

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

L. Peterhans; E. Nicolaidou; P. Diamantis; E. Alloa; M. Leclerc et al. 

Chemistry Of Materials. 2020. Vol. 32, num. 17, p. 7347 – 7362. DOI : 10.1021/acs.chemmater.0c02251.

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

R. Capelli; W. Lyu; V. Bolnykh; S. Meloni; J. M. H. Olsen et al. 

Journal Of Physical Chemistry Letters. 2020. Vol. 11, num. 15, p. 6373 – 6381. DOI : 10.1021/acs.jpclett.0c00999.

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Formamidinium-Based Dion-Jacobson Layered Hybrid Perovskites: Structural Complexity and Optoelectronic Properties

M. C. Gelvez-Rueda; P. Ahlawat; L. Merten; F. Jahanbakhshi; M. Mladenovic et al. 

Advanced Functional Materials. 2020.  p. 2003428. DOI : 10.1002/adfm.202003428.

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Biomolecular Simulation: a Perspective from High Performance Computing

V. Bolnykh; U. Rothlisberger; P. Carloni 

Israel Journal Of Chemistry. 2020. Vol. 60, num. 7, p. 694 – 704. DOI : 10.1002/ijch.202000022.

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Molecular Basis of CLC Antiporter Inhibition by Fluoride

M. G. Chiariello; V. Bolnykh; E. Ippoliti; S. Meloni; J. M. H. Olsen et al. 

Journal Of The American Chemical Society. 2020. Vol. 142, num. 16, p. 7254 – 7258. DOI : 10.1021/jacs.9b13588.

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MiMiC: Multiscale Modeling in Computational Chemistry

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

Frontiers In Molecular Biosciences. 2020. Vol. 7, p. 45. DOI : 10.3389/fmolb.2020.00045.

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Atomistic origins of the limited phase stability of Cs+-rich FAxCs(1-x)PbI3 mixtures

A. Boziki; D. J. Kubicki; A. Mishra; S. Meloni; L. Emsley et al. 

Chemistry of Materials. 2020. Vol. 32, num. 6, p. 2605 – 2614. DOI : 10.1021/acs.chemmater.0c00120.

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From a week to less than a day: Speedup and scaling of coordinate-scaled exact exchange calculations in plane waves

M. P. Bircher; U. Röthlisberger 

Computer Physics Communications. 2020. Vol. 247, p. 106943. DOI : 10.1016/j.cpc.2019.106943.

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Essential role of oxygen vacancies of Cu-Al and Co-Al spinel oxides in their catalytic activity for the reverse water gas shift reaction

A. Bahmanpour; F. E. Héroguel; M. Kiliç; C. J. Baranowski; P. A. Schouwink et al. 

Applied Catalysis B: Environmental. 2020. Vol. 266, p. 118669. DOI : 10.1016/j.apcatb.2020.118669.

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Guanine‐Stabilized Formamidinium Lead Iodide Perovskites

L. Hong; J. V. Milic; P. Ahlawat; M. Mladenovic; D. J. Kubicki et al. 

Angewandte Chemie. 2020. Vol. 59, num. 12, p. 4691 – 4697. DOI : 10.1002/anie.201912051.

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2019

Atomistic Mechanism of the Nucleation of Methylammonium Lead Iodide Perovskite from Solution

P. Ahlawat; M. I. Dar; p. piaggi; M. Graetzel; M. Parrinello et al. 

Chemistry of Materials. 2019. Vol. 32, num. 1, p. 529 – 536. DOI : 10.1021/acs.chemmater.9b04259.

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Microscopic Picture of the Solvent Reorganization During Electron Transfer to Flavin in Water

M. Kilic; B. Ensing 

Journal Of Physical Chemistry B. 2019. Vol. 123, num. 46, p. 9751 – 9761. DOI : 10.1021/acs.jpcb.9b07250.

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

S. C. van Keulen; D. Narzi; U. Rothlisberger 

Biochemistry. 2019. Vol. 58, num. 42, p. 4317 – 4324. DOI : 10.1021/acs.biochem.9b00662.

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

A. Q. M. Alanazi; D. J. Kubicki; D. Prochowicz; E. A. R. Alharbi; M. E. F. Bouduban et al. 

Journal of the American Chemical Society. 2019. Vol. 141, num. 44, p. 17659 – 17669. DOI : 10.1021/jacs.9b07381.

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

N. J. Bruce; D. Narzi; D. Trpevski; S. C. van Keulen; A. G. Nair et al. 

Plos Computational Biology. 2019. Vol. 15, num. 10, p. e1007382. DOI : 10.1371/journal.pcbi.1007382.

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Crosslinking Allosteric Sites on the Nucleosome

L. K. Batchelor; L. De Falco; T. von Erlach; D. Sharma; Z. Adhireksan et al. 

Angewandte Chemie-International Edition. 2019. Vol. 58, num. 44, p. 15660 – 15664. DOI : 10.1002/anie.201906423.

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

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

Journal of Chemical Theory and Computation. 2019. Vol. 15, num. 10, p. 5601 – 5613. DOI : 10.1021/acs.jctc.9b00424.

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

N. Hartmann; S. Bhattacharyya; F. Schlaepfer; M. Volkov; Z. Schumacher et al. 

Physical Chemistry Chemical Physics. 2019. Vol. 21, num. 33, p. 18380 – 18385. DOI : 10.1039/c9cp03138c.

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Halide Versus Nonhalide Salts: The Effects of Guanidinium Salts on the Structural, Morphological, and Photovoltaic Performances of Perovskite Solar Cells

M. H. Alotaibi; Y. A. Alzahrani; N. Arora; A. Alyamani; A. Albadri et al. 

Solar Rrl. 2019.  p. 1900234. DOI : 10.1002/solr.201900234.

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A structure-based mechanism of cisplatin resistance mediated by glutathione transferase P1-1

A. De Luca; L. J. Parker; W. H. Ang; C. Rodolfo; V. Gabbarini et al. 

Proceedings of the National Academy of Sciences. 2019. Vol. 116, num. 28, p. 13943 – 13951. DOI : 10.1073/pnas.1903297116.

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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. Vol. 10, p. 3543 – 3549. DOI : 10.1021/acs.jpclett.9b01111.

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

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

ACS Catalysis. 2019. Vol. 9, num. 7, p. 6243 – 6251. DOI : 10.1021/acscatal.9b01822.

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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. Vol. 15, num. 6, p. 3810 – 3823. DOI : 10.1021/acs.jctc.9b00093.

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Cluster perturbation theory. III. Perturbation series for coupled cluster singles and doubles excitation energies

P. Baudin; F. Pawlowski; D. Bykov; D. Liakh; K. Kristensen et al. 

Journal Of Chemical Physics. 2019. Vol. 150, num. 13, p. 134110. DOI : 10.1063/1.5046935.

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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. Vol. 15, num. 3, p. 2042 – 2052. DOI : 10.1021/acs.jctc.8b00645.

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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. Vol. 15, num. 1, p. 557 – 571. DOI : 10.1021/acs.jctc.8b00897.

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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. Vol. 521, p. 119 – 131. DOI : 10.1016/j.jcis.2018.03.013.

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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. Vol. 115, num. 26, p. 6584 – 6589. DOI : 10.1073/pnas.1802963115.

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Exploiting Coordinate Scaling Relations To Accelerate Exact Exchange Calculations

M. P. Bircher; U. Röthlisberger 

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

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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. Vol. 14, num. 6, p. 3184 – 3195. DOI : 10.1021/acs.jctc.8b00069.

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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. Vol. 120, num. 24, p. 7554 – 7560. DOI : 10.1021/jacs.8b02118.

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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. Vol. 14, num. 6, p. 2834 – 2842. DOI : 10.1021/acs.jctc.7b01189.

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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. Vol. 5, num. 1, p. 019901. DOI : 10.1063/1.5020803.

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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.

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2017

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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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2016

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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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2015

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. Vol. 7, num. 20, p. 10834 – 10842. DOI : 10.1021/acsami.5b01638.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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2013

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

I. Tavernelli 

Physical Review A. 2013. Vol. 87, num. 4, p. 042501. DOI : 10.1103/PhysRevA.87.042501.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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2012

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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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2011

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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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2010

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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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2009

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.

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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.

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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.

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

I. Tavernelli; I. Lin; U. Rothlisberger 

Physical Review B. 2009. Vol. 79, p. 045106. DOI : 10.1103/PhysRevB.79.045106.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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2008

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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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2007

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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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. 023001. DOI : 10.1103/PhysRevLett.98.023001.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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, num. 2, p. 246 – 250. DOI : 10.1021/ct0501699.

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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.

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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.

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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. DOI : 10.1002/jcc.20360.

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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.

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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.

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2005

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.

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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. DOI : 10.1002/cphc.200500066.

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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.

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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.

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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. DOI : 10.1103/PhysRevB.71.195119.

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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. DOI : 10.1103/PhysRevB.71.115110.

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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.

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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.

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Rational design of organo-ruthenium anticancer compounds

C. Gossens; I. Tavernelli; U. Rothlisberger 

Chimia. 2005. Vol. 59, num. 3, p. 81 – 84. DOI : 10.2533/000942905777676795.

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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.

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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.

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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. DOI : 10.2533/000942905777676128.

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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+.

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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.

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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.

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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. DOI : 10.1080/00268970512331339378.

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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.

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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.

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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.

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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. DOI : 10.1021/ja047665b.

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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.

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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.

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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.

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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.

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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.

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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.

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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. DOI : 10.1021/ja048265r.

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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.

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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.

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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.

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2003

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. DOI : 10.1016/S0006-3495(03)74686-4.

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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. DOI : 10.1016/S0006-3495(03)74687-6.

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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.

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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. DOI : 10.1002/cphc.200300650.

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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. DOI : 10.1074/jbc.M305325200.

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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.

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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.

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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.

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Molecular dynamics studies of caspase-3

M. Sulpizi; U. Rothlisberger; P. Carloni 

Biophysical Journal. 2003. Vol. 84, num. 4, p. 2207 – 2215. DOI : 10.1016/S0006-3495(03)75026-7.

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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.

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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.

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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.

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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.

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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. DOI : 10.2533/000942902777680865.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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. DOI : 10.1021/bi026011h.

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2001

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.

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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.

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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.

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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.

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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. DOI : 10.1002/1521-3773(20010216)40:4%3C723::AID-ANIE7230%3E3.0.CO;2-8.

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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+.

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2000

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.

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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. DOI : 10.1007/s007750050368.

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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.

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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.

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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.

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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.

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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.

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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.

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1999

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. DOI : 10.1080/00268979909482837.

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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.

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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.

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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. DOI : 10.1039/A707860I.

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1997

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. DOI : 10.1016/S0006-3495(97)78303-6.

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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.

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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. DOI : 10.1063/1.473988.

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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.

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1996

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. DOI : 10.1063/1.471023.

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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. DOI : 10.1111/j.1432-1033.1996.00996.x.

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1995

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.

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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.

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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. DOI : 10.1039/JM9940400793.

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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 – 395. DOI : 10.1016/0009-2614(94)00852-3.

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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.

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Structure of nanoscale silicon clusters

U. Roethlisberger; W. Andreoni; M. Parrinello 

Physical Review Letters. 1994. Vol. 72, num. 5, p. 665 – 668. DOI : 10.1103/PhysRevLett.72.665.

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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. DOI : 10.1142/S0217979292001730.

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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 – 1256. DOI : 10.1063/1.462161.

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

U. Roethlisberger; W. Andreoni 

Chemical Physics Letters. 1992. Vol. 198, num. 5, p. 478 – 482. DOI : 10.1016/0009-2614(92)80031-6.

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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, p. 8129 – 8151. DOI : 10.1063/1.460096.

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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 – 246. DOI : 10.1007/BF01543983.

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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 – 155. DOI : 10.1002/ijch.199000015.

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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 – 178. DOI : 10.1007/BF01398587.

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1988

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.

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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.

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