Publications by Ivano Tavernelli

Related publications (121)

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

Ursula Röthlisberger, Ivano Tavernelli, Polydefkis Diamantis

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

AMER CHEMICAL SOC2020

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

Ursula Röthlisberger, Ivano Tavernelli, Sara Bonella

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

2014

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

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Marilisa Neri, Pablo Campomanes Ramos, Stefano Vanni, Elizabeth Claire Brunk, Manuel Dömer, Andrey Laktionov, Negar Ashari Astani, Polydefkis Diamantis, Thomas James Penfold, Giulia Palermo

The Laboratory of Computational Chemistry and Biochemistry is active in the development and application of first-principles based simulations of complex chemical and biochemical phenomena. Here, we review some of our recent efforts in extending these metho ...

2011

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

Ursula Röthlisberger, Ivano Tavernelli, Marilisa Neri, Stefano Vanni

Understanding the binding mode of agonists to adrenergic receptors is crucial to enabling improved rational design of new therapeutic agents. However, so far the high conformational flexibility of G protein-coupled receptors has been an obstacle to obtaini ...

Public Library of Science2011

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

Michael Graetzel, Mohammad Khaja Nazeeruddin, Rosario Scopelliti, Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod

A series of homologous bis-cyclometalated iridium(III) complexes Ir(2,4-di-X-phenyl-pyridine)2(picolinate) (X = H, F, Cl, Br) HIrPic, FIrPic, ClIrPic, and BrIrPic has been synthesized and characterized by NMR, X-ray crystallography, UV–vis absorption and e ...

2012

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

Rosario Scopelliti, Paul Joseph Dyson, Ursula Röthlisberger, Ivano Tavernelli, Antoine Dorcier, Christian Gossens

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

2005

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

Ursula Röthlisberger, Ivano Tavernelli, Polydefkis Diamantis

To assess the effect of an 8-oxoguanine (8OG) defect base on the vertical ionization energies (VIEs) and electron affinities (VEAs) of DNA, density functional theory calculations were carried out for native and defect DNA bases and nucleotides, as well as ...

2019

Optical absorption properties of metal-organic frameworks: solid stateversusmolecular perspective

Ivano Tavernelli, Anne-Clémence Corminboeuf, Berend Smit, Maria Fumanal Quintana

The vast chemical space of metal and ligand combinations in Transition Metal Complexes (TMCs) gives rise to a rich variety of electronic excited states with local and non-local character such as intra-ligand (IL), metal-centered (MC), metal-to-ligand (MLCT ...

2020

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

Ursula Röthlisberger, Ivano Tavernelli

The solvation of the Ru(bPy)(3) (bpy = 2,2'-bipyridyl) cation was studied by molecular dynamics simulations, using both a hybrid QM/MM Car-Parrinello scheme and a classical force field. The trajectory analysis reveals that the first solvation sphere ...

2009

Phenomenological theory of variational quantum ground-state preparation

Ivano Tavernelli, Giuseppe Carleo

The variational approach is a cornerstone of computational physics, considering both conventional and quantum computing computational platforms. The variational quantum eigensolver algorithm aims to prepare the ground state of a Hamiltonian exploiting para ...

Amer Physical Soc2023

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

Michael Graetzel, Jacques-Edouard Moser, Mohammad Khaja Nazeeruddin, Robin Humphry-Baker, Joël Teuscher, Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Negar Ashari Astani, Aswani Yella, Julien Edouard Frey, Simon Mathew, Lauren Elizabeth Polander

To improve their efficiency beyond the state-of-the-art, D-pi-A dyes must display increased spectral breadth and account for the physical limitations observed in the dye. sensitized solar cells. In particular, they should be designed to control the electro ...

Amer Chemical Soc2013

Importance of weak interactions in liquid water

Ursula Röthlisberger, Ivano Tavernelli, I-Chun Lin

We present ab initio molecular dynamics studies on liquid water using density functional theory in conjunction with either dispersion-corrected atom-centered potentials or empirical van der Waals corrections. Our results show that improving the description ...

2009

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

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

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

2014

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

Ursula Röthlisberger, Ivano Tavernelli, Marilisa Neri, Stefano Vanni

The mechanism of signal transduction in G-protein-coupled receptors (GPCRs) is a crucial step in cell signaling. However, the molecular details of this process are still largely undetermined. Carrying out submicrosecond molecular dynamics simulations of be ...

Elsevier2010

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

Ursula Röthlisberger, Ivano Tavernelli, Christian Gossens

The reaction of the anticancer compound (eta(6)-benzene)Ru(en)(OH2) (1) toward the nucleobases guanine, adenine, and cytosine is studied computationally using DFT/BP86 calculations. The aqua leaving group of such compounds is known to undergo ligand ...

2009

Quantum mechanical/molecular mechanical (QM/MM) Car-Parrinello simulations in excited states

Ursula Röthlisberger, Leonardo Guidoni, Ivano Tavernelli, Enrico Marko Tapavicza

The combination of time-dependent d. functional theory (TDDFT) for the description of excited states with a hybrid quantum mechanics/mol. mechanics (QM/MM) approach enables the study of photochem. processes in complex environments. Here, we present a short ...

2005

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

Ursula Röthlisberger, Ivano Tavernelli, Pablo Lopez Tarifa

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

2014

Time-dependent density functional theory molecular dynamics simulations of liquid water radiolysis

Ivano Tavernelli

The early stages of the Coulomb explosion of a doubly ionized water molecule immersed in liquid water are investigated with time-dependent density functional theory molecular dynamics (TD-DFT MD) simulations. Our aim is to verify that the double ionization ...

2008

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

Ursula Röthlisberger, Ivano Tavernelli, Anatole von Lilienfeld

Recently, we have introduced a scheme for optimizing atom-based nonlocal external potentials within the framework of d. functional theory (DFT) in order to systematically improve the description of mol. properties [Phys. Rev. Lett. 93, 153004 (2004); J. Ch ...

2005

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

Majed Chergui, Olivier Christian Bräm, Ursula Röthlisberger, Ivano Tavernelli, Frederico Alves Lima, Marco Eli Reinhard, Mercedes Hannelore Rittmann-Frank, Thomas James Penfold, Lotta Susanne Karlsson, Jochen Rittmann, Gloria Capano

We present a static and picosecond X-ray absorption study at the Cu K-edge of bis(2,9-dimethyl-1,10-phenanthroline)copper(I) (Cu(dmp)(2); dmp = 2,9-dimethyl-1,10-phenanthroline) dissolved in acetonitrile and dichloromethane. The steady-state photolumi ...

Amer Chemical Soc2013