Publications by Ivano Tavernelli

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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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

To better understand the complex photophysics of the amino acid tryptophan, which is widely used as a probe of protein structure and dynamics, we have measured electronic spectra of protonated, gas-phase tryptophan solvated with a controlled number of wate ...

We have investigated the mechanism of proton transfer in the lowest photoexcited state of 7-hydroxyquinoline·(NH3)3 using TDDFT based molecular dynamics. We observe a concerted mechanism according to which all protons are transferred simultaneously in a fa ...

In this work, we develop a method to design control pulses for fixed-frequency superconducting qubits coupled via tunable couplers based on local control theory, an approach commonly employed to steer chemical reactions. Local control theory provides an al ...

Ivano Tavernelli

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

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

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

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

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

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

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

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

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

Importance of weak interactions in liquid water

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

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

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

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

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

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

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

Microsolvation effects on the excited state dynamics of protonated tryptophan

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

Local control theory for superconducting qubits