Publications by Polydefkis Diamantis

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

Ursula Röthlisberger, Polydefkis Diamantis, Murat Kiliç

The impact of an 8-oxoguanine (8oxoG) defect on the redox properties of DNA within the nucleosome core particle (NCP) was investigated employing hybrid quantum mechanical/molecular mechanics (QM/MM) molecular dynamics simulations of native and 8oxoG-contai ...

Amer Chemical Soc2023

Hydration dynamics and IR spectroscopy of 4-fluorophenol

Ursula Röthlisberger, Polydefkis Diamantis

Halogenated groups are relevant in pharmaceutical applications and potentially useful spectroscopic probes for infrared spectroscopy. In this work, the structural dynamics and infrared spectroscopy of para-fluorophenol (F-PhOH) and phenol (PhOH) is investi ...

ROYAL SOC CHEMISTRY2022

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

Ursula Röthlisberger, Polydefkis Diamantis, Natalie Renuka Banerji

A promising approach to influence and control the photophysical properties of conjugated polymers is directing their molecular conformation by templating. We explore here the templating effect of single-stranded DNA oligomers (ssDNAs) on cationic polythiop ...

AMER CHEMICAL SOC2020

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

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

Effect of Single-Point Mutations on Nitric Oxide Rebinding and the Thermodynamic Stability of Myoglobin

Polydefkis Diamantis

The effect of single amino acid mutations on the rebinding dynamics of nitrogen monoxide (NO) to myoglobin is investigated using reactive molecular dynamics simulations. In particular, mutations of residues surrounding the heme-active site (Leu29, His64, V ...

AMER CHEMICAL SOC2019

Computational Studies of Redox-Active Chemical and Biological Systems

Polydefkis Diamantis

EPFL2014

Study of the Redox Properties of Singlet and Triplet Tris(2,2 '-bipyridine)ruthenium(II) ([Ru(bpy)(3)](2+)) in Aqueous Solution by Full Quantum and Mixed Quantum/Classical Molecular Dynamics Simulations

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

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

2014

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

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

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