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Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework.
This article presents a time dependent density functional theory (TDDFT) implementation to propagate the Kohn-Sham equations in real time, including the effects of a molecular environment through aExpand
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Insights into the mechanism of the reaction between hydrogen sulfide and peroxynitrite.
Hydrogen sulfide and peroxynitrite are endogenously generated molecules that participate in biologically relevant pathways. A revision of the kinetic features of the reaction between peroxynitriteExpand
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Spectroscopy in Complex Environments from QM-MM Simulations.
The applications of multiscale quantum-classical (QM-MM) approaches have shown an extraordinary expansion and diversification in the last couple of decades. A great proportion of these efforts haveExpand
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Quaternary structure effects on the hexacoordination equilibrium in rice hemoglobin rHb1: Insights from molecular dynamics simulations
Nonsymbiotic hemoglobins (nsHbs) form a widely distributed class of plant proteins, which function remains unknown. Despite the fact that class 1 plant nonsymbiotic hemoglobins are hexacoordinateExpand
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Nitrosodisulfide [S2NO]− (perthionitrite) is a true intermediate during the “cross-talk” of nitrosyl and sulfide
Nitrosodisulfide S2NO- is a controversial intermediate in the reactions of S-nitrosothiols with HS- that produce NO and HNO. QM-MM molecular dynamics simulations combined with TD-DFT analysisExpand
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Electron transport in real time from first-principles.
While the vast majority of calculations reported on molecular conductance have been based on the static non-equilibrium Green's function formalism combined with density functional theory (DFT), inExpand
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Nitrosodisulfide [S2NO]- (perthionitrite) is a true intermediate during the "cross-talk" of nitrosyl and sulfide.
Nitrosodisulfide S2NO- is a controversial intermediate in the reactions of S-nitrosothiols with HS- that produce NO and HNO. QM-MM molecular dynamics simulations combined with TD-DFT analysisExpand
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Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code
In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU),Expand
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Role of Core Electrons in Quantum Dynamics Using TDDFT.
The explicit simulation of time dependent electronic processes requires computationally onerous routes involving the temporal integration of motion equations for the charge density. EfficiencyExpand
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Water Network Dynamics Next to the Oxygen-Evolving Complex of Photosystem II
The influence of the environment on the functionality of the oxygen-evolving complex (OEC) of photosystem II has long been a subject of great interest. In particular, various water channels, whichExpand
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