Search Results - "Gonzalez Lebrero, Mariano C"

Spectroscopy in Complex Environments from QM–MM Simulations by Morzan, Uriel N, Alonso de Armiño, Diego J, Foglia, Nicolás O, Ramírez, Francisco, González Lebrero, Mariano C, Scherlis, Damián A, Estrin, Darío A

“…The applications of multiscale quantum–classical (QM–MM) approaches have shown an extraordinary expansion and diversification in the last couple of decades. A…”
Get full text

Assessment of Embedding Schemes in a Hybrid Machine Learning/Classical Potentials (ML/MM) Approach by Grassano, Juan S., Pickering, Ignacio, Roitberg, Adrian E., González Lebrero, Mariano C., Estrin, Dario A., Semelak, Jonathan A.

“…Machine learning (ML) methods have reached high accuracy levels for the prediction of in vacuo molecular properties. However, the simulation of large systems…”
Get full text

Fluorescence Quantum Yields in Complex Environments from QM-MM TDDFT Simulations: The Case of Indole in Different Solvents by Díaz Mirón, Gonzalo, González Lebrero, Mariano C

“…Fluorescence is commonly exploited to probe microscopic properties. An important example is tryptophan in protein environments, where variations in…”
Get full text

Non-Aromatic Fluorescence in Biological Matter: The Exception or the Rule? by Morzan, Uriel N., Díaz Mirón, Gonzalo, Grisanti, Luca, González Lebrero, Mariano C., Kaminski Schierle, Gabriele S., Hassanali, Ali

“…While in the vast majority of cases fluorescence in biological matter has been attributed to aromatic or conjugated groups, peptides associated with…”
Get full text

Role of Core Electrons in Quantum Dynamics Using TDDFT by Foglia, Nicolás O, Morzan, Uriel N, Estrin, Dario A, Scherlis, Damian A, Gonzalez Lebrero, Mariano C

“…The explicit simulation of time dependent electronic processes requires computationally onerous routes involving the temporal integration of motion equations…”
Get full text

Short hydrogen bonds enhance nonaromatic protein-related fluorescence by Stephens, Amberley D., Qaisrani, Muhammad Nawaz, Ruggiero, Michael T., Mirón, Gonzalo Díaz, Morzan, Uriel N., Lebrero, Mariano C. González, Jones, Saul T. E., Poli, Emiliano, Bond, Andrew D., Woodhams, Philippa J., Kleist, Elyse M., Grisanti, Luca, Gebauer, Ralph, Zeitler, J. Axel, Credgington, Dan, Hassanali, Ali, Schierle, Gabriele S. Kaminski

“…Fluorescence in biological systems is usually associated with the presence of aromatic groups. Here, by employing a combined experimental and computational…”
Get full text

The carbonyl-lock mechanism underlying non-aromatic fluorescence in biological matter by Mirón, Gonzalo Díaz, Semelak, Jonathan A., Grisanti, Luca, Rodriguez, Alex, Conti, Irene, Stella, Martina, Velusamy, Jayaramakrishnan, Seriani, Nicola, Došlić, Nadja, Rivalta, Ivan, Garavelli, Marco, Estrin, Dario A., Kaminski Schierle, Gabriele S., González Lebrero, Mariano C., Hassanali, Ali, Morzan, Uriel N.

“…Challenging the basis of our chemical intuition, recent experimental evidence reveals the presence of a new type of intrinsic fluorescence in biomolecules that…”
Get full text

GPU Accelerated Implementation of Density Functional Theory for Hybrid QM/MM Simulations by Nitsche, Matías A, Ferreria, Manuel, Mocskos, Esteban E, González Lebrero, Mariano C

“…The hybrid simulation tools (QM/MM) evolved into a fundamental methodology for studying chemical reactivity in complex environments. This paper presents an…”
Get full text

Transport and Spectroscopy in Conjugated Molecules: Two Properties and a Single Rationale by Ramirez, Francisco F, Bustamente, Carlos M, González Lebrero, Mariano C, Scherlis, Damián A

“…In the context of electron dynamics simulations, when the charge density of a molecule is subject to a perturbation in the form of a short electric field…”
Get full text

Reaction Path Analysis from Potential Energy Contributions Using Forces: An Accessible Estimator of Reaction Coordinate Adequacy by Foglia, Nicolás O, González Lebrero, Mariano C, Biekofsky, Rodolfo R, Estrin, Darío A

“…The calculation of potential energy and free-energy profiles along complex chemical reactions or rare event processes is of great interest because of their…”
Get full text

Theoretical Insights into the Reaction and Inhibition Mechanism of Metal-Independent Retaining Glycosyltransferase Responsible for Mycothiol Biosynthesis by Blanco Capurro, Juan I., Hopkins, Chad W., Pierdominici Sottile, Gustavo, González Lebrero, Mariano C., Roitberg, Adrian E., Marti, Marcelo A.

“…Understanding enzymatic reactions with atomic resolution has proven in recent years to be of tremendous interest for biochemical research, and thus, the use of…”
Get full text

Molecular Basis of the Mechanism of Thiol Oxidation by Hydrogen Peroxide in Aqueous Solution: Challenging the SN2 Paradigm by Zeida, Ari, Babbush, Ryan, González Lebrero, Mariano C, Trujillo, Madia, Radi, Rafael, Estrin, Darío A

“…The oxidation of cellular thiol-containing compounds, such as glutathione and protein Cys residues, is considered to play an important role in many biological…”
Get full text

Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework by Morzan, Uriel N, Ramírez, Francisco F, Oviedo, M Belén, Sánchez, Cristián G, Scherlis, Damián A, Lebrero, Mariano C González

“…This article presents a time dependent density functional theory (TDDFT) implementation to propagate the Kohn-Sham equations in real time, including the…”
Get more information

Mechanism of cysteine oxidation by peroxynitrite: An integrated experimental and theoretical study by Zeida, Ari, González Lebrero, Mariano C., Radi, Rafael, Trujillo, Madia, Estrin, Darío A.

“…•We explore Cys oxidation by peroxynitrite using fast kinetics and QM/MM simulations.•pH-independent activation thermodynamics parameters were determined.•A…”
Get full text

A helix-coil transition induced by the metal ion interaction with a grafted iron-binding site of the CyaY protein family by Vazquez, Diego S, Agudelo, William A, Yone, Angel, Vizioli, Nora, Arán, Martín, González Flecha, F Luis, González Lebrero, Mariano C, Santos, Javier

“…Iron-protein interactions are involved in electron transfer reactions. Alterations of these processes are present in a number of human pathologies; among them,…”
Get more information

Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code by Marcolongo, Juan P, Zeida, Ari, Semelak, Jonathan A, Foglia, Nicolás O, Morzan, Uriel N, Estrin, Dario A, González Lebrero, Mariano C, Scherlis, Damián A

“…In this work we present the current advances in the development and the applications of , a lab-made code designed for density functional theory calculations…”
Get full text

Dissipative Equation of Motion for Electromagnetic Radiation in Quantum Dynamics by Bustamante, Carlos M, Gadea, Esteban D, Horsfield, Andrew, Todorov, Tchavdar N, González Lebrero, Mariano C, Scherlis, Damián A

“…The dynamical description of the radiative decay of an electronically excited state in realistic many-particle systems is an unresolved challenge. In the…”
Get full text

Bond or Cage Effect:  How Nitrophorins Transport and Release Nitric Oxide by Martí, Marcelo A, Lebrero, Mariano C. González, Roitberg, Adrián E, Estrin, Dario A

“…Most blood-sucking insects possess salivary proteins which, upon injection into the victim's tissue, help them improve their feeding. One group of these…”
Get full text

Modeling heme proteins using atomistic simulations by Bikiel, Damián E, Boechi, Leonardo, Capece, Luciana, Crespo, Alejandro, De Biase, Pablo M, Di Lella, Santiago, González Lebrero, Mariano C, Martí, Marcelo A, Nadra, Alejandro D, Perissinotti, Laura L, Scherlis, Damián A, Estrin, Darío A

“…Heme proteins are found in all living organisms, and perform a wide variety of tasks ranging from electron transport, to the oxidation of organic compounds, to…”
Get more information

QM–MM Ehrenfest dynamics from first principles: photodissociation of diazirine in aqueous solution by Ramírez, Francisco, Díaz Mirón, Gonzalo, González Lebrero, Mariano C., Scherlis, Damian A.

“…This article describes an implementation of Ehrenfest molecular dynamics based on TDDFT and Gaussian basis sets, optimized for hybrid QM–MM simulations in GPU…”
Get full text