A5003907241- Protein Structure and Dynamics
- Photochemistry and Electron Transfer Studies
- Amyotrophic Lateral Sclerosis Research
- Advanced NMR Techniques and Applications
- Porphyrin and Phthalocyanine Chemistry
- Synthesis and Properties of Aromatic Compounds
- Photochromic and Fluorescence Chemistry
- N-Heterocyclic Carbenes in Organic and Inorganic Chemistry
- Spectroscopy and Quantum Chemical Studies
- Machine Learning in Materials Science
- Enzyme Structure and Function
- Chemical Reaction Mechanisms
- Molecular spectroscopy and chirality
- Bioactive Compounds and Antitumor Agents
- Synthesis and Reactivity of Heterocycles
- Advanced Chemical Physics Studies
- Free Radicals and Antioxidants
- Chalcogenide Semiconductor Thin Films
- Metal complexes synthesis and properties
- Organometallic Complex Synthesis and Catalysis
- Crystallography and molecular interactions
- Metalloenzymes and iron-sulfur proteins
- Lipid Membrane Structure and Behavior
- TiO2 Photocatalysis and Solar Cells
- Luminescence and Fluorescent Materials
University of Tarapacá
2024-2025
Universidad de Santiago de Chile
2017-2023
University of Chicago
2023
Université Claude Bernard Lyon 1
2023
Centre National de la Recherche Scientifique
2023
Frankfurt Institute for Advanced Studies
2023
University of Groningen
2023
Universidad Bernardo O'Higgins
2019-2022
Instituto de Química y Fisicoquímica Biológicas
2017-2018
University of Chile
2011-2018
ABSTRACT Coarse-grained modeling has become an important tool to supplement experimental measurements, allowing access spatio-temporal scales beyond all-atom based approaches. The GōMartini model combines structure- and physics-based coarse-grained approaches, balancing computational efficiency accurate representation of protein dynamics with the capabilities studying proteins in different biological environments. This paper introduces enhanced model, which a virtual-site implementation Gō...
Lipid nanoparticles (LNPs) represent a promising platform for advanced drug and gene delivery, yet optimizing these particles specific cargos cell targets poses complex, multifaceted challenge. Furthermore, there is pressing need more comprehensive understanding of the underlying technology. Experimental studies are costly often provide low-resolution information. Molecular dynamics (MD) simulations allow us to study at higher resolution, enhancing our understanding. However, studying...
Coarse-grained modeling has become an important tool to supplement experimental measurements, allowing access spatio-temporal scales beyond all-atom based approaches. The GōMartini model combines structure- and physics-based coarse-grained approaches, balancing computational efficiency accurate representation of protein dynamics with the capabilities studying proteins in different biological environments. This paper introduces enhanced model, which a virtual-site implementation Gō models...
Several different mutations of the protein copper, zinc superoxide dismutase (SOD1) produce neurodegenerative disorder amyotrophic lateral sclerosis (ALS). The molecular mechanism by which diverse converge to a similar pathology is currently unknown. electrostatic loop (EL) SOD1 known be affected in all studied ALS-linked SOD1. In this work, we employ multiscale simulation approach show that perturbation corresponds an increased probability EL detaching from its native position, exposing...
Lipid nanoparticles (LNPs) represent a promising platform for advanced drug and gene delivery, yet optimizing these particles specific cargos cell targets poses complex, multifaceted challenge. Furthermore, there is pressing need more comprehensive understanding of the underlying technology. Experimental studies are costly often provide low-resolution information. Molecular dynamics (MD) simulations allow us to study at higher resolution, enhancing our understanding. However, studying...
Coarse-grained (CG) molecular dynamics (MD) simulations have grown in applicability over the years. The recently released version of Martini CG force field (Martini 3) has been successfully applied to simulate many processes, including protein–ligand binding. However, current ligand parametrization scheme is manual and requires an a priori reference all-atom (AA) simulation for benchmarking. For systems with suboptimal AA parameters, which are often unknown, this translates into model that...
Martini 3 is the new version of a widely used coarse-grained (CG) model that have been extensively parameterized to reproduce experimental and thermodynamic data. Based on building-block approach, shows better coverage chemical space more accurate predictions interactions molecular packing in general. Given these improvements, allows applications such as studies involving protein–ligand interactions. In this chapter, summary key elements presented, followed by an example practical...
Data analysis is a major task for Computational Chemists. The diversity of modeling tools currently available in Chemistry requires the development flexible that can adapt to different systems and output formats. As contribution this need, we report implementation goChem, versatile open-source library multiscale computational chemistry data. library, written Go programming language, allows easy integration levels theory, an easy-to-use API, allowing both one-use complex programs Go. We...
This study evaluated the antioxidant capacity of oxidation products three flavonols using oxygen radical absorbance capacity—fluorescein assay (ORAC-FL), capacity—pyrogallol red (ORAC-PGR), and cellular activity (CAA) in human dermal fibroblast (HFF) cells, with 2,2’-azobis(2-amidinopropane) dihydrochloride (AAPH) as a free generator under controlled pH solvent conditions. At 2 polar aprotic solvent, BZF-OH (benzofuranone-OH) compounds were formed, while methoxylated analogs obtained at 7...
Dye-sensitized solar-cell (DSSC) systems have been investigated by calculating light-absorption and electron-injection processes of zinc-porphyrin-dye based sensitizers adsorbed on a TiO<sub>2</sub> cluster simulating the semiconductor.
Magnetically induced current densities have been investigated for some recently synthesised thieno-bridged porphyrins. The aim of the study is to understand influence direction thieno bridge on aromatic character molecules. calculated ring-current susceptibilities two tautomers 2,3- and 3,4-thieno-bridged porphyrins as well corresponding Zn-containing compounds show that molecules are all according ring criterion. 16.2 nA/T 20.2 around porphyrin 2,3-thieno-bridged somewhat weaker than 22.8...
Three aminocarbonyls were synthesized, and their emissive spectral behavior recorded at various solvent polarities showed marked inverted solvatofluorochromism. The emission energy inversion occurs moderate was found to be triggered by a change in the solute-solvent interaction responsible for stabilization of highly zwitterionic excited state dyes, from dipolarity acidity.
Abstract Comprehensive spectroscopic kinetic studies illustrate an alternative mechanism for the traditional free‐carbene intermediated H/D exchange reaction of 1,3‐dialkylimidazolium salts under neutral (D 2 O) and acidic conditions (DCl/D O 35 wt % solution). The deuteration high purity [bmim]Cl in D is studied at different temperatures, absence catalyst or impurities, to yield activation energy. DFT transition‐state modelling, a small water cluster [bmim] cation, also yields energy which...
Classical force-field parameters of the metal site metalloproteins usually comprise only partial charges involved atoms, as well bond-stretching and bending metal–ligand interactions. Although for certain ligands such histidine residues, torsional motions at play an important role dynamics protein, no terms have been considered to be crucial in parametrization force fields, they therefore omitted parametrization. In this work, we optimized AMBER-compatible reduced state copper, zinc...
Abstract Density functional theory calculations suggest that l -glutamyl- -glutamate [H-Glu-Glu-H] 2– can act as an efficient chelating ligand in basic beryllium carboxylates of type Be 4 O(RCO 2 ) 6 . An exergonic energy balance –10.6 kcal mol –1 for the substitution two [AcO] – anions by one [H-Glu-Glu-OH] dianion O(AcO has been calculated; a second and third substitutions, computed release amounts to –9.3, –11.3 The coordination geometry complexes shows trend toward less deviation from...
Ring deuteration via the SEAr mechanism, which is usually problem-free, found to be troublesome with methylenedioxy substituent aromatics. We report a case where not only partially fails at one of ortho positions but also completely prevented by conformation dependent effect other o-position. Such selectivity discrepancies are important due widespread occurrence substituted natural products. Density functional theory calculations were used elucidate exchange reaction mechanism in...
Nuclear magnetic shieldings have been calculated at the density functional theory (DFT) level for stacks of benzene, hexadehydro[12]annulene, dodecadehydro[18]annulene, and hexabenzocoronene. The due to ring currents in adjacent molecules estimated by calculating nucleus independent molecular monomer atomic positions neighbor molecules. calculations show that shielding model works reasonably well 1H NMR benzene whereas larger 13C interaction between leads effects are least same size as...
Impairment of the Zn(II)-binding site copper, zinc superoxide dismutase (CuZnSOD) protein is involved in a number hypotheses and explanations for still unknown toxic gain function mutant varieties CuZnSOD that are associated with familial forms amyotrophic lateral sclerosis (ALS). In this work, computational chemistry methods have been used studying models metal-binding ALS-linked H46R wild-type variety enzyme. By comparing energy electronic structure these models, plausible explanation...
Solar power is a strong alternative to the currently used fossil fuels in order satisfy world's energy needs. Among them, dye-sensitized solar cells (DSSC) represent low-cost option. Efficient and cheap dyes are needed make DSSCs competitive. Computational chemistry can be guide design of new light-absorbing chromophores. Here, we have computationally studied lowest excited states ZnPBAT, which recently synthesized porphyrinoid chromophore with high light-absorption efficiency. The...
Coarse-grained (CG) molecular dynamics (MD) simulations have grown in applicability over the years. The recently released version of Martini CG force field (Martini 3) has been successfully applied to simulate many processes, including protein-ligand binding. However, current ligand parameterization scheme is manual and requires an a priori reference all-atom (AA) simulation for benchmarking. For systems with suboptimal AA parameters, which are often unknown, this translates into model does...
Coarse-grained (CG) molecular dynamics (MD) simulations have grown in applicability over the years. The recently released version of Martini CG force field (Martini 3) has been successfully applied to simulate many processes, including protein-ligand binding. However, current ligand parameterization scheme is manual and requires an a priori reference all-atom (AA) simulation for benchmarking. For systems with suboptimal AA parameters, which are often unknown, this translates into model does...