Search Results - "Suárez, Dimas"

SARS-CoV‑2 Main Protease: A Molecular Dynamics Study by Suárez, Dimas, Díaz, Natalia

“…Herein, we investigate the structure and flexibility of the hydrated SARS-CoV-2 main protease by means of 2.0 μs molecular dynamics (MD) simulations in…”
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Pyrolytic conversion of glucose into hydroxymethylfurfural and furfural: Benchmark quantum‐chemical calculations by López, Roberto, Suárez, Dimas

“…Quantum chemical methods have been intensively applied to study the pyrolytic conversion of glucose into hydroxymethylfurfural (HMF) and furfural (FF). Herein,…”
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Toward Reliable and Insightful Entropy Calculations on Flexible Molecules by Díaz, Natalia, Suárez, Dimas

“…The absolute entropy of a flexible molecule can be approximated by the sum of a rigid-rotor-harmonic-oscillator (RRHO) entropy and a Gibbs–Shannon entropy…”
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A Quantum Chemical Topology Picture of Intermolecular Electrostatic Interactions and Charge Penetration Energy by Jiménez-Grávalos, Fernando, Suárez, Dimas

“…Based on the Interacting Quantum Atoms approach, we present herein a conceptual and theoretical framework of short-range electrostatic interactions, whose…”
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Affinity Calculations of Cyclodextrin Host–Guest Complexes: Assessment of Strengths and Weaknesses of End-Point Free Energy Methods by Suarez, Dimas, Diaz, Natalia

“…The end-point methods like MM/PBSA or MM/GBSA estimate the free energy of a biomolecule by combining its molecular mechanics energy with solvation free energy…”
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Understanding the Conformational Properties of Fluorinated Polypeptides: Molecular Modelling of Unguisin A by Díaz, Natalia, Suárez, Dimas

“…In this work, we investigate the conformational properties of unguisin A, a natural macrocyclic heptapeptide that incorporates a γ-aminobutyric acid (Gaba),…”
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Amphiphilic cyclodextrins: Dimerization and diazepam binding explored by molecular dynamics simulations by Suárez, Dimas, Díaz, Natalia

“…[Display omitted] •β-CD dimerization is marginal in aqueous solution.•Alkyl side chains in the amphiphilic β-CDs tend to be self-included within the ring.•Long…”
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Ligand Strain and Entropic Effects on the Binding of Macrocyclic and Linear Inhibitors: Molecular Modeling of Penicillopepsin Complexes by Suárez, Dimas, Díaz, Natalia

“…Using extensive molecular dynamics simulations, we investigate the structure and dynamics of the complexes formed between penicillopepsin and two…”
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Direct methods for computing single-molecule entropies from molecular simulations by Suarez, Dimas, Diaz, Natalia

“…Assessing the actual role of entropic forces in controlling both the stability and activity of flexible molecules and macromolecules is a theoretical challenge…”
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Alkali and Alkaline‐Earth Cations in Complexes with Small Bioorganic Ligands: Ab Initio Benchmark Calculations and Bond Energy Decomposition by López, Roberto, Díaz, Natalia, Suárez, Dimas

“…Herein, we report a computational database for the complexes of alkali [Li(I), Na(I), K(I)] and alkaline‐earth [Be(II), Mg(II) and Ca(II)] cations with 25…”
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Role of the Protonation State on the Structure and Dynamics of Albumin by Diaz, Natalia, Suarez, Dimas

“…Human serum albumin undergoes reversible conformational transitions associated with ligand binding or pH changes. Among them, the neutral to base (N → B)…”
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Entropy Calculations of Single Molecules by Combining the Rigid–Rotor and Harmonic-Oscillator Approximations with Conformational Entropy Estimations from Molecular Dynamics Simulations by Suárez, Ernesto, Díaz, Natalia, Suárez, Dimas

“…As shown by previous theoretical and computational work, absolute entropies of small molecules that populate different conformers can be predicted accurately…”
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Sampling Assessment for Molecular Simulations Using Conformational Entropy Calculations by Suárez, Dimas, Díaz, Natalia

“…The extent and significance of conformational sampling is a major factor determining the reliability of long-scale molecular simulations of large and flexible…”
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Extensive Simulations of the Full-Length Matrix Metalloproteinase‑2 Enzyme in a Prereactive Complex with a Collagen Triple-Helical Peptide by Díaz, Natalia, Suárez, Dimas

“…Collagen hydrolysis catalyzed by matrix metalloproteinases is an important and complex process involved in a variety of physiological and pathological…”
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Application of the Interacting Quantum Atoms Approach to the S66 and Ionic‐Hydrogen‐Bond Datasets for Noncovalent Interactions by Suárez, Dimas, Díaz, Natalia, Francisco, Evelio, Martín Pendás, Angel

“…The interacting quantum atoms (IQA) method can assess, systematically and in great detail, the strength and physics of both covalent and noncovalent…”
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Molecular Dynamics Studies of Matrix Metalloproteases by Díaz, Natalia, Suárez, Dimas

“…Matrix metalloproteases are multidomain enzymes with a remarkable proteolytic activity located in the extracellular environment. Their catalytic activity and…”
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Multibody local approximation: application to conformational entropy calculations on biomolecules by Suárez, Ernesto, Suárez, Dimas

“…Multibody type expansions like mutual information expansions are widely used for computing or analyzing properties of large composite systems. The power of…”
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CENCALC: A computational tool for conformational entropy calculations from molecular simulations by Suárez, Ernesto, Díaz, Natalia, Méndez, Jefferson, Suárez, Dimas

“…We present the CENCALC software that has been designed to estimate the conformational entropy of single molecules from extended Molecular Dynamics (MD)…”
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Molecular Modeling of Bioorganometallic Compounds: Thermodynamic Properties of Molybdocene-Glutathione Complexes and Mechanism of Peptide Hydrolysis by Suarez, Dimas, Diaz, Natalia

“…The computational study of bioinorganic complexes between transition metals and flexible ligands is still challenging, given that, besides requiring extensive…”
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Unraveling the Molecular Structure of the Catalytic Domain of Matrix Metalloproteinase‑2 in Complex with a Triple-Helical Peptide by Means of Molecular Dynamics Simulations by Díaz, Natalia, Suárez, Dimas, Valdés, Haydeé

“…Herein, we present the results of a computational study that employed various simulation methodologies to build and validate a series of molecular models of a…”
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