Publications (30) NATALIA DIAZ FERNANDEZ publications View referenced research data.

filter_list Organic Chemistry

2022

  1. Amphiphilic cyclodextrins: Dimerization and diazepam binding explored by molecular dynamics simulations

    Journal of Molecular Liquids, Vol. 349

2021

  1. Understanding the Conformational Properties of Fluorinated Polypeptides: Molecular Modelling of Unguisin A

    Journal of Chemical Information and Modeling, Vol. 61, Núm. 1, pp. 223-237

2020

  1. Aptamers targeting protein-specific glycosylation in tumor biomarkers: general selection, characterization and structural modeling

    Chemical Science, Vol. 11, Núm. 35, pp. 9402-9413

  2. SARS-CoV-2 Main Protease: A Molecular Dynamics Study

    Journal of Chemical Information and Modeling, Vol. 60, Núm. 12, pp. 5815-5831

2017

  1. Conformational and entropy analyses of extended molecular dynamics simulations of α-, β- And γ-cyclodextrins and of the β-cyclodextrin/nabumetone complex

    Physical Chemistry Chemical Physics, Vol. 19, Núm. 2, pp. 1431-1440

  2. Ligand Strain and Entropic Effects on the Binding of Macrocyclic and Linear Inhibitors: Molecular Modeling of Penicillopepsin Complexes

    Journal of Chemical Information and Modeling, Vol. 57, Núm. 8, pp. 2045-2055

2014

  1. A combined semiempirical and DFT computational protocol for studying bioorganometallic complexes: Application to molybdocene-cysteine complexes

    Journal of Computational Chemistry, Vol. 35, Núm. 4, pp. 324-334

  2. An integrated computational and experimental approach to gaining selectivity for MMP-2 within the gelatinase subfamily

    ChemBioChem, Vol. 15, Núm. 3, pp. 399-412

2013

  1. CENCALC: A computational tool for conformational entropy calculations from molecular simulations

    Journal of Computational Chemistry, Vol. 34, Núm. 23, pp. 2041-2054

  2. 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

    Biochemistry, Vol. 52, Núm. 47, pp. 8556-8569

2012

  1. Alternative interdomain configurations of the full-length MMP-2 enzyme explored by molecular dynamics simulations

    Journal of Physical Chemistry B, Vol. 116, Núm. 9, pp. 2677-2686

2011

  1. Ab initio benchmark calculations on Ca(II) complexes and assessment of density functional theory methodologies

    Journal of Physical Chemistry A, Vol. 115, Núm. 41, pp. 11331-11343

  2. Entropy calculations of single molecules by combining the rigid-rotor and harmonic-oscillator approximations with conformational entropy estimations from molecular dynamics simulations

    Journal of Chemical Theory and Computation, Vol. 7, Núm. 8, pp. 2638-2653

2010

  1. Kinetic and binding effects in peptide substrate selectivity of matrix metalloproteinase-2: Molecular dynamics and QM/MM calculations

    Proteins: Structure, Function and Bioinformatics, Vol. 78, Núm. 1, pp. 1-11

  2. Understanding regioselective cleavage in peptide hydrolysis by a palladium(II) aqua complex: A theoretical point of view

    Journal of Physical Chemistry B, Vol. 114, Núm. 25, pp. 8525-8535

2009

  1. Thermochemical fragment energy method for biomolecules: Application to a collagen model peptide

    Journal of Chemical Theory and Computation, Vol. 5, Núm. 6, pp. 1667-1679

2008

  1. Entropic control of the relative stability of triple-helical collagen peptide models

    Journal of Physical Chemistry B, Vol. 112, Núm. 47, pp. 15248-15255

  2. Peptide hydrolysis catalyzed by matrix metalloproteinase 2: A computational study

    Journal of Physical Chemistry B, Vol. 112, Núm. 28, pp. 8412-8424

2006

  1. A computational study of the deacylation mechanism of human butyrylcholinesterase

    Biochemistry, Vol. 45, Núm. 24, pp. 7529-7543

2003

  1. A Combined Theoretical and Experimental Research Project into the Aminolysis of β-Lactam Antibiotics: The Importance of Bifunctional Catalysis

    European Journal of Organic Chemistry, pp. 4161-4172