Now showing items 1-20 of 42

    • 1H nuclear spin relaxation of liquid water from molecular dynamics simulations 

      Calero Borrallo, Carles; Martí Rabassa, Jordi; Guàrdia Manuel, Elvira (2015-01-13)
      Article
      Restricted access - publisher's policy
      We have investigated the nuclear spin relaxation properties of 1H in liquid water with the help of molecular dynamics simulations. We have computed the 1H nuclear spin relaxation times T1 and T2 and determined the contribution ...
    • A comparative molecular dynamics study of sulfuric and methanesulfonic acids 

      Canales Gabriel, Manel; Guàrdia Manuel, Elvira (2016-12-01)
      Article
      Open Access
      The molecular dynamics computer simulation method has been used to study sulfuric and methanesulfonic acids. Calculations have been carried out between 200 K and 400 K using reliable force fields. Thermodynamic properties, ...
    • A continuous mixture of two different dimers in liquid water 

      Pardo Soto, Luis Carlos; Henao Aristizábal, Andrés; Busch, Sebastian; Guàrdia Manuel, Elvira; Tamarit Mur, José Luis (2014-01-01)
      Article
      Restricted access - publisher's policy
      It is hitherto thought that liquid water is composed of tetrahedrally coordinated molecules with an asymmetric interaction of the central molecule with neighboring molecules. Kuhne et al., Nat. Commun., 2013, 4, 1450 ...
    • Aqueous electrolytes confined within functionalized silica nanopores 

      Videla, Pablo; Sala Viñas, Jonàs; Martí Rabassa, Jordi; Guàrdia Manuel, Elvira; Laria, Daniel (2011-09-09)
      Article
      Open Access
      Molecular dynamics simulations have been carried out to investigate structural and dynamical characteristics of NaCl aqueous solutions confined within silica nanopores in contact with a “bulk-like” reservoir. Two types of ...
    • Aqueous halide potentials from force matching of Car-Parrinello data 

      Spangberg, Daniel; Guàrdia Manuel, Elvira; Masia, Marco (Elsevier, 2012-02-15)
      Article
      Restricted access - publisher's policy
      Recently many various research groups have devoted a huge effort to develop a realistic classical force field for ions in water. The parametrization techniques used could be gathered into two classes: (i) fit of the ...
    • Characterization of the methane–graphene hydrophobic interaction in aqueous solution from ab initio simulations 

      Calero Borrallo, Carles; Martí Rabassa, Jordi; Guàrdia Manuel, Elvira; Masia, Marco (2013-09-17)
      Article
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      In this article, the interaction between a methane molecule and a graphene plane in liquid water has been characterized employing DFT-based free energy Molecular Dynamics calculations. This system represents a good model ...
    • Competing structures within the first shell of liquid C2Cl6: a molecular dynamics study 

      Henao Aristizábal, Andrés; Pothoczki, Szilvia; Canales Gabriel, Manel; Guàrdia Manuel, Elvira; Pardo Soto, Luis Carlos (2014-02-28)
      Article
      Open Access
      We present a detailed study on the liquid structure of hexachloroethane (C2Cl6) within the first shell using the proper Euler-angles convention. Molecular dynamics is used and the van der Waals picture of a liquid is taken ...
    • Computer simulation of liquid methanol ii:system size effects 

      Casulleras Ambrós, Joaquín; Guàrdia Manuel, Elvira (1991-01)
      Article
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      A series of molecular dynamics simulations of liquid methanol has been carried out on a supernode transputer array. Four system sizes from 125 to 512 molecules have been considered, in order to study the effect of system ...
    • Dielectric properties of liquid ethanol: a computer simulation study 

      Saiz, L; Guàrdia Manuel, Elvira; Padro Cardenas, Joan Angel (2000-08)
      Article
      Open Access
      Static and dynamic dielectric properties of liquidethanol have been studied as a function of the wave-vector number by computer simulation.Molecular dynamics simulations at room temperature have been performed using the ...
    • Dynamical aspects of the Na+ - Cl- ion pair association in water 

      Rey Oriol, Rosendo; Guàrdia Manuel, Elvira (1992-05-01)
      Article
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      Molecular dynamics is applied to analyze the association-dissociation process that takes place between contact and solvent-separated ion pairs for aqueous sodium chloride. A flexible single point charge model for water has ...
    • Effect of the local hydrogen bonding network on the reorientational and translational dynamics in supercritical water 

      Skarmoutsos, Ioannis; Guàrdia Manuel, Elvira (2010-02)
      Article
      Open Access
      Molecular dynamics simulations have been performed in a wide range of densities along a near critical isotherm of supercritical water in order to reveal the interconnection between the local hydrogen bonding (HB) network ...
    • Effect of the water model in simulations of protein–protein recognition and association 

      Emperador Badimon, Agustín; Crehuet Simón, Ramon; Guàrdia Manuel, Elvira (Multidisciplinary Digital Publishing Institute (MDPI), 2021-01-06)
      Article
      Open Access
      We study self-association of ubiquitin and the disordered protein ACTR using the most commonly used water models. We find that dissociation events are found only with TIP4P-EW and TIP4P/2005, while the widely used TIP3P ...
    • Effects of concentration on structure, dielectric, and dynamic properties of aqueous NaCl solutions using a polarizable model 

      Sala Viñas, Jonàs; Guàrdia Manuel, Elvira; Martí Rabassa, Jordi (American Institute of Physics (AIP), 2010-06-03)
      Article
      Restricted access - publisher's policy
      The study of NaCl solutions in water at finite concentration, explicitly including polarization in water molecules and ions, has been carried out by molecular dynamics simulations. A comparison of the RPOL polarizable model ...
    • Excess protons in mesoscopic water-acetone nanoclusters 

      Semino, Rocío; Martí Rabassa, Jordi; Guàrdia Manuel, Elvira; Laria, Daniel (2012-11-19)
      Article
      Open Access
      We carried out molecular dynamics simulation experiments to examine equilibrium and dynamical characteristics of the solvation of excess protons in mesoscopic, [m:n] binary polar clusters comprising m = 50 water molecules ...
    • Exploring the picosecond time domain of the solvation dynamics of coumarin 153 within beta-cyclodextrins 

      RODRIGUEZ, J; Martí Rabassa, Jordi; Guàrdia Manuel, Elvira; Laria, D (2008-07)
      Article
      Restricted access - publisher's policy
      We report molecular dynamics simulation results of equilibrium and dynamical characteristics pertaining to the solvation of the dye coumarin 153 (C153) trapped within hydrophobic cavities of di- and trimethylated ß-cyclodextrins ...
    • Fitting properties from density functional theory based molecular dynamics simulations to parameterize a rigid water force field 

      Sala Viñas, Jonàs; Guàrdia Manuel, Elvira; Martí Rabassa, Jordi; Spangberg, Daniel; Masia, Marco (2012-02-02)
      Article
      Restricted access - publisher's policy
      In the quest towards coarse-grained potentials and new water models, we present an extension of the force matching technique to parameterize an all-atom force field for rigid water. The methodology presented here allows ...
    • Hydration structure and dynamics of the favipiravir antiviral drug: a molecular modelling approach 

      Skarmoutsos, Ioannis; Maurin, Guillaume; Guàrdia Manuel, Elvira; Samios, Jannis (2020-11-15)
      Article
      Open Access
      The hydration structure of the Favipiravir antiviral drug, at infinite dilution in water, was investigated by employing a systematic molecular modelling approach. An effective interaction potential model was employed for ...
    • Hydrogen bonding and related properties in liquid water: a Car-Parrinello molecular dynamics simulation study 

      Guàrdia Manuel, Elvira; Skarmoutsos, Ioannis; Masia, Marco (2015-07-23)
      Article
      Open Access
      The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. The radial distribution functions and coordination numbers around ...
    • Improving the force matching algorithm: Application to a simple point charge flexible model of water 

      Sala Viñas, Jonàs; Guàrdia Manuel, Elvira; Masia, Marco (2011-09)
      Article
      Restricted access - publisher's policy
      In the last years the force matching algorithm has appeared to be a promising method for deriving next generation classical force fields. Recently it has been successfully utilized to parameterize new water models based ...
    • Ionic association of Na+-Cl-, Na+-Na+ and Cl--Cl- in methanol: mean force potentials and friction kernels 

      Sesé Castel, Gemma; Guàrdia Manuel, Elvira; Padro Cardenas, Joan Angel (1995-08)
      Article
      Restricted access - publisher's policy
      Kinetic investigation of 1-octene bromination in AOT-isooctane-water microemulsions (13 = w = [H2O]/[AOT] = 24 and 6 = z = [IO]/[AOT] = 57) shows that the reaction is first-order in alkene and first-order in bromine, as ...