Descripción: Fil:Chernomoretz, A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.

Descripción: Solvation of excess electrons in supercritical ammonia along the T = 450 K isotherm was investigated. Equilibrium aspects of solvation were analyzed using combined path integral-molecular dynamics techniques. Observations showed transition from localized to quasifree states at approximately one fourth of the triple point density.

Descripción: Molecular dynamics simulations have been carried out to investigate the structure and dynamics of liquid methanol confined in 3.3 nm diameter cylindrical silica pores. Three cavities differing in the characteristics of the functional groups at their walls have been examined: (i) smooth hydrophobic pores in which dispersive forces prevail, (ii) hydrophilic cavities with surfaces covered by polar silanol groups, and (iii) a much more rugged pore in which 60% of the previous interfacial hydroxyl groups were replaced by the bulkier trimethylsilyl ones. Confinement promotes a considerable structure at the vicinity of the pore walls which is enhanced in the case of hydroxylated surfaces. Moreover, in the presence of the trimethylsilyl groups, the propagation of this interface-induced spatial ordering extends down to the central region of the pore. Concerning the dynamical modes, we observed an overall slowdown in both the translational and rotational motions. An analysis of these mobilities from a local perspective shows that the largest retardations operate at the vicinity of the interfaces. The gross features of the rotational dynamics were analyzed in terms of contributions arising from bulk and surface states. Compared to the bulk dynamical behavior, the characteristic timescales associated with the rotational motions show the most dramatic increments. A dynamical analysis of hydrogen bond formation and breaking processes is also included. © 2010 American Institute of Physics.

Descripción: Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such a continuum approach in a density functional theory framework using plane-wave basis sets and periodic boundary conditions. Our work stems from a recent model designed for Car-Parrinello simulations of quantum solutes in a dielectric medium [D. A. Scherlis, J. Chem. Phys. 124, 074103 (2006)], for which the permittivity of the solvent is defined as a function of the electronic density of the solute. This strategy turns out to be inadequate for systems extended in two dimensions: the dependence of the dielectric function on the electronic density introduces a new term in the Kohn-Sham potential, which becomes unphysically large at the interfacial region, seriously affecting the convergence of the self-consistent calculations. If the dielectric medium is properly redefined as a function of the atomic coordinates, a good convergence is obtained and the constant of motion is conserved during the molecular dynamics simulations. The Poisson problem is solved using a multigrid method, and in this way Car-Parrinello molecular dynamics simulations of solid-liquid interfaces can be performed at a very moderate computational cost. This scheme is employed to investigate the acid-base equilibrium at the TiO2 -water interface. The aqueous behavior of titania surfaces has stimulated a large amount of experimental research, but many open questions remain concerning the molecular mechanisms determining the chemistry of the interface. Here we make an attempt to answer some of them, putting to the test our continuum model. © 2009 American Institute of Physics.

Descripción: In this work we studied the effect of NaCl on the thermodynamic and dynamic properties of supercooled water, for salt concentrations between 0.19 and 1.33mol kg-1, using molecular dynamic simulations for TIP5PE water model and ion parameters specially designed to be used in combination with this potential. We studied the isobaric heat capacity (Cp) temperature dependence and observed a maximum in Cp, occurring at Tm, that moves to lower temperature values with increasing salt concentration. Many characteristic changes were observed at scaled temperature TTm ∼ 0.96, namely a minimum in the density of the system, a reduction of the slope of the number of hydrogen bonds vs. temperature, and a crossover from Vogel-Tamman-Fulcher to Arrhenius dynamics. Finally, at low temperatures we observed that water dynamics become heterogeneous with an apparently common relationship between the fraction of immobile molecules and T/Tm for all studied systems. © 2011 American Institute of Physics.

Descripción: Pineal hormone melatonin (N-acetyl-5-methoxytryptamine) is thought to modulate the calcium/calmodulin signaling pathway either by changing intracellular Ca2+ concentration via activation of its G-protein-coupled membrane receptors, or through a direct interaction with calmodulin (CaM). The present work studies the direct interaction of melatonin with intact calcium-saturated CaM both experimentally, by fluorescence and nuclear magnetic resonance spectroscopies, and theoretically, by molecular dynamics simulations. The analysis of the experimental data shows that the interaction is calcium-dependent. The affinity, as obtained from monitoring 15N and 1H chemical shift changes for a melatonin titration, is weak (in the millimolar range) and comparable for the N- and C-terminal domains. Partial replacement of diamagnetic Ca2+ by paramagnetic Tb3+ allowed the measurement of interdomain NMR pseudocontact shifts and residual dipolar couplings, indicating that each domain movement in the complex is not correlated with the other one. Molecular dynamics simulations allow us to follow the dynamics of melatonin in the binding pocket of CaM. Overall, this study provides an example of how a combination of experimental and theoretical approaches can shed light on a weakly interacting system of biological and pharmacological significance.

Descripción: A theoretical study of the relation between the relativistic formulation of the nuclear magnetic shielding and spin-rotation tensors is presented. To this end a theoretical expression of the relativistic spin-rotation tensor is formulated, considering a molecular Hamiltonian of relativistic electrons and non-relativistic nuclei. Molecular rotation effects are introduced considering the terms of the Born-Oppenheimer decomposition, which couple the electrons and nuclei dynamics. The loss of the simple relation linking both spectral parameters in the non-relativistic formulation is further analyzed carrying out a perturbative expansion of relativistic effects by means of the linear response within the elimination of the small component approach. It is concluded that relativistic effects on the spin-rotation tensor are less important than those of the nuclear magnetic shielding tensor. © 2012 American Institute of Physics.

Descripción: New insights into equilibrium and dynamical aspects of electron photodetachment reactions in small water clusters were given. It focuses on assessing the effects of thermal and polarization fluctuations provided by three cluster environments with different extents of spatial confinement, on the microscopic mechanisms that drive the reaction. These fluctuations, in turn, determine the characteristics of the electron localization and the subsequent detachment following photoexcitation of the probe.

Descripción: We use ring-polymer-molecular-dynamics (RPMD) techniques and the semi-empirical q-TIP4P/F water model to investigate the relationship between hydrogen bond connectivity and the characteristics of nuclear position fluctuations, including explicit incorporation of quantum effects, for the energetically low lying isomers of the prototype cluster [H2O] 8 at T = 50 K and at 150 K. Our results reveal that tunneling and zero-point energy effects lead to sensible increments in the magnitudes of the fluctuations of intra and intermolecular distances. The degree of proton spatial delocalization is found to map logically with the hydrogen-bond connectivity pattern of the cluster. Dangling hydrogen bonds exhibit the largest extent of spatial delocalization and participate in shorter intramolecular O-H bonds. Combined effects from quantum and polarization fluctuations on the resulting individual dipole moments are also examined. From the dynamical side, we analyze the characteristics of the infrared absorption spectrum. The incorporation of nuclear quantum fluctuations promotes red shifts and sensible broadening relative to the classical profile, bringing the simulation results in much more satisfactory agreement with direct experimental information in the mid and high frequency range of the stretching band. While RPMD predictions overestimate the peak position of the low frequency shoulder, the overall agreement with that reported using an accurate, parameterized, many-body potential is reasonable, and far superior to that one obtains by implementing a partially adiabatic centroid molecular dynamics approach. Quantum effects on the collective dynamics, as reported by instantaneous normal modes, are also discussed. © 2013 AIP Publishing LLC.

Descripción: The resolution of molecular electric dipole polarizabilities into atomic contributions was studied in the context of methyl and ethyl derivatives, CH3-X and CH3-CH2-X. The reliability of the partitioning schemes allowing for adhoc quantum chemical tools was also tested. Results depicted a good degree of the transferability from molecule to molecule as shown by the evaluation of gross atomic isotropic contributions for carbon, hydrogen, and heteroatoms.

Descripción: Diosgeninlactone (1), a natural product from Solanum vespertilio, was stereo-selectively synthesized in high yield from 3β-hydroxy-5-androstene.

Descripción: Dimethyl sulfoxide (DMSO) has been known to enhance cell membrane permeability of drugs or DNA. Molecular dynamics (MD) simulations with single-component lipid bilayers predicted the existence of three regimes of action of DMSO: membrane loosening, pore formation and bilayer collapse. We show here that these modes of action are also reproduced in the presence of cholesterol in the bilayer, and we provide a description at the atomic detail of the DMSO-mediated process of pore formation in cholesterol-containing lipid membranes. We also successfully explore the applicability of DMSO to promote plasma membrane permeability to water, calcium ions (Ca2+) and Yo-Pro-1 iodide (Yo-Pro-1) in living cell membranes. The experimental results on cells in culture can be easily explained according to the three expected regimes: in the presence of low doses of DMSO, the membrane of the cells exhibits undulations but no permeability increase can be detected, while at intermediate DMSO concentrations cells are permeabilized to water and calcium but not to larger molecules as Yo-Pro-1. These two behaviors can be associated to the MD-predicted consequences of the effects of the DMSO at low and intermediate DMSO concentrations. At larger DMSO concentrations, permeabilization is larger, as even Yo-Pro-1 can enter the cells as predicted by the DMSO-induced membrane-destructuring effects described in the MD simulations. © 2012 de Ménorval et al.

Descripción: An information theory description of finite systems explicitly evolving in time is presented. We impose a MaxEnt variational principle on the Shannon entropy at a given time while the constraints are set at a former time. The resulting density matrix contains explicit time odd components in the form of collective flows. As a specific application we consider the dynamics of the expansion in connection with heavy ion experiments. Lattice gas and classical molecular dynamics simulations are shown. © 2007 American Institute of Physics.

Descripción: Since the elucidation of the myoglobin (Mb) structure, a histidine residue on the E helix (His-E7) has been proposed to act as a gate with an open or closed conformation controlling access to the active site. Although it is believed that at low pH, the His-E7 gate is in its open conformation, the full relationship between the His-E7 protonation state, its conformation, and ligand migration in Mb is hotly debated. We used molecular dynamics simulations to first address the effect of His-E7 protonation on its conformation. We observed the expected shift from the closed to the open conformation upon protonation, but more importantly, noted a significant difference between the conformations of the two neutral histidine tautomers. We further computed free energy profiles for oxygen migration in each of the possible His-E7 states as well as in two instructive Mb mutants: Ala-E7 and Trp-E7. Our results show that even in the closed conformation, the His-E7 gate does not create a large barrier to oxygen migration and permits oxygen entry with only a small rotation of the imidazole side chain and movement of the E helix. We identify, instead, a hydrophobic site in the E7 channel that can accommodate an apolar diatomic ligand and enhances ligand uptake particularly in the open His-E7 conformation. This rate enhancement is diminished in the closed conformation. Taken together, our results provide a new conceptual framework for the histidine gate hypothesis. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.

Descripción: We have studied the hydration and diffusion of the hydroxyl radical O H0 in water using classical molecular dynamics. We report the atomic radial distribution functions, hydrogen-bond distributions, angular distribution functions, and lifetimes of the hydration structures. The most frequent hydration structure in the O H0 has one water molecule bound to the O H0 oxygen (57% of the time), and one water molecule bound to the O H0 hydrogen (88% of the time). In the hydrogen bonds between the O H0 and the water that surrounds it the O H0 acts mainly as proton donor. These hydrogen bonds take place in a low percentage, indicating little adaptability of the molecule to the structure of the solvent. All hydration structures of the O H0 have shorter lifetimes than those corresponding to the hydration structures of the water molecule. The value of the diffusion coefficient of the O H0 obtained from the simulation was 7.1× 10-9 m2 s-1, which is higher than those of the water and the O H-. © 2005 American Institute of Physics.

Descripción: A scheme for resolving average optical rotatory power of a molecule into atomic contributions, applied to hydrogen peroxide, is presented. The scheme is based on the acceleration gauge for the electric dipole, and the torque formalism. Calculations are carried out to test the reliability of the partition method. The force and torque gauges provide different numerical values for atomic contributions.

Descripción: This work describes simple decompositions of the energy of molecular systems according to schemes that partition the three-dimensional space. The components of those decompositions depend on one and two atomic domains thus providing a meaningful chemical information about the nature of different bondings among the atoms which compose the system. Our algorithms can be applied at any level of theory (correlated or uncorrelated wave functions). The results reported here, obtained at the Hartree-Fock level in selected molecules, show a good agreement with the chemical picture of molecules and require a low computational cost in comparison with other previously reported decompositions.

Descripción: This work studies the partitioning of the electron density into two contributions which are interpreted as the paired and the effectively unpaired electron densities. The topological features of each density field as well as of the total density are described localizing the corresponding critical points in simple selected molecules (local formalism). The results show that unpaired electron-density concentrations occur out of the topological bonding regions whereas the paired electron densities present accumulations inside those regions. A comparison of these results with those arising from population analysis techniques (nonlocal or integrated formalisms) is reported. © 2005 American Institute of Physics.

Descripción: This work describes a simple spatial decomposition of the first-order reduced density matrix corresponding to an N -electron system into first-order density matrices, each of them associated to an atomic domain defined in the theory of atoms in molecules. A study of the representability of the density matrices arisen from this decomposition is reported and analyzed. An appropriate treatment of the eigenvectors of the matrices defined over atomic domains or over unions of these domains allows one to describe satisfactorily molecular properties and chemical bondings within a determined molecule and among its fragments. Numerical determinations, performed in selected molecules, confirm the reliability of our proposal. © 2005 American Institute of Physics.