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    ABSTRACT: The formation of methane hydrates represents a problem for natural gas production, transportation, and processing, as it may clog up the pipelines, with potentially catastrophic consequences. Two types of inhibitors are used[1] to prevent the occlusion: thermodynamic, that shift the liquid-hydrate boundary on the phase diagram by altering the chemical potential, and kinetic, that are designed either to delay the nucleation or to maintain aceptable rheological properties with the crystals that may grow. The choice of an inhibitor for a specific situation, and eventually its chemical modification or design, requires a better understanding of the gathering of water molecules to encage individual gas molecules and of the accretion of the crystal. Whereas the shapes and the number of water molecules of the gas-containing cavities in the crystal structures of gas hydrates are well established, the same is not true for the ordering of water molecules around non-polar solutes in aqueous solution. Though the number of water molecules around the methane molecule has been determined to be 20 from a MAS-NMR study[2], an analysis of a large number of hydration shells obtained from numerical simulations[3], it was concluded that the probability of occurrence of a 512 cage around methane in aqueous solution is much less than 107. Because the results from numerical simulations depend on the force-field employed, in this work a similar analysis is presented, but using a novel four-site water model (TIP4Q) combined with three different models for CH4, one of them being a united-atom model. The all-atom models are used to estimate the rotational barrier of CH4 within the dodecahedral cage. Furthermore, the study is extended to analyze the interactions between two hydrated methane molecules as a function of their distance. ------------------------- [1] Carver, T. J., Drew, M. G. B., Rodger, P. M., J. Chem. Soc. Faraday Trans., 1995, 91(19), 3449. [2] Dec, S. F., Bowler, K. E., Stadterman, L. L., Koh, C. A., Sloan Jr., E. D., J. Amer. Chem. Soc., 2006, 128, 414-415 [3] Guo, G.-J., Zhang, Y.-G., Li, M., Wu, Ch.-H., J. Chem. Phys., 2008, 128, Art. No. 194504 Extended Abstract: File Not Uploaded
    12 AIChE Annual Meeting; 10/2012
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    ABSTRACT: AbstractA search for stable local minima CH4 ‐ (H2O)n closed methane clathrates was done at the ωB97X‐D/aug‐cc‐pVDZ level of the theory, for n up to 20, starting from various different configurations for each size. The reliability of the method was validated by comparison to the complete basis set limit (CBSL) values of the methane–water interactions, of the water–water interactions and of the binding energies of (H2O)20 clusters. A potential model fitted to reproduce the CBSL interaction energy of the optimal CH4 ‐ (H2O)n pair was also used in Monte Carlo optimizations. Confinement was found to occur already at n = 14. Optimizations with two empirical models for numerical simulations resulted in the same configurations. The addition of more water molecules, though, favored an increase of the size of the cage, instead of making an external hydrogen bond with the other water molecules in the cluster. An analysis was made at the ωB97X‐D/aug‐cc‐pVDZ level of the interactions of methane with the confining clusters. In all cases, the interaction energy was negative, and for the dodecahedral cavity, the confinement of methane resulted in a significant stabilization relative to the unperturbed empty (H2O)20 cluster and an external methane molecule. Another analysis was made of the energetic cost of rotating the methane within the dodecahedral cavity. The corresponding barrier was lower than K BT at ambient temperature. © 2012 Wiley Periodicals, Inc.
    International Journal of Quantum Chemistry 01/2012; 112(22). · 1.17 Impact Factor
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    ABSTRACT: A four-site rigid water model is presented, whose parameters are fitted to reproduce the experimental static dielectric constant at 298 K, the maximum density of liquid water and the equation of state at low pressures. The model has a positive charge on each of the three atomic nuclei and a negative charge located at the bisector of the HOH bending angle. This charge distribution allows increasing the molecular dipole moment relative to four-site models with only three charges and improves the liquid dielectric constant at different temperatures. Several other properties of the liquid and of ice Ih resulting from numerical simulations with the model are in good agreement with experimental values over a wide range of temperatures and pressures. Moreover, the model yields the minimum density of supercooled water at 190 K and the minimum thermal compressibility at 310 K, close to the experimental values. A discussion is presented on the structural changes of liquid water in the supercooled region where the derivative of density with respect to temperature is a maximum.
    Physical Chemistry Chemical Physics 09/2011; 13(44):19728-40. · 4.20 Impact Factor
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    ABSTRACT: Ab initio calculations were performed on gas-phase calcium and magnesium dications chelated with various anionic pyrophosphate species: H2P2O72-, HP2O73-, and P2O74-. The cleavage of the pyrophosphate into a metaphosphate and an orthophosphate complexed to either calcium or magnesium was also investigated. The studied isomerization reaction of the metal−pyrophosphate complexes can be written as [M·HNP2O7]N-2 → [PO3·M·HNPO4]N-2 where M = Mg, Ca, and N = 0, 1, 2. Geometries for the complexes were optimized with the self-consistent-field (SCF) level of theory, and the total energy for each system was subsequently calculated with the second-order Møller−Plesset perturbation (MP2) method using 6-31+G** basis functions for the H, O, and P atoms and valence double-ζ basis functions polarization augmented with a diffuse function (pVDZ+) for the Mg and Ca atoms. Zero-point energies (ZPE) and entropies were calculated with the SCF harmonic frequencies from which enthalpies and Gibbs free energies were also estimated. The ab initio isomerization energies of all of the calcium-containing complexes were positive and had a large contribution of correlation, while those of the magnesium-containing complexes were negative and had a significantly lower contribution of correlation. These calculated gas-phase isomerization energies may provide an explanation to the observation that pyrophosphatases utilize magnesium complexes as substrates for the hydrolysis of pyrophosphates but do not utilize calcium complexes.
    ChemInform 09/2010; 29(36).
  • Biophysical Journal 01/2010; 98(3). · 3.67 Impact Factor
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    ABSTRACT: An infinitely diluted aqueous solution of Rb+ was studied using ab initio-based model potentials in classical Monte Carlo simulations to describe its structural and thermodynamic features. An existing flexible and polarizable model [Saint-Martin et al. in J Chem Phys 113(24) 10899, 2000] was used for water–water interactions, and the parameters of the Rb+–water potential were fitted to reproduce the polarizability of the cation and a sample of ab initio pair interaction energies. It was necessary to calibrate the basis set to be employed as a reference, which resulted in a new determination of the complete basis set (CBS) limit energy of the optimal Rb+–OH2 configuration. Good agreement was found for the values produced by the model with ab initio calculations of three- and four-body nonadditive contributions to the energy, as well as with ab initio and experimental data for the energies, the enthalpies and the geometric parameters of Rb+(H2O) n clusters, with n=1, 2,…,8. Thus validated, the potential was used for simulations of the aqueous solution with three versions of the MCDHO water model; this allowed to assess the relative importance of including flexibility and polarizability in the molecular model. In agreement with experimental data, the Rb+–O radial distribution function (RDF) showed three maxima, and hence three hydration shells. The average coordination number was found to be 6.9, with a broad distribution from 4 to 12. The dipole moment of the water molecules in the first hydration shell was tilted to 55° with respect to the ion’s electric field and had a lower value than the average in bulk water; this latter value was recovered at the second shell. The use of the nonpolarizable version of the MCDHO water model resulted in an enhanced alignment to the ion’s electric field, not only in the first, but also in the second hydration shell. The hydration enthalpy was determined from the numerical simulation, taking into account corrections to the interfacial potential and to the spurious effects due to the periodicity imposed by the Ewald sums; the resulting value lied within the range of the various different experimental data. An analysis of the interaction energies between the ion and the water molecules in the different hydration shells and the bulk showed the same partition of the hydration enthalpy as for K+. The reason for this similarity is that at distances longer than 3Å, the ion–water interaction is dominated by the charge-(enhanced) dipole term. Thus, it was concluded that starting at K+, the hydration properties of the heavier alkali metal cations should be very similar. KeywordsRubidium ion hydration-Polarizable force fields-Monte Carlo simulation
    Theoretical Chemistry Accounts 01/2010; 126(3):197-211. · 2.14 Impact Factor
  • Alessandra Villa, Berk Hess, Humberto Saint-Martin
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    ABSTRACT: Aqueous solutions of a light (Nd3+), a middle (Gd3+), and a heavy (Yb3+) lanthanide ion were studied using ab initio based flexible and polarizable analytical potentials in classical molecular dynamics simulations to describe their thermodynamic, structural, and dynamic features. To avoid the spurious demise of O-H bonds, it was necessary to reparametrize an existing water model, which resulted in an improved description of pure water. The good agreement of the results from the simulations with the experimental hydration enthalpies, the Ln(III)-water radial distribution functions, and the water-exchange rates validated the potentials, though the r(Ln-Ow) distances were 6% longer than the experimentally determined values. A nona-coordinated state was found for Nd3+ in 95% of the simulation, with a tricapped trigonal prism (TCTP) geometry; the corresponding water-exchange mechanism was found to be of dissociative interchange (Id) character through a short-lived octa-coordinated transition state in a square antiprism (SQA) geometry. An octa-coordinated state in SQA geometry was found for Yb3+ in 99% of the simulation, and the observed exchange events exhibited characteristics of an interchange (I) mechanism. For Gd3+ an equilibrium was observed between 8-fold SQA and 9-fold TCTP coordinated states that was maintained by the frequent exchange of a water molecule from the first hydration shell with the bulk, thus producing significant deviations from the ideal geometries, and a fast exchange rate. Though strong water-water interactions prevented a full alignment of the dipoles to the ion's electric field, the screening was found large enough as to limit its range to 5 A; water molecules further apart from the ion were found to have the same dipole as the molecules in the bulk, and a random orientation. The interplay among the water-ion and the water-water interactions determined the different coordination numbers and the different dynamics of the water exchange in the first hydration shell for each ion.
    The Journal of Physical Chemistry B 05/2009; 113(20):7270-81. · 3.61 Impact Factor
  • Rogelio Antonio Hernández-López, Humberto Saint-Martin Posada, Ivan Ortega-Blake
    Biophysical Journal 01/2009; 96(3). · 3.67 Impact Factor
  • Humberto Saint‐Martin
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    ABSTRACT: Since the resolution of the structure of the KcsA potassium channel was published [Science 280: 69–77, 1998], there have been numerous experimental and theoretical studies looking for an explanation of the highly refined selectivity to ions of biological channels. Most numerical simulations have dealt with a complex representation of the system, but with a simple modelling of the interactions. Our group has undertaken the opposite approach, simulating simple systems with complex interactions, consisting of ionic solutions inside structureless cylinders. This approach requires proper validation by comparison to experimental data of simple systems, which can be obtained from water‐filled single‐wall nanotubes (SWNT). The design of analytical models for simulating nanosolutions is discussed in this work; the reliability of the models is tested by comparison to data from experiments on SWNT. The implications for the molecular mechanism of ion selectivity obtained from simulations with these models can then be assessed on a more quantitative manner.
    AIP Conference Proceedings. 03/2008; 979(1):156-165.
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    ABSTRACT: Monte Carlo simulations of liquid methanol were performed using a refined ab initio derived potential which includes polarizability, nonadditivity, and intramolecular relaxation. The results present good agreement between the energetic and structural properties predicted by the model and those predicted by ab initio calculations of methanol clusters and experimental values of gas and condensed phases. The molecular level picture of methanol shows the existence of both rings and linear polymers in the methanol liquid phase.
    The Journal of Chemical Physics 12/2007; 127(22):224507-224507-14. · 3.12 Impact Factor
  • Maksym Volobuyev, Humberto Saint-Martin, Ludwik Adamowicz
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    ABSTRACT: A computational model, which includes both tunneling and thermal hopping mechanisms, has been applied to study the charge transfer in DNA (GC)n and (AT)n strands. The calculations revealed the crucial role played by the A or G NH2-group vibrations in the hole transfer in both types of strands. Charge-transfer rates in the two strands have been determined based on the molecular dynamics calculations. They are in good agreement with the available experimental data. The modeling approach used here may be employed in the theoretical study of the charge transfer in natural and artificial DNA strands containing AT and GC pairs.
    The Journal of Physical Chemistry B 10/2007; 111(37):11083-9. · 3.61 Impact Factor
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    ABSTRACT: Using a simple model, it is shown that the cost of constraining a hydrated potassium ion inside a narrow pore is smaller than the cost of constraining hydrated sodium or lithium ions in pores of radius around 1.5 A. The opposite is true for pores of radius around 2.5 A. The reason for the selectivity in the first region is that the potassium ion allows for a greater distortion of its hydration shell and can therefore maintain a better coordination, and the reason for the reverse selectivity in the second region is that the smaller ions retain their hydration shells in these pores. This is relevant to the molecular basis of ion selective channels, and since this mechanism does not depend on the molecular details of the pore, it could also operate in all sorts of nanotubes.
    Biophysical Chemistry 01/2007; 124(3):243-50. · 2.28 Impact Factor
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    ABSTRACT: Four water models that have the same analytical potential but different degrees of freedom were used to examine the hydration of Li+: (a) a polarizable and flexible molecule with constraints that account for the quantal nature of the vibration, (b) a polarizable and classically flexible molecule, (c) a polarizable and rigid molecule, and finally (d) a nonpolarizable and rigid molecule. The goal was to determine how individual molecular properties affect the correct description of the hydration of ions by comparing the structural and thermodynamic predictions for the aqueous solution as made by the different models, which ranged from a very refined one to a simple effective potential. The length of the Monte Carlo runs was large enough to ensure convergence and provide statistically meaningful results; the four models attained good agreement with the experimental data available for the hydration of Li+, as well as with the results of the most refined simulations. A well-defined first hydration shell was found. It had four water molecules whose dipoles were not aligned to the electric field of the ion because of their hydrogen-bonding with water molecules in outer shells. In the case of the most refined water model, the results showed this pattern clearly. On the other hand, the rigid nonpolarizable version produced a slightly higher hydration number and an almost complete alignment of the dipoles to the ion’s electric field. Moreover, a detailed analysis of a microscopic molecular model of hydration showed that the average intramolecular geometry of the water molecules in the first hydration shell was the same as the one for those in the bulk, whereas the electric field of the ion induced a dipole 0.2 D higher in the water molecules of the first hydration shell. The value of the bulk was recovered at the second shell, which explains the good performance of the simplest model. Thus, despite the differences found in the description of the first hydration shell between the polarizable and the nonpolarizable models, the major effect on the polarization of the water molecules resulted from the water-water interaction.
    Theoretical Chemistry Accounts 02/2006; 115(2):177-189. · 2.14 Impact Factor
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    ABSTRACT: Coexistence properties for water near the critical point using several ab initio models were calculated using grand canonical Monte Carlo simulations with multiple histogram reweighting techniques. These models, that have proved to yield a good reproduction of the water properties at ambient conditions, perform rather well, improving the performance of a previous ab initio model. It is also shown that bulk geometry and dipole values, predicted by the simulation, can be used and a good approximation obtained with a polarizable rigid water model but not when polarization is excluded.
    The Journal of Chemical Physics 08/2005; 123(4):044506. · 3.12 Impact Factor
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    Humberto Saint-Martin, Jorge Hernández-Cobos, Iván Ortega-Blake
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    ABSTRACT: Up to now it has not been possible to neatly assess whether a deficient performance of a model is due to poor parametrization of the force field or the lack of inclusion of enough molecular properties. This work compares several molecular models in the framework of the same force field, which was designed to include many-body nonadditive effects: (a) a polarizable and flexible molecule with constraints that account for the quantal nature of the vibration [B. Hess, H. Saint-Martin, and H. J. C. Berendsen, J. Chem. Phys. 116, 9602 (2002), H. Saint-Martin, B. Hess, and H. J. C. Berendsen, J. Chem. Phys. 120, 11133 (2004)], (b) a polarizable and classically flexible molecule [H. Saint-Martin, J. Hernandez-Cobos, M. I. Bernal-Uruchurtu, I. Ortega-Blake, and H. J. C. Berendsen, J. Chem. Phys. 113, 10899 (2000)], (c) a polarizable and rigid molecule, and finally (d) a nonpolarizable and rigid molecule. The goal is to determine how significant the different molecular properties are. The results indicate that all factors--nonadditivity, polarizability, and intramolecular flexibility--are important. Still, approximations can be made in order to diminish the computational cost of the simulations with a small decrease in the accuracy of the predictions, provided that those approximations are counterbalanced by the proper inclusion of an effective molecular property, that is, an average molecular geometry or an average dipole. Hence instead of building an effective force field by parametrizing it in order to reproduce the properties of a specific phase, a building approach is proposed that is based on adequately restricting the molecular flexibility and/or polarizability of a model potential fitted to unimolecular properties, pair interactions, and many-body nonadditive contributions. In this manner, the same parental model can be used to simulate the same substance under a wide range of thermodynamic conditions. An additional advantage of this approach is that, as the force field improves by the quality of the molecular calculations, all levels of modeling can be improved.
    The Journal of Chemical Physics 07/2005; 122(22):224509. · 3.12 Impact Factor
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    ABSTRACT: Using a simple model it is shown that the cost of constraining a hydrated potassium ion inside a narrow nanopore is smaller than the cost of constraining the smaller hydrated sodium ion. The former allows for a greater distortion of its hydration shell and can therefore maintain a better coordination. We propose that in this way the larger ion can go through narrow pores more easily. This is relevant to the molecular basis of ion selective nanopores and since this mechanism does not depend on the molecular details of the pore, it could also operate in all sorts of nanotubes, from biological to synthetic.
    Physical Review Letters 11/2004; 93(16):168104. · 7.73 Impact Factor
  • Humberto Saint-Martin, Berk Hess, Herman J C Berendsen
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    ABSTRACT: The method of flexible constraints was implemented in a Monte Carlo code to perform numerical simulations of liquid water and ice Ih in the constant number of molecules, volume, and temperature and constant pressure, instead of volume ensembles, using the polarizable and flexible mobile charge densities in harmonic oscillators (MCDHO) model. The structural and energetic results for the liquid at T=298 K and rho=997 kg m(-3) were in good agreement with those obtained from molecular dynamics. The density obtained at P=1 atm with flexible constraints, rho=1008 kg m(-3), was slightly lower than with the classical sampling of the intramolecular vibrations, rho=1010 kg m(-3). The comparison of the structures and energies found for water hexamers and for ice Ih with six standard empirical models to those obtained with MCDHO, show this latter to perform better in describing water far from ambient conditions: the MCDHO minimum lattice energy, density, and lattice constants were in good agreement with experiment. The average angle HOH of the water molecule in ice was predicted to be slightly larger than in the liquid, yet 1.2% smaller than the experimental value.
    The Journal of Chemical Physics 07/2004; 120(23):11133-43. · 3.12 Impact Factor
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    ABSTRACT: The hydrations of Na+ and K+ were investigated by means of Monte Carlo simulations with refined ab initio based potentials. These interaction potentials include intramolecular relaxation, polarizability and many-body nonadditive effects. Care was taken to ensure proper convergence of the MC runs and that the statistical samples were large enough. As a result, agreement was attained with all experimental data available for the hydration of the ions. The water molecules in the first hydration shell were found to have the same intramolecular geometries and dipole moments as those of the bulk. Furthermore, their dipoles were not aligned to the electric field produced by the ion, but quite tilted. The hydration number for the sodium was found to be 5 or 6 water molecules, whereas the potassium’s hydration number had a probability distribution ranging from 5 to 10. From an analysis of the energetic contributions of each hydration shell to the total enthalpy of hydration we propose that the hydrated ions have a distinct behavior. Sodium has a stronger interaction with its first hydration shell than potassium, giving the latter a more flexible structure.© 2003 American Institute of Physics.
    The Journal of Chemical Physics 04/2003; 118(15):7062-7073. · 3.12 Impact Factor
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    ABSTRACT: This work presents the development of first-principles bromide ion–water interaction potentials using the mobile charge density in harmonic oscillators-type model. This model allows for a flexible and polarizable character of the interacting molecules and has already been parametrized for water–water interactions. The prospected potential energy surfaces of the bromide ion-water system were computed quantum-mechanically at Hartree–Fock and Møller–Plesset second-order perturbation levels. In addition to the ion–solvent molecule pair, structures formed by the anion and two or three water molecules were considered in order to include many body effects. Minimizations of hydrated bromide clusters in gas phase [Br(H2O)n]− (n = 1–6,10,15,20) and Monte Carlo computations of bromide aqueous solutions were performed to test the new potentials. Both structural and thermodynamic properties have been studied in detail and compared to the available experimental and theoretical values. From these comparisons, it was concluded the importance of including basis set superposition error corrections for the two-body interactions, and the small role of both electron correlation on the three-body terms and the four-body terms. Monte Carlo simulation results have also been used to investigate if the presence of the anion significantly affects the intramolecular geometry of the water molecules and the degree of disruption of the water solvent structure in its vicinity.© 2002 American Institute of Physics.
    The Journal of Chemical Physics 12/2002; 117(23):10512-10524. · 3.12 Impact Factor
  • Berk Hess, Humberto Saint-Martin, Herman J. C. Berendsen
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    ABSTRACT: In classical molecular simulations chemical bonds and bond angles have been modeled either as rigid constraints, or as nearly harmonic oscillators. However, neither model is a good description of a chemical bond, which is a quantum oscillator that in most cases occupies the ground state only. A quantum oscillator in the ground state can be represented more faithfully by a flexible constraint. This means that the constraint length adapts itself, in time, to the environment, such that the rotational and potential forces on the constraint cancel out. An accurate algorithm for flexible constraints is presented in this work and applied to study liquid water with the flexible and the polarizable “mobile charge densities in harmonic oscillators” model. The iterations for the flexible constraints are done simultaneously with those for the electronic polarization, resulting in negligible additional computational costs. A comparison with fully flexible and rigidly constrained simulations shows little effect on structure and energetics of the liquid, while the dynamics is somewhat faster with flexible constraints. © 2002 American Institute of Physics.
    The Journal of Chemical Physics 06/2002; 116(22):9602-9610. · 3.12 Impact Factor

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