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At least 1,315 records · Page 73Linked to original sources
PubMed2005

Water mediated proton transfer in a mesostructured aluminosilicate framework: an ab initio molecular dynamics study.

The proton transfer process mediated by water molecules adsorbed in an aluminosilicate framework has been studied using ab initio molecular dynamics simulations. This investigation has been carried out using a quasi-one-dimensional model simulating the mesoporous aluminosilicate channel structures. The effects of both the water loading and temperature of the system have been considered. At low coverage (one water molecule per acid site), the hydroxonium ion (H(3)O)(+) is found to be a transition state, in agreement with earlier studies on zeolites. At a higher water coverage (two water molecules per acid site), the (H(5)O(2))(+) species and the hydrogen bonded "neutral complex" structure are both found to be stable complexes at finite temperatures. The vibrational frequency spectrum is simulated by performing a Fourier transform of the velocity autocorrelation function (VAF), and the peak positions in the VAF are compared with IR measurements and zero-temperature calculations.

Adsorption↗
PubMed2005

Prediction of supercritical ethane bulk solvent densities for pyrazine solvation shell average occupancy by 1, 2, 3, and 4 ethanes: combined experimental and ab initio approach.

We introduce a method that addresses the elusive local density at the solute in the highly compressible regime of a supercritical fluid. Experimentally, the red shift of the pyrazine n-pi electronic transition was measured at infinite dilution in supercritical ethane as a function of pressure from 0 to about 3000 psia at two temperatures, one close (35.0 degrees C) to the critical temperature and the other remote (55.0 degrees C). Computationally, stationary points were located on the potential surfaces for pyrazine and one, two, three, and four ethanes at the MP2/6-311++G(d,p) level. The vertical n-pi ((1)B(3u)) transition energies were computed for each of these geometries with a TDDFT/B3LYP/6-311++G(d,p) method. The combination of experiment and computation allows prediction of supercritical ethane bulk densities at which the pyrazine primary solvation shell contains an average of one, two, three, and four ethane molecules. These density predictions were achieved by graphical superposition of calculated shifts on the experimental shift versus density curves for 35.0 and 55.0 degrees C. Predicted densities are 0.0635, 0.0875, and 0.0915 g cm(-3) for average pyrazine primary solvation shell occupancy by one, two, and three ethanes at both 35.0 and 55.0 degrees C. Predicted densities are 0.129 and 0.150 g cm(-3) for occupancy by four ethanes at 35.0 and 55.0 degrees C, respectively. An alternative approach, designed to "average out" geometry specific shifts, is based on the relationship Deltanu = -23.9n cm(-1), where n = ethane number. Graphical treatment gives alternative predicted densities of 0.0490, 0.0844, and 0.120 g cm(-3) for average pyrazine primary solvation shell occupancy by one, two, and three ethanes at both 35.0 and 55.0 degrees C, and densities of 0.148 and 0.174 g cm(-3) for occupancy by four ethanes at 35.0 and 55.0 degrees C, respectively.

Computer Simulation↗
PubMed2006

Time dependent density functional theory modeling of chiroptical properties of small amino acids in solution.

Time dependent density functional theory (TDDFT) and the conductor-like screening model (COSMO) of solvation were used to model the specific rotation and optical rotatory dispersion (ORD) of alanine, proline and serine solutions. Zwitterionic, cationic and anionic forms of amino acids were investigated and the results compared with experimental literature data obtained in neutral, acidic and basic conditions, respectively. It was found that TDDFT consistently underestimated the electronic excitation energies of the molecules, leading to calculated optical rotations that are of the correct sign but somewhat larger in magnitude than those of experiment. An additional challenge was encountered in the modeling of serine, an amino acid with a strong tendency to form intramolecular hydrogen bonds. The model used overestimated the extent of such hydrogen bonding for the zwitterions while possibly underestimating such bonding for the cationic form. This effect on the calculated mole fractions of the different conformers had an impact on the specific rotation.

Alanine↗
PubMed2006

Conformational study of monomeric 2,3-butanediols by matrix-isolation infrared spectroscopy and DFT calculations.

The FT-IR spectra of two diastereomers of 2,3-butanediol, (R,S) and (S,S), isolated in low-temperature argon and xenon matrixes were studied, allowing the identification of two different conformers for each compound. These conformers were characterized by a +/-gauche arrangement around the O-C-C-O dihedral angle, thus enabling the establishment of a very weak intramolecular hydrogen bond of the O...H-O type. No other forms of these compounds were identified in matrixes, despite the fact that these four conformers had calculated relative energies from 0 to 5.1 kJ mol(-1) and were expected to be thermally populated from 50 to 6% in the gaseous phase of each compound. The nonobservation of additional conformers was explained in terms of low barriers to intramolecular rotation, resulting in the conformational relaxation of the compounds during deposition of the matrixes. The barriers to internal rotation of the OH groups were computed to be less than 4 kJ mol(-1) and are easily overcome in matrixes within the family of conformers with the same heavy atom backbone. The barriers for intramolecular rearrangement of the O-C-C-O dihedral angle in both diastereomers were calculated to range from 20 to 30 kJ mol(-1). Interconversions between the latter conformers were not observed in matrixes, even after annealing up to 65 K. Energy calculations, barriers, and calculated infrared spectra were carried out at the DFT(B3LYP)/6-311++G theory. Additional MP2/6-311++G calculations of energies and vibrational frequencies were performed on the most relevant conformers. Finally, independent estimations of the hydrogen-bond enthalpy in the studied molecules were also obtained based on theoretical structural data and from vibrational frequencies (using well-established empirical correlations). The obtained values for -DeltaH for both diastereomers of 2,3-butanediol amount to ca. 6-8 kJ mol(-1).

Butylene Glycols↗
PubMed2006

Protonolysis of the Hg-C bond of chloromethylmercury and dimethylmercury. A DFT and QTAIM study.

Possible mechanisms for degrading chloromethylmercury (CH(3)HgCl) and dimethylmercury [(CH3)2Hg] involving thiol and ammonium residues were investigated by DFT and atoms-in-molecules (QTAIM) calculations. Using H2S and HS- as models for thiol and thiolate groups RSH and RS-, respectively, we obtained transition states and energy barriers for possible decomposition routes to Hg(SH)2 based on a model proposed by Moore and Pitts (Moore, M. J.; Distefano, M. D.; Zydowsky, L. D.; Cummings, R. T.; Walsh, C. T. Acc. Chem. Res. 1990, 23, 301. Pitts, K. E.; Summers, A. O. Biochemistry 2002, 41, 10287). Demethylation was found to be a multistep process that involved initial substitution of Cl- by RS-. We found that successive coordination of Hg with thiolates leads to increased negative charge on the methyl group and facilitates the protonolysis of the Hg-C bond by H-SH. This was also found to be the case for (CH3)2Hg. We found that NH4(+) readily protonolyzes the Hg-C bond of these thiolate complexes, suggesting that ammonium residues of protonated amino acids might also act as effective proton donors.

Carbon↗
PubMed2006

Structures of dense glycine and alanine adlayers on chiral Cu(3,1,17) surfaces.

Density Functional Theory calculations have been used to predict the structures of dense glycine and alanine adlayers on Cu(3,1,17)(S). Facets of this chiral Cu surface result from adsorbate-induced surface reconstruction when glycine or alanine are adsorbed and annealed on Cu(100). We have calculated the surface energy changes associated with this surface reconstruction. Our results allow the enantiospecificity of this reconstruction following adsorption of enantiopure or racemic alanine on Cu(100) to be discussed. The overall stability of glycine and alanine adlayers on Cu(3,1,17)(S) arises from an interplay between the formation of chemical bonds with the Cu surface, deformations in the adsorbed molecules during adsorption, and intermolecular hydrogen bonds within the adlayer; none of these factors individually dominates.

Alanine↗
PubMed2006

General internal coordinate gradient vectors and the vibrational kinetic energy operator of centrally-connected penta-atomic systems. Part I.

New internal coordinate gradients, s-vectors, are derived using geometric algebra. The internal coordinates are based on a completely general description of the molecular geometry in terms of internal vectors. The internal coordinate gradients allow kinetic energy operators to be easily expressed in terms of orthogonal or non-orthogonal coordinate systems. Using this approach, a new exact vibrational kinetic energy operator for centrally-connected penta-atomic systems is derived for an internal polyspherical coordinate system based on orthogonal internal vectors. Difficulties associated with the well known coordinate redundancy in centrally-connected penta-atomic systems are discussed and overcome.

Computer Simulation↗
PubMed2005

The He-LiH potential energy surface revisited. II. Rovibrational energy transfer on a three-dimensional surface.

We use our rigid rotor He-LiH potential energy surface [B. K. Taylor and R. J. Hinde, J. Phys. Chem. 111, 973 (1999)] as a starting point to develop a three-dimensional potential surface that describes the interaction between He and a rotating and vibrating LiH molecule. We use a fully quantum treatment of the collision dynamics on the current potential surface to compute rovibrational state-to-state cross sections. We compute excitation and relaxation vibrational rate constants as a function of temperature by integrating these cross sections over a Maxwell-Boltzmann translational energy distribution and summing over Boltzmann-weighted initial rotational levels. The rate constants for vibrational excitation of LiH are very small for temperatures below 300 K. Rate constants for vibrational relaxation of excited LiH molecules, however, are several orders of magnitude larger and show very little temperature dependence, suggesting that the collisions that result in vibrational relaxation are governed by long-range attractive interactions.

Journal Article↗
PubMed2005

Fast localized orthonormal virtual orbitals which depend smoothly on nuclear coordinates.

We present here an algorithm for computing stable, well-defined localized orthonormal virtual orbitals which depend smoothly on nuclear coordinates. The algorithm is very fast, limited only by diagonalization of two matrices with dimension the size of the number of virtual orbitals. Furthermore, we require no more than quadratic (in the number of electrons) storage. The basic premise behind our algorithm is that one can decompose any given atomic-orbital (AO) vector space as a minimal basis space (which includes the occupied and valence virtual spaces) and a hard-virtual (HV) space (which includes everything else). The valence virtual space localizes easily with standard methods, while the hard-virtual space is constructed to be atom centered and automatically local. The orbitals presented here may be computed almost as quickly as projecting the AO basis onto the virtual space and are almost as local (according to orbital variance), while our orbitals are orthonormal (rather than redundant and nonorthogonal). We expect this algorithm to find use in local-correlation methods.

Algorithms↗
PubMed2006

Towards a spin-adapted coupled-cluster theory for high-spin open-shell states.

A spin-adapted coupled-cluster (SA-CC) scheme based on the additional consideration of spin constraints is proposed for the quantum chemical treatment of high-spin open-shell cases. Its computational feasibility is demonstrated via a pilot implementation within the singles and doubles approximation. Test calculations indicate that the suggested SA-CC scheme provides results of similar accuracy as the more traditional schemes without spin adaptation.

Journal Article↗
PubMed2006

A justification for a nonadiabatic surface hopping Herman-Kluk semiclassical initial value representation of the time evolution operator.

A justification is given for the validity of a nonadiabatic surface hopping Herman-Kluk (HK) semiclassical initial value representation (SC-IVR) method. The method is based on a propagator that combines the single surface HK SC-IVR method [J. Chem. Phys. 84, 326 (1986)] and Herman's nonadiabatic semiclassical surface hopping theory [J. Chem. Phys. 103, 8081 (1995)], which was originally developed using the primitive semiclassical Van Vleck propagator. We show that the nonadiabatic HK SC-IVR propagator satisfies the time-dependent Schrodinger equation to the first order of variant Planck's over 2pi and the error is O(variant Planck's over 2pi(2)). As a required lemma, we show that the stationary phase approximation, under current assumptions, has an error term variant Planck's over 2pi(1) order higher than the leading term. Our derivation suggests some changes to the previous development, and it is shown that the numerical accuracy in applications to Tully's three model systems in low energies is improved.

Algorithms↗
PubMed2007

Molecular properties from variational reduced-density-matrix theory with three-particle N-representability conditions.

Molecular ground-state energies and two-electron reduced density matrices (2-RDMs) have recently been computed without the many-electron wave function by constraining the 2-RDM to satisfy a complete set of three-positivity conditions for N representability [D. A. Mazziotti, Phys. Rev. A 74, 032501 (2006)]. Energies at both equilibrium and nonequilibrium geometries are obtained within 0.3% of the correlation energy. In this paper the authors extend this work to examine the accuracy of molecular properties, including multipole moments and components of the ground-state energy, relative to full configuration interaction (FCI). Comparisons are also made with 2-RDM methods with two-positivity conditions and two-positivity plus the generalized T1T2 conditions as well as several approximate wave function methods. Using the 2-RDM method with three-positivity conditions, the authors obtain dipole, quadrupole, and octupole moments for BeH2, BH, H2O, CO, and NH3 at equilibrium geometries that are within 0.04% of their FCI values. In addition, for the potential energy surface of N2, the 2-RDM method with three-positivity yields not only accurate total ground-state energies but also accurate expectation values of the kinetic energy operator, the electron-nuclei potential, and electron-electron repulsion.

Algorithms↗
PubMed2002

Lattice Boltzmann simulations of binary fluid flow through porous media.

The lattice Boltzmann equation is often advocated as a simulation tool that is particularly effective for complex fluids such as multiphase and multicomponent flows through porous media. We construct a three-dimensional 19 velocity lattice Boltzmann model for immiscible binary fluids with variable viscosities and density ratio based on the model proposed by Gunstensen. The model is tested for the following binary fluid flow problems: a stationary planar interface among two fluids; channel flow of immiscible binary fluids; the Laplace problem; and a rising bubble. The results agree well with semi-analytic results in a range of the Eötvös, Morton and Reynolds number. We also present preliminary simulation results for two large-scale realistic applications: the flow of an air-water mixture in a waste-water batch reactor and the saturation hysteresis effect in soil flow. We discuss some limitations of the lattice Boltzmann method in the simulation of realistic and difficult multiphase problems.

Biological Transport↗
PubMed2002

Numerical simulation and measurement of liquid hold-up in biporous media containing discrete stagnant zones.

We have studied hydrodynamic dispersion in single-phase incompressible liquid flow through a fixed bed made of spherical, permeable (porous) particles. The observed behaviour was contrasted with the corresponding fluid dynamics in a random packing of impermeable (non-porous) spheres with an interparticle void fraction of 0.37. Experimental data were obtained in the laminar flow regime by pulsed field gradient nuclear magnetic resonance and were complemented by numerical simulations employing a hierarchical transport model with a discrete (lattice Boltzmann) interparticle flow field. Finite-size effects in the simulation associated with the spatial discretization of support particles or dimension and boundaries of the bed were minimized and the simulation results are in reasonable agreement with experiment.

Biological Transport↗
PubMed2002

Lattice Boltzmann simulation of the flow of binary immiscible fluids with different viscosities using the Shan-Chen microscopic interaction model.

We present a lattice Boltzmann study of the flow of a binary fluid where the fluid components have different viscosities. For this purpose, a microscopic interaction model (due to Shan & Chen) is used. The model is validated for Poiseuille flow of layered immiscible binary fluids and the dispersion of a capillary wave. We then study the unstable displacement of a viscous fluid by a less viscous fluid in a two-dimensional channel. Although a finger-like structure was observed in many simulations, it is not clear if this structure was produced due to viscous fingering or due to other effects.

Colloids↗
PubMed2003

Self-organization from structural refrigeration.

The self-organization of a classical current is studied, in an exactly solvable model where both the quantum statistics over microhistories of particles, and the macroscopic phenomenology, can be computed in closed form. It is shown that for thermodynamically reversible systems, the Jaynes formulation of statistical mechanics naturally extends to include explicit macroscopic dynamics and heterogeneities in temperature, while preserving the structure of partition functions, effective potentials, and ground states of the equilibrium theory. Self-organization in such reversible systems is constrained by entropy transport through engine and refrigeration cycles, rather than by diffusion in gradients. Limitations in the ability to decompose such systems sensibly into components with additive entropies, and in the extrapolation of entropy functions from equilibrium forms, are discussed with examples.

Journal Article↗
PubMed2001

Transport theory for a two-flavor color superconductor.

QCD with two light-quark flavors at high baryonic density is a color superconductor. The diquark condensate breaks the SU(3) gauge symmetry down to an SU(2) subgroup. We study thermal fluctuations of the superconductor for temperatures below the gap. These are described by a simple transport equation. In the collisionless limit and close to equilibrium, it gives rise to the "hard superconducting loop" effective theory for the SU(2) gauge fields. This theory describes Debye screening and Landau damping of the gauge fields in the presence of the diquark condensate. We explain how our effective theory follows to one-loop order from quantum field theory. Our approach provides a convenient starting point for the computation of transport coefficients of the two-flavor color superconductor.

Journal Article↗
PubMed2006

Detecting topological order in a ground state wave function.

A large class of topological orders can be understood and classified using the string-net condensation picture. These topological orders can be characterized by a set of data (N, di, F(lmn)(ijk), delta(ijk). We describe a way to detect this kind of topological order using only the ground state wave function. The method involves computing a quantity called the "topological entropy" which directly measures the total quantum dimension D= Sum(id2i).

Journal Article↗