A self-consistent reaction field model of solvation using distributed multipoles. I. Energy and energy derivatives

The self-consistent reaction field model developed previously by the authors in the case of single center multipole expansion of the electronic structure of the solute has been extended to the case of a distributed multipole expansion. Three different expansions have been tested and two of them have proved to be rapidly convergent. The performances of the code are illustrated by the density functional theory treatment of few test systems: guanine, cytosine, and cytosine hydrated with one and three water molecules. A robust fast computer code has been tested to get the electronic structure, the electrostatic contribution to the solute-solvent free energy of interaction, and the optimized molecular geometry in solution.     

Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field

The hydration free energy, structure, and dynamics of the zinc divalent cation are studied using a polarizable force field in molecular dynamics simulations. Parameters for the Zn(2+) are derived from gas-phase ab initio calculation of Zn(2+)-water dimer. The Thole-based dipole polarization is adjusted based on the Constrained Space Orbital Variations (CSOV) calculation while the Symmetry Adapted Perturbation Theory (SAPT) approach is also discussed. The vdW parameters of Zn(2+) have been obtained by comparing the AMOEBA Zn(2+)-water dimerization energy with results from several theory levels and basis sets over a range of distances. Molecular dynamics simulations of Zn(2+) solvation in bulk water are subsequently performed with the polarizable force field. The calculated first-shell water coordination number, water residence time and free energy of hydration are consistent with experimental and previous theoretical values. The study is supplemented with extensive Reduced Variational Space (RVS) and Electron Localization Function (ELF) computations in order to unravel the nature of the bonding in Zn(2+)(H(2)O)(n) (n=1,6) complexes and to analyze the charge transfer contribution to the complexes. Results show that the importance of charge transfer decreases as the size of Zn-water cluster grows due to anticooperativity and to changes in the nature of the metal-ligand bonds. Induction could be dominated by polarization when the system approaches condensed-phase and the covelant effects are eliminated from the Zn(II)-water interaction. To construct an "effective" classical polarizable potential for Zn(2+) in bulk water, one should therefore avoid over-fitting to the ab initio charge transfer energy of Zn(2+)-water dimer. Indeed, in order to avoid overestimation of condensed-phase many-body effects, which is crucial to the transferability of polarizable molecular dynamics, charge transfer should not be included within the classical polarization contribution and should preferably be either incorporated in to the pairwise van der Waals contribution or treated explicitly.     

Accuracy of distributed multipoles and polarizabilities: comparison between the LoProp and MpProp models

Localized multipole moments up to the fifth moment as well as localized dipole polarizabilities are calculated with the MpProp and the newly developed LoProp methods for a total of 20 molecules, predominantly derived from amino acids. A comparison of electrostatic potentials calculated from the multipole expansion obtained by the two methods with ab initio results shows that both methods reproduce the electrostatic interaction with an elementary charge with a mean absolute error of approximately 1.5 kJ/mol at contact distance and less than 0.1 kJ/mol at distances 2 A further out when terms up to the octupole moments are included. The polarizabilities are tested with homogenous electric fields and are found to have similar accuracy. The MpProp method gives better multipole moments unless diffuse basis sets are used, whereas LoProp gives better polarizabilities.     

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

A re-parameterization of the standard TIP4P water model for use with Ewald techniques is introduced, providing an overall global improvement in water properties relative to several popular nonpolarizable and polarizable water potentials. Using high precision simulations, and careful application of standard analytical corrections, we show that the new TIP4P-Ew potential has a density maximum at approximately 1 degrees C, and reproduces experimental bulk-densities and the enthalpy of vaporization, DeltaH(vap), from -37.5 to 127 degrees C at 1 atm with an absolute average error of less than 1%. Structural properties are in very good agreement with x-ray scattering intensities at temperatures between 0 and 77 degrees C and dynamical properties such as self-diffusion coefficient are in excellent agreement with experiment. The parameterization approach used can be easily generalized to rehabilitate any water force field using available experimental data over a range of thermodynamic points.     

Microencapsulation using an oil-in-water-in-air 'dry water emulsion'

We describe the first example of a tri-phasic oil-in-water-in-air 'dry water emulsion'. The method combines highly stable oil-in-water emulsions prepared using branched copolymer surfactants, with aqueous droplet encapsulation using 'dry water' technology.     

Computer simulation study of water using a fluctuating charge model

Hydrogen bonding in small water clusters is studied through computer simulation methods using a sophisticated, empirical model of interaction developed by Ricket al (S W Rick, S J Stuart and B J Berne 1994J. Chem. Phys. 101 6141) and others. The model allows for the charges on the interacting sites to fluctuate as a function of time, depending on their local environment. The charge flow is driven by the difference in the electronegativity of the atoms within the water molecule, thus effectively mimicking the effects of polarization of the charge density. The potential model is thus transferable across all phases of water. Using this model, we have obtained the minimum energy structures of water clusters up to a size often. The cluster structures agree well with experimental data. In addition, we are able to distinctly identify the hydrogens that form hydrogen bonds based on their charges alone, a feature that is not possible in simulations using fixed charge models. We have also studied the structure of liquid water at ambient conditions using this fluctuating charge model.     

Thermogravimetric and kinetic analysis of energy crop Jerusalem artichoke using the distributed activation energy model

Jerusalem artichoke has great potential as future feedstock for bioenergy production because of its high tuber yield (up to 90 t ha^?1), appropriate biomass characteristics, low input demand, and positive environmental impact. The pyrolytic and kinetic characteristics of Jerusalem artichoke tubers were analyzed at heating rates of 5, 10, 20 and 30 °C min^?1. TG and DTG curves in an inert (nitrogen) atmosphere suggested that there were three distinct stages of mass loss and the major loss occurs between about 190–380 °C. Heating rate brought a lateral shift toward right in the temperature. And, it not only affects the temperature at which the highest mass loss rate reached, but also affect the maximum rate of mass loss. The distributed activation energy model (DAEM) was used to study the pyrolysis kinetics and provided reasonable fits to the experimental data. The activation energy (E) of tubers ranged from 146.40 to 232.45 kJ mol^?1, and the frequency factor (A) changed greatly corresponding to E values at different mass conversion.     

Development of an efficient geometry optimization method for water clusters

A geometry optimization method for water clusters (H(2)O)(n) was developed in the present study. The method was applied to the TIP3P and TIP4P water clusters in the range of n < or = 30, and the resulting structures were compared with the global-minimum structures in the literature (n < or = 25 for the TIP3P potential and n < or = 30 for the TIP4P potential). The method failed to reproduce the previously reported global minimum of the n = 24 TIP4P cluster. However, it was possible to find new global minima for the n = 24, 26-30 TIP3P cluster and the TIP4P clusters of 25, 28, 29, and 30 molecules.     

Extractability of dioxins from suspended substances in distributed water

The extractability of dioxins from suspended substances (SS) in distributed water was evaluated. Dioxins adsorbed on the collected SS were extracted by pressurized liquid extraction with various solvents. High-polarity solvents (acetone, alcohols) extracted considerably higher amounts of some lower-chlorinated dibenzo-p-dioxins (LoCDDs) than did low-polarity solvents (dichloromethane, toluene), whereas the extracted amounts of higher-chlorinated dibenzo-p-dioxins (HiCDDs) were roughly the same, regardless of the solvent. The extractability of the LoCDDs depended on the isomer. Daily variations in quantities for PCDDs, organic matter (OM), and iron in the SS were examined, and the results suggested that in the SS, LoCDDs and HiCDDs were associated, respectively, with raw water-derived organic matter and microparticles sequestered in iron oxy(hydr)oxide floc. It was also suggested that the low extractability of certain congeners was not attributable to the enormously coexisting ferric compounds but was probably attributable to OM with which they strongly associate.     

A polarizable,charge transfer model of water using the drude oscillator

The transfer of small amounts of charge between neighboring particles can be a significant part of interactions among particles. A model is developed for treating charge transfer (CT) combined with the Drude model for polarizability to create an efficient model for liquid water which includes both CT and polarizability. The model is shown to be accurate for a variety of liquid properties, including the density as a function of temperature and the dielectric constant. A new model for water with CT and polarization is developed and applied to the liquid. The inclusion of CT increases the accuracy of many properties, like the density as a function of temperature, indicating the importance of charge redistribution as induced by other particles. © 2016 Wiley Periodicals, Inc.     

Interactions between particles with an undulated contact line at a fluid interface: capillary multipoles of arbitrary order

A colloidal particle adsorbed at a fluid interface could have an undulated, or irregular contact line in the presence of surface roughness and/or chemical inhomogeneity. The contact-line undulations produce distortions in the surrounding liquid interface, whose overlap engenders capillary interaction between the particles. The convex and concave local deviations of the meniscus shape from planarity can be formally treated as positive and negative "capillary charges," which form "capillary multipoles." Here, we derive theoretical expressions for the interaction between two capillary multipoles of arbitrary order. Depending on the angle of mutual orientation, the interaction energy could exhibit a minimum, or it could represent a monotonic attraction. For undulation amplitudes larger than 5 nm, the interaction energy is typically much greater than the thermal energy kT. As a consequence, a monolayer from capillary multipoles exhibits considerable shear elasticity, and such monolayer is expected to behave as a two-dimensional elastic solid. These theoretical results could be helpful for the understanding of phenomena related to aggregation and ordering of particles adsorbed at a fluid interface, and for the interpretation of rheological properties of particulate monolayers. Related research fields are the particle-stabilized (Pickering) emulsions and the two-dimensional self-assembly of microscopic particles.     

Kinetic analyses of biomass tar pyrolysis using the distributed activation energy model by TG/DTA technique

Volatile compounds of iridium(I): (acetylacetonato)(1,5-cyclooctadiene)iridium(I) Ir(acac)(cod), (methylcyclopentadienyl) (1,5-cyclooctadiene)iridium(I) Ir(Cp’)(cod), (pentamethylcyclopentadienyl)(dicarbonyl) iridium(I) Ir(Cp*)(CO)₂ and (acetylacetonato)(dicarbonyl)iridium(I) Ir(acac)(CO)₂ were synthesized and identified by means of element analysis, NMR-spectroscopy, mass spectrometry. Thermal properties in solid phase for synthesized iridium(I) complexes were studied by means of thermogravimetric analysis in inert atmosphere (He). By effusion Knudsen method with mass spectrometric registration of gas phase composition the temperature dependencies of saturated vapor pressure were measured for iridium(I) compounds and the thermodynamic characteristics of vaporization processes enthalpy ΔH _T* and entropy ΔS _T⁰ were determined. The energy of intermolecular interaction in the crystals of complexes was calculated.     

Photocatalytic hydroxylation of aromatic ring by using water as an oxidant

Electrophilic oxygen species photocatalytically derived from water molecules can selectively react with the aromatic ring of both benzene and its derivatives to produce the corresponding phenols and hydrogen over platinum-loaded titanium oxide when illuminated with light of appropriate wavelength in the absence of oxygen.     

Estimation of the degree of self-association of water using a novel retention model

Summary An attempt has been made to gain a semi-quantitative insight into the self-association of water molecules through hydrogen bonds. This was only possible with the use of a new solute retention model for the chromatographic systems by considering intermolecular interactions between the constituents of binary mobile phases. Four different sizes of the average associative aqueous multimer were assumed. By comparing measured and calculated retention values, the existence of associated aqueous multimers consisting of 100 aqueous monomer units is postulated as an average multimer structure.     

Development of parallel density functional program using distributed matrix to calculate all-electron canonical wavefunction of large molecules

We developed a new parallel density-functional canonical molecular-orbital program for large molecules based on the resolution of the identity method. In this study, all huge matrices were decomposed and saved to the distributed local memory. The routines of the analytical molecular integrals and numerical integrals of the exchange-correlation terms were parallelized using the single program multiple data method. A conventional linear algebra matrix library, ScaLAPACK, was used for matrix operations, such as diagonalization, multiplication, and inversion. Anderson's mixing method was adopted to accelerate the self-consistent field (SCF) convergence. Using this program, we calculated the canonical wavefunctions of a 306-residue protein, insulin hexamer (26,790 orbitals), and a 133-residue protein, interleukin (11,909 orbitals) by the direct-SCF method. In regard to insulin hexamer, the total parallelization efficiency of the first SCF iteration was estimated to be 82% using 64 Itanium 2 processors connected at 3.2 GB/s (SGI Altix3700), and the calculation successfully converged at the 17-th SCF iteration. By adopting the update method, the computational time of the first and the final SCF loops was 229 min and 156 min, respectively. The whole computational time including the calculation before the SCF loop was 2 days and 17 h. This study put the calculations of the canonical wavefunction of 30,000 orbitals to practical use.     

Modeling of enzymatic reaction in an airlift reactor using an axial dispersion model

This work was focused on modeling of biochemical processes in a 40-L internal-loop airlift reactor. Due to different mixing in the specific zones of the reactor four main sections, bottom, riser, separator and downcomer, were recognized. Each zone was modeled by an adequate mixing model: bottom and separator sections by the model of ideally-stirred reactor; riser and downcomer sections by the model of plug-flow reactor with axial dispersion. In the model, the effects of mass transfer, hydrodynamics, and reaction kinetics were taken into account. The model of the reactor was experimentally verified by the aerobic enzymatic oxidation of glucose to gluconic acid. Simulations are in good agreement with experimental data. Presented at the 34th International Conference of the Slovak Society of Chemical Engineering, Tatranské Matliare, 21–25 May 2007.