Variation and decomposition of the partial molar volume of small gas molecules in different organic solvents derived from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Klähn, Marco; Martin, Alistair; Cheong, Daniel W.; Garland, Marc V.

2013-12-01

The partial molar volumes, bar V_i, of the gas solutes H2, CO, and CO2, solvated in acetone, methanol, heptane, and diethylether are determined computationally in the limit of infinite dilution and standard conditions. Solutions are described with molecular dynamics simulations in combination with the OPLS-aa force field for solvents and customized force field for solutes. bar V_i is determined with the direct method, while the composition of bar V_i is studied with Kirkwood-Buff integrals (KBIs). Subsequently, the amount of unoccupied space and size of pre-formed cavities in pure solvents is determined. Additionally, the shape of individual solvent cages is analyzed. Calculated bar V_i deviate only 3.4 cm3 mol-1 (7.1%) from experimental literature values. Experimental bar V_i variations across solutions are reproduced qualitatively and also quantitatively in most cases. The KBI analysis identifies differences in solute induced solvent reorganization in the immediate vicinity of H2 (<0.7 nm) and solvent reorganization up to the third solvation shell of CO and CO2 (<1.6 nm) as the origin of bar V_i variations. In all solutions, larger bar V_i are found in solvents that exhibit weak internal interactions, low cohesive energy density and large compressibility. Weak internal interactions facilitate solvent displacement by thermal solute movement, which enhances the size of solvent cages and thus bar V_i. Additionally, attractive electrostatic interactions of CO2 and the solvents, which do not depend on internal solvent interactions only, partially reversed the bar V_i trends observed in H2 and CO solutions where electrostatic interactions with the solvents are absent. More empty space and larger pre-formed cavities are found in solvents with weak internal interactions, however, no evidence is found that solutes in any considered solvent are accommodated in pre-formed cavities. Individual solvent cages are found to be elongated in the negative direction of solute movement. This wake behind the moving solute is more pronounced in case of mobile H2 and in solvents with weaker internal interactions. However, deviations from a spherical solvent cage shape do not influence solute-solvent radial distribution functions after averaging over all solvent cage orientations and hence do not change bar V_i. Overall, the applied methodology reproduces bar V_i and its variations reliably and the used bar V_i decompositions identify the underlying reasons behind observed bar V_i variations.

Spectroscopic and DFT study of solvent effects on the electronic absorption spectra of sulfamethoxazole in neat and binary solvent mixtures

NASA Astrophysics Data System (ADS)

Almandoz, M. C.; Sancho, M. I.; Blanco, S. E.

2014-01-01

The solvatochromic behavior of sulfamethoxazole (SMX) was investigated using UV-vis spectroscopy and DFT methods in neat and binary solvent mixtures. The spectral shifts of this solute were correlated with the Kamlet and Taft parameters (α, β and π*). Multiple lineal regression analysis indicates that both specific hydrogen-bond interaction and non specific dipolar interaction play an important role in the position of the absorption maxima in neat solvents. The simulated absorption spectra using TD-DFT methods were in good agreement with the experimental ones. Binary mixtures consist of cyclohexane (Cy)-ethanol (EtOH), acetonitrile (ACN)-dimethylsulfoxide (DMSO), ACN-dimethylformamide (DMF), and aqueous mixtures containing as co-solvents DMSO, ACN, EtOH and MeOH. Index of preferential solvation was calculated as a function of solvent composition and non-ideal characteristics are observed in all binary mixtures. In ACN-DMSO and ACN-DMF mixtures, the results show that the solvents with higher polarity and hydrogen bond donor ability interact preferentially with the solute. In binary mixtures containing water, the SMX molecules are solvated by the organic co-solvent (DMSO or EtOH) over the whole composition range. Synergistic effect is observed in the case of ACN-H2O and MeOH-H2O, indicating that at certain concentrations solvents interact to form association complexes, which should be more polar than the individual solvents of the mixture.

Specific interactions of alcohols and non-alcohols with a biologically active boronic acid derivative: a spectroscopic study.

PubMed

Geethanjali, H S; Melavanki, R M; Nagaraja, D; Patil, N R; Thipperudrappa, J; Kusanur, R A

2016-08-01

The photophysical properties of 4-fluoro-2-methoxyphenyl boronic acid (4FMPBA) are characterized using absorption and fluorescence techniques in series of non-alcohols and alcohols. The results are analyzed using different solvent polarity functions and Kamlet and Catalan's multiple regression approaches. The excited state dipole moment and change in dipole moment are calculated using both the solvatochromic shift method and Reichardt's microscopic solvent polarity parameter ETN. The ground state dipole moment is evaluated using quantum chemical calculations. It is found that general solute-solvent and hydrogen bond interactions are operative in this system. A red shift of ~ 9 nm in the emission spectra is observed with an increase in the solvent polarity, which depicts π→π(*) transitions, as well as the possibility of an intramolecular charge transfer (ICT) character in the emitting singlet state of 4FMPBA. The relative quantum yield, radiative and non-radiative decay constants are calculated in alkanes and alcohols using the single point method. It is found that the quantum yield of the molecule varies from 16.81% to 50.79% with the change in solvent polarity, indicating the dependence of fluorescence on the solvent environment. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

On the nature of solvatochromic effect: The riboflavin absorption spectrum as a case study

NASA Astrophysics Data System (ADS)

Daidone, Isabella; Amadei, Andrea; Aschi, Massimiliano; Zanetti-Polzi, Laura

2018-03-01

We present here the calculation of the absorption spectrum of riboflavin in acetonitrile and dimethyl sulfoxide using a hybrid quantum/classical approach, namely the perturbed matrix method, based on quantum mechanical calculations and molecular dynamics simulations. The calculated spectra are compared to the absorption spectrum of riboflavin previously calculated in water and to the experimental spectra obtained in all three solvents. The experimentally observed variations in the absorption spectra upon change of the solvent environment are well reproduced by the calculated spectra. In addition, the nature of the excited states of riboflavin interacting with different solvents is investigated, showing that environment effects determine a recombination of the gas-phase electronic states and that such a recombination is strongly affected by the polarity of the solvent inducing significant changes in the absorption spectra.

Diffusion of Small Solute Particles in Viscous Liquids: Cage Diffusion, a Result of Decoupling of Solute-Solvent Dynamics, Leads to Amplification of Solute Diffusion.

PubMed

Acharya, Sayantan; Nandi, Manoj K; Mandal, Arkajit; Sarkar, Sucharita; Bhattacharyya, Sarika Maitra

2015-08-27

We study the diffusion of small solute particles through solvent by keeping the solute-solvent interaction repulsive and varying the solvent properties. The study involves computer simulations, development of a new model to describe diffusion of small solutes in a solvent, and also mode coupling theory (MCT) calculations. In a viscous solvent, a small solute diffuses via coupling to the solvent hydrodynamic modes and also through the transient cages formed by the solvent. The model developed can estimate the independent contributions from these two different channels of diffusion. Although the solute diffusion in all the systems shows an amplification, the degree of it increases with solvent viscosity. The model correctly predicts that when the solvent viscosity is high, the solute primarily diffuses by exploiting the solvent cages. In such a scenario the MCT diffusion performed for a static solvent provides a correct estimation of the cage diffusion.

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.

PubMed

Vorobjev, Y N; Almagro, J C; Hermans, J

1998-09-01

A new method for calculating the total conformational free energy of proteins in water solvent is presented. The method consists of a relatively brief simulation by molecular dynamics with explicit solvent (ES) molecules to produce a set of microstates of the macroscopic conformation. Conformational energy and entropy are obtained from the simulation, the latter in the quasi-harmonic approximation by analysis of the covariance matrix. The implicit solvent (IS) dielectric continuum model is used to calculate the average solvation free energy as the sum of the free energies of creating the solute-size hydrophobic cavity, of the van der Waals solute-solvent interactions, and of the polarization of water solvent by the solute's charges. The reliability of the solvation free energy depends on a number of factors: the details of arrangement of the protein's charges, especially those near the surface; the definition of the molecular surface; and the method chosen for solving the Poisson equation. Molecular dynamics simulation in explicit solvent relaxes the protein's conformation and allows polar surface groups to assume conformations compatible with interaction with solvent, while averaging of internal energy and solvation free energy tend to enhance the precision. Two recently developed methods--SIMS, for calculation of a smooth invariant molecular surface, and FAMBE, for solution of the Poisson equation via a fast adaptive multigrid boundary element--have been employed. The SIMS and FAMBE programs scale linearly with the number of atoms. SIMS is superior to Connolly's MS (molecular surface) program: it is faster, more accurate, and more stable, and it smooths singularities of the molecular surface. Solvation free energies calculated with these two programs do not depend on molecular position or orientation and are stable along a molecular dynamics trajectory. We have applied this method to calculate the conformational free energy of native and intentionally misfolded globular conformations of proteins (the EMBL set of deliberately misfolded proteins) and have obtained good discrimination in favor of the native conformations in all instances.

Non-uniform Continuum Model for Solvated Species Based on Frozen-Density Embedding Theory: The Study Case of Solvatochromism of Coumarin 153.

PubMed

Shedge, Sapana V; Zhou, Xiuwen; Wesolowski, Tomasz A

2014-09-01

Recent application of the Frozen-Density Embedding Theory based continuum model of the solvent, which is used for calculating solvatochromic shifts in the UV/Vis range, are reviewed. In this model, the solvent is represented as a non-uniform continuum taking into account both the statistical nature of the solvent and specific solute-solvent interactions. It offers, therefore, a computationally attractive alternative to methods in which the solvent is described at atomistic level. The evaluation of the solvatochromic shift involves only two calculations of excitation energy instead of at least hundreds needed to account for inhomogeneous broadening. The present review provides a detailed graphical analysis of the key quantities of this model: the average charge density of the solvent (<ρB>) and the corresponding Frozen-Density Embedding Theory derived embedding potential for coumarin 153.

A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solution based upon a mixed quantum-classical approximation. II. Proton transfer reaction in non-polar solvent

NASA Astrophysics Data System (ADS)

Kojima, H.; Yamada, A.; Okazaki, S.

2015-05-01

The intramolecular proton transfer reaction of malonaldehyde in neon solvent has been investigated by mixed quantum-classical molecular dynamics (QCMD) calculations and fully classical molecular dynamics (FCMD) calculations. Comparing these calculated results with those for malonaldehyde in water reported in Part I [A. Yamada, H. Kojima, and S. Okazaki, J. Chem. Phys. 141, 084509 (2014)], the solvent dependence of the reaction rate, the reaction mechanism involved, and the quantum effect therein have been investigated. With FCMD, the reaction rate in weakly interacting neon is lower than that in strongly interacting water. However, with QCMD, the order of the reaction rates is reversed. To investigate the mechanisms in detail, the reactions were categorized into three mechanisms: tunneling, thermal activation, and barrier vanishing. Then, the quantum and solvent effects were analyzed from the viewpoint of the reaction mechanism focusing on the shape of potential energy curve and its fluctuations. The higher reaction rate that was found for neon in QCMD compared with that found for water solvent arises from the tunneling reactions because of the nearly symmetric double-well shape of the potential curve in neon. The thermal activation and barrier vanishing reactions were also accelerated by the zero-point energy. The number of reactions based on these two mechanisms in water was greater than that in neon in both QCMD and FCMD because these reactions are dominated by the strength of solute-solvent interactions.

Study of molecular interactions in binary mixtures of 2-chloro-4'methoxy benzoin with various solvents through ultrasonic speed measurements

NASA Astrophysics Data System (ADS)

Thanuja, B.; Kanakam, C.; Nithya, G.

2013-12-01

Density ( ρ) and ultrasonic velocity ( U), for binary mixtures of 2-chloro-4'-methoxy benzoin with ethanol, chloroform, acetonitrile, benzene and 1,4-dioxane of different compositions have been measured at 298 K and explanation of solute solvent interactions and effect of polarity of the solvent on type of interactions are presented in this paper. From the above data, adiabatic compressibility ( β), intermolecular free length ( L f ) and relative association ( R A ) have been calculated. Other useful parameters such as excess density, excess velocity, excess intermolecular freelength and excess adiabatic compressibility have also been calculated. These parameters have been used to study the nature and extent of intermolecular interactions between component molecules in present binary mixtures.

Generation and detection of the cyclohexadienyl radical in phosphonium ionic liquids.

PubMed

Lauzon, J M; Arseneau, D J; Brodovitch, J C; Clyburne, J A C; Cormier, P; McCollum, B; Ghandi, K

2008-10-21

The formation of the cyclohexadienyl radical, C(6)H(6)Mu, in ionic and molecular solvents has been compared. This is the first time that a muoniated free radical is reported in an ionic liquid. In marked contrast to molecular liquids, free radical generation in ionic liquids is significantly enhanced. Comparison of the hyperfine interactions in the ionic liquid and in molecular solvents and with theoretical calculations, suggests significant and unforeseen solvent interaction with the cyclohexadienyl radical.

Unexpected solvent effects on the UV/Vis absorption spectra of o-cresol in toluene and benzene: in contrast with non-aromatic solvents

PubMed Central

Zheng, Dong; Yuan, Xiang-Ai; Ma, Haibo; Li, Xiaoxiong; Wang, Xizhang; Liu, Ziteng

2018-01-01

Cresol is a prototype molecule in understanding intermolecular interactions in material and biological systems, because it offers different binding sites with various solvents and protonation states under different pH values. It is found that the UV/Vis absorption spectra of o-cresol in aromatic solvents (benzene, toluene) are characterized by a sharp peak, unlike the broad double-peaks in 11 non-aromatic solvents. Both molecular dynamics simulations and electronic structure calculations revealed the formation of intermolecular π-complexation between o-cresol and aromatic solvents. The thermal movements of solvent and solute molecules render the conformations of o-cresol changing between trans and cis isomers. The π-interaction makes the cis configuration a dominant isomer, hence leading to the single keen-edged UV/Vis absorption peak at approximately 283 nm. The free conformation changes between trans and cis in aqueous solution rationalize the broader absorption peaks in the range of 260–280 nm. The pH dependence of the UV/Vis absorption spectra in aqueous solutions is also rationalized by different protonation states of o-cresol. The explicit solvent model with long-ranged interactions is vital to describe the effects of π-complexation and electrostatic interaction on the UV/Vis absorption spectra of o-cresol in toluene and alkaline aqueous (pH > 10.3) solutions, respectively. PMID:29657794

Unexpected solvent effects on the UV/Vis absorption spectra of o-cresol in toluene and benzene: in contrast with non-aromatic solvents.

PubMed

Zheng, Dong; Yuan, Xiang-Ai; Ma, Haibo; Li, Xiaoxiong; Wang, Xizhang; Liu, Ziteng; Ma, Jing

2018-03-01

Cresol is a prototype molecule in understanding intermolecular interactions in material and biological systems, because it offers different binding sites with various solvents and protonation states under different pH values. It is found that the UV/Vis absorption spectra of o -cresol in aromatic solvents (benzene, toluene) are characterized by a sharp peak, unlike the broad double-peaks in 11 non-aromatic solvents. Both molecular dynamics simulations and electronic structure calculations revealed the formation of intermolecular π-complexation between o -cresol and aromatic solvents. The thermal movements of solvent and solute molecules render the conformations of o -cresol changing between trans and cis isomers. The π-interaction makes the cis configuration a dominant isomer, hence leading to the single keen-edged UV/Vis absorption peak at approximately 283 nm. The free conformation changes between trans and cis in aqueous solution rationalize the broader absorption peaks in the range of 260-280 nm. The pH dependence of the UV/Vis absorption spectra in aqueous solutions is also rationalized by different protonation states of o -cresol. The explicit solvent model with long-ranged interactions is vital to describe the effects of π-complexation and electrostatic interaction on the UV/Vis absorption spectra of o -cresol in toluene and alkaline aqueous (pH > 10.3) solutions, respectively.

Interaction between morin and AOT reversed micelles--studies with UV-vis at 25 °C.

PubMed

Bhattarai, Ajaya; Wilczura-Wachnik, H

2014-01-30

The precise measurements of morin absorbance in presence of surfactant/solvent/water systems at 25 °C by UV-vis technique are reported. The surfactant used in presented study was sodium bis(2-ethylhexyl) sulfosuccinate called Aerosol-OT or AOT. The solvents selected were: ethanol, ethylene glycol, and n-decanol. The concentrations of AOT were varied between 0.001 and 0.4 mol/kg. Morin concentration in quvette during UV-vis registration was not equals in all solvent because of its different solubility and absorption intensity depending on the solvent. Water concentration in the studied systems was defined by R parameter according to relation: R=[H2O]/[AOT] and was equal 0, 30 and 40 in ethanol; 0, 10, 20 and 30 in ethylene glycol and 0, 10, 20, 30, and 40 in n-decanol. In presented work a Nernstian distribution of morin between the organic and micellar phases was assumed. The intensity of morin absorbance as a function of AOT concentration was analyzed. Using Non-linear Regression Procedure (NLREG) morin binding constant (K' [mol/kg]), and morin distribution constant (K) between organic phase and AOT micellar phase have been calculated. The experimental results have shown a significant influence of solvent, surfactant and water presence on morin UV-vis spectrum. Calculated data pointed out on different transfer of morin molecules from the organic to micellar phase depending on the solvent. Moreover, results of calculations indicate on competition between morin and water molecules interacting with AOT polar heads. Morin molecules privileged location in AOT reversed micelles strongly depends on the solvent. In case of systems with ethylene glycol as solvent is possible morin molecules location in polar cores of AOT reversed micelles as results of strong interaction between AOT polar heads and morin hydroxyl groups, whereas in case of ethanol and n-decanol morin molecules are located in palisade layer. Copyright © 2013 Elsevier B.V. All rights reserved.

The solvation of L-serine in mixtures of water with some aprotic solvents at 298.15 K

NASA Astrophysics Data System (ADS)

Mezhevoi, I. N.; Badelin, V. G.

2009-03-01

The integral enthalpies of solution Δsol H m of L-serine in mixtures of water with acetonitrile, 1,4-dioxane, dimethylsulfoxide (DMSO), and acetone were measured by solution calorimetry at organic component concentrations up to 0.31 mole fractions. The standard enthalpies of solution (Δsol H°), transfer (Δtr H°), and solvation (Δsolv H°) of L-serine from water into mixed solvents were calculated. The dependences of Δsol H°, Δsolv H°, and Δtr H° on the composition of aqueous-organic solvents contained extrema. The calculated enthalpy coefficients of pair interactions of the amino acid with cosolvent molecules were positive and increased in the series acetonitrile, 1,4-dioxane, DMSO, acetone. The results obtained were interpreted from the point of view of various types of interactions in solutions and the influence of the nature of organic solvents on the thermochemical characteristics of solutions.

Mechanism of protein precipitation and stabilization by co-solvents

NASA Astrophysics Data System (ADS)

Timasheff, Serge N.; Arakawa, Tsutomu

1988-07-01

The interactions between proteins and a number of substances which, when present at high concentration, stabilize or precipitate proteins, have been analyzed in terms of the preferential interactions of these co-solvents with proteins. In all cases, stabilization or precipitation was accompanied by preferential exclusion of the co-solvent from the immediate domain of the protein, i.e., preferential hydration of the protein. This means that addition of the co-solvent to the aqueous protein solution increased the chemical potentials of both components. The thermodynamic interaction parameters derived from such data make it possible to calculate the salting out constant, Ks, as well as to construct a phase isotherm for any given solvent mixture which indicates the limiting protein solubility. The salting-out effect can be decomposed into contributions from non-specific preferential exclusion and specific binding of the ligand to the protein, the balance leading to solubilization or precipitation. In reactions, such as denaturation, the effect of co-solvent on the reaction depends on the difference in the preferential interactions of the two end states of the protein. Principal sources of preferential exclusion have been identified as steric exclusion, increase of the surface tension of water by the co-solvent, repulsion by charged loci on the protein and solvophobicity.

Molecular dynamics simulation of solute diffusion in Lennard-Jones fluids

NASA Astrophysics Data System (ADS)

Yamaguchi, T.; Kimura, Y.; Hirota, N.

We performed a molecular dynamics (MD) simulation for a system of 5 solute molecules in 495 solvent molecules interacting through the Lennard-Jones (LJ) 12-6 potential, in order to study solvent density effects on the diffusion coefficients in supercritical fluids. The effects of the size of the solute and the strength of the solute-solvent attractive interaction on the diffusion coefficient of the solute were examined. The diffusion coefficients of the solute molecules were calculated at T = 1.5 (in the LJ reduced unit), slightly above the critical temperature, from rho = 0.1 to rho = 0.95, where rho is the number density in the LJ reduced unit. The memory function in the generalized Langevin equation was calculated, in order to know the molecular origin of the friction on a solute. The memory function is separated into fast and slow components. The former arises from the solute-solvent repulsive interaction, and is interpreted as collisional Enskog-like friction. The interaction strength dependence of the collisional friction is larger in the low- and medium-density regions, which is consistent with the 'clustering' picture, i.e., the local density enhancement due to the solute-solvent attractive interaction. However, the slow component of the memory function suppresses the effect of the local density on the diffusion coefficients, and as a result the effect of the attractive interaction is smaller on the diffusion coefficients than on the local density. Nonetheless, the solvent density dependence of the effect of the attraction on the diffusion coefficient varies with the local density, and it is concluded that the local density is the principal factor that determines the interaction strength dependence of the diffusion coefficient in the low- and medium-density regions (p < 0.6).

Electronic excitation spectra of molecules in solution calculated using the symmetry-adapted cluster-configuration interaction method in the polarizable continuum model with perturbative approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fukuda, Ryoichi, E-mail: fukuda@ims.ac.jp; Ehara, Masahiro; Elements Strategy Initiative for Catalysts and Batteries

A perturbative approximation of the state specific polarizable continuum model (PCM) symmetry-adapted cluster-configuration interaction (SAC-CI) method is proposed for efficient calculations of the electronic excitations and absorption spectra of molecules in solutions. This first-order PCM SAC-CI method considers the solvent effects on the energies of excited states up to the first-order with using the zeroth-order wavefunctions. This method can avoid the costly iterative procedure of the self-consistent reaction field calculations. The first-order PCM SAC-CI calculations well reproduce the results obtained by the iterative method for various types of excitations of molecules in polar and nonpolar solvents. The first-order contribution ismore » significant for the excitation energies. The results obtained by the zeroth-order PCM SAC-CI, which considers the fixed ground-state reaction field for the excited-state calculations, are deviated from the results by the iterative method about 0.1 eV, and the zeroth-order PCM SAC-CI cannot predict even the direction of solvent shifts in n-hexane for many cases. The first-order PCM SAC-CI is applied to studying the solvatochromisms of (2,2{sup ′}-bipyridine)tetracarbonyltungsten [W(CO){sub 4}(bpy), bpy = 2,2{sup ′}-bipyridine] and bis(pentacarbonyltungsten)pyrazine [(OC){sub 5}W(pyz)W(CO){sub 5}, pyz = pyrazine]. The SAC-CI calculations reveal the detailed character of the excited states and the mechanisms of solvent shifts. The energies of metal to ligand charge transfer states are significantly sensitive to solvents. The first-order PCM SAC-CI well reproduces the observed absorption spectra of the tungsten carbonyl complexes in several solvents.« less

A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solution based upon a mixed quantum–classical approximation. II. Proton transfer reaction in non-polar solvent

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kojima, H.; Yamada, A.; Okazaki, S., E-mail: okazaki@apchem.nagoya-u.ac.jp

2015-05-07

The intramolecular proton transfer reaction of malonaldehyde in neon solvent has been investigated by mixed quantum–classical molecular dynamics (QCMD) calculations and fully classical molecular dynamics (FCMD) calculations. Comparing these calculated results with those for malonaldehyde in water reported in Part I [A. Yamada, H. Kojima, and S. Okazaki, J. Chem. Phys. 141, 084509 (2014)], the solvent dependence of the reaction rate, the reaction mechanism involved, and the quantum effect therein have been investigated. With FCMD, the reaction rate in weakly interacting neon is lower than that in strongly interacting water. However, with QCMD, the order of the reaction rates ismore » reversed. To investigate the mechanisms in detail, the reactions were categorized into three mechanisms: tunneling, thermal activation, and barrier vanishing. Then, the quantum and solvent effects were analyzed from the viewpoint of the reaction mechanism focusing on the shape of potential energy curve and its fluctuations. The higher reaction rate that was found for neon in QCMD compared with that found for water solvent arises from the tunneling reactions because of the nearly symmetric double-well shape of the potential curve in neon. The thermal activation and barrier vanishing reactions were also accelerated by the zero-point energy. The number of reactions based on these two mechanisms in water was greater than that in neon in both QCMD and FCMD because these reactions are dominated by the strength of solute–solvent interactions.« less

Thermophoresis of dissolved molecules and polymers: Consideration of the temperature-induced macroscopic pressure gradient

NASA Astrophysics Data System (ADS)

Semenov, Semen; Schimpf, Martin

2004-01-01

The movement of molecules and homopolymer chains dissolved in a nonelectrolyte solvent in response to a temperature gradient is considered a consequence of temperature-induced pressure gradients in the solvent layer surrounding the solute molecules. Local pressure gradients are produced by nonuniform London van der Waals interactions, established by gradients in the concentration (density) of solvent molecules. The density gradient is produced by variations in solvent thermal expansion within the nonuniform temperature field. The resulting expression for the velocity of the solute contains the Hamaker constants for solute-solvent and solute-solute interactions, the radius of the solute molecule, and the viscosity and cubic coefficient of thermal expansion of the solvent. In this paper we consider an additional force that arises from directional asymmetry in the interaction between solvent molecules. In a closed cell, the resulting macroscopic pressure gradient gives rise to a volume force that affects the motion of dissolved solutes. An expression for this macroscopic pressure gradient is derived and the resulting force is incorporated into the expression for the solute velocity. The expression is used to calculate thermodiffusion coefficients for polystyrene in several organic solvents. When these values are compared to those measured in the laboratory, the consistency is better than that found in previous reports, which did not consider the macroscopic pressure gradient that arises in a closed thermodiffusion cell. The model also allows for the movement of solute in either direction, depending on the relative values of the solvent and solute Hamaker constants.

Enthalpy characteristics of L-proline dissolution in certain water-organic mixtures at 298.15 K

NASA Astrophysics Data System (ADS)

Badelin, V. G.; Smirnov, V. I.

2017-01-01

A thermochemical study of the processes of L-proline dissolution in aqueous solutions of acetonitrile, 1,4-dioxane, acetone, dimethyl sulfoxide, nitromethane and tetrahydrofuran at T = 298.15 K in the range of organic solvent concentrations x2 = 0-0.25 mole fractions is performed. Standard values of the enthalpies of solution and transfer of L-proline from water to mixed solvent, and the enthalpy coefficients of pairwise interactions between L-proline and molecules of organic solvents, are calculated. The effect the composition of a water-organic mixture and the structure of organic solvents have on the enthalpy characteristics of L-proline dissolution and transfer is examined. The effect the energy properties of intermolecular interactions between components of a mixed solvent has on the intermolecular interactions between L-proline and molecules of cosolvent is estimated. The correlation between the enthalpy characteristics of L-proline dissolution and electron-donor properties of organic cosolvent in aqueous solutions is determined.

Interactions between Nanoparticles and Polymer Brushes: Molecular Dynamics Simulations and Self-consistent Field Theory Calculations

NASA Astrophysics Data System (ADS)

Cheng, Shengfeng; Wen, Chengyuan; Egorov, Sergei

2015-03-01

Molecular dynamics simulations and self-consistent field theory calculations are employed to study the interactions between a nanoparticle and a polymer brush at various densities of chains grafted to a plane. Simulations with both implicit and explicit solvent are performed. In either case the nanoparticle is loaded to the brush at a constant velocity. Then a series of simulations are performed to compute the force exerted on the nanoparticle that is fixed at various distances from the grafting plane. The potential of mean force is calculated and compared to the prediction based on a self-consistent field theory. Our simulations show that the explicit solvent leads to effects that are not captured in simulations with implicit solvent, indicating the importance of including explicit solvent in molecular simulations of such systems. Our results also demonstrate an interesting correlation between the force on the nanoparticle and the density profile of the brush. We gratefully acknowledge the support of NVIDIA Corporation with the donation of the Tesla K40 GPU used for this research.

Efficient implementation of three-dimensional reference interaction site model self-consistent-field method: Application to solvatochromic shift calculations

NASA Astrophysics Data System (ADS)

Minezawa, Noriyuki; Kato, Shigeki

2007-02-01

The authors present an implementation of the three-dimensional reference interaction site model self-consistent-field (3D-RISM-SCF) method. First, they introduce a robust and efficient algorithm for solving the 3D-RISM equation. The algorithm is a hybrid of the Newton-Raphson and Picard methods. The Jacobian matrix is analytically expressed in a computationally useful form. Second, they discuss the solute-solvent electrostatic interaction. For the solute to solvent route, the electrostatic potential (ESP) map on a 3D grid is constructed directly from the electron density. The charge fitting procedure is not required to determine the ESP. For the solvent to solute route, the ESP acting on the solute molecule is derived from the solvent charge distribution obtained by solving the 3D-RISM equation. Matrix elements of the solute-solvent interaction are evaluated by the direct numerical integration. A remarkable reduction in the computational time is observed in both routes. Finally, the authors implement the first derivatives of the free energy with respect to the solute nuclear coordinates. They apply the present method to "solute" water and formaldehyde in aqueous solvent using the simple point charge model, and the results are compared with those from other methods: the six-dimensional molecular Ornstein-Zernike SCF, the one-dimensional site-site RISM-SCF, and the polarizable continuum model. The authors also calculate the solvatochromic shifts of acetone, benzonitrile, and nitrobenzene using the present method and compare them with the experimental and other theoretical results.

Efficient implementation of three-dimensional reference interaction site model self-consistent-field method: application to solvatochromic shift calculations.

PubMed

Minezawa, Noriyuki; Kato, Shigeki

2007-02-07

The authors present an implementation of the three-dimensional reference interaction site model self-consistent-field (3D-RISM-SCF) method. First, they introduce a robust and efficient algorithm for solving the 3D-RISM equation. The algorithm is a hybrid of the Newton-Raphson and Picard methods. The Jacobian matrix is analytically expressed in a computationally useful form. Second, they discuss the solute-solvent electrostatic interaction. For the solute to solvent route, the electrostatic potential (ESP) map on a 3D grid is constructed directly from the electron density. The charge fitting procedure is not required to determine the ESP. For the solvent to solute route, the ESP acting on the solute molecule is derived from the solvent charge distribution obtained by solving the 3D-RISM equation. Matrix elements of the solute-solvent interaction are evaluated by the direct numerical integration. A remarkable reduction in the computational time is observed in both routes. Finally, the authors implement the first derivatives of the free energy with respect to the solute nuclear coordinates. They apply the present method to "solute" water and formaldehyde in aqueous solvent using the simple point charge model, and the results are compared with those from other methods: the six-dimensional molecular Ornstein-Zernike SCF, the one-dimensional site-site RISM-SCF, and the polarizable continuum model. The authors also calculate the solvatochromic shifts of acetone, benzonitrile, and nitrobenzene using the present method and compare them with the experimental and other theoretical results.

Exploring Solute-Solvent Interactions of -Amino Acids in Aqueous [] Arrangements by Volumetric, Viscometric, Refractometric, and Acoustic Approach

NASA Astrophysics Data System (ADS)

Roy, Mahendra Nath; Roy, Milan Chandra; Basak, Saptarshi

2014-05-01

Qualitative and quantitative analysis of molecular interaction prevailing in glycine, l-alanine, l-valine, and aqueous solution of ionic liquid (IL) [1-ethylpyridinium tetrafluoroborate (] have been investigated by thermophysical properties. The apparent molar volume (), viscosity -coefficient, molal refraction (), and adiabatic compressibility ( of glycine, l-alanine, and l-valine have been studied in 0.001 mol , 0.003 mol , and 0.005 mol aqueous 1-ethylpyridinium tetrafluoroborate [] solutions at 298.15 K from the values of densities , viscosities (), refractive index (, and speed of sound , respectively. The extent of interaction, i.e., the solute-solvent interaction is expressed in terms of the limiting apparent molar volume (, viscosity -coefficient, and limiting apparent molar adiabatic compressibility (. The limiting apparent molar volumes (, experimental slopes ( derived from the Masson equation, and viscosity - and -coefficients using the Jones-Dole equation have been interpreted in terms of ion-ion and ion-solvent interactions, respectively. Molal refractions ( have been calculated with the help of the Lorentz-Lorenz equation. The role of the solvent (aqueous IL solution) and the contribution of solute-solute and solute-solvent interactions to the solution complexes have also been analyzed through the derived properties.

Study of the solvent effects on the molecular structure and Cdbnd O stretching vibrations of flurbiprofen

NASA Astrophysics Data System (ADS)

Tekin, Nalan; Pir, Hacer; Sagdinc, Seda

2012-12-01

The effects of 15 solvents on the C=O stretching vibrational frequency of flurbiprofen (FBF) were determined to investigate solvent-solute interactions. Solvent effects on the geometry and C=O stretching vibrational frequency, ν(C=O), of FBF were studied theoretically at the DFT/B3LYP and HF level in combination with the polarizable continuum model and experimentally using attenuated total reflection infrared spectroscopy (ATR-IR). The calculated C=O stretching frequencies in the liquid phase are in agreement with experimental values. Moreover, the wavenumbers of ν(C=O) of FBF in different solvents have been obtained and correlated with the Kirkwood-Bauer-Magat equation (KBM), the solvent acceptor numbers (ANs), and the linear solvation energy relationships (LSERs). The solvent-induced stretching vibrational frequency shifts displayed a better correlation with the LSERs than with the ANs and KBM.

Surface interactions between silica particles and water and organic solvents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Douillard, J.M.; Elwafir, M.; Partyka, S.

1994-04-01

A silica sample has been studied by vapor adsorption and by microcalorimetric methods. The combination of these two methods in the case of water allows one to calculate all the thermodynamic terms related to the adhesion on this silica. Adhesion between silica and miscellaneous solvents has been studied by immersion microcalorimetry. The silica is slightly hydrophobic, but the enthalpy of immersion into water is the most energetic one of all the solvents studied. It appears a clear graduation of the enthalpies of immersion due to the presence of delocalized electrons in the studied solvents.

Solvation effects on chemical shifts by embedded cluster integral equation theory.

PubMed

Frach, Roland; Kast, Stefan M

2014-12-11

The accurate computational prediction of nuclear magnetic resonance (NMR) parameters like chemical shifts represents a challenge if the species studied is immersed in strongly polarizing environments such as water. Common approaches to treating a solvent in the form of, e.g., the polarizable continuum model (PCM) ignore strong directional interactions such as H-bonds to the solvent which can have substantial impact on magnetic shieldings. We here present a computational methodology that accounts for atomic-level solvent effects on NMR parameters by extending the embedded cluster reference interaction site model (EC-RISM) integral equation theory to the prediction of chemical shifts of N-methylacetamide (NMA) in aqueous solution. We examine the influence of various so-called closure approximations of the underlying three-dimensional RISM theory as well as the impact of basis set size and different treatment of electrostatic solute-solvent interactions. We find considerable and systematic improvement over reference PCM and gas phase calculations. A smaller basis set in combination with a simple point charge model already yields good performance which can be further improved by employing exact electrostatic quantum-mechanical solute-solvent interaction energies. A larger basis set benefits more significantly from exact over point charge electrostatics, which can be related to differences of the solvent's charge distribution.

Theoretical investigation of the weak interaction between graphene and alcohol solvents

NASA Astrophysics Data System (ADS)

Wang, Haining; Chen, Sian; Lu, Shanfu; Xiang, Yan

2017-05-01

The dispersion of graphene in five different alcohol solvents was investigated by evaluating the binding energy between graphene and alcohol molecules using DFT-D method. The calculation showed the most stable binding energy appeared at the distance of ∼3.5 Å between graphene and alcohol molecules and increased linearly as changing the alcohol from methanol to 1-pentanol. The weak interaction was further graphically illustrated using the reduced density gradient method. The theoretical study revealed alcohols with more carbon atoms could be a good starting point for screening suitable solvents for graphene dispersion.

Thermodynamic Parameters of the Dissolution of 4-Hydroxy-L-Proline and L-Phenylalanine in Mixed Aqueous Solvents at 298 K

NASA Astrophysics Data System (ADS)

Smirnov, V. I.; Badelin, V. G.

2018-01-01

The enthalpies of solution of 4-hydroxy-L-proline and L-phenylalanine in binary mixed aqueous solvents containing acetonitrile (AN), 1,4-dioxane (1,4-DO), or acetone (AC) at mole fractions of 0 to 0.25 are determined at T = 298.15 K via isothermal calorimetry. The standard enthalpies of solution (Δsol H°) and transfer (Δtr H°) of 4-hydroxy-L-proline and L-phenylalanine from water to mixed aqueous solvents are calculated using the experimental calorimetric data, as are the enthalpy coefficients of paired interactions ( h xy ) between the molecules of the investigated amino acids and the organic solvents. The effects the mixed aqueous solvent composition and the structure of the organic solvent molecules have on the enthalpies of solution and transfer for the investigated amino acids are considered. The correlation between the enthalpy of solution of the amino acids and the electron-donating properties of the organic solvents in the mixed aqueous solvent systems is established.

Theoretical study of structure and stability of small gadolinium carboxylate complexes in liquid scintillator solvents.

PubMed

Huang, Pin-Wen

2014-09-01

The structural properties of three small gadolinium carboxylate complexes in three liquid scintillator solvents (pseudocumene, linear alkylbenzene, and phenyl xylylethane) were theoretically investigated using density functional theory (B3LYP/LC-RECP) and polarizable continuum model (PCM). The average interaction energy between gadolinium atom and carboxylate ligand (E(int)) and the energy difference of the highest singly occupied molecular orbital and lowest unoccupied molecular orbital (Δ(SL)) were calculated to evaluate and compare the relative stability of these complexes in solvents. The calculation results show that the larger (with a longer alkyl chain) gadolinium carboxylate complex has greater stability than the smaller one, while these gadolinium carboxylates in linear alkylbenzene were found to have greater stability than those in the other two solvents.

Solvent effects on the crystal growth structure and morphology of the pharmaceutical dirithromycin

NASA Astrophysics Data System (ADS)

Wang, Yuan; Liang, Zuozhong

2017-12-01

Solvent effects on the crystal structure and morphology of pharmaceutical dirithromycin molecules were systematically investigated using both experimental crystallization and theoretical simulation. Dirithromycin is one of the new generation of macrolide antibiotics with two polymorphic forms (Form I and Form II) and many solvate forms. Herein, six solvates of the dirithromycin, including acetonitrile, acetonitrile/water, acetone, 1-propanol, N,N-dimethylformamide (DMF) and cyclohexane, were studied. Experimentally, we crystallized the dirithromycin molecules in different solvents by the solvent evaporating method and measured the crystal structures with the X-ray diffraction (XRD). We compared these crystal structures of dirithromycin solvates and analyzed the solvent property-determined structure evolution. The solvents have a strong interaction with the dirithromycin molecule due to the formation of inter-molecular interactions (such as the hydrogen bonding and close contacts (sum of vdW radii)). Theoretically, we calculated the ideal crystal habit based on the solvated structures with the attachment growth (AE) model. The predicted morphologies and aspect ratios of dirithromycin solvates agree well with the experimental results. This work could be helpful to better understand the structure and morphology evolution of solvates controlled by solvents and guide the crystallization of active pharmaceutical ingredients in the pharmaceutical industry.

Calculation of activities of ions in molten salts with potential application to the pyroprocessing of nuclear waste.

PubMed

Salanne, Mathieu; Simon, Christian; Turq, Pierre; Madden, Paul A

2008-01-31

The ability to separate fission products by electrodeposition from molten salts depends, in part, on differences between the interactions of the different fission product cations with the ions present in the molten salt "solvent". These differences may be expressed as ratios of activity coefficients, which depend on the identity of the solvent and other factors. Here, we demonstrate the ability to calculate these activity coefficient ratios using molecular dynamics simulations with sufficient precision to guide the choice of suitable solvent systems in practical applications. We use polarizable ion interaction potentials which have previously been shown to give excellent agreement with structural, transport, and spectroscopic information of the molten salts, and the activity coefficients calculated in this work agree well with experimental data. The activity coefficients are shown to vary systematically with cation size for a set of trivalent cations.

Solvent Reaction Field Potential inside an Uncharged Globular Protein: A Bridge between Implicit and Explicit Solvent Models?

PubMed Central

Baker, Nathan A.; McCammon, J. Andrew

2008-01-01

The solvent reaction field potential of an uncharged protein immersed in Simple Point Charge/Extended (SPC/E) explicit solvent was computed over a series of molecular dynamics trajectories, intotal 1560 ns of simulation time. A finite, positive potential of 13 to 24 kbTec−1 (where T = 300K), dependent on the geometry of the solvent-accessible surface, was observed inside the biomolecule. The primary contribution to this potential arose from a layer of positive charge density 1.0 Å from the solute surface, on average 0.008 ec/Å3, which we found to be the product of a highly ordered first solvation shell. Significant second solvation shell effects, including additional layers of charge density and a slight decrease in the short-range solvent-solvent interaction strength, were also observed. The impact of these findings on implicit solvent models was assessed by running similar explicit-solvent simulations on the fully charged protein system. When the energy due to the solvent reaction field in the uncharged system is accounted for, correlation between per-atom electrostatic energies for the explicit solvent model and a simple implicit (Poisson) calculation is 0.97, and correlation between per-atom energies for the explicit solvent model and a previously published, optimized Poisson model is 0.99. PMID:17949217

Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models?

NASA Astrophysics Data System (ADS)

Cerutti, David S.; Baker, Nathan A.; McCammon, J. Andrew

2007-10-01

The solvent reaction field potential of an uncharged protein immersed in simple point charge/extended explicit solvent was computed over a series of molecular dynamics trajectories, in total 1560ns of simulation time. A finite, positive potential of 13-24 kbTec-1 (where T =300K), dependent on the geometry of the solvent-accessible surface, was observed inside the biomolecule. The primary contribution to this potential arose from a layer of positive charge density 1.0Å from the solute surface, on average 0.008ec/Å3, which we found to be the product of a highly ordered first solvation shell. Significant second solvation shell effects, including additional layers of charge density and a slight decrease in the short-range solvent-solvent interaction strength, were also observed. The impact of these findings on implicit solvent models was assessed by running similar explicit solvent simulations on the fully charged protein system. When the energy due to the solvent reaction field in the uncharged system is accounted for, correlation between per-atom electrostatic energies for the explicit solvent model and a simple implicit (Poisson) calculation is 0.97, and correlation between per-atom energies for the explicit solvent model and a previously published, optimized Poisson model is 0.99.

Stereochemistry and solvent role in protein folding: nuclear magnetic resonance and molecular dynamics studies of poly-L and alternating-L,D homopolypeptides in dimethyl sulfoxide.

PubMed

Srivastava, Kinshuk Raj; Kumar, Anil; Goyal, Bhupesh; Durani, Susheel

2011-05-26

The competing interactions folding and unfolding protein structure remain obscure. Using homopolypeptides, we ask if poly-L structure may have a role. We mutate the structure to alternating-L,D stereochemistry and substitute water as the fold-promoting solvent with methanol and dimethyl sulfoxide (DMSO) as the fold-denaturing solvents. Circular dichroism and molecular dynamics established previously that, while both isomers were folded in water, the poly-L isomer was unfolded and alternating-L,D isomer folded in methanol. Nuclear magnetic resonance and molecular dynamics establish now that both isomers are unfolded in DMSO. We calculated energetics of folding-unfolding equilibrium with water and methanol as solvents. We have now calculated interactions of unfolded polypeptide structures with DMSO as solvent. Methanol was found to unfold and water fold poly-L structure as a dielectric. DMSO has now been found to unfold both poly-L and alternating-L,D structures by strong solvation of peptides to disrupt their hydrogen bonds. Accordingly, we propose that while linked peptides fold protein structure with hydrogen bonds they unfold the structure electrostatically due to the stereochemical effect of the poly-L structure. Protein folding to ordering of peptide hydrogen bonds with water as canonical solvent may thus involve two specific and independent solvent effects-one, strong screening of electrostatics of poly-L linked peptides, and two, weak dipolar solvation of peptides. Correspondingly, protein denaturation may involve two independent solvent effects-one, weak dielectric to unfold poly-L structure electrostatically, and two, strong polarity to disrupt peptide hydrogen bonds by solvation of peptides.

Solvatochromic Effects on the Absorption Spectrum of 2-Thiocytosine

PubMed Central

2017-01-01

The solvatochromic effects of six different solvents on the UV absorption spectrum of 2-thiocytosine have been studied by a combination of experimental and theoretical techniques. The steady-state absorption spectra show significant shifts of the absorption bands, where in more polar solvents the first absorption maximum shifts to higher transition energies and the second maximum to lower energies. The observed solvatochromic shifts have been rationalized using three popular solvatochromic scales and with high-level multireference quantum chemistry calculations including implicit and explicit solvent effects. It has been found that the dipole moments of the excited states account for some general shifts in the excitation energies, whereas the explicit solvent interactions explain the differences in the spectra recorded in the different solvents. PMID:28452483

Electric dipole moments of the fluorescent probes Prodan and Laurdan: experimental and theoretical evaluations.

PubMed

Vequi-Suplicy, Cíntia C; Coutinho, Kaline; Lamy, M Teresa

2014-03-01

Several experimental and theoretical approaches can be used for a comprehensive understanding of solvent effects on the electronic structure of solutes. In this review, we revisit the influence of solvents on the electronic structure of the fluorescent probes Prodan and Laurdan, focusing on their electric dipole moments. These biologically used probes were synthesized to be sensitive to the environment polarity. However, their solvent-dependent electronic structures are still a matter of discussion in the literature. The absorption and emission spectra of Prodan and Laurdan in different solvents indicate that the two probes have very similar electronic structures in both the ground and excited states. Theoretical calculations confirm that their electronic ground states are very much alike. In this review, we discuss the electric dipole moments of the ground and excited states calculated using the widely applied Lippert-Mataga equation, using both spherical and spheroid prolate cavities for the solute. The dimensions of the cavity were found to be crucial for the calculated dipole moments. These values are compared to those obtained by quantum mechanics calculations, considering Prodan in vacuum, in a polarizable continuum solvent, and using a hybrid quantum mechanics-molecular mechanics methodology. Based on the theoretical approaches it is evident that the Prodan dipole moment can change even in the absence of solute-solvent-specific interactions, which is not taken into consideration with the experimental Lippert-Mataga method. Moreover, in water, for electric dipole moment calculations, it is fundamental to consider hydrogen-bonded molecules.

Testing the nature of reaction coordinate describing interaction of H2 with carbonyl carbon, activated by Lewis acid complexation, and the Lewis basic solvent: A Born-Oppenheimer molecular dynamics study with explicit solvent

NASA Astrophysics Data System (ADS)

Heshmat, Mojgan; Privalov, Timofei

2017-09-01

Using Born-Oppenheimer molecular dynamics (BOMD), we explore the nature of interactions between H2 and the activated carbonyl carbon, C(carbonyl), of the acetone-B(C6F5)3 adduct surrounded by an explicit solvent (1,4-dioxane). BOMD simulations at finite (non-zero) temperature with an explicit solvent produced long-lasting instances of significant vibrational perturbation of the H—H bond and H2-polarization at C(carbonyl). As far as the characteristics of H2 are concerned, the dynamical transient state approximates the transition-state of the heterolytic H2-cleavage. The culprit is the concerted interactions of H2 with C(carbonyl) and a number of Lewis basic solvent molecules—i.e., the concerted C(carbonyl)⋯H2⋯solvent interactions. On one hand, the results presented herein complement the mechanistic insight gained from our recent transition-state calculations, reported separately from this article. But on the other hand, we now indicate that an idea of the sufficiency of just one simple reaction coordinate in solution-phase reactions can be too simplistic and misleading. This article goes in the footsteps of the rapidly strengthening approach of investigating molecular interactions in large molecular systems via "computational experimentation" employing, primarily, ab initio molecular dynamics describing reactants-interaction without constraints of the preordained reaction coordinate and/or foreknowledge of the sampling order parameters.

Self-assembly mechanism of 1,3:2,4-di(3,4-dichlorobenzylidene)-D-sorbitol and control of the supramolecular chirality.

PubMed

Li, Jingjing; Fan, Kaiqi; Guan, Xidong; Yu, Yingzhe; Song, Jian

2014-11-11

Dibenzylidene-D-sorbitol (DBS) and its derivatives are known to form gels in organic solvents; however, the mechanism of the gel formation has been a subject of much debate. The present work is undertaken to elucidate the organization mechanism of a DBS derivative, 1,3:2,4-di(3,4-dichlorobenzylidene)-D-sorbitol (DCDBS), by taking into account the solvent effects and comparing the experiment data with theoretical calculation. These molecules form smooth nonhelical fibers with a rest circular dichroism (CD) signal in polar solvents, in contrast to rope-liked left-helical fibers with a strong negative CD signal observed in nonpolar solvents. The molecular complexes thus formed were characterized by means of Fourier transform infrared spectra, ultraviolet-visible spectra, X-ray diffraction patterns, static contact angles, and theoretical calculations. It was proposed that the interactions between the gelator and the solvents could subtly change the stacking of the molecules and hence their self-assembled nanostructures. In nonpolar solvents, the gelator molecules appear as a distorted T-shaped structure with the 6-OH forming intermolecular hydrogen bonds with the acetal oxygens of adjacent gelator molecule. In addition, because of differential stacking interactions on both sides of the 10-member ring skeleton of the gelator, the oligomers may assemble in a helix fashion to minimize the energy, leading to helical fibers. In polar solvents, however, the gelator molecules show a rigid planelike structure and thus stack on top of each other because of strong parallel-displaced π interactions. The balanced driving force on both sides of the 10-member ring skeleton made it difficult for the dimers to bend, thus resulting in nonhelical nanostructure. As expected from the mechanisms proposed here, twisted ribbon fibers with a medium strength CD signal were obtained when solvents of different polarities were mixed. Thus, solvent effects revealed in this work represent an effective means of realizing in situ tuning of nanostructures and control of the expression of chirality at supramolecular levels.

Nonpolar Solvation Free Energy from Proximal Distribution Functions

PubMed Central

Ou, Shu-Ching; Drake, Justin A.; Pettitt, B. Montgomery

2017-01-01

Using precomputed near neighbor or proximal distribution functions (pDFs) that approximate solvent density about atoms in a chemically bonded context one can estimate the solvation structures around complex solutes and the corresponding solute–solvent energetics. In this contribution, we extend this technique to calculate the solvation free energies (ΔG) of a variety of solutes. In particular we use pDFs computed for small peptide molecules to estimate ΔG for larger peptide systems. We separately compute the non polar (ΔGvdW) and electrostatic (ΔGelec) components of the underlying potential model. Here we show how the former can be estimated by thermodynamic integration using pDF-reconstructed solute–solvent interaction energy. The electrostatic component can be approximated with Linear Response theory as half of the electrostatic solute–solvent interaction energy. We test the method by calculating the solvation free energies of butane, propanol, polyalanine, and polyglycine and by comparing with traditional free energy simulations. Results indicate that the pDF-reconstruction algorithm approximately reproduces ΔGvdW calculated by benchmark free energy simulations to within ~ kcal/mol accuracy. The use of transferable pDFs for each solute atom allows for a rapid estimation of ΔG for arbitrary molecular systems. PMID:27992228

Using MD simulations to calculate how solvents modulate solubility

PubMed Central

Liu, Shuai; Cao, Shannon; Hoang, Kevin; Young, Kayla L.; Paluch, Andrew S.; Mobley, David L.

2016-01-01

Here, our interest is in predicting solubility in general, and we focus particularly on predicting how the solubility of particular solutes is modulated by the solvent environment. Solubility in general is extremely important, both for theoretical reasons – it provides an important probe of the balance between solute-solute and solute-solvent interactions – and for more practical reasons, such as how to control the solubility of a given solute via modulation of its environment, as in process chemistry and separations. Here, we study how the change of solvent affects the solubility of a given compound. That is, we calculate relative solubilities. We use MD simulations to calculate relative solubility and compare our calculated values with experiment as well as with results from several other methods, SMD and UNIFAC, the latter of which is commonly used in chemical engineering design. We find that straightforward solubility calculations based on molecular simulations using a general small-molecule force field outperform SMD and UNIFAC both in terms of accuracy and coverage of the relevant chemical space. PMID:26878198

Diffusion coefficients of nitric oxide in water: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Pokharel, Sunil; Pantha, Nurapati; Adhikari, N. P.

2016-09-01

Self-diffusion coefficients along with the mutual diffusion coefficients of nitric oxide (NO) and SPC/E water (H2O) as solute and solvent of the mixture, have been studied within the framework of classical molecular dynamics level of calculations using GROMACS package. The radial distribution function (RDF) of the constituent compounds are calculated to study solute-solute, solute-solvent and solvent-solvent molecular interactions as a function of temperature. A dilute solution of five NO molecules (mole fraction 0.018) and 280 H2O molecules (mole fraction 0.982) has been taken as the sample. The self-diffusion coefficient of the solvent is calculated by using mean square displacement (MSD) where as that for solute (NO) is calculated by using MSD and velocity auto-correlation function (VACF). The results are then compared with the available experimental values. The results from the present work for water come in good agreement, very precise at low temperatures, with the experimental values. The diffusion coefficients of NO, on the other hands, agree well with the available theoretical studies, and also with experiment at low temperatures (up to 310 K). The results at the higher temperatures (up to 333 K), however, deviate significantly with the experimental observations. Also, the mutual diffusion coefficients of NO in water have been calculated by using Darken’s relation. The temperature dependence of the calculated diffusion coefficients follow the Arrhenius behavior.

Extended Hansen solubility approach: naphthalene in individual solvents.

PubMed

Martin, A; Wu, P L; Adjei, A; Beerbower, A; Prausnitz, J M

1981-11-01

A multiple regression method using Hansen partial solubility parameters, delta D, delta p, and delta H, was used to reproduce the solubilities of naphthalene in pure polar and nonpolar solvents and to predict its solubility in untested solvents. The method, called the extended Hansen approach, was compared with the extended Hildebrand solubility approach and the universal-functional-group-activity-coefficient (UNIFAC) method. The Hildebrand regular solution theory was also used to calculate naphthalene solubility. Naphthalene, an aromatic molecule having no side chains or functional groups, is "well-behaved', i.e., its solubility in active solvents known to interact with drug molecules is fairly regular. Because of its simplicity, naphthalene is a suitable solute with which to initiate the difficult study of solubility phenomena. The three methods tested (Hildebrand regular solution theory was introduced only for comparison of solubilities in regular solution) yielded similar results, reproducing naphthalene solubilities within approximately 30% of literature values. In some cases, however, the error was considerably greater. The UNIFAC calculation is superior in that it requires only the solute's heat of fusion, the melting point, and a knowledge of chemical structures of solute and solvent. The extended Hansen and extended Hildebrand methods need experimental solubility data on which to carry out regression analysis. The extended Hansen approach was the method of second choice because of its adaptability to solutes and solvents from various classes. Sample calculations are included to illustrate methods of predicting solubilities in untested solvents at various temperatures. The UNIFAC method was successful in this regard.

Combined effects of exposure to occupational noise and mixed organic solvents on blood pressure in car manufacturing company workers.

PubMed

Attarchi, Mirsaeed; Golabadi, Majid; Labbafinejad, Yasser; Mohammadi, Saber

2013-02-01

Recent studies suggest that occupational exposures such as noise and organic solvents may affect blood pressure. The aim of this study was to investigate interaction of noise and mixed organic solvents on blood pressure. Four hundred seventy-one workers of a car manufacturing plant were divided into four groups: group one or G1 workers exposed to noise and mixed organic solvents in the permitted limit or control group, G3 exposed to noise only, G2 exposed to solvents only, and G4 workers exposed to noise and mixed organic solvents at higher than the permitted limit or co-exposure group. Biological interaction of two variables on hypertension was calculated using the synergistic index. The workers of co-exposure group (G4), noise only group (G3), and solvents only group (G2) had significantly higher mean values of SBP and DBP than workers of control group (G1) or office workers (P < 0.05). Also logistic regression analysis showed a significant association between hypertension and exposure to noise and mixture of organic solvents. Odds ratio for hypertension in the co-exposure group and the noise only and solvents only exposed groups was 14.22, 9.43, and 4.38, respectively, compared to control group. In this study, the estimated synergism index was 1.11. Our results indicate that exposure to noise or a mixture of organic solvents may be associated with the prevalence of hypertension in car manufacturing company workers and co-exposure to noise and a mixture of solvents has an additive effect in this regard. Therefore appropriate preventive programs in these workers recommended. Copyright © 2012 Wiley Periodicals, Inc.

Solvent as electron donor: Donor/acceptor electronic coupling is a dynamical variable

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castner, E.W. Jr.; Kennedy, D.; Cave, R.J.

2000-04-06

The authors combine analysis of measurements by femtosecond optical spectroscopy, computer simulations, and the generalized Mulliken-Hush (GMH) theory in the study of electron-transfer reactions and electron donor-acceptor interactions. The study focus is on ultrafast photoinduced electron-transfer reactions from aromatic amine solvent donors to excited-state acceptors. The experimental results from femtosecond dynamical measurements fall into three categories: six coumarin acceptors reductively quenched by N,N-dimethylaniline (DMA), eight electron-donating amine solvents reductively quenching coumarin 152 (7-(dimethylamino)-4-(trifluoromethyl)-coumarin), and reductive quenching dynamics of two coumarins by DMA as a function of dilution in the nonreactive solvents toluene and chlorobenzene. Applying a combination of molecular dynamicsmore » trajectories, semiempirical quantum mechanical calculations (of the relevant adiabatic electronic states), and GMH theory to the C152/DMA photoreaction, the authors calculate the electron donor/acceptor interaction parameter H{sub DA} at various time frames, H{sub DA} is strongly modulated by both inner-sphere and outer-sphere nuclear dynamics, leading us to conclude that H{sub DA} must be considered as a dynamical variable.« less

Molecular near-field antenna effect in resonance hyper-Raman scattering: Intermolecular vibronic intensity borrowing of solvent from solute through dipole-dipole and dipole-quadrupole interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shimada, Rintaro; Hamaguchi, Hiro-o, E-mail: hhama@nctu.edu.tw

2014-05-28

We quantitatively interpret the recently discovered intriguing phenomenon related to resonance Hyper-Raman (HR) scattering. In resonance HR spectra of all-trans-β-carotene (β-carotene) in solution, vibrations of proximate solvent molecules are observed concomitantly with the solute β-carotene HR bands. It has been shown that these solvent bands are subject to marked intensity enhancements by more than 5 orders of magnitude under the presence of β-carotene. We have called this phenomenon the molecular-near field effect. Resonance HR spectra of β-carotene in benzene, deuterated benzene, cyclohexane, and deuterated cyclohexane have been measured precisely for a quantitative analysis of this effect. The assignments of themore » observed peaks are made by referring to the infrared, Raman, and HR spectra of neat solvents. It has been revealed that infrared active and some Raman active vibrations are active in the HR molecular near-field effect. The observed spectra in the form of difference spectra (between benzene/deuterated benzene and cyclohexane/deuterated cyclohexane) are quantitatively analyzed on the basis of the extended vibronic theory of resonance HR scattering. The theory incorporates the coupling of excited electronic states of β-carotene with the vibrations of a proximate solvent molecule through solute–solvent dipole–dipole and dipole–quadrupole interactions. It is shown that the infrared active modes arise from the dipole–dipole interaction, whereas Raman active modes from the dipole–quadrupole interaction. It is also shown that vibrations that give strongly polarized Raman bands are weak in the HR molecular near-field effect. The observed solvent HR spectra are simulated with the help of quantum chemical calculations for various orientations and distances of a solvent molecule with respect to the solute. The observed spectra are best simulated with random orientations of the solvent molecule at an intermolecular distance of 10 Å.« less

Investigation of migrant-polymer interaction in pharmaceutical packaging material using the linear interaction energy algorithm.

PubMed

Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes

2014-10-01

The interaction between drug products and polymeric packaging materials is an important topic in the pharmaceutical industry and often associated with high costs because of the required elaborative interaction studies. Therefore, a theoretical prediction of such interactions would be beneficial. Often, material parameters such as the octanol water partition coefficient are used to predict the partitioning of migrant molecules between a solvent and a polymeric packaging material. Here, we present the investigation of the partitioning of various migrant molecules between polymers and solvents using molecular dynamics simulations for the calculation of interaction energies. Our results show that the use of a model for the interaction between the migrant and the polymer at atomistic detail can yield significantly better results when predicting the polymer solvent partitioning than a model based on the octanol water partition coefficient. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Effect of Tryptophan and Asparagine Structure on the Enthalpic Characteristics of Their Dissolution in Aqueous Solutions of Sodium Dodecyl Sulfate

NASA Astrophysics Data System (ADS)

Mezhevoi, I. N.; Badelin, V. G.; Tyunina, E. Yu.; Kamkina, S. V.

2018-03-01

The integral enthalpies of dissolution of L-tryptophan and L-asparagine in aqueous solutions of sodium dodecyl sulfate (surfactant) at surfactant concentrations of up to 0.05 mol/kg of the solvent are determined and estimated calorimetrically. Standard values of the enthalpies of dissolution and transfer of amino acids from water to a mixed solvent are calculated. The calculated enthalpy coefficients of pair interactions between amino acids and surfactant molecules have positive values. Hydrophobic interactions between amino acids and surfactants have the dominant effect on the enthalpy characteristics of the interaction in a three-component solution.

Environment effect on spectral and charge distribution characteristics of some drugs of folate derivatives

NASA Astrophysics Data System (ADS)

Khadem Sadigh, M.; Zakerhamidi, M. S.; Seyed Ahmadian, S. M.; Johari-Ahar, M.; Zare Haghighi, L.

2017-01-01

Molecular surrounding media as an important factor can effect on the operation of wide variety of drugs. For more study in this paper, spectral properties of Methotrexate and Folinic acid have been studied in various solvents. Our results show that the photo-physical of solute molecules depend strongly on solute-solvent interactions and active groups in their chemical structures. In order to investigate the contribution of specific and nonspecific interactions on the various properties of drug molecules, the linear solvation energy relationships concept is used. Moreover, charge distribution characteristics of used samples with various resonance structures in solvent environments were calculated by means of solvatochromic method. The high value of dipole moments in excited state show that local intramolecular charge transfer can occur by excitation. These results about molecular interactions can be extended to biological systems and can indicate completely the behaviors of Methotrexate and Folinic acid in polar solvents such as water in body system.

Molecular modelling of protein-protein/protein-solvent interactions

NASA Astrophysics Data System (ADS)

Luchko, Tyler

The inner workings of individual cells are based on intricate networks of protein-protein interactions. However, each of these individual protein interactions requires a complex physical interaction between proteins and their aqueous environment at the atomic scale. In this thesis, molecular dynamics simulations are used in three theoretical studies to gain insight at the atomic scale about protein hydration, protein structure and tubulin-tubulin (protein-protein) interactions, as found in microtubules. Also presented, in a fourth project, is a molecular model of solvation coupled with the Amber molecular modelling package, to facilitate further studies without the need of explicitly modelled water. Basic properties of a minimally solvated protein were calculated through an extended study of myoglobin hydration with explicit solvent, directly investigating water and protein polarization. Results indicate a close correlation between polarization of both water and protein and the onset of protein function. The methodology of explicit solvent molecular dynamics was further used to study tubulin and microtubules. Extensive conformational sampling of the carboxy-terminal tails of 8-tubulin was performed via replica exchange molecular dynamics, allowing the characterisation of the flexibility, secondary structure and binding domains of the C-terminal tails through statistical analysis methods. Mechanical properties of tubulin and microtubules were calculated with adaptive biasing force molecular dynamics. The function of the M-loop in microtubule stability was demonstrated in these simulations. The flexibility of this loop allowed constant contacts between the protofilaments to be maintained during simulations while the smooth deformation provided a spring-like restoring force. Additionally, calculating the free energy profile between the straight and bent tubulin configurations was used to test the proposed conformational change in tubulin, thought to cause microtubule destabilization. No conformational change was observed but a nucleotide dependent 'softening' of the interaction was found instead, suggesting that an entropic force in a microtubule configuration could be the mechanism of microtubule collapse. Finally, to overcome much of the computational costs associated with explicit soIvent calculations, a new combination of molecular dynamics with the 3D-reference interaction site model (3D-RISM) of solvation was integrated into the Amber molecular dynamics package. Our implementation of 3D-RISM shows excellent agreement with explicit solvent free energy calculations. Several optimisation techniques, including a new multiple time step method, provide a nearly 100 fold performance increase, giving similar computational performance to explicit solvent.

Miscibility Evaluation Of The Next Generation Solvent With Polymers Currently Used At DWPF, MCU, And Saltstone

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fondeur, F. F.

The Office of Waste Processing, within the Office of Technology Innovation and Development, funded the development of an enhanced Caustic-Side Solvent Extraction (CSSX) solvent for deployment at the Savannah River Site for removal of cesium from High Level Waste. This effort lead to the development of the Next Generation Solvent (NGS) with Tris (3,7-dimethyl octyl) guanidine (TiDG). The first deployment target for the NGS solvent is within the Modular CSSX Unit (MCU). Deployment of a new chemical within an existing facility requires verification that the new chemical components are compatible with the installed equipment. In the instance of a newmore » organic solvent, the primary focus is on compatibility of the solvent with organic polymers used in the affected facility. This report provides the calculated data from exposing these polymers to the Next Generation Solvent. An assessment of the dimensional stability of polymers known to be used or present in the MCU, Defense Waste Processing Facility (DWPF), and Saltstone facilities that will be exposed to the NGS showed that TiDG could selectively affect the elastomers and some thermoplastics to varying extents, but the typical use of these polymers in a confined geometry will likely prevent the NGS from impacting component performance. The polymers identified as of primary concern include Grafoil® (flexible graphite), Tefzel®, Isolast®, ethylene-propylene-diene monomer (EPDM) rubber, nitrile-butadiene rubber (NBR), styrene-butadiene rubber (SBR), ultra high molecular weight polyethylene (UHMWPE), and fluorocarbon rubber (FKM). Certain polymers like NBR and EPDM were found to interact mildly with NGS but their calculated swelling and the confined geometry will impede interaction with NGS. In addition, it was found that Vellumoid (cellulose fibers-reinforced glycerin and protein) may leach protein and Polyvinyl Chloride (PVC) may leach plasticizer (such as Bis-Ethylhexyl-Phthalates) into the NGS solvent. Either case will not impact decontamination or immobilization operations at Savannah River Site (SRS). Some applications have zero tolerance for dimensional changes such as the operation of valves while other applications a finite dimensional change improves the function of the application such as seals and gaskets. Additional considerations are required before using the conclusions from this work to judge outcomes in field applications. Decane, a component of Isopar L that is most likely to interact with the polymers, mildly interacted with the elastomers and the propylene based polymers but their degree of swelling is at most 10% and the confined geometry that they are typically placed in indicate this is not significant. In addition, it was found that Vellumoid may leach protein into the NGS solvent. Since Vellumoid is used at the mixer in Saltstone where it sees minimum quantities of solvent, this leaching has no effect on the extraction process at MCU or the immobilization process at saltstone. No significant interaction is expected between MaxCalix and the polymers and elastomers used at MCU, DWPF, and Saltstone. Overall, minimal and insignificant interactions are expected on extraction and immobilization operations when MCU switches from CSSX to NGS solvent. It is expected that contacting NGS will not accelerate the aging rate of polymers and elastomers under radiation and heat. This is due to the minimal interaction between NGS and the polymers and the confined geometries for these polymers. SRNL recommends the use of the HSP method (for screening) and some testing to evaluate the impact of other organic such as alcohols, glycolate, and their byproducts on the polymers used throughout the site.« less

Computer simulations of the solvatochromism of betaine-30

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mente, S.R.; Maroncelli, M.

1999-09-09

Monte Carlo simulations of the pyridinium N-phenolate dye betaine-30 in 12 solvents (20 solvent representations) were performed in order to explore the molecular basis of the E{sub T}(30) scale of solvent polarity. Ab initio (HF/6-31G{sup *}) and semiempirical (AM1 and INDO/S) electronic structure calculations were used to determine the geometry and charge distribution of betaine-30 in its S{sub 0} and S{sub 1} states. The solvent effect on the betaine absorption spectrum was assumed to derive from electrostatic interactions between the effective charge distributions of solvent molecules and the charge shift brought about by the S{sub 0} {r_arrow} S{sub 1} transition.more » Two models for this charge shift, one obtained from INDO/S calculations and the other an idealized two-site model, were used for the spectral calculations. Good agreement between simulated and observed {Delta}E{sub T} shifts (E{sub T}(30) values measured relative to the nonpolar standard tetramethylsilane) was found for both charge-shift models. In water and other hydroxylic solvents, the O atom of the betaine solute was observed to form moderately strong hydrogen bonds to between one and two solvent molecules. The contribution of these specifically coordinated molecules to the {Delta}E{sub T} shift was found to be large, (30--60%) and comparable to experimental estimates. Additional simulations of acetonitrile and methanol in equilibrium with the S{sub 1} state of betaine-30 were used to determine reorganization energies in these solvents and to decide the extent to which the solvent response to the S{sub 0} {leftrightarrow} S{sub 1} transition conforms to linear response predictions. In both solvents, the spectral distributions observed in the S{sub 0} state simulations were {approximately} 15% narrower than those in the S{sub 1} simulations, indicating only a relatively small departure from linear behavior. Reorganization energies were also estimated for a number of other solvents and compared to values reported in previous experimental and theoretical studies.« less

Electronic excitation of molecules in solution calculated using the symmetry-adapted cluster–configuration interaction method in the polarizable continuum model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fukuda, Ryoichi, E-mail: fukuda@ims.ac.jp; Ehara, Masahiro; Elements Strategy Initiative for Catalysts and Batteries

2015-12-31

The effects from solvent environment are specific to the electronic states; therefore, a computational scheme for solvent effects consistent with the electronic states is necessary to discuss electronic excitation of molecules in solution. The PCM (polarizable continuum model) SAC (symmetry-adapted cluster) and SAC-CI (configuration interaction) methods are developed for such purposes. The PCM SAC-CI adopts the state-specific (SS) solvation scheme where solvent effects are self-consistently considered for every ground and excited states. For efficient computations of many excited states, we develop a perturbative approximation for the PCM SAC-CI method, which is called corrected linear response (cLR) scheme. Our test calculationsmore » show that the cLR PCM SAC-CI is a very good approximation of the SS PCM SAC-CI method for polar and nonpolar solvents.« less

Effect of dynamic surface polarization on the oxidative stability of solvents in nonaqueous Li-O 2 batteries

NASA Astrophysics Data System (ADS)

Khetan, Abhishek; Pitsch, Heinz; Viswanathan, Venkatasubramanian

2017-09-01

Polarization-induced renormalization of the frontier energy levels of interacting molecules and surfaces can cause significant shifts in the excitation and transport behavior of electrons. This phenomenon is crucial in determining the oxidative stability of nonaqueous electrolytes in high-energy density electrochemical systems such as the Li-O2 battery. On the basis of partially self-consistent first-principles Sc G W0 calculations, we systematically study how the electronic energy levels of four commonly used solvent molecules, namely, dimethylsulfoxide (DMSO), dimethoxyethane (DME), tetrahydrofuran (THF), and acetonitrile (ACN), renormalize when physisorbed on the different stable surfaces of Li2O2 , the main discharge product. Using band level alignment arguments, we propose that the difference between the solvent's highest occupied molecular orbital (HOMO) level and the surface's valence-band maximum (VBM) is a refined metric of oxidative stability. This metric and a previously used descriptor, solvent's gas phase HOMO level, agree quite well for physisorbed cases on pristine surfaces where ACN is oxidatively most stable followed by DME, THF, and DMSO. However, this effect is intrinsically linked to the surface chemistry of the solvent's interaction with the surface states and defects, and depends strongly on their nature. We conclusively show that the propensity of solvent molecules to oxidize will be significantly higher on Li2O2 surfaces with defects as compared to pristine surfaces. This suggests that the oxidative stability of a solvent is dynamic and is a strong function of surface electronic properties. Thus, while gas phase HOMO levels could be used for preliminary solvent candidate screening, a more refined picture of solvent stability requires mapping out the solvent stability as a function of the state of the surface under operating conditions.

Analytical RISM-MP2 free energy gradient method: Application to the Schlenk equilibrium of Grignard reagent

NASA Astrophysics Data System (ADS)

Mori, Toshifumi; Kato, Shigeki

2007-03-01

We present a method to evaluate the analytical gradient of reference interaction site model Møller-Plesset second order free energy with respect to solute nuclear coordinates. It is applied to calculate the geometries and energies in the equilibria of the Grignard reagent (CH 3MgCl) in dimethylether solvent. The Mg-Mg and Mg-Cl distances as well as the binding energies of solvents are largely affected by the dynamical electron correlation. The solvent effect on the Schlenk equilibrium is examined.

Amino Acid Side Chain Interactions in the Presence of Salts

PubMed Central

Hassan, Sergio A.

2005-01-01

The effects of salt on the intermolecular interactions between polar/charged amino acids are investigated through molecular dynamics simulations. The mean forces and associated potentials are calculated for NaCl salt in the 0–2 M concentration range at 298 K. It is found that the addition of salt may stabilize or destabilize the interactions, depending on the nature of the interacting molecules. The degree of (de)stabilization is quantified, and the origin of the salt-dependent modulation is discussed based upon an analysis of solvent density profiles. To gain insight into the molecular origin of the salt modulation, spatial distribution functions (sdf’s) are calculated, revealing a high degree of solvent structuredness in all cases. The peaks in the sdf’s are consistent with long-range hydrogen-bonding networks connecting the solute hydrophilic groups, and that contribute to their intermolecular solvent-induced forces. The restructuring of water around the solutes as they dissociate from close contact is analyzed. This analysis offers clues on how the solvent structure modulates the effective intermolecular interactions in complex solutes. This modulation results from a critical balance between bulk electrostatic forces and those exerted by (i) the water molecules in the structured region between the monomers, which is disrupted by ions that transiently enter the hydration shells, and (ii) the ions in the hydration shells in direct interactions with the solutes. The implications of these findings in protein/ligand (noncovalent) association/dissociation mechanisms are briefly discussed. PMID:16479276

Solution influence on biomolecular equilibria - Nucleic acid base associations

NASA Technical Reports Server (NTRS)

Pohorille, A.; Pratt, L. R.; Burt, S. K.; Macelroy, R. D.

1984-01-01

Various attempts to construct an understanding of the influence of solution environment on biomolecular equilibria at the molecular level using computer simulation are discussed. First, the application of the formal statistical thermodynamic program for investigating biomolecular equilibria in solution is presented, addressing modeling and conceptual simplications such as perturbative methods, long-range interaction approximations, surface thermodynamics, and hydration shell. Then, Monte Carlo calculations on the associations of nucleic acid bases in both polar and nonpolar solvents such as water and carbon tetrachloride are carried out. The solvent contribution to the enthalpy of base association is positive (destabilizing) in both polar and nonpolar solvents while negative enthalpies for stacked complexes are obtained only when the solute-solute in vacuo energy is added to the total energy. The release upon association of solvent molecules from the first hydration layer around a solute to the bulk is accompanied by an increase in solute-solvent energy and decrease in solvent-solvent energy. The techniques presented are expectd to displace less molecular and more heuristic modeling of biomolecular equilibria in solution.

Viscosity-dependent diffusion of fluorescent particles using fluorescence correlation spectroscopy.

PubMed

Jung, Chanbae; Lee, Jaeran; Kang, Manil; Kim, Sok Won

2014-11-01

Fluorescent particles show the variety characteristics by the interaction with other particles and solvent. In order to investigate the relationship between the dynamic properties of fluorescent particles and solvent viscosity, particle diffusion in various solvents was evaluated using a fluorescence correlation spectroscopy. Upon analyzing the correlation functions of AF-647, Q-dot, and beads with different viscosity values, the diffusion time of all particles was observed to increase with increasing solvent viscosity, and the ratio of diffusion time to solvent viscosity, τ D /η, showed a linear dependence on particle size. The particle diffusion coefficients calculated from the diffusion time decreased with increasing solvent viscosity. Further, the hydrodynamic radii of AF-647, Q-dot, and beads were 0.98 ± 0.1 nm, 64.8 ± 3.23 nm, and 89.8 ± 4.91 nm, respectively, revealing a linear dependence on τ D /η, which suggests that the hydrodynamic radius of a particle strongly depends on both the physical size of the particle and solvent viscosity.

Gibbs Ensemble Simulations of the Solvent Swelling of Polymer Films

NASA Astrophysics Data System (ADS)

Gartner, Thomas; Epps, Thomas, III; Jayaraman, Arthi

Solvent vapor annealing (SVA) is a useful technique to tune the morphology of block polymer, polymer blend, and polymer nanocomposite films. Despite SVA's utility, standardized SVA protocols have not been established, partly due to a lack of fundamental knowledge regarding the interplay between the polymer(s), solvent, substrate, and free-surface during solvent annealing and evaporation. An understanding of how to tune polymer film properties in a controllable manner through SVA processes is needed. Herein, the thermodynamic implications of the presence of solvent in the swollen polymer film is explored through two alternative Gibbs ensemble simulation methods that we have developed and extended: Gibbs ensemble molecular dynamics (GEMD) and hybrid Monte Carlo (MC)/molecular dynamics (MD). In this poster, we will describe these simulation methods and demonstrate their application to polystyrene films swollen by toluene and n-hexane. Polymer film swelling experiments, Gibbs ensemble molecular simulations, and polymer reference interaction site model (PRISM) theory are combined to calculate an effective Flory-Huggins χ (χeff) for polymer-solvent mixtures. The effects of solvent chemistry, solvent content, polymer molecular weight, and polymer architecture on χeff are examined, providing a platform to control and understand the thermodynamics of polymer film swelling.

Predicting solvatochromic shifts and colours of a solvated organic dye: The example of nile red

NASA Astrophysics Data System (ADS)

Zuehlsdorff, T. J.; Haynes, P. D.; Payne, M. C.; Hine, N. D. M.

2017-03-01

The solvatochromic shift, as well as the change in colour of the simple organic dye nile red, is studied in two polar and two non-polar solvents in the context of large-scale time-dependent density-functional theory (TDDFT) calculations treating large parts of the solvent environment from first principles. We show that an explicit solvent representation is vital to resolve absorption peak shifts between nile red in n-hexane and toluene, as well as acetone and ethanol. The origin of the failure of implicit solvent models for these solvents is identified as being due to the strong solute-solvent interactions in form of π-stacking and hydrogen bonding in the case of toluene and ethanol. We furthermore demonstrate that the failures of the computationally inexpensive Perdew-Burke-Ernzerhof (PBE) functional in describing some features of the excited state potential energy surface of the S1 state of nile red can be corrected for in a straightforward fashion, relying only on a small number of calculations making use of more sophisticated range-separated hybrid functionals. The resulting solvatochromic shifts and predicted colours are in excellent agreement with experiment, showing the computational approach outlined in this work to yield very robust predictions of optical properties of dyes in solution.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deng, Xuchu; Hu, Mary Y.; Wei, Xiaoliang

Understanding the solvation structures of electrolytes should prove conducive for the development of nonaqueous redox flow batteries that hold considerable potential for future large scale energy storage systems. The utilization of an emerging ionic-derivatived ferrocene compound, ferrocenylmethyl dimethyl ethyl ammonium bis(trifluoromethanesulfonyl)imide (Fc1N112-TFSI), has recently overcome the issue of solubility in the supporting electrolyte. In this work, 13C, 1H and 17O NMR investigations were carried out using electrolyte solutions consisting of Fc1N112-TFSI as the solute and the mixed alkyl carbonate as the solvent. It was observed that the spectra of 13C experience changes of chemical shifts while those of 17O undergomore » linewidth broadening, indicating interactions between solute and solvent molecules. Quantum chemistry calculations of both molecular structures and chemical shifts (13C, 1H and 17O) are performed for interpreting experimental results and of understanding the detailed solvation structures and molecular dynamics. The results indicate that Fc1N112-TFSI is dissociated at varying degrees in mixed solvent depending on concentrations. Solvent molecules encircle Fc1N112 and TFSI respectively as solvation shells, rapidly exchanging with both bulk solvent and TFSI. Additionally, the solvent with high dielectric constant is more capable of dissociating Fc1N112-TFSI molecules compared with those with low dielectric constant. At saturated concentration, contact ion pairs are formed and the solvent molecules are interacting with the Fc rings rather than interacting with the ionic pendant arm of Fc1N112-TFSI. These studies will contribute to the development of nonaqueous electrolytes of storage systems.« less

3D RISM theory with fast reciprocal-space electrostatics.

PubMed

Heil, Jochen; Kast, Stefan M

2015-03-21

The calculation of electrostatic solute-solvent interactions in 3D RISM ("three-dimensional reference interaction site model") integral equation theory is recast in a form that allows for a computational treatment analogous to the "particle-mesh Ewald" formalism as used for molecular simulations. In addition, relations that connect 3D RISM correlation functions and interaction potentials with thermodynamic quantities such as the chemical potential and average solute-solvent interaction energy are reformulated in a way that calculations of expensive real-space electrostatic terms on the 3D grid are completely avoided. These methodical enhancements allow for both, a significant speedup particularly for large solute systems and a smoother convergence of predicted thermodynamic quantities with respect to box size, as illustrated for several benchmark systems.

Enthalpy characteristics of the dissolution of L-valine in water/formamide mixtures at 298.15 K

NASA Astrophysics Data System (ADS)

Smirnov, V. I.; Badelin, V. G.

2016-11-01

The thermochemical dissolution of L-valine in solvent mixtures H2O + (formamide, N-methylformamide, and N, N-dimethylformamide) is studied at an organic component concentration of x 2 = 0-0.35 molar fractions and a temperature of 298.15 K. The experimental data are used to calculate standard enthalpies of dissolution, the transferring of L-valine from water to a mixed solvent, and the enthalpy coefficients of pairwise interactions ( h xy ) with organic solvent molecules. The correlation between the enthalpy characteristics of the dissolution of L-valine with the composition of aqueous organic mixtures and the nature of the organic solvent (its physicochemical properties) is determined. A comparative analysis of the values of h xy of a number of aliphatic L-amino acids in similar solvent mixtures with the hydrophobicity parameters of their side chains is performed.

Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes.

PubMed

Gkionis, Konstantinos; Kruse, Holger; Šponer, Jiří

2016-04-12

Modern dispersion-corrected DFT methods have made it possible to perform reliable QM studies on complete nucleic acid (NA) building blocks having hundreds of atoms. Such calculations, although still limited to investigations of potential energy surfaces, enhance the portfolio of computational methods applicable to NAs and offer considerably more accurate intrinsic descriptions of NAs than standard MM. However, in practice such calculations are hampered by the use of implicit solvent environments and truncation of the systems. Conventional QM optimizations are spoiled by spurious intramolecular interactions and severe structural deformations. Here we compare two approaches designed to suppress such artifacts: partially restrained continuum solvent QM and explicit solvent QM/MM optimizations. We report geometry relaxations of a set of diverse double-quartet guanine quadruplex (GQ) DNA stems. Both methods provide neat structures without major artifacts. However, each one also has distinct weaknesses. In restrained optimizations, all errors in the target geometries (i.e., low-resolution X-ray and NMR structures) are transferred to the optimized geometries. In QM/MM, the initial solvent configuration causes some heterogeneity in the geometries. Nevertheless, both approaches represent a decisive step forward compared to conventional optimizations. We refine earlier computations that revealed sizable differences in the relative energies of GQ stems computed with AMBER MM and QM. We also explore the dependence of the QM/MM results on the applied computational protocol.

Dielectric Interactions and the Prediction of Retention Times of Pesticides in Supercritical Fluid Chromatography with CO2

NASA Astrophysics Data System (ADS)

Alvarez, Guillermo A.; Baumanna, Wolfram

2005-02-01

A thermodynamic model for the partition of a solute (pesticide) between two immiscible phases, such as the stationary and mobile phases of supercritical fluid chromatography with CO2, is developed from first principles. A key ingredient of the model is the result of the calculation made by Liptay of the energy of interaction of a polar molecule with a dielectric continuum, which represents the solvent. The strength of the interaction between the solute and the solvent, which may be considered a measure of the solvent power, is characterized by a function g = (ɛ - 1)/(2ɛ +1), where ɛ is the dielectric constant of the medium, which is a function of the temperature T and the pressure P. Since the interactions between the nonpolar supercritical CO2 solvent and the slightly polar pesticide molecules are considered to be extremely weak, a regular solution model is appropriate from the thermodynamic point of view. At constant temperature, the model predicts a linear dependence of the logarithm of the capacity factor (lnk) of the chromatographic experiment on the function g = g(P), as the pressure is varied, with a slope which depends on the dipole moment of the solute, dispersion interactions and the size of the solute cavity in the solvent. At constant pressure, once the term containing the g (solvent interaction) factor is subtracted from lnk, a plot of the resulting term against the inverse of temperature yields the enthalpy change of transfer of the solute from the mobile (supercritical CO2) phase to the stationary (adsorbent) phase. The increase in temperature with the consequent large volume expansion of the supercritical fluid lowers its solvent strength and hence the capacity factor of the column (or solute retention time) increases. These pressure and temperature effects, predicted by the model, agree excellently with the experimental retention times of seven pesticides. Beyond a temperature of about 393 K, where the liquid solvent densities approach those of a gas (and hence the solvent strength becomes negligible), a dramatic loss of the retention times of all pesticides is observed in the experiments; this is attributed to desorption of the solute from the stationary phase, as predicted by Le Châtelier's principle for the (exothermic) adsorption process.

Combined multireference configuration interaction/ molecular dynamics approach for calculating solvatochromic shifts: application to the n(O) --> pi* electronic transition of formaldehyde.

PubMed

Xu, ZongRong; Matsika, Spiridoula

2006-11-02

A combined quantum mechanics/molecular mechanics method is described here for considering the solvatochromic shift of excited states in solution. The quantum mechanical solute is described using high level multireference configuration interaction methods (MRCI), while molecular dynamics is used for obtaining the structure of the solvent around the solute. The electrostatic effect of the solvent is included in the quantum description of the solute in an averaged way. This method is used to study solvent effects on the n(O) --> pi* electronic transition of formaldehyde in aqueous solution. The effects of solute polarization, basis sets, and dynamical correlation on the solvatochromic shift, and on dipole moments, have been investigated.

Would the solvent effect be the main cause of band shift in the theoretical absorption spectrum of large lanthanide complexes?

NASA Astrophysics Data System (ADS)

Freire, Ricardo O.; Rodrigues, Nailton M.; Rocha, Gerd B.; Gimenez, Iara F.; da Costa Junior, Nivan B.

2011-06-01

As most reactions take place in solution, the study of solvent effects on relevant molecular properties - either by experimental or theoretical methods - is crucial for the design of new processes and prediction of technological properties. In spite of this, only few works focusing the influence of the solvent nature specifically on the spectroscopic properties of lanthanide complexes can be found in the literature. The present work describes a theoretical study of the solvent effect on the prediction of the absorption spectra for lanthanide complexes, but other possible relevant factors have been also considered such as the molecular geometry and the excitation window used for interaction configuration (CI) calculations. The [Eu(ETA) 2· nH 2O] +1 complex has been chosen as an ideal candidate for this type of study due to its small number of atoms (only 49) and also because the absorption spectrum exhibits a single band. Two Monte Carlo simulations were performed, the first one considering the [Eu(ETA) 2] +1 complex in 400 water molecules, evidencing that the complex presents four coordinated water molecules. The second simulation considered the [Eu(ETA) 2·4H 2O] +1 complex in 400 ethanol molecules, in order to evaluate the solvent effect on the shift of the maximum absorption in calculated spectra, compared to the experimental one. Quantum chemical studies were also performed in order to evaluate the effect of the accuracy of calculated ground state geometry on the prediction of absorption spectra. The influence of the excitation window used for CI calculations on the spectral shift was also evaluated. No significant solvent effect was found on the prediction of the absorption spectrum for [Eu(ETA) 2·4H 2O] +1 complex. A small but significant effect of the ground state geometry on the transition energy and oscillator strength was also observed. Finally it must be emphasized that the absorption spectra of lanthanide complexes can be predicted with great accuracy by the combined use of semiempirical Sparkle/AM1 and INDO/S-CIS as long as the largest possible excitation window is used in the configuration interaction calculation.

Measuring the relative hydrogen-bonding strengths of alcohols in aprotic organic solvents.

PubMed

Tessensohn, Malcolm E; Lee, Melvyn; Hirao, Hajime; Webster, Richard D

2015-01-12

Voltammetric experiments with 9,10-anthraquinone and 1,4-benzoquinone performed under controlled moisture conditions indicate that the hydrogen-bond strengths of alcohols in aprotic organic solvents can be differentiated by the electrochemical parameter ΔEp (red) =|Ep (red(1)) -Ep (red(2)) |, which is the potential separation between the two one-electron reduction processes. This electrochemical parameter is inversely related to the strength of the interactions and can be used to differentiate between primary, secondary, tertiary alcohols, and even diols, as it is sensitive to both their steric and electronic properties. The results are highly reproducible across two solvents with substantially different hydrogen-bonding properties (CH3 CN and CH2 Cl2 ) and are supported by density functional theory calculations. This indicates that the numerous solvent-alcohol interactions are less significant than the quinone-alcohol hydrogen-bonding interactions. The utility of ΔEp (red) was illustrated by comparisons between 1) 3,3,3-trifluoro-n-propanol and 1,3-difluoroisopropanol and 2) ethylene glycol and 2,2,2-trifluoroethanol. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Order of wetting transitions in electrolyte solutions.

PubMed

Ibagon, Ingrid; Bier, Markus; Dietrich, S

2014-05-07

For wetting films in dilute electrolyte solutions close to charged walls we present analytic expressions for their effective interface potentials. The analysis of these expressions renders the conditions under which corresponding wetting transitions can be first- or second-order. Within mean field theory we consider two models, one with short- and one with long-ranged solvent-solvent and solvent-wall interactions. The analytic results reveal in a transparent way that wetting transitions in electrolyte solutions, which occur far away from their critical point (i.e., the bulk correlation length is less than half of the Debye length) are always first-order if the solvent-solvent and solvent-wall interactions are short-ranged. In contrast, wetting transitions close to the bulk critical point of the solvent (i.e., the bulk correlation length is larger than the Debye length) exhibit the same wetting behavior as the pure, i.e., salt-free, solvent. If the salt-free solvent is governed by long-ranged solvent-solvent as well as long-ranged solvent-wall interactions and exhibits critical wetting, adding salt can cause the occurrence of an ion-induced first-order thin-thick transition which precedes the subsequent continuous wetting as for the salt-free solvent.

Understanding the influence of solvent field and fluctuations on the stability of photo-induced charge-separated state in molecular triad

NASA Astrophysics Data System (ADS)

Balamurugan, D.; Aquino, Adelia; Lischka, Hans; Dios, Francis; Flores, Lionel; Cheung, Margaret

2013-03-01

Molecular triad composed of fullerene, porphyrin, and carotene is an artificial analogue of natural photosynthetic system and is considered for applications in solar energy conversion because of its ability to produce long-lived photo-induced charge separated state. The goal of the present multiscale simulation is to understand how the stability of photo-induced charge-separated state in molecular triad is influenced by a polar organic solvent, namely tetrahydrofuran (THF). The multiscale approach is based on combined quantum, classical molecular dynamics, and statistical physics calculations. The quantum chemical calculations were performed on the triad using the second order algebraic diagrammatic perturbation and time-dependent density functional theory. Molecular dynamics simulations were performed on triad in a box of THF solvent with the replica exchange method. The two methods on different length and time scales are bridged through an important sampling technique. We have analyzed the free energy landscape, structural fluctuations, and the long- range electrostatic interactions between triad and solvent molecules. The results suggest that the polarity and re-organization of the solvent is critical in stabilization of charge-separated state in triad. Supported by DOE (DE-FG02-10ER16175)

Keto-enol tautomerism of (E)-2-[(3,4-dimethylphenylimino)methyl]-4-nitrophenol: Synthesis, X-ray, FT-IR, UV-Vis, NMR and quantum chemical characterizations

NASA Astrophysics Data System (ADS)

Özek Yıldırım, Arzu; Yıldırım, M. Hakkı; Albayrak Kaştaş, Çiǧdem

2017-01-01

(E)-2-((3,4-dimethylphenylimino)methyl)-4-nitrophenol, which is a new Schiff base compound, was synthesized and characterized by experimental and computational methods. Molecular geometry, harmonic oscillator model of aromaticity (HOMA) indices, intra- and inter-molecular interactions in the crystal structure were determined by using single crystal X-ray diffraction technique. The optimized structures, which are obtained by Gaussian and Slater type orbitals, were compared to experimental structures to determine how much correlation is found between the experimental and the calculated properties. Intramolecular and hyperconjugative interactions of bonds have been found by Natural Bond Orbital analysis. The experimental infrared spectrum of the compound has been analyzed in detail by the calculated infrared spectra and Potential Energy Distribution analysis. To find out about the correlation between the solvent polarity and the enol-keto equilibrium, experimental UV-Visible spectra of the compound were obtained in benzene, CHCl3, EtOH and DMSO solvents. In these solvents, the UV-Vis spectra and relaxed potential energy surface scan (PES) calculations have been performed to get more insight into the equilibrium dynamics. Solvent effects in UV-Vis and PES calculations have been taken into account by using Polarizable Continuum Modelling method. 1H and 13C NMR spectra of the compound (in DMSO) were analyzed. The computational study of nonlinear optical properties shows that the compound can be used for the development of nonlinear optical materials.

Dynamical discrete/continuum linear response shells theory of solvation: convergence test for NH4+ and OH- ions in water solution using DFT and DFTB methods.

PubMed

de Lima, Guilherme Ferreira; Duarte, Hélio Anderson; Pliego, Josefredo R

2010-12-09

A new dynamical discrete/continuum solvation model was tested for NH(4)(+) and OH(-) ions in water solvent. The method is similar to continuum solvation models in a sense that the linear response approximation is used. However, different from pure continuum models, explicit solvent molecules are included in the inner shell, which allows adequate treatment of specific solute-solvent interactions present in the first solvation shell, the main drawback of continuum models. Molecular dynamics calculations coupled with SCC-DFTB method are used to generate the configurations of the solute in a box with 64 water molecules, while the interaction energies are calculated at the DFT level. We have tested the convergence of the method using a variable number of explicit water molecules and it was found that even a small number of waters (as low as 14) are able to produce converged values. Our results also point out that the Born model, often used for long-range correction, is not reliable and our method should be applied for more accurate calculations.

Quantifying the Molecular Origins of Opposite Solvent Effects on Protein-Protein Interactions

PubMed Central

Vagenende, Vincent; Han, Alvin X.; Pek, Han B.; Loo, Bernard L. W.

2013-01-01

Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens protein-protein interactions for others. This is exemplified by the puzzling observation that addition of glycerol oppositely affects the association constants of two antibodies, D1.3 and D44.1, with lysozyme. To resolve this conundrum, we develop a methodology based on the thermodynamic principles of preferential interaction theory and the quantitative characterization of local protein solvation from molecular dynamics simulations. We find that changes of preferential solvent interactions at the protein-protein interface quantitatively account for the opposite effects of glycerol on the antibody-antigen association constants. Detailed characterization of local protein solvation in the free and associated protein states reveals how opposite solvent effects on protein-protein interactions depend on the extent of dewetting of the protein-protein contact region and on structural changes that alter cooperative solvent-protein interactions at the periphery of the protein-protein interface. These results demonstrate the direct relationship between macroscopic solvent effects on protein-protein interactions and atom-scale solvent-protein interactions, and establish a general methodology for predicting and understanding solvent effects on protein-protein interactions in diverse biological environments. PMID:23696727

Quantifying the molecular origins of opposite solvent effects on protein-protein interactions.

PubMed

Vagenende, Vincent; Han, Alvin X; Pek, Han B; Loo, Bernard L W

2013-01-01

Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens protein-protein interactions for others. This is exemplified by the puzzling observation that addition of glycerol oppositely affects the association constants of two antibodies, D1.3 and D44.1, with lysozyme. To resolve this conundrum, we develop a methodology based on the thermodynamic principles of preferential interaction theory and the quantitative characterization of local protein solvation from molecular dynamics simulations. We find that changes of preferential solvent interactions at the protein-protein interface quantitatively account for the opposite effects of glycerol on the antibody-antigen association constants. Detailed characterization of local protein solvation in the free and associated protein states reveals how opposite solvent effects on protein-protein interactions depend on the extent of dewetting of the protein-protein contact region and on structural changes that alter cooperative solvent-protein interactions at the periphery of the protein-protein interface. These results demonstrate the direct relationship between macroscopic solvent effects on protein-protein interactions and atom-scale solvent-protein interactions, and establish a general methodology for predicting and understanding solvent effects on protein-protein interactions in diverse biological environments.

Material Science Smart Coatings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rubinstein, A. I.; Sabirianov, R. F.; Namavar, Fereydoon

2014-07-01

The contribution of electrostatic interactions to the free energy of binding between model protein and a ceramic implant surface in the aqueous solvent, considered in the framework of the nonlocal electrostatic model, is calculated as a function of the implant low-frequency dielectric constant. We show that the existence of a dynamically ordered (low-dielectric) interfacial solvent layer at the protein-solvent and ceramic-solvent interface markedly increases charging energy of the protein and ceramic implant, and consequently makes the electrostatic contribution to the protein-ceramic binding energy more favorable (attractive). Our analysis shows that the corresponding electrostatic energy between protein and oxide ceramics dependsmore » nonmonotonically on the dielectric constant of ceramic, ε C. Obtained results indicate that protein can attract electrostatically to the surface if ceramic material has a moderate ε C below or about 35 (in particularly ZrO 2 or Ta 2O 5). This is in contrast to classical (local) consideration of the solvent, which demonstrates an unfavorable electrostatic interaction of protein with typical metal oxide ceramic materials (ε C>10). Thus, a solid implant coated by combining oxide ceramic with a reduced dielectric constant can be beneficial to strengthen the electrostatic binding of the protein-implant complex.« less

Estimation of ground and excited state dipole moment of laser dyes C504T and C521T using solvatochromic shifts of absorption and fluorescence spectra.

PubMed

Basavaraja, Jana; Suresh Kumar, H M; Inamdar, S R; Wari, M N

2016-02-05

The absorption and fluorescence spectra of laser dyes: coumarin 504T (C504T) and coumarin 521T (C521T) have been recorded at room temperature in a series of non-polar and polar solvents. The spectra of these dyes showed bathochromic shift with increasing in solvent polarity indicating the involvement of π→π⁎ transition. Kamlet-Taft and Catalan solvent parameters were used to analyze the effect of solvents on C504T and C521T molecules. The study reveals that both general solute-solvent interactions and specific interactions are operative in these two systems. The ground state dipole moment was estimated using Guggenheim's method and also by quantum mechanical calculations. The solvatochromic data were used to determine the excited state dipole moment (μ(e)). It is observed that dipole moment value of excited state (μ(e)) is higher than that of the ground state in both the laser dyes indicating that these dyes are more polar in nature in the excited state than in the ground state. Copyright © 2015. Published by Elsevier B.V.

SO2 absorption in EmimCl-TEG deep eutectic solvents.

PubMed

Yang, Dezhong; Zhang, Shaoze; Jiang, De-En; Dai, Sheng

2018-06-06

Deep eutectic solvents (DESs) based on 1-ethyl-3-methylimidazolium chloride (EmimCl) and triethylene glycol (TEG) with different molar ratios (from 6 : 1 to 1 : 1) were prepared. FTIR and theoretical calculation indicated that the C2-H on the imidazolium ring form hydrogen bonds with the hydroxyl group rather than the ether O atom of the TEG. The EmimCl-TEG DESs can efficiently capture SO2; in particular, EmimCl-TEG (6 : 1) can capture 0.54 g SO2 per gram of solvent at 0.10 atm and 20 °C, the highest absorption amount for DESs under the same conditions. Theoretical calculation showed that the high SO2 absorption capacity was mainly due to the strong charge-transfer interaction between SO2 and the anion Cl-. Moreover, SO2 desorption in the DESs can be controlled by tuning the interaction between EmimCl and TEG, and the DESs can be cycled many times.

The influence of solvent on conformational properties of peptides with Aib residue-a DFT study.

PubMed

Wałęsa, Roksana; Broda, Małgorzata A

2017-11-21

The conformational propensities of the Aib residue on the example of two model peptides Ac-Aib-NHMe (1) and Ac-Aib-NMe 2 (2), were studied by B3LYP and M06-2X functionals, in the gas phase and in the polar solvents. To verify the reliability of selected functionals, we also performed MP2 calculations for the tested molecules in vacuum. Polarizable continuum models (PCM and SMD) were used to estimate the solvent effect. Ramachandran maps were calculated to find all energy minima. Noncovalent intramolecular interactions due to hydrogen-bonds and dipole attractions between carbonyl groups are responsible for the relative stabilities of the conformers. In order to verify the theoretical results, the available conformations of similar X-ray structures from the Cambridge Crystallographic Data Center (CCDC) were analyzed. The results of the calculations show that both derivatives with the Aib residue in the gas phase prefer structures stabilized by intramolecular N-H⋯O hydrogen bonds, i.e., C 5 and C 7 conformations, while polar solvent promotes helical conformation with φ, ψ values equal to +/-60°, +/-40°. In addition, in the case of molecule 2, the helical conformation is the only one available in the polar environment. This result is fully consistent with the X-ray data. Graphical abstract Effect of solvent on the Ramachandran maps of the model peptides with Aib residue.

Synthesis, stabilization, and characterization of metal nanoparticles

NASA Astrophysics Data System (ADS)

White, Gregory Von, II

Wet chemical synthesis techniques offer the ability to control various nanoparticle characteristics including size, shape, dispersibility in both aqueous and organic solvents, and tailored surface chemistries appropriate for different applications. Large quantities of stabilizing ligands or surfactants are often required during synthesis to achieve these nanoparticle characteristics. Unfortunately, excess reaction byproducts, surfactants, and ligands remaining in solution after nanoparticle synthesis can impede application, and therefore post-synthesis purification must be employed. A liquid-liquid solvent/antisolvent pair (typically ethanol/toluene or ethanol/hexane for gold nanoparticles, GNPs) can be used to both purify and size-selectively fractionate hydrophobically modified nanoparticles. Alternatively, carbon dioxide may be used in place of a liquid antisolvent, a "green" approach, enabling both nanoparticle purification and size-selective fractionation while simultaneously eliminating mixed solvent waste and allowing solvent recycle. We have used small-angle neutron scattering (SANS) to investigate the ligand structure and composition response of alkanethiol modified gold and silver nanoparticles at varying anti-solvent conditions (CO2 or ethanol). The ligand lengths and ligand solvation for alkanethiol gold and silver NPs were found to decrease with increased antisolvent concentrations directly impacting their dispersibility in solution. Calculated Flory-Huggins interaction parameters support our SANS study for dodecanethiol dispersibility in the mixed organic solvents. This research has led to a greater understanding of the liquid-liquid precipitation process for metal nanoparticles, and provides critical results for future interaction energy modeling.

Nonadiabatic dynamics of electron transfer in solution: Explicit and implicit solvent treatments that include multiple relaxation time scales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwerdtfeger, Christine A.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon, E-mail: shs3@illinois.edu

2014-01-21

The development of efficient theoretical methods for describing electron transfer (ET) reactions in condensed phases is important for a variety of chemical and biological applications. Previously, dynamical dielectric continuum theory was used to derive Langevin equations for a single collective solvent coordinate describing ET in a polar solvent. In this theory, the parameters are directly related to the physical properties of the system and can be determined from experimental data or explicit molecular dynamics simulations. Herein, we combine these Langevin equations with surface hopping nonadiabatic dynamics methods to calculate the rate constants for thermal ET reactions in polar solvents formore » a wide range of electronic couplings and reaction free energies. Comparison of explicit and implicit solvent calculations illustrates that the mapping from explicit to implicit solvent models is valid even for solvents exhibiting complex relaxation behavior with multiple relaxation time scales and a short-time inertial response. The rate constants calculated for implicit solvent models with a single solvent relaxation time scale corresponding to water, acetonitrile, and methanol agree well with analytical theories in the Golden rule and solvent-controlled regimes, as well as in the intermediate regime. The implicit solvent models with two relaxation time scales are in qualitative agreement with the analytical theories but quantitatively overestimate the rate constants compared to these theories. Analysis of these simulations elucidates the importance of multiple relaxation time scales and the inertial component of the solvent response, as well as potential shortcomings of the analytical theories based on single time scale solvent relaxation models. This implicit solvent approach will enable the simulation of a wide range of ET reactions via the stochastic dynamics of a single collective solvent coordinate with parameters that are relevant to experimentally accessible systems.« less

Combined Quantum Chemical/Raman Spectroscopic Analyses of Li+ Cation Solvation: Cyclic Carbonate Solvents - Ethylene Carbonate and Propylene Earbonate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allen, Joshua L.; Borodin, Oleg; Seo, D. M.

2014-12-01

Combined computational/Raman spectroscopic analyses of ethylene carbonate (EC) and propylene carbonate (PC) solvation interactions with lithium salts are reported. It is proposed that previously reported Raman analyses of (EC)n-LiX mixtures have utilized faulty assumptions. In the present studies, density functional theory (DFT) calculations have provided corrections in terms of both the scaling factors for the solvent's Raman band intensity variations and information about band overlap. By accounting for these factors, the solvation numbers obtained from two different EC solvent bands are in excellent agreement with one another. The same analysis for PC, however, was found to be quite challenging. Commerciallymore » available PC is a racemic mixture of (S)- and (R)-PC isomers. Based upon the quantum chemistry calculations, each of these solvent isomers may exist as multiple conformers due to a low energy barrier for ring inversion, making deconvolution of the Raman bands daunting and inherently prone to significant error. Thus, Raman spectroscopy is able to accurately determine the extent of the EC...Li+ cation solvation interactions using the provided methodology, but a similar analysis of PC...Li+ cation solvation results in a significant underestimation of the actual solvation numbers.« less

The solvent effects on dimethyl phthalate investigated by FTIR characterization, solvent parameter correlation and DFT computation

NASA Astrophysics Data System (ADS)

Chen, Yi; Zhang, Hui; Zhou, Wenzhao; Deng, Chao; Liao, Jian

2018-06-01

This study set out with the aim of investigating the solvent effects on dimethyl phthalate (DMP) using FTIR characterization, solvent parameter correlation and DFT calculation. DMP exposed to 17 organic solvents manifested varying shift in the carbonyl stretching vibration frequency (νCdbnd O). Non-alkanols induced Band I and alkanols produced Band I and Band II. Through correlating the νCdbnd O with the empirical solvent scales including acceptor parameter (AN), Schleyer's linear free energy parameter (G), and linear free salvation energy relationships (LSER), Band I was mainly ascribed to non-specific effects from either non-alkanols or alkanol polymers ((alkanol)n). νCdbnd O of the latter indicated minor red shift and less variability compared to the former. An assumption was made and validated about the sequestering of hydroxyl group by the bulky hydrophobic chain in (alkanol)n, creating what we refer to as "screening effects". Ab initio calculation, on the other hand, provided insights for possible hydrogen binding between DMP and (ethanol)n or between ethanol monomers. The two components of Band I observed in inert solvents were assigned to the two Cdbnd O groups adopting differentiated conformations. This in turn prompted our consideration that hydrogen binding was highly selective in favor of lowly associated (alkanol)n and the particular Cdbnd O group having relatively less steric hindrance and stronger electron-donating capacity. Band II was therefore believed to derive from hydrogen-bond interactions mainly in manner of 1:1 and 1:2 DMP-(alkanol)n complexes.

Role of solvent in metal-on-metal surface diffusion: A case for rational solvent selection for materials synthesis

NASA Astrophysics Data System (ADS)

Imandi, Venkataramana; Jagannath, Mantha Sai Pavan; Chatterjee, Abhijit

2018-09-01

The effect of solvent on diffusion at metal surfaces is poorly understood despite its importance to morphological evolution during materials processing, corrosion and catalysis. In this article, we probe the metal-solvent interfacial structure, effective nature of interactions and dynamics when a solvent is in contact with a metal using a novel accelerated molecular dynamics simulation technique called temperature programmed molecular dynamics (TPMD). TPMD simulations reveal that surface diffusion of metal-on-metal can be made to vary over orders-of-magnitude by tuning the metal-solvent interaction. Ultimately, the solvent can have an indirect effect on diffusion. As the solvent tugs at the metal surface the separation between the adsorbed metal atom (adatom) and the surface layer can be modulated via metal-solvent interactions. The resulting adatom-surface separation can cause stronger/weaker binding of the adatom to the metal surface, which in turn results in the observed slower/enhanced diffusion in the presence of solvent. We believe this effect is ubiquitous in pure metal and metal alloys and in principle one could rationally select solvent to control the material structural evolution. Implications on materials synthesis are discussed in the context of formation of nanoporous materials.

Density functional theory of freezing of a system of highly elongated ellipsoidal oligomer solutions

NASA Astrophysics Data System (ADS)

Dwivedi, Shikha; Mishra, Pankaj

2017-05-01

We have used the density functional theory of freezing to study the liquid crystalline phase behavior of a system of highly elongated ellipsoidal conjugated oligomers dispersed in three different solvents namely chloroform, toluene and their equimolar mixture. The molecules are assumed to interact via solvent-implicit coarse-grained Gay-Berne potential. Pair correlation functions needed as input in the density functional theory have been calculated using the Percus-Yevick (PY) integral equation theory. Considering the isotropic and nematic phases, we have calculated the isotropic-nematic phase transition parameters and presented the temperature-density and pressure-temperature phase diagrams. Different solvent conditions are found not only to affect the transition parameters but also determine the capability of oligomers to form nematic phase in various thermodynamic conditions. In principle, our results are verifiable through computer simulations.

Solvent effects in time-dependent self-consistent field methods. I. Optical response calculations

DOE PAGES

Bjorgaard, J. A.; Kuzmenko, V.; Velizhanin, K. A.; ...

2015-01-22

In this study, we implement and examine three excited state solvent models in time-dependent self-consistent field methods using a consistent formalism which unambiguously shows their relationship. These are the linear response, state specific, and vertical excitation solvent models. Their effects on energies calculated with the equivalent of COSMO/CIS/AM1 are given for a set of test molecules with varying excited state charge transfer character. The resulting solvent effects are explained qualitatively using a dipole approximation. It is shown that the fundamental differences between these solvent models are reflected by the character of the calculated excitations.

1H NMR-based metabolomics reveals interactive effects between the carrier solvent methanol and a pharmaceutical mixture in an amphibian developmental bioassay with Limnodynastes peronii.

PubMed

Melvin, Steven D; Jones, Oliver A H; Carroll, Anthony R; Leusch, Frederic D L

2018-05-01

Organic carrier solvents are used in aquatic toxicity testing to improve chemical solubility and facilitate the exploration of dose-response relationships. Both water- and solvent-control groups are normally included in these scenarios to ensure that the solvent itself has no effect on the test organism, but this fails to consider possible interactive effects between carrier solvents and contaminants of interest. We explored this topic by exposing Limnodynastes peronii tadpoles to a mixture of common water-soluble pharmaceuticals (diclofenac, metformin and valproic acid) in the presence and absence of the carrier solvent methanol, according to standard developmental bioassay methodology. Nuclear Magnetic Resonance (NMR) spectroscopy was applied as a platform for untargeted metabolomics, to compare broad sub-lethal hepatotoxicity in solvent- and solvent-free exposure scenarios. Considerable interactive effects were identified between the pharmaceutical mixture and a typical dose of methanol (0.003%). Specifically, pronounced differences were observed between the solvent- and solvent-free exposure groups for leucine, acetate, glutamine, citrate, glycogen, tyrosine, arginine, purine nucleotides and an unidentified metabolite at 6.53 ppm. Various other metabolites exhibited similar disparity related to the use of carrier solvent, but the interactions were non-significant. These results raise important questions about the use of carrier solvents for chemical exposures in aquatic ecotoxicology, and particularly for studies interested in sub-lethal mechanistic information and/or biomarker discovery. Copyright © 2018 Elsevier Ltd. All rights reserved.

Lipase-catalyzed synthesis of xylitol monoesters: solvent engineering approach.

PubMed

Castillo, E; Pezzotti, F; Navarro, A; López-Munguía, A

2003-05-08

A solvent engineering strategy was applied to the lipase-catalyzed synthesis of xylitol-oleic acid monoesters. The different esterification degrees for this polyhydroxylated molecule were examined in different organic solvent mixtures. In this context, conditions for high selectivity towards monooleoyl xylitol synthesis were enhanced from 6 mol% in pure n-hexane to 73 mol% in 2-methyl-2-propanol/dimethylsulfoxide (DMSO) 80:20 (v/v). On the contrary, the highest production of di- and trioleoyl xylitol, corresponding to 94 mol%, was achieved in n-hexane. Changes in polarity of the reaction medium and in the molecular interactions between solvents and reactants were correlated with the activity coefficients of products. Based on experimental results and calculated thermodynamic activities, the effect of different binary mixtures of solvents on the selective production of xylitol esters is reported. From this analysis, it is concluded that in the more polar conditions (100% dimethylsulfoxide (DMSO)), the synthesis of xylitol monoesters is favored. However, these conditions are unfavorable in terms of enzyme stability. As an alternative, binary mixtures of solvents were proposed. Each mixture of solvents was characterized in terms of the quantitative polarity parameter E(T)(30) and related with the activity coefficients of xylitol esters. To our knowledge, the characterization of solvent mixtures in terms of this polarity parameter and its relationship with the selectivity of the process has not been previously reported.

Comparative theoretical study of the structures and stabilities of four typical gadolinium carboxylates in different scintillator solvents.

PubMed

Huang, Pin-Wen

2016-03-01

The structural properties and stabilities of four typical gadolinium carboxylates (Gd-CBX) in toluene, linear alkyl benzene (LAB), and phenyl xylyl ethane (PXE) solvents were theoretically studied using density functional theory (DFT/B3LYP with the basis sets 6-311G(d) and MWB54) and the polarizable continuum model (PCM). The average Gd-ligand interaction energies (E int, corrected for dispersion) and the values of the energy gap between the highest occupied molecular orbital and lowest unoccupied molecular orbital (ΔHL) for the gadolinium complexes were calculated to compare the relative stabilities of the four Gd-CBX molecules in the three liquid scintillator solvents. According to the calculations, the values of E int and ΔHL for Gd-CBX in LAB are larger than the corresponding values in PXE and toluene. Gd-CBX may therefore be more compatible with LAB than with PXE and toluene. It was also found that, in the three scintillator solvents, the stabilities of the four Gd-CBX molecules increase in the order Gd-2EHA < Gd-2MVA < Gd-pivalate < Gd-TMHA.

Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field

PubMed Central

Mohamed, Noor Asidah; Bradshaw, Richard T.

2016-01-01

The effects of electronic polarization in biomolecular interactions will differ depending on the local dielectric constant of the environment, such as in solvent, DNA, proteins, and membranes. Here the performance of the AMOEBA polarizable force field is evaluated under nonaqueous conditions by calculating the solvation free energies of small molecules in four common organic solvents. Results are compared with experimental data and equivalent simulations performed with the GAFF pairwise‐additive force field. Although AMOEBA results give mean errors close to “chemical accuracy,” GAFF performs surprisingly well, with statistically significantly more accurate results than AMOEBA in some solvents. However, for both models, free energies calculated in chloroform show worst agreement to experiment and individual solutes are consistently poor performers, suggesting non‐potential‐specific errors also contribute to inaccuracy. Scope for the improvement of both potentials remains limited by the lack of high quality experimental data across multiple solvents, particularly those of high dielectric constant. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:27757978

Detailed solvent, structural, quantum chemical study and antimicrobial activity of isatin Schiff base

NASA Astrophysics Data System (ADS)

Brkić, Dominik R.; Božić, Aleksandra R.; Marinković, Aleksandar D.; Milčić, Miloš K.; Prlainović, Nevena Ž.; Assaleh, Fathi H.; Cvijetić, Ilija N.; Nikolić, Jasmina B.; Drmanić, Saša Ž.

2018-05-01

The ratios of E/Z isomers of sixteen synthesized 1,3-dihydro-3-(substituted phenylimino)-2H-indol-2-one were studied using experimental and theoretical methodology. Linear solvation energy relationships (LSER) rationalized solvent influence of the solvent-solute interactions on the UV-Vis absorption maxima shifts (νmax) of both geometrical isomers using the Kamlet-Taft equation. Linear free energy relationships (LFER) in the form of single substituent parameter equation (SSP) was used to analyze substituent effect on pKa, NMR chemical shifts and νmax values. Electron charge density was obtained by the use of Quantum Theory of Atoms in Molecules, i.e. Bader's analysis. The substituent and solvent effect on intramolecular charge transfer (ICT) were interpreted with the aid of time-dependent density functional (TD-DFT) method. Additionally, the results of TD-DFT calculations quantified the efficiency of ICT from the calculated charge-transfer distance (DCT) and amount of transferred charge (QCT). The antimicrobial activity was evaluated using broth microdilution method. 3D QSAR modeling was used to demonstrate the influence of substituents effect as well as molecule geometry on antimicrobial activity.

40 CFR 63.5749 - How do I calculate the organic HAP content of aluminum wipedown solvents?

Code of Federal Regulations, 2010 CFR

2010-07-01

... content of aluminum wipedown solvents? 63.5749 Section 63.5749 Protection of Environment ENVIRONMENTAL... Manufacturing Standards for Aluminum Recreational Boat Surface Coating Operations § 63.5749 How do I calculate the organic HAP content of aluminum wipedown solvents? (a) Use equation 1 of this section to calculate...

Electric Dipole Transition Moments and Solvent-Dependent Interactions of Fluorescent Boron-Nitrogen Substituted Indole Derivatives.

PubMed

Saif, Mari; Widom, Julia R; Xu, Senmiao; Abbey, Eric R; Liu, Shih-Yuan; Marcus, Andrew H

2015-06-25

Fluorescent analogues of the indole side chain of tryptophan can be useful spectroscopic probes of protein-protein and protein-DNA interactions. Here we present linear dichroism and solvent-dependent spectroscopic studies of two fluorescent analogues of indole, in which the organic C═C unit is substituted with the isosteric inorganic B-N unit. We studied the so-called "external" BN indole, which has C2v symmetry, and the "fused" BN indole with Cs symmetry. We performed a combination of absorption and fluorescence spectroscopy, ultraviolet linear dichroism (UV-LD) in stretched poly(ethylene) (PE) films, and quantum chemical calculations on both BN indole compounds. Our measurements allowed us to characterize the degree of alignment for both molecules in stretched PE films. We thus determined the orientations and magnitudes of the two lowest energy electric dipole transition moments (EDTMs) for external BN indole, and the two lowest energy EDTMs for fused BN indole within the 30 000-45 000 cm(-1) spectral range. We compared our experimental results to those of quantum chemical calculations using standard density functional theory (DFT). Our theoretical predictions for the low-energy EDTMs are in good agreement with our experimental data. The absorption and fluorescence spectra of the external and the fused BN indoles are sensitive to solvent polarity. Our results indicate that the fused BN indole experiences much greater solvation interactions with polar solvents than does the external BN indole.

Solvent effects on infrared spectra of progesterone in CHCl 3/ cyclo-C 6H 12 binary solvent systems

NASA Astrophysics Data System (ADS)

Liu, Qing; Wang, Xiao-yan; Zhang, Hui

2007-01-01

The infrared spectroscopy studies of the C 3 and C 20 carbonyl stretching vibrations ( υ(C dbnd O)) of progesterone in CHCl 3/ cyclo-C 6H 12 binary solvent systems were undertaken to investigate the solute-solvent interactions. With the mole fraction of CHC1 3 in the binary solvent mixtures increase, three types of C 3 and C 20 carbonyl stretching vibration band of progesterone are observed, respectively. The assignments of υ(C dbnd O) of progesterone are discussed in detail. In the CHCl 3-rich binary solvent systems or pure CHCl 3 solvent, two kinds of solute-solvent hydrogen bonding interactions coexist for C 20 C dbnd O. Comparisons are drawn for the solvent sensitivities of υ(C dbnd O) for acetophenone and 5α-androstan-3,17-dione, respectively.

Solvatochromism of 9,10-phenanthrenequinone: An electronic and resonance Raman spectroscopic study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ravi Kumar, Venkatraman; Rajkumar, Nagappan; Umapathy, Siva, E-mail: umapathy@ipc.iisc.ernet.in

2015-01-14

Solvent effects play a vital role in various chemical, physical, and biological processes. To gain a fundamental understanding of the solute-solvent interactions and their implications on the energy level re-ordering and structure, UV-VIS absorption, resonance Raman spectroscopic, and density functional theory calculation studies on 9,10-phenanthrenequinone (PQ) in different solvents of diverse solvent polarity has been carried out. The solvatochromic analysis of the absorption spectra of PQ in protic dipolar solvents suggests that the longest (1n-π{sup 1}*; S{sub 1} state) and the shorter (1π-π{sup 1}*; S{sub 2} state) wavelength band undergoes a hypsochromic and bathochromic shift due to intermolecular hydrogen bondmore » weakening and strengthening, respectively. It also indicates that hydrogen bonding plays a major role in the differential solvation of the S{sub 2} state relative to the ground state. Raman excitation profiles of PQ (400–1800 cm{sup −1}) in various solvents followed their corresponding absorption spectra therefore the enhancements on resonant excitation are from single-state rather than mixed states. The hyperchromism of the longer wavelength band is attributed to intensity borrowing from the nearby allowed electronic transition through vibronic coupling. Computational calculation with C{sub 2ν} symmetry constraint on the S{sub 2} state resulted in an imaginary frequency along the low-frequency out-of-plane torsional modes involving the C=O site and therefore, we hypothesize that this mode could be involved in the vibronic coupling.« less

Quantification of the hydrophobic interaction by simulations of the aggregation of small hydrophobic solutes in water

PubMed Central

Raschke, Tanya M.; Tsai, Jerry; Levitt, Michael

2001-01-01

The hydrophobic interaction, the tendency for nonpolar molecules to aggregate in solution, is a major driving force in biology. In a direct approach to the physical basis of the hydrophobic effect, nanosecond molecular dynamics simulations were performed on increasing numbers of hydrocarbon solute molecules in water-filled boxes of different sizes. The intermittent formation of solute clusters gives a free energy that is proportional to the loss in exposed molecular surface area with a constant of proportionality of 45 ± 6 cal/mol⋅Å2. The molecular surface area is the envelope of the solute cluster that is impenetrable by solvent and is somewhat smaller than the more traditional solvent-accessible surface area, which is the area transcribed by the radius of a solvent molecule rolled over the surface of the cluster. When we apply a factor relating molecular surface area to solvent-accessible surface area, we obtain 24 cal/mol⋅Å2. Ours is the first direct calculation, to our knowledge, of the hydrophobic interaction from molecular dynamics simulations; the excellent qualitative and quantitative agreement with experiment proves that simple van der Waals interactions and atomic point-charge electrostatics account for the most important driving force in biology. PMID:11353861

Absorption Spectra and Photoreactivity of p-Aminobenzophenone by Time-dependent Density Functional Theory

NASA Astrophysics Data System (ADS)

Cheng, Xue-mei; Huang, Yao; Ma, Jian-yi; Li, Xiang-yuan

2007-06-01

The absorption spectral properties of para-aminobenzophenone (p-ABP) were investigated in gas phase and in solution by time-dependent density functional theory. Calculations suggest that the singlet states vary greatly with the solvent polarities. In various polar solvents, including acetonitrile, methanol, ethanol, dimethyl sulfoxide, and dimethyl formamide, the excited S1 states with charge transfer character result from π → π* transitions. However, in nonpolar solvents, cyclohexane, and benzene, the S1 states are the result of n → π* transitions related to local excitation in the carbonyl group. The excited T1 states were calculated to have ππ* character in various solvents. From the variation of the calculated excited states, the band due to π → π* transition undergoes a redshift with an increase in solvent polarity, while the band due to n → π* transition undergoes a blueshift with an increase in solvent polarity. In addition, the triplet yields and the photoreactivities of p-ABP in various solvents are discussed.

Efficient molecular density functional theory using generalized spherical harmonics expansions.

PubMed

Ding, Lu; Levesque, Maximilien; Borgis, Daniel; Belloni, Luc

2017-09-07

We show that generalized spherical harmonics are well suited for representing the space and orientation molecular density in the resolution of the molecular density functional theory. We consider the common system made of a rigid solute of arbitrary complexity immersed in a molecular solvent, both represented by molecules with interacting atomic sites and classical force fields. The molecular solvent density ρ(r,Ω) around the solute is a function of the position r≡(x,y,z) and of the three Euler angles Ω≡(θ,ϕ,ψ) describing the solvent orientation. The standard density functional, equivalent to the hypernetted-chain closure for the solute-solvent correlations in the liquid theory, is minimized with respect to ρ(r,Ω). The up-to-now very expensive angular convolution products are advantageously replaced by simple products between projections onto generalized spherical harmonics. The dramatic gain in speed of resolution enables to explore in a systematic way molecular solutes of up to nanometric sizes in arbitrary solvents and to calculate their solvation free energy and associated microscopic solvent structure in at most a few minutes. We finally illustrate the formalism by tackling the solvation of molecules of various complexities in water.

Preferential solvation of Brooker's merocyanine in binary solvent mixtures composed of formamides and hydroxylic solvents.

PubMed

Bevilaqua, Tharly; da Silva, Domingas C; Machado, Vanderlei G

2004-03-01

The ET polarity values of 4-[(1-methyl-4(1H)-pyridinylidene)-ethylidene]-2,5-cyclohexadien-1-one (Brooker's merocyanine) were collected in mixed-solvent systems comprising a formamide [N,N-dimethylformamide (DMF), N-methylformamide (NMF) or formamide (FA)] and a hydroxylic (water, methanol, ethanol, propan-2-ol or butan-1-ol) solvent. Binary mixtures involving DMF and the other formamides (NMF and FA) as well as NMF and FA were also studied. These data were employed in the investigation of the preferential solvation (PS) of the probe. Each solvent system was analyzed in terms of both solute-solvent and solvent-solvent interactions. These latter interactions were responsible for the synergism observed in many binary mixtures. This synergistic behaviour was observed for DMF-propan-2-ol, DMF-butan-1-ol, FA-methanol, FA-ethanol and for the mixtures of the alcohols with NMF. All data were successfully fitted to a model based on solvent-exchange equilibria, which allowed the separation of the different contributions of the solvent species in the solvation shell of the dye. The results suggest that both hydrogen bonding and solvophobic interactions contribute to the formation of the solvent complexes responsible for the observed synergistic effects in the PS of the dye.

Communication: Cosolvency and cononsolvency explained in terms of a Flory-Huggins type theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dudowicz, Jacek, E-mail: dudowicz@jfi.uchicago.edu; Freed, Karl F.; Douglas, Jack F.

2015-10-07

Standard Flory-Huggins (FH) theory is utilized to describe the enigmatic cosolvency and cononsolvency phenomena for systems of polymers dissolved in mixed solvents. In particular, phase boundaries (specifically upper critical solution temperature spinodals) are calculated for solutions of homopolymers B in pure solvents and in binary mixtures of small molecule liquids A and C. The miscibility (or immiscibility) patterns for the ternary systems are classified in terms of the FH binary interaction parameters (χ{sub αβ}) and the ratio r = ϕ{sub A}/ϕ{sub C} of the concentrations ϕ{sub A} and ϕ{sub C} of the two solvents. The trends in miscibility are comparedmore » to those observed for blends of random copolymers (A{sub x}C{sub 1−x}) with homopolymers (B) and to those deduced for A/B/C solutions of polymers B in liquid mixtures of small molecules A and C that associate into polymeric clusters (A{sub p}C{sub q}){sub i}, (i = 1, 2, …, ∞). Although the classic FH theory is able to explain cosolvency and cononsolvency phenomena, the theory does not include a consideration of the mutual association of the solvent molecules and the competitive association between the solvent molecules and the polymer. These interactions can be incorporated in refinements of the FH theory, and the present paper provides a foundation for such extensions for modeling the rich thermodynamics of polymers in mixed solvents.« less

Physicochemical properties and ion-solvent interactions in aqueous sodium, ammonium, and lead acetate solution

NASA Astrophysics Data System (ADS)

Deosarkar, S. D.; Mendkudle, M. S.

2014-09-01

Densities (ρ), viscosities (η) and refractive indices ( n D) of aqueous sodium acetate (SA), ammonium acetate (AA), and lead acetate (LA) solutions have been measured for different concentrations of salts at 302.15 K. Apparent molar volumes (φv) for studied solutions were calculated from density data, and fitted to Masson's relation and partial molar volume (φ{v/o}) was determined. Viscosity data were fitted to Jones-Dole equation and viscosity A- and B-coefficients were determined. Refractive index and density data were fitted to Lorentz and Lorenz equation and specific refraction ( R D) were calculated. Behavior of various physicochemical properties indicated presence of strong ion-solvent interactions in present systems and the acetate salts structure maker in water.

Vibrational energy transfer between carbon nanotubes and liquid water: a molecular dynamics study.

PubMed

Nelson, Tammie R; Chaban, Vitaly V; Kalugin, Oleg N; Prezhdo, Oleg V

2010-04-08

The rates and magnitudes of vibrational energy transfer between single-wall carbon nanotubes (CNTs) and water are investigated by classical molecular dynamics. The interactions between the CNT and solvent confined inside of the tube, the CNT and solvent surrounding the tube, as well as the solvent inside and outside of the tube are considered for the (11,11), (15,15), and (19,19) armchair CNTs. The vibrational energy transfer exhibits two time scales, subpicosecond and picosecond, of roughly equal importance. Solvent molecules confined within CNTs are more strongly coupled to the tubes than the outside molecules. The energy exchange is facilitated by slow collective motions, including CNT radial breathing modes (RBM). The transfer rate between CNTs and the inside solvent shows strong dependence on the CNT diameter. In smaller tubes, the transfer is faster and the solvent coupling to RBMs is stronger. The magnitude of the CNT-outside solvent interaction scales with the CNT surface area, while that of the CNT-inside solvent exhibits scaling that is intermediate between the CNT volume and surface. The Coulomb interaction between the solvent molecules inside and outside of the CNTs is much weaker than the CNT-solvent interactions. The results indicate that the excitation energy supplied to CNTs in chemical and biological applications is rapidly deposited to the active molecular agents and should remain localized sufficiently long in order to perform the desired function.

Incorporation of the TIP4P water model into a continuum solvent for computing solvation free energy

NASA Astrophysics Data System (ADS)

Yang, Pei-Kun

2014-10-01

The continuum solvent model is one of the commonly used strategies to compute solvation free energy especially for large-scale conformational transitions such as protein folding or to calculate the binding affinity of protein-protein/ligand interactions. However, the dielectric polarization for computing solvation free energy from the continuum solvent is different than that obtained from molecular dynamic simulations. To mimic the dielectric polarization surrounding a solute in molecular dynamic simulations, the first-shell water molecules was modeled using a charge distribution of TIP4P in a hard sphere; the time-averaged charge distribution from the first-shell water molecules were estimated based on the coordination number of the solute, and the orientation distribution of the first-shell waters and the intermediate water molecules were treated as that of a bulk solvent. Based on this strategy, an equation describing the solvation free energy of ions was derived.

Thermodynamic properties of deep eutectic solvent and ionic liquid mixtures at temperatures from 293.15 K to 343.15 K

NASA Astrophysics Data System (ADS)

Achsah, R. S.; Shyam, S.; Mayuri, N.; Anantharaj, R.

2018-04-01

Deep eutectic solvents (DES) and ionic liquids (ILs) have their applications in various fields of research and in industries due to their attractive physiochemical properties. In this study, the combined thermodynamic properties of DES (choline chloride-glycerol) + IL1 (1-butyl-3-methylimiazolium acetate) and DES(choline chloride-glycerol) + IL2 (1-ethyl-3-methylimadzolium ethyl sulphate) have been studied. The thermodynamic properties such as excess molar volume, partial molar volume, excess partial molar volume and apparent molar volume were calculated for different mole fractions ranging from 0 to 1 and varying temperatures from 293.15 K to 343.15 K. In order to know the solvent properties of DESs and ILs mixtures at different temperatures and their molecular interactions to enhance the solvent performance and process efficiency at fixed composition and temperature the thermodynamic properties were analyzed.

Diversity and Hierarchy in Supramolecular Assemblies of Triphenylalanine: From Laminated Helical Ribbons to Toroids.

PubMed

Mayans, Enric; Casanovas, Jordi; Gil, Ana M; Jiménez, Ana I; Cativiela, Carlos; Puiggalí, Jordi; Alemán, Carlos

2017-04-25

Microstructures from small phenylalanine-based peptides have attracted great attention lately because these compounds are considered to be a new class of tunable materials. In spite of the extensive studies on uncapped diphenylalanine and tetraphenylalanine peptides, studies on the self-assembly of uncapped triphenylananine (FFF) are very scarce and nonsystematic. In this work, we demonstrate that FFF assemblies can organize in a wide number of well-defined supramolecular structures, which include laminated helical-ribbons, leaflike dendrimers, doughnut-, needle-, and flower-shapes. These organizations are produced by the attractive or repulsive interactions between already formed assemblies and therefore can be controlled through the choice of solvents used as the incubation medium. Thus, the formation of the desired supramolecular structures is regulated through the protonation/deprotonation of the terminal groups, the polarity of the incubation medium, which affects both peptide···solvent interactions and the cavity solvation energy (i.e., solvent···solvent interactions), and the steric interactions between own assemblies that act as building blocks. Finally, the β-sheet disposition in the latter structural motifs has been examined using both theoretical calculations and Fourier transform infrared spectroscopy. Results indicate that FFF molecules can adopt both parallel and antiparallel β-sheets. However, the former one is the most energetically favored because of the formation of π-π stacking interactions between the aromatic rings of hydrogen-bonded strands.

Vapor-phase interactions and diffusion of organic solvents in the unsaturated zone

USGS Publications Warehouse

Roy, W.R.; Griffin, R.A.

1990-01-01

This article presents an analysis of the interactions and static movement of 37 organic solvents as vapors through the unsaturated soil zone. The physicochemical interactions of the organic vapors with unsaturated soil materials were emphasized with focus on diffusive, and adsorptive interactions. Fick's Law and porous media diffusion coefficients for most of the solvent vapors were either compiled or estimated; coefficients were not available for some of the fluorinated solvents. The adsorption of some of the solvent vapors by silica was concluded to be due to hydrogen bond formation with surface silanol groups. Heats of adsorption data for different adsorbents were also compiled. There were very few data on the adsorption of these solvent vapors by soils, but it appears that the magnitude of adsorption of nonpolar solvents is reduced as the relative humidity of the vapor-solid system is increased. Consequently, the interaction of the vapors may then separated into two processes; (1) gas-water partitioning described by Henry's Law constants, and (2) solid-water adsorption coefficients which may be estimated from liquid-solid partition coefficients (Kd values). ?? 1990 Springer-Verlag New York Inc.

Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations.

PubMed

Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro

2018-01-01

Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. More recently outstanding advancement in both implicit solvent models and in entropy calculations are making the goal of free energy estimation from end-point simulations more feasible than ever before. We review briefly the basic theory and discuss the advancements in light of practical applications.

Solvent dependent triphenylamine based D-(pi-A)n type dye molecules and optical properties.

PubMed

Li, Xiaochuan; Son, Young-A; Kim, Young-Sung; Kim, Sung-Hoon; Kun, Jun; Shin, Jong-Il

2012-02-01

D-(pi-A)n type dyes of triphenylamine derivatives were synthesized and their absorption and luminescence in different solvents were examined to investigate solvent dependent properties observed for their emissions in solvents with different dielectric constants. The emission wavelengths showed a dramatic blue shift with increasing solvent polarity. The results of molecular orbital calculations by computer simulation, based on Material Studio suite of programs, were found to reasonably account for the spectral properties. Relative levels of HOMO and LUMO were measured and calculated and all derivatives exhibited strong solid fluorescence with distinctively different FWHMs.

Energetics of the molecular interactions of L-cysteine, L-serine, and L-asparagine in aqueous propylene glycol solutions at 298.15 K

NASA Astrophysics Data System (ADS)

Mezhevoi, I. N.; Badelin, V. G.

2015-03-01

Integral enthalpies of dissolution Δsol H m of L-cysteine, L-serine, and L-asparagine in aqueous solutions of 1,3-propylene glycol at organic solvent concentrations of up to 0.26 mole fraction are measured via the thermochemistry of dissolution. Standard enthalpies of dissolution (Δsol H ○) and transfer (Δtr H ○) of amino acids from water to a mixed solvent are calculated. It is found that the calculated enthalpy coefficients of pair interactions of the amino acids with polyhydric alcohol molecules have positive values. The effect the arrangement of the hydroxyl group in the structure of polyhydric alcohols has on the enthalpy of interaction of amino acids in aqueous solutions is revealed. The effect of different types of interactions in solutions and the structural features of biomolecules and cosolvents on the enthalpy of dissolution of amino acids is analyzed.

Dynamic solvophobic effect and its cooperativity in the hydrogen-bonding liquids studied by dielectric and nuclear magnetic resonance relaxation.

PubMed

Yamaguchi, Tsuyoshi; Furuhashi, Hiroki; Matsuoka, Tatsuro; Koda, Shinobu

2008-12-25

The reorientational relaxation of solvent molecules in the mixture of nonpolar solutes and hydrogen-bonding liquids including water, alcohols, and amides are studied by dielectric and 2H-nuclear magnetic resonance (NMR) spin-lattice relaxations. The retardation of the reorientational motion of the solvent by weak solute-solvent interaction is observed in all the solvent systems. On the other hand, no clear correlation between the strength of the solute-solvent interaction and the slowing down of the solvent motion is found in N,N-dimethylacetamide, which suggests the importance of the hydrogen bonding in the dynamic solvophobic effect. The cooperativity of the reorientational relaxation is investigated by the comparison between the collective relaxation measured by the dielectric spectroscopy and the single-molecular reorientation determined by NMR. The modification of the dielectric relaxation time caused by the dissolution of the solute is larger than that of the single-molecular reorientational relaxation time in all the solvents studied here. The effect of the static correlation between the dipole moments of different molecules is calculated from the static dielectric constant, and the effect of the dynamic correlation is estimated. The difference in the effects of the solutes on the collective and single-molecular reorientational relaxation is mainly ascribed to the dynamic cooperativity in the cases of water and alcohols, which is consistent with the picture on the dynamic solvophobicity derived by our previous theoretical analysis (Yamaguchi, T.; Matsuoka, T.; Koda, S. J. Chem. Phys. 2004, 120, 7590). On the other hand, the static correlation plays the principal role in the case of N-methylformamide.

Nuclear magnetic resonance studies of the solvation structures of a high-performance nonaqueous redox flow electrolyte

NASA Astrophysics Data System (ADS)

Deng, Xuchu; Hu, Mary; Wei, Xiaoliang; Wang, Wei; Mueller, Karl T.; Chen, Zhong; Hu, Jian Zhi

2016-03-01

Understanding the solvation structures of electrolytes is important for developing nonaqueous redox flow batteries that hold considerable potential for future large scale energy storage systems. The utilization of an emerging ionic-derivatived ferrocene compound, ferrocenylmethyl dimethyl ethyl ammonium bis(trifluoromethanesulfonyl)imide (Fc1N112-TFSI), has recently overcome the issue of solubility in the supporting electrolyte. In this work, 13C, 1H and 17O NMR investigations were carried out using electrolyte solutions consisting of Fc1N112-TFSI as the solute and the mixed alkyl carbonate as the solvent. It was observed that the spectra of 13C experience changes of chemical shifts while those of 17O undergo linewidth broadening, indicating interactions between solute and solvent molecules. Quantum chemistry calculations of both molecular structures and chemical shifts (13C, 1H and 17O) are performed for interpreting experimental results and for understanding the detailed solvation structures. The results indicate that Fc1N112-TFSI is dissociated at varying degrees in mixed solvent depending on concentrations. At dilute solute concentrations, most Fc1N112+ and TFSI- are fully disassociated with their own solvation shells formed by solvent molecules. At saturated concentration, Fc1N112+-TFSI- contact ion pairs are formed and the solvent molecules are preferentially interacting with the Fc rings rather than interacting with the ionic pendant arm of Fc1N112-TFSI.

Probing the Early Stages of Solvation of cis-Pinate Dianions by Water, Acetonitrile, and Methanol: A Photoelectron Spectroscopy and Theoretical Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hou, Gao-Lei; Kong, Xiang-Tao; Valiev, Marat

2016-01-01

Cis-pinic acid is one of the most important oxidation products of α-pinene – a key monoterpene compound in biogenic emission processes affecting the atmosphere. Molecular level understanding of interactions involved in the cluster formations around cis-pinic acid is an important and necessary prerequisite toward ascertaining its role in the aerosol formation processes. In this work, we studied the structures and energetics of the solvated clusters of cis-pinate (cis-PA²⁻), the doubly deprotonated dicarboxylate of cis-pinic acid, with H₂O, CH₃OH, and CH₃CN by negative ion photoelectron spectroscopy and ab initio theoretical calculations. We found that cis-PA²⁻ prefers being solvated alternately on themore » two -CO₂⁻ groups with increase of solvent coverage, a well-known solvation pattern that has been observed in microhydrated linear dicarboxylate dianion (DC n²⁻) clusters. Experiments and calculations further reveal an intriguing feature for the existence of the asymmetric type isomers for cis-PA2–(H2O)2 and cis-PA²⁻(CH₃OH)₂, in which both solvent molecules interact with only one of the -CO²⁻ groups – a phenomena that has not been observed in DCn²⁻ water clusters and exhibits the subtle effect of the rigid four-membered carbon ring brought in on the cis-PA²⁻ solvation. The dominant interactions between cis-PA²⁻ and solvent molecules are forming bidentate O–···H–O H-bonds for H₂O, O–···H–O and O–···H–C H-bonds for CH₃OH, and tridentate O–···H–C H-bonds for CH₃CN. The formation of inter-solvent H-bonds between H₂O and CH₃CN is found to be favorable in mixed solvent clusters, distinctly different from that between H₂O and CH₃OH. These findings have important implications for understanding the mechanism of cluster growth and nucleation of atmospheric organic aerosols and the nature of structure-function relationship of proteins containing carboxylate groups under various solvent environments.« less

Probing the early stages of solvation of cis-pinate dianions by water, acetonitrile, and methanol: a photoelectron spectroscopy and theoretical study.

PubMed

Hou, Gao-Lei; Kong, Xiang-Tao; Valiev, Marat; Jiang, Ling; Wang, Xue-Bin

2016-02-07

cis-Pinic acid is one of the most important oxidation products of α-pinene--a key monoterpene compound in biogenic emission processes. Molecular level understanding of its interaction with water in cluster formation is an important and necessary prerequisite for ascertaining its role in the aerosol formation processes. In this work, we studied the structures and energetics of the solvated clusters of cis-pinate (cis-PA(2-)), the doubly deprotonated dicarboxylate of cis-pinic acid, with H2O, CH3OH, and CH3CN by negative ion photoelectron spectroscopy and ab initio theoretical calculations. We found that cis-PA(2-) prefers being solvated alternately on the two -CO2(-) groups with increase of solvent coverage, a well-known solvation pattern that has been observed in microhydrated linear dicarboxylate dianion (DCn(2-)) clusters. Experiments and calculations further reveal an intriguing feature for the existence of the asymmetric type isomers for cis-PA(2-)(H2O)2 and cis-PA(2-)(CH3OH)2, in which both solvent molecules interact with only one of the -CO2(-) groups, a phenomenon that has not been observed in DCn(2-) water clusters and exhibits that the subtle effect of the rigid four-membered carbon ring brought on the cis-PA(2-) solvation. The dominant interactions between cis-PA(2-) and solvent molecules form bidentate O(-)...H-O H-bonds for H2O, O(-)...H-O and O(-)...H-C H-bonds for CH3OH, and tridentate O(-)...H-C H-bonds for CH3CN. The formation of inter-solvent H-bonds between H2O and CH3CN is found to be favorable in mixed solvent clusters, different from that between H2O and CH3OH. These findings have important implications for understanding the mechanism of cluster growth and the formation of atmospheric organic aerosols, as well as for rationalizing the nature of structure-function relationship of proteins containing carboxylate groups in various solvent environments.

Universal calculational recipe for solvent-mediated potential: based on a combination of integral equation theory and density functional theory

NASA Astrophysics Data System (ADS)

Zhou, Shiqi

2004-07-01

A universal formalism, which enables calculation of solvent-mediated potential (SMP) between two equal or non-equal solute particles with any shape immersed in solvent reservior consisting of atomic particle and/or polymer chain or their mixture, is proposed by importing a density functional theory externally into OZ equation systems. Only if size asymmetry of the solvent bath components is moderate, the present formalism can calculate the SMP in any complex fluids at the present development stage of statistical mechanics, and therefore avoids all of limitations of previous approaches for SMP. Preliminary calculation indicates the reliability of the present formalism.

Solubility determination of raloxifene hydrochloride in ten pure solvents at various temperatures: Thermodynamics-based analysis and solute-solvent interactions.

PubMed

Ahad, Abdul; Shakeel, Faiyaz; Alfaifi, Omar Ali; Raish, Mohammad; Ahmad, Ajaz; Al-Jenoobi, Fahad I; Al-Mohizea, Abdullah M

2018-06-10

The purpose of the present study was to determine the solubility of raloxifene hydrochloride (RHCl) in ten solvents: water, ethanol, isopropyl alcohol (IPA), ethylene glycol (EG), propylene glycol (PG), polyethylene glycol-400 (PEG-400), Transcutol, 1-butanol, dimethyl sulfoxide (DMSO), and ethyl acetate (EA) at temperatures of 298.2-323.2 K and a pressure of 0.1 MPa. The solubility data obtained was fitted upon "Apelblat and Van't Hoff" equations. The maximum mole fraction solubility of RHCl was obtained in DMSO (5.02 × 10 -2 at 323.2 K), followed by PEG-400 (5.92 × 10 -3 at 323.2 K), EA (3.11 × 10 -3 at 323.2 K), Transcutol (1.22 × 10 -3 at 323.2 K), PG (2.19 × 10 -4 at 323.2 K), 1-butanol (1.96 × 10 -4 at 323.2 K), IPA (1.47 × 10 -4 at 323.2 K), ethanol (7.90 × 10 -5 at 323.2 K), EG (6.65 × 10 -5 at 323.2 K), and water (3.60 × 10 -5 at 323.2 K). Similar fashions were noticed at each studied temperature. The higher solubility of RHCl in DMSO, PEG-400, EA, and Transcutol was possibly referable to their lower polarity in comparison with water. The molecular interactions between the solute and solvent molecules were estimated by calculating parameters like activity coefficients, and more prominent solute-solvent molecular interactions were noted for RHCl-DMSO, RHCl-EA, and RHCl-PEG-400 in comparison with the other solute-solvent combinations. The outcomes of the "apparent thermodynamic analysis" showed that the dissolution of RHCl was "endothermic, spontaneous and entropy-driven" in all investigated solvents. The obtained solubility data of RHCl in commonly used solvents could be useful in the purification, recrystallization, and dosage form design of the drug. Copyright © 2018 Elsevier B.V. All rights reserved.

Effects analysis of substituent characteristics and solvents on the photodegradation of polybrominated diphenyl ethers.

PubMed

Jiang, Long; Qiu, Youli; Li, Yu

2017-10-01

The ultraviolet spectra and electron transition information of 209 polybrominated diphenyl ethers (PBDEs) in gas were first calculated via time-dependent density functional theory using Gaussian 09 software. The main and second-order interactional effects of substituent characteristics on the photodegradation of PBDEs were then analysed using a full factorial experimental design. Solvent effects were considered to research the effect and promotion mechanism of solvent molecules on the photodegradation of PBDEs compared with that in gas. The results showed that the introduction of substituents at each position promoted excitation of PBDEs from their ground states to excited states to induce photodegradation. The different positions affected the photodegradation of PBDEs with magnitudes of para > meta > ortho. The congeners with a concentrated distribution of substituents can always be photodegraded more easily than those with separated substituents. From the viewpoint of light-induced reactions, the electron transfer reactions between molecules of PBDE* T1 and Solvent* T1 are the main driving force for the enhanced photodegradation of PBDEs in solvents compared with that in gas. Copyright © 2017 Elsevier Ltd. All rights reserved.

On the Helix Propensity in Generalized Born Solvent Descriptions of Modeling the Dark Proteome

PubMed Central

Olson, Mark A.

2017-01-01

Intrinsically disordered proteins that populate the so-called “Dark Proteome” offer challenging benchmarks of atomistic simulation methods to accurately model conformational transitions on a multidimensional energy landscape. This work explores the application of parallel tempering with implicit solvent models as a computational framework to capture the conformational ensemble of an intrinsically disordered peptide derived from the Ebola virus protein VP35. A recent X-ray crystallographic study reported a protein-peptide interface where the VP35 peptide underwent a folding transition from a disordered form to a helix-β-turn-helix topological fold upon molecular association with the Ebola protein NP. An assessment is provided of the accuracy of two generalized Born solvent models (GBMV2 and GBSW2) using the CHARMM force field and applied with temperature-based replica exchange dynamics to calculate the disorder propensity of the peptide and its probability density of states in a continuum solvent. A further comparison is presented of applying an explicit/implicit solvent hybrid replica exchange simulation of the peptide to determine the effect of modeling water interactions at the all-atom resolution. PMID:28197405

On the Helix Propensity in Generalized Born Solvent Descriptions of Modeling the Dark Proteome.

PubMed

Olson, Mark A

2017-01-01

Intrinsically disordered proteins that populate the so-called "Dark Proteome" offer challenging benchmarks of atomistic simulation methods to accurately model conformational transitions on a multidimensional energy landscape. This work explores the application of parallel tempering with implicit solvent models as a computational framework to capture the conformational ensemble of an intrinsically disordered peptide derived from the Ebola virus protein VP35. A recent X-ray crystallographic study reported a protein-peptide interface where the VP35 peptide underwent a folding transition from a disordered form to a helix-β-turn-helix topological fold upon molecular association with the Ebola protein NP. An assessment is provided of the accuracy of two generalized Born solvent models (GBMV2 and GBSW2) using the CHARMM force field and applied with temperature-based replica exchange dynamics to calculate the disorder propensity of the peptide and its probability density of states in a continuum solvent. A further comparison is presented of applying an explicit/implicit solvent hybrid replica exchange simulation of the peptide to determine the effect of modeling water interactions at the all-atom resolution.

Co-solvent effects on reaction rate and reaction equilibrium of an enzymatic peptide hydrolysis.

PubMed

Wangler, A; Canales, R; Held, C; Luong, T Q; Winter, R; Zaitsau, D H; Verevkin, S P; Sadowski, G

2018-04-25

This work presents an approach that expresses the Michaelis constant KaM and the equilibrium constant Kth of an enzymatic peptide hydrolysis based on thermodynamic activities instead of concentrations. This provides KaM and Kth values that are independent of any co-solvent. To this end, the hydrolysis reaction of N-succinyl-l-phenylalanine-p-nitroanilide catalysed by the enzyme α-chymotrypsin was studied in pure buffer and in the presence of the co-solvents dimethyl sulfoxide, trimethylamine-N-oxide, urea, and two salts. A strong influence of the co-solvents on the measured Michaelis constant (KM) and equilibrium constant (Kx) was observed, which was found to be caused by molecular interactions expressed as activity coefficients. Substrate and product activity coefficients were used to calculate the activity-based values KaM and Kth for the co-solvent free reaction. Based on these constants, the co-solvent effect on KM and Kx was predicted in almost quantitative agreement with the experimental data. The approach presented here does not only reveal the importance of understanding the thermodynamic non-ideality of reactions taking place in biological solutions and in many technological applications, it also provides a framework for interpreting and quantifying the multifaceted co-solvent effects on enzyme-catalysed reactions that are known and have been observed experimentally for a long time.

Effect of Solvent and Substrate on the Surface Binding Mode of Carboxylate-Functionalized Aromatic Molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Domenico, Janna; Foster, Michael E.; Spoerke, Erik D.

Here, the efficiency of dye-sensitized solar cells (DSSCs) is strongly influenced by dye molecule orientation and interactions with the substrate. Understanding the factors controlling the surface orientation of sensitizing organic molecules will aid in the improvement of both traditional DSSCs and other devices that integrate molecular linkers at interfaces. Here, we describe a general approach to understand relative dye–substrate orientation and provide analytical expressions predicting orientation. We consider the effects of substrate, solvent, and protonation state on dye molecule orientation. In the absence of solvent, our model predicts that most carboxylic acid-functionalized molecules prefer to lie flat (parallel) on themore » surface, due to van der Waals interactions, as opposed to a tilted orientation with respect to the surface that is favored by covalent bonding of the carboxylic acid group to the substrate. When solvation effects are considered, however, the molecules are predicted to orient perpendicular to the surface. We extend this approach to help understand and guide the orientation of metal–organic framework (MOF) thin-film growth on various metal–oxide substrates. A two-part analytical model is developed on the basis of the results of DFT calculations and ab initio MD simulations that predicts the binding energy of a molecule by chemical and dispersion forces on rutile and anatase TiO 2 surfaces, and quantifies the dye solvation energy for two solvents. The model is in good agreement with the DFT calculations and enables rapid prediction of dye molecule and MOF linker binding preference on the basis of the size of the adsorbing molecule, identity of the surface, and the solvent environment. We establish the threshold molecular size, governing dye molecule orientation, for each condition.« less

Effect of Solvent and Substrate on the Surface Binding Mode of Carboxylate-Functionalized Aromatic Molecules

DOE PAGES

Domenico, Janna; Foster, Michael E.; Spoerke, Erik D.; ...

2018-04-25

Here, the efficiency of dye-sensitized solar cells (DSSCs) is strongly influenced by dye molecule orientation and interactions with the substrate. Understanding the factors controlling the surface orientation of sensitizing organic molecules will aid in the improvement of both traditional DSSCs and other devices that integrate molecular linkers at interfaces. Here, we describe a general approach to understand relative dye–substrate orientation and provide analytical expressions predicting orientation. We consider the effects of substrate, solvent, and protonation state on dye molecule orientation. In the absence of solvent, our model predicts that most carboxylic acid-functionalized molecules prefer to lie flat (parallel) on themore » surface, due to van der Waals interactions, as opposed to a tilted orientation with respect to the surface that is favored by covalent bonding of the carboxylic acid group to the substrate. When solvation effects are considered, however, the molecules are predicted to orient perpendicular to the surface. We extend this approach to help understand and guide the orientation of metal–organic framework (MOF) thin-film growth on various metal–oxide substrates. A two-part analytical model is developed on the basis of the results of DFT calculations and ab initio MD simulations that predicts the binding energy of a molecule by chemical and dispersion forces on rutile and anatase TiO 2 surfaces, and quantifies the dye solvation energy for two solvents. The model is in good agreement with the DFT calculations and enables rapid prediction of dye molecule and MOF linker binding preference on the basis of the size of the adsorbing molecule, identity of the surface, and the solvent environment. We establish the threshold molecular size, governing dye molecule orientation, for each condition.« less

A QSPR study on the solvent-induced frequency shifts of acetone and dimethyl sulfoxide in organic solvents.

PubMed

Ou, Yu Heng; Chang, Chia Ming; Chen, Ying Shao

2016-06-05

In this study, solvent-induced frequency shifts (SIFS) in the infrared spectrum of acetone and dimethyl sulfoxide in organic solvents were investigated by using four types of quantum-chemical reactivity descriptors. The results showed that the SIFS of acetone is mainly affected by the electron-acceptance chemical potential and the maximum nucleophilic condensed local softness of organic solvents, which represent the electron flow and the polarization between acetone and solvent molecules. On the other hand, the SIFS of dimethyl sulfoxide changes with the maximum positive charge of hydrogen atom and the inverse of apolar surface area of solvent molecules, showing that the electrostatic and hydrophilic interactions are main mechanisms between dimethyl sulfoxide and solvent molecules. The introduction of the four-element theory model-based quantitative structure-property relationship approach improved the assessing quality and provided a basis for interpreting the solute-solvent interactions. Copyright © 2016 Elsevier B.V. All rights reserved.

Aprotic solvents effect on the UV-visible absorption spectra of bixin.

PubMed

Rahmalia, Winda; Fabre, Jean-François; Usman, Thamrin; Mouloungui, Zéphirin

2014-10-15

We describe here the effects of aprotic solvents on the spectroscopic characteristics of bixin. Bixin was dissolved in dimethyl sulfoxide, acetone, dichloromethane, ethyl acetate, chloroform, dimethyl carbonate, cyclohexane and hexane, separately, and its spectra in the resulting solutions were determined by UV-visible spectrophotometry at normal pressure and room temperature. We analyzed the effect of aprotic solvents on λmax according to Onsager cavity model and Hansen theory, and determined the approximate absorption coefficient with the Beer-Lambert law. We found that the UV-visible absorption spectra of bixin were found to be solvent dependent. The S0→S2 transition energy of bixin in solution was dependent principally on the refractive index of the solvents and the bixin-solvent dispersion interaction. There was a small influence of the solvents dielectric constant, permanent dipole interaction and hydrogen bonding occurred between bixin and solvents. The absorbance of bixin in various solvents, with the exception of hexane, increased linearly with concentration. Copyright © 2014 Elsevier B.V. All rights reserved.

Aprotic solvents effect on the UV-visible absorption spectra of bixin

NASA Astrophysics Data System (ADS)

Rahmalia, Winda; Fabre, Jean-François; Usman, Thamrin; Mouloungui, Zéphirin

2014-10-01

We describe here the effects of aprotic solvents on the spectroscopic characteristics of bixin. Bixin was dissolved in dimethyl sulfoxide, acetone, dichloromethane, ethyl acetate, chloroform, dimethyl carbonate, cyclohexane and hexane, separately, and its spectra in the resulting solutions were determined by UV-visible spectrophotometry at normal pressure and room temperature. We analyzed the effect of aprotic solvents on λmax according to Onsager cavity model and Hansen theory, and determined the approximate absorption coefficient with the Beer-Lambert law. We found that the UV-visible absorption spectra of bixin were found to be solvent dependent. The S0 → S2 transition energy of bixin in solution was dependent principally on the refractive index of the solvents and the bixin-solvent dispersion interaction. There was a small influence of the solvents dielectric constant, permanent dipole interaction and hydrogen bonding occurred between bixin and solvents. The absorbance of bixin in various solvents, with the exception of hexane, increased linearly with concentration.

Polar and low polar solvents media effect on dipole moments of some diazo Sudan dyes

NASA Astrophysics Data System (ADS)

Zakerhamidi, M. S.; Golghasemi Sorkhabi, Sh.; Shamkhali, A. N.

2014-06-01

Absorption and fluorescence spectra of three Sudan dyes (SudanIII, SudanIV and Sudan black B) were recorded in various solvents with different polarity in the range of 300-800 nm, at room temperature. The solvatochromic method was used to investigate dipole moments of these dyes in ground and excited states, in different media. The solvatochromic behavior of these substances and their solvent-solute interactions were analyzed via solvent polarity parameters. Obtained results express the effects of solvation on tautomerism and molecular configuration (geometry) of Sudan dyes in solvent media with different polarity. Furthermore, analyze of solvent-solute interactions and value of ground and excited states dipole moments suggests different forms of resonance structures for Sudan dyes in polar and low-polar solvents.

Determination of Abraham model solute descriptors for the monomeric and dimeric forms of trans-cinnamic acid using measured solubilities from the Open Notebook Science Challenge.

PubMed

Bradley, Jean-Claude; Abraham, Michael H; Acree, William E; Lang, Andrew Sid; Beck, Samantha N; Bulger, David A; Clark, Elizabeth A; Condron, Lacey N; Costa, Stephanie T; Curtin, Evan M; Kurtu, Sozit B; Mangir, Mark I; McBride, Matthew J

2015-01-01

Calculating Abraham descriptors from solubility values requires that the solute have the same form when dissolved in all solvents. However, carboxylic acids can form dimers when dissolved in non-polar solvents. For such compounds Abraham descriptors can be calculated for both the monomeric and dimeric forms by treating the polar and non-polar systems separately. We illustrate the method of how this can be done by calculating the Abraham descriptors for both the monomeric and dimeric forms of trans-cinnamic acid, the first time that descriptors for a carboxylic acid dimer have been obtained. Abraham descriptors were calculated for the monomeric form of trans-cinnamic acid using experimental solubility measurements in polar solvents from the Open Notebook Science Challenge together with a number of water-solvent partition coefficients from the literature. Similarly, experimental solubility measurements in non-polar solvents were used to determine Abraham descriptors for the trans-cinnamic acid dimer. Abraham descriptors were calculated for both the monomeric and dimeric forms of trans-cinnamic acid. This allows for the prediction of further solubilities of trans-cinnamic acid in both polar and non-polar solvents with an error of about 0.10 log units. Graphical abstractMolar concentration of trans-cinnamic acid in various polar and non-polar solvents.

Activity and conformation of lysozyme in molecular solvents, protic ionic liquids (PILs) and salt-water systems.

PubMed

Wijaya, Emmy C; Separovic, Frances; Drummond, Calum J; Greaves, Tamar L

2016-09-21

Improving protein stabilisation is important for the further development of many applications in the pharmaceutical, specialty chemical, consumer product and agricultural sectors. However, protein stabilization is highly dependent on the solvent environment and, hence, it is very complex to tailor protein-solvent combinations for stable protein maintenance. Understanding solvent features that govern protein stabilization will enable selection or design of suitable media with favourable solution environments to retain protein native conformation. In this work the structural conformation and activity of lysozyme in 29 solvent systems were investigated to determine the role of various solvent features on the stability of the enzyme. The solvent systems consisted of 19 low molecular weight polar solvents and 4 protic ionic liquids (PILs), both at different water content levels, and 6 aqueous salt solutions. Small angle X-ray scattering, Fourier transform infrared spectroscopy and UV-vis spectroscopy were used to investigate the tertiary and secondary structure of lysozyme along with the corresponding activity in various solvation systems. At low non-aqueous solvent concentrations (high water content), the presence of solvents and salts generally maintained lysozyme in its native structure and enhanced its activity. Due to the presence of a net surface charge on lysozyme, electrostatic interactions in PIL-water systems and salt solutions enhanced lysozyme activity more than the specific hydrogen-bond interactions present in non-ionic molecular solvents. At higher solvent concentrations (lower water content), solvents with a propensity to exhibit the solvophobic effect, analogous to the hydrophobic effect in water, retained lysozyme native conformation and activity. This solvophobic effect was observed particularly for solvents which contained hydroxyl moieties. Preferential solvophobic effects along with bulky chemical structures were postulated to result in less competition with water at the specific hydration layer around the protein, thus reducing protein-solvent interactions and retaining lysozyme's native conformation. The structure-property links established in this study are considered to be applicable to other proteins.

The docking of chiral analytes on proline-based chiral stationary phases: A molecular dynamics study of selectivity.

PubMed

Ashtari, M; Cann, N M

2015-08-28

Molecular dynamics simulations are employed to examine the selectivity of four proline-based chiral stationary phases in two solvent environments, a relatively apolar n-hexane/2-propanol solvent and a polar water/methanol solvent. The four chiral surfaces are based on a BOC-terminated diproline, a TMA-terminated diproline, a TMA-terminated triproline and a TMA-terminated hexaproline. This range of chiral selectors allows an analysis of the impact of oligomer length and terminal group on selectivity while the two solvent environments indicate the impact of solvent hydrogen bonding and polarity. The selector-analyte interactions are examined for six closely related analytes that each have an aromatic moiety, a hydrogen, and an alcohol group directly bonded to the stereocenter. The analytes differ in the nature of the aromatic group (phenyl or anthracyl), in the attachment point (to the central ring or a side ring in the anthracyl), and in the fourth group bonded to the carbon (CH3, CF3, or C2H5). For each of the 48 solvent+selector+analyte systems, selectivity factors are calculated and, when possible, compared to experiment. The docking mode for these proline-based selectors is analyzed. Copyright © 2015 Elsevier B.V. All rights reserved.

Solubility of pharmaceuticals: A comparison between SciPharma, a PC-SAFT-based approach, and NRTL-SAC

NASA Astrophysics Data System (ADS)

Bouillot, Baptiste; Spyriouni, Theodora; Teychené, Sébastien; Biscans, Béatrice

2017-04-01

The solubility of seven pharmaceutical compounds (paracetamol, benzoic acid, 4-aminobenzoic acid, salicylic acid, ibuprofen, naproxen and temazepam) in pure and mixed solvents as a function of temperature is calculated with SciPharma, a semi-empirical approach based on PC-SAFT, and the NRTL-SAC model. To conduct a fair comparison between the approaches, the parameters of the compounds were regressed against the same solubility data, chosen to account for hydrophilic, polar and hydrophobic interactions. Only these solubility data were used by both models for predicting solubility in other pure and mixed solvents for which experimental data were available for comparison. A total of 386 pure solvent data points were used for the comparison comprising one or more temperatures per solvent. SciPharma is found to be more accurate than NRTL-SAC on the pure solvent data used especially in the description of the temperature dependence. This is due to the appropriate parameterization of the pharmaceuticals and the temperature-dependent description of the activity coefficient in PC-SAFT. The solubility in mixed solvents is predicted satisfactorily with SciPharma. NRTL-SAC tends to overestimate the solubility in aqueous solutions of alcohols or shows invariable solubility with composition in other cases.

Preferential Solvation of an Asymmetric Redox Molecule

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, Kee Sung; Rajput, Nav Nidhi; Vijayakumar, M.

2016-12-15

The fundamental correlations between inter-molecular interactions, solvation structure and functionality of electrolytes are in many cases unknown, particularly for multi-component liquid systems. In this work, we explore such correlations by investigating the complex interplay between solubility and solvation structure for the electrolyte system comprising N-(ferrocenylmethyl)-N,N-dimethyl-N-ethylammonium bistrifluoromethylsulfonimide (Fc1N112-TFSI) dissolved in a ternary carbonate solvent mixture using combined NMR relaxation and computational analyses. Probing the evolution of the solvent-solvent, ion-solvent and ion-ion interactions with an increase in solute concentration provides a molecular level understanding of the solubility limit of the Fc1N112-TFSI system. An increase in solute con-centration leads to pronounced Fc1N112-TFSI contact-ionmore » pair formation by diminishing solvent-solvent and ion-solvent type interactions. At the solubility limit, the precipitation of solute is initiated through agglomeration of contact-ion pairs due to overlapping solvation shells.« less

Solute-solvent interactions in solutions of 2-hydroxy-5-chloro-3-nitroacetophenone isonicotinoylhydrazone in N, N-dimethylformamide at 298-313 K according to ultrasonic and viscometric data

NASA Astrophysics Data System (ADS)

Dikkar, A. B.; Pethe, G. B.; Aswar, A. S.

2015-12-01

Density (ρ), speed of sound ( u), and viscosity (η), measurements have been carried on 2-hydroxy- 5-chloro-3-nitroacetophenone isonicotinoylhydrazone (HCNAIH) in N, N-dimethylformamide at 298.15, 303.15, 308.15, and 313.15 K. Adiabatic compressibility (βs), intermolecular free length ( L f), acoustic impedance ( Z), internal pressure ( P int), the apparent molar volume ( V w), limiting apparent molar volume ( V w 0), partial molar expansibility (wE 0), apparent molar adiabatic compressibility ( K w), limiting apparent molar adiabatic compressibility ( K w 0), viscosity B coefficients of Jones-Dole equation have been calculated. The activation free energy (Δμ 2 0 *) for viscous flow in solution have been calculated from B coefficient and partial molar volume data. The calculated parameters are used to interpret the solute-solvent interactions and structure forming/breaking ability of solute in DMF.

FT-IR spectroscopy combined with DFT calculation to explore solvent effects of vinyl acetate

NASA Astrophysics Data System (ADS)

Chen, Yi; Zhang, Hui; Liu, Qing

The infrared vibration frequencies of vinyl acetate (VAc) in 18 different solvents were theoretically computed at Density Function Theory (DFT) B3LYP/6-311G* level based on Polarizable Continuum Model (PCM) and experimentally recorded by FT-IR spectroscopy. The solvent-induced long-range bulk electrostatic solvation free energies of VAc (ΔGelec) were calculated by the SMD model. The Cdbnd O stretching vibration frequencies of VAc were utilized as a measure of the chemical reactivities of the Cdbnd C group in VAc. The calculated and experimental Cdbnd O stretching vibration frequencies of VAc (νcal(Cdbnd O) and νexp(Cdbnd O)) were correlated with empirical solvent parameters including the KBM equation, the Swain equation and the linear solvation energy relationships (LSER). Through ab initio calculation, assignments of the two Cdbnd O absorption bands of VAc in alcohol solvents were achieved. The PCM, SMD and ab initio calculation offered supporting evidence to explain the FT-IR experimental observations from differing aspects.

Quantum Monte Carlo studies of solvated systems

NASA Astrophysics Data System (ADS)

Schwarz, Kathleen; Letchworth Weaver, Kendra; Arias, T. A.; Hennig, Richard G.

2011-03-01

Solvation qualitatively alters the energetics of diverse processes from protein folding to reactions on catalytic surfaces. An explicit description of the solvent in quantum-mechanical calculations requires both a large number of electrons and exploration of a large number of configurations in the phase space of the solvent. These problems can be circumvented by including the effects of solvent through a rigorous classical density-functional description of the liquid environment, thereby yielding free energies and thermodynamic averages directly, while eliminating the need for explicit consideration of the solvent electrons. We have implemented and tested this approach within the CASINO Quantum Monte Carlo code. Our method is suitable for calculations in any basis within CASINO, including b-spline and plane wave trial wavefunctions, and is equally applicable to molecules, surfaces, and crystals. For our preliminary test calculations, we use a simplified description of the solvent in terms of an isodensity continuum dielectric solvation approach, though the method is fully compatible with more reliable descriptions of the solvent we shall employ in the future.

Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

PubMed Central

Nagy, Peter I.

2014-01-01

A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed. PMID:25353178

TES buffer-induced phase separation of aqueous solutions of several water-miscible organic solvents at 298.15 K: phase diagrams and molecular dynamic simulations.

PubMed

Taha, Mohamed; Lee, Ming-Jer

2013-06-28

Water and the organic solvents tetrahydrofuran, 1,3-dioxolane, 1,4-dioxane, 1-propanol, 2-propanol, tert-butanol, acetonitrile, or acetone are completely miscible in all proportions at room temperature. Here, we present new buffering-out phase separation systems that the above mentioned organic aqueous solutions can be induced to form two liquid phases in the presence of a biological buffer 2-[[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]amino]ethanesulfonic acid (TES). The lower liquid phase is rich in water and buffer, and the upper phase is organic rich. This observation has both practical and mechanistic interests. The phase diagrams of these systems were constructed by experimental measurements at ambient conditions. Molecular dynamic (MD) simulations were performed for TES + water + THF system to understand the interactions between TES, water, and organic solvent at molecular level. Several composition-sets for this system, beyond and inside the liquid-liquid phase-splitting region, have been simulated. Interestingly, the MD simulation for compositions inside the phase separation region showed that THF molecules are forced out from the water network to start forming a new liquid phase. The hydrogen-bonds, hydrogen-bonds lifetimes, hydrogen-bond energies, radial distribution functions, coordination numbers, the electrostatic interactions, and the van der Waals interactions between the different pairs have been calculated. Additionally, MD simulations for TES + water + tert-butanol∕acetonitrile∕acetone phase separation systems were simulated. The results from MD simulations provide an explanation for the buffering-out phenomena observed in [TES + water + organic solvent] systems by a mechanism controlled by the competitive interactions of the buffer and the organic solvent with water. The molecular mechanism reported here is helpful for designing new benign separation materials.

STABILITY OF A CYLINDRICAL SOLUTE-SOLVENT INTERFACE: EFFECT OF GEOMETRY, ELECTROSTATICS, AND HYDRODYNAMICS.

PubMed

Li, B O; Sun, Hui; Zhou, Shenggao

The solute-solvent interface that separates biological molecules from their surrounding aqueous solvent characterizes the conformation and dynamics of such molecules. In this work, we construct a solvent fluid dielectric boundary model for the solvation of charged molecules and apply it to study the stability of a model cylindrical solute-solvent interface. The motion of the solute-solvent interface is defined to be the same as that of solvent fluid at the interface. The solvent fluid is assumed to be incompressible and is described by the Stokes equation. The solute is modeled simply by the ideal-gas law. All the viscous force, hydrostatic pressure, solute-solvent van der Waals interaction, surface tension, and electrostatic force are balanced at the solute-solvent interface. We model the electrostatics by Poisson's equation in which the solute-solvent interface is treated as a dielectric boundary that separates the low-dielectric solute from the high-dielectric solvent. For a cylindrical geometry, we find multiple cylindrically shaped equilibrium interfaces that describe polymodal (e.g., dry and wet) states of hydration of an underlying molecular system. These steady-state solutions exhibit bifurcation behavior with respect to the charge density. For their linearized systems, we use the projection method to solve the fluid equation and find the dispersion relation. Our asymptotic analysis shows that, for large wavenumbers, the decay rate is proportional to wavenumber with the proportionality half of the ratio of surface tension to solvent viscosity, indicating that the solvent viscosity does affect the stability of a solute-solvent interface. Consequences of our analysis in the context of biomolecular interactions are discussed.

Solvent effects on adsorption of CO over CuCl(1 1 1) surface: A density functional theory study

NASA Astrophysics Data System (ADS)

Zhang, Riguang; Ling, Lixia; Wang, Baojun; Huang, Wei

2010-09-01

DFT calculations have been performed to investigate the effect of dielectric responses of the solvent environment on the CO adsorption over CuCl(1 1 1) surface by using COSMO (conductor-like solvent model) model in Dmol 3. Different dielectric constants, including vacuum, liquid paraffin, methylene chloride, methanol and water solution, are considered. The effects of solvent model on the structural parameters, adsorption energies and vibrational frequency of CO adsorption over CuCl(1 1 1) surface have been investigated. The calculation results suggest that solvent effects can improve the stability of CO adsorption and reduce the intensity of C-O bond, which might mean that solvent is in favor of C-O bond activation and improve the reaction activity of oxidative carbonylation in a slurry reactor.

3DRISM-HI-D2MSA: an improved analytic theory to compute solvent structure around hydrophobic solutes with proper treatment of solute–solvent electrostatic interactions

NASA Astrophysics Data System (ADS)

Cao, Siqin; Zhu, Lizhe; Huang, Xuhui

2018-04-01

The 3D reference interaction site model (3DRISM) is a powerful tool to study the thermodynamic and structural properties of liquids. However, for hydrophobic solutes, the inhomogeneity of the solvent density around them poses a great challenge to the 3DRISM theory. To address this issue, we have previously introduced the hydrophobic-induced density inhomogeneity theory (HI) for purely hydrophobic solutes. To further consider the complex hydrophobic solutes containing partial charges, here we propose the D2MSA closure to incorporate the short-range and long-range interactions with the D2 closure and the mean spherical approximation, respectively. We demonstrate that our new theory can compute the solvent distributions around real hydrophobic solutes in water and complex organic solvents that agree well with the explicit solvent molecular dynamics simulations.

Volumetric Properties of the Ionic Liquid, 1-Butyl-3-methylimidazolium Tetrafluoroborate, in Organic Solvents at T = 298.15K

NASA Astrophysics Data System (ADS)

Shekaari, Hemayat; Zafarani-Moattar, Mohammed Taghi

2008-04-01

Apparent molar volumes, V_φ , and compressibilities, kappa _φ , of 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIm][BF4]) have been determined from precise density and speed-of-sound measurements in organic solvents, methanol (MeOH), acetonitrile (MeCN), tetrahydrofuran (THF), N, N-dimethylacetamide (DMA), and dimethylsulfoxide (DMSO) in the dilute region of the ionic liquid. Corresponding values at infinite dilution are estimated by the Redlich-Mayer and Pitzer equations. The results have been interpreted by the interaction of the [BMIm][BF4] in the organic solvents. Results show that the structure and dielectric constant of the organic solvents play an important role for the ion-solvent interactions in these mixtures. It was found that the strength of interaction between [BMIm][BF4] with the studied organic solvents has the order DMSO > DMA > MeOH > MeCN > THF.

Prediction of the solvent affecting site and the computational design of stable Candida antarctica lipase B in a hydrophilic organic solvent.

PubMed

Park, Hyun June; Joo, Jeong Chan; Park, Kyungmoon; Kim, Yong Hwan; Yoo, Young Je

2013-02-10

Enzyme reactions in organic solvent such as for organic synthesis have great industrial potential. However, enzymes lose their stability in hydrophilic organic solvents due to the deformation of the enzyme by the solvent. It is thus important to enhance the stability of enzymes in hydrophilic organic solvents. Previous approaches have not considered on the interaction between enzymes and solvents due to the lack of information. In this study, the structural motions of the enzyme in methanol cosolvent and the interaction between the enzyme surface and the solvent molecule were investigated using molecular dynamics simulation (MD). By analyzing the MD simulation results, the surface residues of Candida antarctica lipase B (CalB) with higher root mean square deviation (RMSD) in a methanol solvent were considered as methanol affecting site and selected for site-directed mutagenesis. The methanol affecting site was computationally redesigned by lowering the RMSD. Among the candidate mutants, the A8T, A92E, N97Q and T245S mutants showed higher organic solvent stability at various methanol concentrations. The rational approach developed in this study could be applied to the stabilization of other industrial enzymes used in organic solvents. Copyright © 2012 Elsevier B.V. All rights reserved.

Insights into the effects of solvent properties in graphene based electric double-layer capacitors with organic electrolytes

NASA Astrophysics Data System (ADS)

Zhang, Shuo; Bo, Zheng; Yang, Huachao; Yang, Jinyuan; Duan, Liangping; Yan, Jianhua; Cen, Kefa

2016-12-01

Organic electrolytes are widely used in electric double-layer capacitors (EDLCs). In this work, the microstructure of planar graphene-based EDLCs with different organic solvents are investigated with molecular dynamics simulations. Results show that an increase of solvent polarity could weaken the accumulation of counter-ions nearby the electrode surface, due to the screen of electrode charges and relatively lower ionic desolvation. It thus suggests that solvents with low polarity could be preferable to yield high EDL capacitance. Meanwhile, the significant effects of the size and structure of solvent molecules are reflected by non-electrostatic molecule-electrode interactions, further influencing the adsorption of solvent molecules on electrode surface. Compared with dimethyl carbonate, γ-butyrolactone, and propylene carbonate, acetonitrile with relatively small-size and linear structure owns weak non-electrostatic interactions, which favors the easy re-orientation of solvent molecules. Moreover, the shift of solvent orientation in surface layer, from parallel orientation to perpendicular orientation relative to the electrode surface, deciphers the solvent twin-peak behavior near negative electrode. The as-obtained insights into the roles of solvent properties on the interplays among particles and electrodes elucidate the solvent influences on the microstructure and capacitive behavior of EDLCs using organic electrolytes.

Docking glycosaminoglycans to proteins: analysis of solvent inclusion

NASA Astrophysics Data System (ADS)

Samsonov, Sergey A.; Teyra, Joan; Pisabarro, M. Teresa

2011-05-01

Glycosaminoglycans (GAGs) are anionic polysaccharides, which participate in key processes in the extracellular matrix by interactions with protein targets. Due to their charged nature, accurate consideration of electrostatic and water-mediated interactions is indispensable for understanding GAGs binding properties. However, solvent is often overlooked in molecular recognition studies. Here we analyze the abundance of solvent in GAG-protein interfaces and investigate the challenges of adding explicit solvent in GAG-protein docking experiments. We observe PDB GAG-protein interfaces being significantly more hydrated than protein-protein interfaces. Furthermore, by applying molecular dynamics approaches we estimate that about half of GAG-protein interactions are water-mediated. With a dataset of eleven GAG-protein complexes we analyze how solvent inclusion affects Autodock 3, eHiTs, MOE and FlexX docking. We develop an approach to de novo place explicit solvent into the binding site prior to docking, which uses the GRID program to predict positions of waters and to locate possible areas of solvent displacement upon ligand binding. To investigate how solvent placement affects docking performance, we compare these results with those obtained by taking into account information about the solvent position in the crystal structure. In general, we observe that inclusion of solvent improves the results obtained with these methods. Our data show that Autodock 3 performs best, though it experiences difficulties to quantitatively reproduce experimental data on specificity of heparin/heparan sulfate disaccharides binding to IL-8. Our work highlights the current challenges of introducing solvent in protein-GAGs recognition studies, which is crucial for exploiting the full potential of these molecules for rational engineering.

Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations.

PubMed

Godschalk, Frithjof; Genheden, Samuel; Söderhjelm, Pär; Ryde, Ulf

2013-05-28

Molecular mechanics with generalised Born and surface area solvation (MM/GBSA) is a popular method to calculate the free energy of the binding of ligands to proteins. It involves molecular dynamics (MD) simulations with an explicit solvent of the protein-ligand complex to give a set of snapshots for which energies are calculated with an implicit solvent. This change in the solvation method (explicit → implicit) would strictly require that the energies are reweighted with the implicit-solvent energies, which is normally not done. In this paper we calculate MM/GBSA energies with two generalised Born models for snapshots generated by the same methods or by explicit-solvent simulations for five synthetic N-acetyllactosamine derivatives binding to galectin-3. We show that the resulting energies are very different both in absolute and relative terms, showing that the change in the solvent model is far from innocent and that standard MM/GBSA is not a consistent method. The ensembles generated with the various solvent models are quite different with root-mean-square deviations of 1.2-1.4 Å. The ensembles can be converted to each other by performing short MD simulations with the new method, but the convergence is slow, showing mean absolute differences in the calculated energies of 6-7 kJ mol(-1) after 2 ps simulations. Minimisations show even slower convergence and there are strong indications that the energies obtained from minimised structures are different from those obtained by MD.

Anion-π aromatic neutral tweezers complexes: are they stable in polar solvents?

PubMed

Sánchez-Lozano, Marta; Otero, Nicolás; Hermida-Ramón, Jose M; Estévez, Carlos M; Mandado, Marcos

2011-03-17

The impact of the solvent environment on the stabilization of the complexes formed by fluorine (T-F) and cyanide (T-CN) substituted tweezers with halide anions has been investigated theoretically. The study was carried out using computational methodologies based on density functional theory (DFT) and symmetry adapted perturbation theory (SAPT). Interaction energies were obtained at the M05-2X/6-31+G* level. The obtained results show a large stability of the complexes in solvents with large dielectric constant and prove the suitability of these molecular tweezers as potential hosts for anion recognition in solution. A detailed analysis of the effects of the solvent on the electron withdrawing ability of the substituents and its influence on the complex stability has been performed. In particular, the interaction energy in solution was split up into intermonomer and solvent-complex terms. In turn, the intermonomer interaction energy was partitioned into electrostatic, exchange, and polarization terms. Polar resonance structures in T-CN complexes are favored by polar solvents, giving rise to a stabilization of the intermonomer interaction, the opposite is found for T-F complexes. The solvent-complex energy increases with the polarity of the solvent in T-CN complexes, nonetheless the energy reaches a maximum and then decreases slowly in T-F complexes. An electron density analysis was also performed before and after complexation, providing an explanation to the trends followed by the interaction energies and their different components in solution.

Effects of water-alcohol binary solvents on the thermochemical characteristics of L-tryptophane dissolution at 298.15 K

NASA Astrophysics Data System (ADS)

Badelin, V. G.; Smirnov, V. I.

2013-01-01

The enthalpies of L-tryptophane solution in water-methanol, water-ethanol, water-1-propanol, and water-2-propanol mixtures at alcohol concentrations of x 2 = 0-0.4 mole fractions were measured by calorimetry. The standard enthalpies of L-tryptophane solution (Δsol H ∘) and transfer (Δtr H ∘) from water to the binary solvent were calculated. The influence of the composition of the water-alcohol mixture and the structure and properties of L-tryptophane on the enthalpy characteristics of the latter was considered. The enthalpy coefficients of pair interactions ( h xy ) of L-tryptophane with alcohol molecules were calculated. The coefficients were positive and increased in the series: methanol (MeOH), ethanol (EtOH), 1-propanol (1-PrOH), and 2-propanol (2-PrOH). The solution and transfer enthalpies of L-tryptophane were compared with those of aliphatic amino acids (glycine, L-threonine, DL-alanine, L-valine, and L-phenylalanine) in similar binary solvents.

SAMPL5: 3D-RISM partition coefficient calculations with partial molar volume corrections and solute conformational sampling.

PubMed

Luchko, Tyler; Blinov, Nikolay; Limon, Garrett C; Joyce, Kevin P; Kovalenko, Andriy

2016-11-01

Implicit solvent methods for classical molecular modeling are frequently used to provide fast, physics-based hydration free energies of macromolecules. Less commonly considered is the transferability of these methods to other solvents. The Statistical Assessment of Modeling of Proteins and Ligands 5 (SAMPL5) distribution coefficient dataset and the accompanying explicit solvent partition coefficient reference calculations provide a direct test of solvent model transferability. Here we use the 3D reference interaction site model (3D-RISM) statistical-mechanical solvation theory, with a well tested water model and a new united atom cyclohexane model, to calculate partition coefficients for the SAMPL5 dataset. The cyclohexane model performed well in training and testing ([Formula: see text] for amino acid neutral side chain analogues) but only if a parameterized solvation free energy correction was used. In contrast, the same protocol, using single solute conformations, performed poorly on the SAMPL5 dataset, obtaining [Formula: see text] compared to the reference partition coefficients, likely due to the much larger solute sizes. Including solute conformational sampling through molecular dynamics coupled with 3D-RISM (MD/3D-RISM) improved agreement with the reference calculation to [Formula: see text]. Since our initial calculations only considered partition coefficients and not distribution coefficients, solute sampling provided little benefit comparing against experiment, where ionized and tautomer states are more important. Applying a simple [Formula: see text] correction improved agreement with experiment from [Formula: see text] to [Formula: see text], despite a small number of outliers. Better agreement is possible by accounting for tautomers and improving the ionization correction.

SAMPL5: 3D-RISM partition coefficient calculations with partial molar volume corrections and solute conformational sampling

NASA Astrophysics Data System (ADS)

Luchko, Tyler; Blinov, Nikolay; Limon, Garrett C.; Joyce, Kevin P.; Kovalenko, Andriy

2016-11-01

Implicit solvent methods for classical molecular modeling are frequently used to provide fast, physics-based hydration free energies of macromolecules. Less commonly considered is the transferability of these methods to other solvents. The Statistical Assessment of Modeling of Proteins and Ligands 5 (SAMPL5) distribution coefficient dataset and the accompanying explicit solvent partition coefficient reference calculations provide a direct test of solvent model transferability. Here we use the 3D reference interaction site model (3D-RISM) statistical-mechanical solvation theory, with a well tested water model and a new united atom cyclohexane model, to calculate partition coefficients for the SAMPL5 dataset. The cyclohexane model performed well in training and testing (R=0.98 for amino acid neutral side chain analogues) but only if a parameterized solvation free energy correction was used. In contrast, the same protocol, using single solute conformations, performed poorly on the SAMPL5 dataset, obtaining R=0.73 compared to the reference partition coefficients, likely due to the much larger solute sizes. Including solute conformational sampling through molecular dynamics coupled with 3D-RISM (MD/3D-RISM) improved agreement with the reference calculation to R=0.93. Since our initial calculations only considered partition coefficients and not distribution coefficients, solute sampling provided little benefit comparing against experiment, where ionized and tautomer states are more important. Applying a simple pK_{ {a}} correction improved agreement with experiment from R=0.54 to R=0.66, despite a small number of outliers. Better agreement is possible by accounting for tautomers and improving the ionization correction.

Dynamic Stacking Pathway of Perylene Dimers in Aromatic and Nonaromatic Solvents.

PubMed

Hollfelder, Manuel; Gekle, Stephan

2015-08-13

Using molecular dynamics simulations, we elucidate in detail the dynamics of the π-π stacking process of a perylene bisimide (PBI) dimer solvated in toluene. Our calculations show that the transition from the open (unstacked) to the stacked configuration is hindered by a small free energy barrier of approximately 1kBT in toluene but not in the nonaromatic solvent hexane. A similar effect is observed tor two non-covalently linked monomers. The origin of this barrier is traced back to π-π interactions between perylene and the aromatic solvent which are very similar in nature to those between two PBI monomers. The stacking process proceeds in three phases via two well-defined transition states: (i) in the first phase, the two PBI molecules share part of their respective solvation shells forming the first transition state. Further approach needs to squeeze out the shared solvent layer, thus creating the energy barrier. (ii) After removal of the separating solvent, the two PBIs form a second transition state with one monomer located at a random position in the other's solvation shell. (iii) Finally, the two PBIs slide on top of each other into their final stacked position.

Vibrational spectroscopic determination of local solvent electric field, solute-solvent electrostatic interaction energy, and their fluctuation amplitudes.

PubMed

Lee, Hochan; Lee, Gayeon; Jeon, Jonggu; Cho, Minhaeng

2012-01-12

IR probes have been extensively used to monitor local electrostatic and solvation dynamics. Particularly, their vibrational frequencies are highly sensitive to local solvent electric field around an IR probe. Here, we show that the experimentally measured vibrational frequency shifts can be inversely used to determine local electric potential distribution and solute-solvent electrostatic interaction energy. In addition, the upper limits of their fluctuation amplitudes are estimated by using the vibrational bandwidths. Applying this method to fully deuterated N-methylacetamide (NMA) in D(2)O and examining the solvatochromic effects on the amide I' and II' mode frequencies, we found that the solvent electric potential difference between O(═C) and D(-N) atoms of the peptide bond is about 5.4 V, and thus, the approximate solvent electric field produced by surrounding water molecules on the NMA is 172 MV/cm on average if the molecular geometry is taken into account. The solute-solvent electrostatic interaction energy is estimated to be -137 kJ/mol, by considering electric dipole-electric field interaction. Furthermore, their root-mean-square fluctuation amplitudes are as large as 1.6 V, 52 MV/cm, and 41 kJ/mol, respectively. We found that the water electric potential on a peptide bond is spatially nonhomogeneous and that the fluctuation in the electrostatic peptide-water interaction energy is about 10 times larger than the thermal energy at room temperature. This indicates that the peptide-solvent interactions are indeed important for the activation of chemical reactions in aqueous solution.

IR, Raman and Vibrational Optical Activity Spectra of Methyl Glycidate in Chloroform and Water: The Clusters-in-a-Liquid Solvation Model.

PubMed

Xu, Yunjie; Perera, Angelo Shehan; Cheramy, Joseph; Merten, Christian; Thomas, Javix

2018-05-16

Solvent effects, in particular those involving water as the solvent, are of significant interest to chemistry and physics communities. IR, vibrational circular dichroism (VCD), Raman, and Raman optical activity (ROA) spectra of methyl glycidate in two very different solvents, namely CCl4 and water, have been measured experimentally and simulated theoretically. While the observed spectra in CCl4 could be well modelled using the polarizable continuum model for the solvent, the situation is much different in water. The experimental VCD spectrum of methyl glycidate in water reveals strong induced VCD signatures in the water bending region, indicating the presence of the relatively long-lived methyl glycidate-watern complexes. We applied the clusters-in-a-liquid approach to identify the dominant methyl glycidate-water1,2 complexes which are the long-lived species responsible for all the spectra observed in water. We examined the influences of solvent dielectric environment and the hydrogen-bonding interactions on the conformational distribution of methyl glycidate. The geometry optimizations, frequency calculations, IR, VCD, Raman and ROA intensity calculations were performed at the B3LYP/6-311++G(2d,p) and aug-cc-pVTZ levels of theory with D3BJ dispersion correction. It is particularly satisfying to note that the clusters-in-a-liquid approach has captured all main experimental features in IR, VCD, Raman and ROA spectra of methyl glycidate in water. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cluster-continuum quasichemical theory calculation of the lithium ion solvation in water, acetonitrile and dimethyl sulfoxide: an absolute single-ion solvation free energy scale.

PubMed

Carvalho, Nathalia F; Pliego, Josefredo R

2015-10-28

Absolute single-ion solvation free energy is a very useful property for understanding solution phase chemistry. The real solvation free energy of an ion depends on its interaction with the solvent molecules and on the net potential inside the solute cavity. The tetraphenyl arsonium-tetraphenyl borate (TATB) assumption as well as the cluster-continuum quasichemical theory (CC-QCT) approach for Li(+) solvation allows access to a solvation scale excluding the net potential. We have determined this free energy scale investigating the solvation of the lithium ion in water (H2O), acetonitrile (CH3CN) and dimethyl sulfoxide (DMSO) solvents via the CC-QCT approach. Our calculations at the MP2 and MP4 levels with basis sets up to the QZVPP+diff quality, and including solvation of the clusters and solvent molecules by the dielectric continuum SMD method, predict the solvation free energy of Li(+) as -116.1, -120.6 and -123.6 kcal mol(-1) in H2O, CH3CN and DMSO solvents, respectively (1 mol L(-1) standard state). These values are compatible with the solvation free energy of the proton of -253.4, -253.2 and -261.1 kcal mol(-1) in H2O, CH3CN and DMSO solvents, respectively. Deviations from the experimental TATB scale are only 1.3 kcal mol(-1) in H2O and 1.8 kcal mol(-1) in DMSO solvents. However, in the case of CH3CN, the deviation reaches a value of 9.2 kcal mol(-1). The present study suggests that the experimental TATB scale is inconsistent for CH3CN. A total of 125 values of the solvation free energy of ions in these three solvents were obtained. These new data should be useful for the development of theoretical solvation models.

Ab initio and DFT study of hydrogen bond interactions between ascorbic acid and dimethylsulfoxide based on FT-IR and FT-Raman spectra

NASA Astrophysics Data System (ADS)

Niazazari, Naser; Zatikyan, Ashkhen L.; Markarian, Shiraz A.

2013-06-01

The hydrogen bonding of 1:1 complexes formed between L-ascorbic acid (LAA) and dimethylsulfoxide (DMSO) has been studied by means of ab initio and density functional theory (DFT) calculations. Solutions of L-ascorbic acid (AA) in dimethylsulfoxide (DMSO) have been studied by means of both FT-IR (4000-220 cm-1) and FT-Raman spectroscopy. Ab initio Hartree-Fock (HF) and DFT methods have been used to determine the structure and energies of stable conformers of various types of L-AA/DMSO complexes in gas phase and solution. The basis sets 6-31++G∗∗ and 6-311+G∗ were used to describe the structure, energy, charges and vibrational frequencies of interacting complexes in the gas phase. The optimized geometric parameters and interaction energies for various complexes at different theories have been estimated. Binding energies have been corrected for basis set superposition error (BSSE) and harmonic vibrational frequencies of the structures have been calculated to obtain the stable forms of the complexes. The self-consistent reaction field (SCRF) has been used to calculate the effect of DMSO as the solvent on the geometry, energy and charges of complexes. The solvent effect has been studied using the Onsager models. It is shown that the polarity of the solvent plays an important role on the structures and relative stabilities of different complexes. The results obtained show that there is a satisfactory correlation between experimental and theoretical predictions.

A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer

NASA Astrophysics Data System (ADS)

Kawaguchi, Kazutomo; Nakagawa, Satoshi; Kurniawan, Isman; Kodama, Koichi; Arwansyah, Muhammad Saleh; Nagao, Hidemi

2018-03-01

We present a simple coarse-grained model of the effective interaction for charged amino acid residues, such as Glu and Lys, in a water solvent. The free-energy profile as a function of the distance between two charged amino acid side-chain analogues in an explicit water solvent is calculated with all-atom molecular dynamics simulation and thermodynamic integration method. The calculated free-energy profile is applied to the coarse-grained potential of the effective interaction between two amino acid residues. The Langevin dynamics simulations with our coarse-grained potential are performed for association of a small protein complex, GCN4-pLI tetramer. The tetramer conformation reproduced by our coarse-grained model is similar to the X-ray crystallographic structure. We show that the effective interaction between charged amino acid residues stabilises association and orientation of protein complex. We also investigate the association pathways of GCN4-pLI tetramer.

Comparison of experimental and DFT-calculated NMR chemical shifts of 2-amino and 2-hydroxyl substituted phenyl benzimidazoles, benzoxazoles and benzothiazoles in four solvents using the IEF-PCM solvation model.

PubMed

Pierens, Gregory K; Venkatachalam, T K; Reutens, David C

2016-04-01

A comparative study of experimental and calculated NMR chemical shifts of six compounds comprising 2-amino and 2-hydroxy phenyl benzoxazoles/benzothiazoles/benzimidazoles in four solvents is reported. The benzimidazoles showed interesting spectral characteristics, which are discussed. The proton and carbon chemical shifts were similar for all solvents. The largest chemical shift deviations were observed in benzene. The chemical shifts were calculated with density functional theory using a suite of four functionals and basis set combinations. The calculated chemical shifts revealed a good match to the experimentally observed values in most of the solvents. The mean absolute error was used as the primary metric. The use of an additional metric is suggested, which is based on the order of chemical shifts. The DP4 probability measures were also used to compare the experimental and calculated chemical shifts for each compound in the four solvents. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Solvent-Polarity-Induced Active Layer Morphology Control in Crystalline Diketopyrrolopyrrole-Based Low Band Gap Polymer Photovoltaics

NASA Astrophysics Data System (ADS)

Ferdous, Sunzida; Liu, Feng; Wang, Dong; Russell, Thomas

2014-03-01

The effects of various processing solvents on the morphology of diketopyrrolopyrrole (DPP)-based low band gap polymer (PDPPBT) and phenyl-C71-butyric acid methyl ester (PC71BM) blends are studied. The quality of the processing solvents was varied systematically using a mixture of a non-aromatic polar primary solvent with high boiling point secondary solvents of increasing polarities. An unfavorable solvent-PC71BM interaction affects the growth process of polymer crystallites inside the blend. When non-aromatic polar solvent was used, large PC71BM aggregates were formed that increase in size with the addition of non-polar secondary solvents. When polar solvents were instead used as the secondary solvents, the size scales of the aggregates decrease markedly, creating a percolated fibrillar network. Power conversion efficiencies of 0.03% to 5% are obtained, depending on the solvent system used.

Water equivalence of NIPAM based polymer gel dosimeters with enhanced sensitivity for x-ray CT

NASA Astrophysics Data System (ADS)

Gorjiara, Tina; Hill, Robin; Bosi, Stephen; Kuncic, Zdenka; Baldock, Clive

2013-10-01

Two new formulations of N-isopropylacrylamide (NIPAM) based three dimensional (3D) gel dosimeters have recently been developed with improved sensitivity to x-ray CT readout, one without any co-solvent and the other one with isopropanol co-solvent. The water equivalence of the NIPAM gel dosimeters was investigated using different methods to calculate their radiological properties including: density, electron density, number of electrons per grams, effective atomic number, photon interaction probabilities, mass attenuation and energy absorption coefficients, electron collisional, radiative and total mass stopping powers and electron mass scattering power. Monte Carlo modelling was also used to compare the dose response of these gel dosimeters with water for kilovoltage and megavoltage x-ray beams and for megavoltage electron beams. We found that the density and electron density of the co-solvent free gel dosimeter are more water equivalent with less than a 2.6% difference compared to a 5.7% difference for the isopropanol gel dosimeter. Both the co-solvent free and isopropanol solvent gel dosimeters have lower effective atomic numbers than water, differing by 2.2% and 6.5%, respectively. As a result, their photoelectric absorption interaction probabilities are up to 6% and 19% different from water, respectively. Compton scattering and pair production interaction probabilities of NIPAM gel with isopropanol differ by up to 10% from water while for the co-solvent free gel, the differences are 3%. Mass attenuation and energy absorption coefficients of the co-solvent free gel dosimeter and the isopropanol gel dosimeter are up to 7% and 19% lower than water, respectively. Collisional and total mass stopping powers of both gel dosimeters differ by less than 2% from those of water. The dose response of the co-solvent free gel dosimeter is water equivalent (with <1% discrepancy) for dosimetry of x-rays with energies <100 keV while the discrepancy increases (up to 5%) for the isopropanol gel dosimeter over the same energy range. For x-ray beams over the energy range 180 keV-18 MV, both gel dosimeters have less than 2% discrepancy with water. For megavoltage electron beams, the dose differences with water reach 7% and 14% for the co-solvent free gel dosimeter and the isopropanol gel dosimeter, respectively. Our results demonstrate that for x-ray beam dosimetry with photon energies higher than 100 keV and megavoltage electron beams, correction factors are needed for both NIPAM gels to be used as water equivalent dosimeters.

Spectral behaviour of eosin Y in different solvents and aqueous surfactant media.

PubMed

Chakraborty, Moumita; Panda, Amiya Kumar

2011-10-15

Photophysical behaviour of the anionic xanthene dye, eosin Y (EY) was investigated in solvents of different polarities as well as in the presence of aqueous cationic surfactants. From the correlation between E(T)(30) and Kosower Z values of EY in different solvents, subsequent parameters for EY were determined in the presence of surfactants. A red shift, both in the absorption and emission spectra of EY, was observed with decreasing solvent polarity. Dimerisation of EY was found to be dependent on solvent polarity. Cationic surfactants retarded the process of dimerisation, which were evident from the lower dimerisation constant (K(D)) values, compared to that of in pure water. Dye-surfactant interaction constants were determined at different temperatures (298-318 K) and subsequently the thermodynamic parameters, viz., ΔG°, ΔH° and ΔS° were evaluated using the interaction constant values. The fluorescence spectra of EY followed the same trend as in the absorption spectra, although with lesser extents. Stokes shifts were calculated and correlated with the polarity of the medium. Fluorescence of EY was initially quenched by the cationic surfactants in their pre-micellar region, which then followed a red shift with intensity enhancement. Fluorescence quenching was found to be of Stern-Volmer type where the excited state lifetime of EY remained unchanged in different surfactant media. However, the anisotropy value of EY was changed in the post micellar region of surfactants. Copyright © 2011 Elsevier B.V. All rights reserved.

Prediction of enhanced solvent-induced enantioselectivity for a ring opening with a bifurcating reaction path

DOE PAGES

Carpenter, Barry K.; Harvey, Jeremy N.; Glowacki, David R.

2014-12-11

Classical molecular dynamics simulations are reported for the deazetisation and ring opening of meso-2,3-difluoro-2,3-dimethyldiazocyclopropane in three solvents: CHCl 3, CHFClBr and CH 3CH(OH)CF 3 (TFIPA). In this study, the achiral reactant leads to enantiomeric allene products, and the question addressed in the study is whether either of the chiral, enantiomerically pure solvents can induce significant enantiomeric excess in the products. The direct dynamics calculations use an empirical valence bond potential for the solute, with empirical parameters optimised against M06-2X/cc-pVTZ density functional results. The results reveal that the exothermic N 2 loss and ring opening promote transient strong solvent–solute interactions withinmore » the first ~100 fs of the reaction. Because of the bifurcating reaction path, these interactions occur at time when the “decision” about which enantiomer of the product to form has yet to be made (at least for many of the trajectories). Hence, it is possible in principle that the solvent could exert a larger-than-normal influence on the course of the reaction. In fact, the results reveal no such effect for CHFClBr but do predict that TFIPA should induce 15.2 ± 2.1% enantiomeric excess. This is roughly an order of magnitude larger than solvent-induced enantiomeric excesses found experimentally in reactions where the conversion of reactant(s) to enantiomeric products occur over separate transition states.« less

The solvent-gelator interaction as the origin of different diffusivity behavior of diols in gels formed with sugar-based low-molecular-mass gelator.

PubMed

Kowalczuk, Joanna; Bielejewski, Michał; Lapiński, Andrzej; Luboradzki, Roman; Tritt-Goc, Jadwiga

2014-04-10

Organogels are soft materials consisting of low-molecular-mass gelators (LMOGs) self-assembled through noncovalent interactions into 3D structures, in which free spaces are filled by organic solvents. 4,6,4',6'-O-terephthylidene-bis(methyl-α-d-glucopyranoside) (1) is found to be a new LMOG. It gelatinizes only a limited number of solvents. Here, the gels of 1 with ethylene glycol (EG) and 1,3-propanediol (PG) are investigated with FT-IR, Raman, and UV-vis spectroscopies, the NMR relaxometry and diffusometry methods, and microscopic observation. The chemical structures of both solvents are closely related, but the variety of physical characteristics of the gels is large. The 1/PG gels are thermally more stable compared to 1/EG gels. The types of aggregates are most likely the H- and J-type in 1/EG gels and the J-type in 1/PG gels. Different microstructures are observed: bundles of crossing fibers for 1/EG and a honeycomb-like matrix for 1/PG gels. The diffusivity of the EG solvent in gels with 1 behaves as expected, decreasing with increasing gelator concentration, whereas the opposite behavior is observed for the PG solvent. This is a most fascinating result. To explain the diffusion enhancement, we suggest that a dynamic hydrogen bonding network of PG solvent in gel matrixes is disrupted due to solvent-gelator interaction. The direct proof of this interaction is given by the observed low frequency dispersion of the spin-lattice relaxation time of solvents in the gel matrixes.

Toxic hepatitis in occupational exposure to solvents

PubMed Central

Malaguarnera, Giulia; Cataudella, Emanuela; Giordano, Maria; Nunnari, Giuseppe; Chisari, Giuseppe; Malaguarnera, Mariano

2012-01-01

The liver is the main organ responsible for the metabolism of drugs and toxic chemicals, and so is the primary target organ for many organic solvents. Work activities with hepatotoxins exposures are numerous and, moreover, organic solvents are used in various industrial processes. Organic solvents used in different industrial processes may be associated with hepatotoxicity. Several factors contribute to liver toxicity; among these are: species differences, nutritional condition, genetic factors, interaction with medications in use, alcohol abuse and interaction, and age. This review addresses the mechanisms of hepatotoxicity. The main pathogenic mechanisms responsible for functional and organic damage caused by solvents are: inflammation, dysfunction of cytochrome P450, mitochondrial dysfunction and oxidative stress. The health impact of exposure to solvents in the workplace remains an interesting and worrying question for professional health work. PMID:22719183

Ion-dipole interactions in concentrated organic electrolytes.

PubMed

Chagnes, Alexandre; Nicolis, Stamatios; Carré, Bernard; Willmann, Patrick; Lemordant, Daniel

2003-06-16

An algorithm is proposed for calculating the energy of ion-dipole interactions in concentrated organic electrolytes. The ion-dipole interactions increase with increasing salt concentration and must be taken into account when the activation energy for the conductivity is calculated. In this case, the contribution of ion-dipole interactions to the activation energy for this transport process is of the same order of magnitude as the contribution of ion-ion interactions. The ion-dipole interaction energy was calculated for a cell of eight ions, alternatingly anions and cations, placed on the vertices of an expanded cubic lattice whose parameter is related to the mean interionic distance (pseudolattice theory). The solvent dipoles were introduced randomly into the cell by assuming a randomness compacity of 0.58. The energy of the dipole assembly in the cell was minimized by using a Newton-Raphson numerical method. The dielectric field gradient around ions was taken into account by a distance parameter and a dielectric constant of epsilon = 3 at the surfaces of the ions. A fair agreement between experimental and calculated activation energy has been found for systems composed of gamma-butyrolactone (BL) as solvent and lithium perchlorate (LiClO4), lithium tetrafluoroborate (LiBF4), lithium hexafluorophosphate (LiPF6), lithium hexafluoroarsenate (LiAsF6), and lithium bis(trifluoromethylsulfonyl)imide (LiTFSI) as salts.

Heterofunctionality interaction with donor solvent coal liquefaction. Final progress report, August 1982-April 1984

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cronauer, D.C.

1984-05-01

This project was undertaken to understand the role of the coal liquefaction solvent through a study of the interaction between the hydrogen donor solvent characteristics and the heterofunctionality of the solvent. Specifically, hydroxyl- and nitrogen-containing solvents were studied and characterized. A series of coal liquefaction experiments were carried out at 450/sup 0/C in a continuous feed stirred-tank reactor (CSTR) to observe the effect of adding phenolics to anthracene oil (AO) and SRC-II recycle solvents. The addition of phenol to AO at a ratio of 5/65 resulted in a nominal increase in coal conversion to THF solubles, but the amount ofmore » asphaltenes more than doubled resulting in a sizable net loss of solvent. The addition of m-cresol to both AO and SRC-II solvents had a positive effect on coal conversion to both THF and pentane solubles (oils). The partial removal of an OH-concentrate from SRC-II solvent was carried out using Amberlyst IRA-904 ion exchange resin. The resin-treated oil was only marginally better than raw SRC-II recycle solvent for coal liquefaction. Hydroaromatics having nitrogen functionality should be good solvents for coal liquefaction considering their effective solvent power, ability to penetrate and swell coal, and their ability to readily transfer hydrogen, particularly in the presence of oxygen functionality. However, these benefits are overshadowed by the strong tendency of the nitrogen-containing species to adduct with themselves and coal-derived materials.« less

Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.

PubMed

Marenich, Aleksandr V; Cramer, Christopher J; Truhlar, Donald G

2009-05-07

We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the "D" stands for "density" to denote that the full solute electron density is used without defining partial atomic charges. "Continuum" denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where "universal" denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which a few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonhomogeneous Poisson equation for electrostatics in terms of the integral-equation-formalism polarizable continuum model (IEF-PCM). The cavities for the bulk electrostatic calculation are defined by superpositions of nuclear-centered spheres. The second component is called the cavity-dispersion-solvent-structure term and is the contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. This contribution is a sum of terms that are proportional (with geometry-dependent proportionality constants called atomic surface tensions) to the solvent-accessible surface areas of the individual atoms of the solute. The SMD model has been parametrized with a training set of 2821 solvation data including 112 aqueous ionic solvation free energies, 220 solvation free energies for 166 ions in acetonitrile, methanol, and dimethyl sulfoxide, 2346 solvation free energies for 318 neutral solutes in 91 solvents (90 nonaqueous organic solvents and water), and 143 transfer free energies for 93 neutral solutes between water and 15 organic solvents. The elements present in the solutes are H, C, N, O, F, Si, P, S, Cl, and Br. The SMD model employs a single set of parameters (intrinsic atomic Coulomb radii and atomic surface tension coefficients) optimized over six electronic structure methods: M05-2X/MIDI!6D, M05-2X/6-31G, M05-2X/6-31+G, M05-2X/cc-pVTZ, B3LYP/6-31G, and HF/6-31G. Although the SMD model has been parametrized using the IEF-PCM protocol for bulk electrostatics, it may also be employed with other algorithms for solving the nonhomogeneous Poisson equation for continuum solvation calculations in which the solute is represented by its electron density in real space. This includes, for example, the conductor-like screening algorithm. With the 6-31G basis set, the SMD model achieves mean unsigned errors of 0.6-1.0 kcal/mol in the solvation free energies of tested neutrals and mean unsigned errors of 4 kcal/mol on average for ions with either Gaussian03 or GAMESS.

Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marenich, Aleksandr; Cramer, Christopher J; Truhlar, Donald G

2009-04-30

We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the “D” stands for “density” to denote that the full solute electron density is used without defining partial atomic charges. “Continuum” denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where “universal” denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which amore » few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonhomogeneous Poisson equation for electrostatics in terms of the integral-equation-formalism polarizable continuum model (IEF-PCM). The cavities for the bulk electrostatic calculation are defined by superpositions of nuclear-centered spheres. The second component is called the cavity-dispersion-solvent-structure term and is the contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. This contribution is a sum of terms that are proportional (with geometry-dependent proportionality constants called atomic surface tensions) to the solvent-accessible surface areas of the individual atoms of the solute. The SMD model has been parametrized with a training set of 2821 solvation data including 112 aqueous ionic solvation free energies, 220 solvation free energies for 166 ions in acetonitrile, methanol, and dimethyl sulfoxide, 2346 solvation free energies for 318 neutral solutes in 91 solvents (90 nonaqueous organic solvents and water), and 143 transfer free energies for 93 neutral solutes between water and 15 organic solvents. The elements present in the solutes are H, C, N, O, F, Si, P, S, Cl, and Br. The SMD model employs a single set of parameters (intrinsic atomic Coulomb radii and atomic surface tension coefficients) optimized over six electronic structure methods: M05-2X/MIDI!6D, M05-2X/6-31G*, M05-2X/6-31+G**, M05-2X/cc-pVTZ, B3LYP/6-31G*, and HF/6-31G*. Although the SMD model has been parametrized using the IEF-PCM protocol for bulk electrostatics, it may also be employed with other algorithms for solving the nonhomogeneous Poisson equation for continuum solvation calculations in which the solute is represented by its electron density in real space. This includes, for example, the conductor-like screening algorithm. With the 6-31G* basis set, the SMD model achieves mean unsigned errors of 0.6-1.0 kcal/mol in the solvation free energies of tested neutrals and mean unsigned errors of 4 kcal/mol on average for ions with either Gaussian03 or GAMESS.« less

High throughput research and evaporation rate modeling for solvent screening for ethylcellulose barrier membranes in pharmaceutical applications.

PubMed

Schoener, Cody A; Curtis-Fisk, Jaime L; Rogers, True L; Tate, Michael P

2016-10-01

Ethylcellulose is commonly dissolved in a solvent or formed into an aqueous dispersion and sprayed onto various dosage forms to form a barrier membrane to provide controlled release in pharmaceutical formulations. Due to the variety of solvents utilized in the pharmaceutical industry and the importance solvent can play on film formation and film strength it is critical to understand how solvent can influence these parameters. To systematically study a variety of solvent blends and how these solvent blends influence ethylcellulose film formation, physical and mechanical film properties and solution properties such as clarity and viscosity. Using high throughput capabilities and evaporation rate modeling, thirty-one different solvent blends composed of ethanol, isopropanol, acetone, methanol, and/or water were formulated, analyzed for viscosity and clarity, and narrowed down to four solvent blends. Brookfield viscosity, film casting, mechanical film testing and water permeation were also completed. High throughput analysis identified isopropanol/water, ethanol, ethanol/water and methanol/acetone/water as solvent blends with unique clarity and viscosity values. Evaporation rate modeling further rank ordered these candidates from excellent to poor interaction with ethylcellulose. Isopropanol/water was identified as the most suitable solvent blend for ethylcellulose due to azeotrope formation during evaporation, which resulted in a solvent-rich phase allowing the ethylcellulose polymer chains to remain maximally extended during film formation. Consequently, the highest clarity and most ductile films were formed. Employing high throughput capabilities paired with evaporation rate modeling allowed strong predictions between solvent interaction with ethylcellulose and mechanical film properties.

Influence of solvent polarity and supersaturation on template-induced nucleation of carbamazepine crystal polymorphs

NASA Astrophysics Data System (ADS)

Parambil, Jose V.; Poornachary, Sendhil K.; Tan, Reginald B. H.; Heng, Jerry Y. Y.

2017-07-01

Studies on the use of template surfaces to induce heterogeneous crystal nucleation have gained momentum in recent years-with potential applications in selective crystallisation of polymorphs and in the generation of seed crystals in a continuous crystallisation process. In developing a template-assisted solution crystallisation process, the kinetics of homogeneous versus heterogeneous crystal nucleation could be influenced by solute-solvent, solute-template, and solvent-template interactions. In this study, we report the effect of solvents of varying polarity on the nucleation of carbamazepine (CBZ) crystal polymorphs, a model active pharmaceutical ingredient. The experimental results demonstrate that functionalised template surfaces are effective in promoting crystallisation of either the metastable (form II) or stable (form III) polymorphs of CBZ only in moderately (methanol, ethanol, isopropanol) and low polar (toluene) solvents. A solvent with high polarity (acetonitrile) is thought to mask the template effect on heterogeneous nucleation due to strong solute-solvent and solvent-template interactions. The current study highlights that a quality-by-design (QbD) approach-considering the synergistic effects of solute concentration, solvent type, solution temperature, and template surface chemistry on crystal nucleation-is critical to the development of a template-induced crystallisation process.

Crystal Nucleation of Tolbutamide in Solution: Relationship to Solvent, Solute Conformation, and Solution Structure.

PubMed

Zeglinski, Jacek; Kuhs, Manuel; Khamar, Dikshitkumar; Hegarty, Avril C; Devi, Renuka K; Rasmuson, Åke C

2018-04-03

The influence of the solvent in nucleation of tolbutamide, a medium-sized, flexible and polymorphic organic molecule, has been explored by measuring nucleation induction times, estimating solvent-solute interaction enthalpies using molecular modelling and calorimetric data, probing interactions and clustering with spectroscopy, and modelling solvent-dependence of molecular conformation in solution. The nucleation driving force required to reach the same induction time is strongly solvent-dependent, increasing in the order: acetonitrile

SLTCAP: A Simple Method for Calculating the Number of Ions Needed for MD Simulation.

PubMed

Schmit, Jeremy D; Kariyawasam, Nilusha L; Needham, Vince; Smith, Paul E

2018-04-10

An accurate depiction of electrostatic interactions in molecular dynamics requires the correct number of ions in the simulation box to capture screening effects. However, the number of ions that should be added to the box is seldom given by the bulk salt concentration because a charged biomolecule solute will perturb the local solvent environment. We present a simple method for calculating the number of ions that requires only the total solute charge, solvent volume, and bulk salt concentration as inputs. We show that the most commonly used method for adding salt to a simulation results in an effective salt concentration that is too high. These findings are confirmed using simulations of lysozyme. We have established a web server where these calculations can be readily performed to aid simulation setup.

Translational, rotational and vibrational relaxation dynamics of a solute molecule in a non-interacting solvent.

PubMed

Grubb, Michael P; Coulter, Philip M; Marroux, Hugo J B; Hornung, Balazs; McMullen, Ryan S; Orr-Ewing, Andrew J; Ashfold, Michael N R

2016-11-01

Spectroscopically observing the translational and rotational motion of solute molecules in liquid solutions is typically impeded by their interactions with the solvent, which conceal spectral detail through linewidth broadening. Here we show that unique insights into solute dynamics can be made with perfluorinated solvents, which interact weakly with solutes and provide a simplified liquid environment that helps to bridge the gap in our understanding of gas- and liquid-phase dynamics. Specifically, we show that in such solvents, the translational and rotational cooling of an energetic CN radical can be observed directly using ultrafast transient absorption spectroscopy. We observe that translational-energy dissipation within these liquids can be modelled through a series of classic collisions, whereas classically simulated rotational-energy dissipation is shown to be distinctly faster than experimentally measured. We also observe the onset of rotational hindering from nearby solvent molecules, which arises as the average rotational energy of the solute falls below the effective barrier to rotation induced by the solvent.

Structural elucidation, molecular representation and solvent interactions of vitrinite-rich and inertinite-rich South African coals

NASA Astrophysics Data System (ADS)

van Niekerk, Daniel

The structural differences and similarities of two Permian-aged South African coals, vitrinite-rich Waterberg and inertinite-rich Highveld coals (similar rank, carbon content and Permian age), were evaluated. With South African coals the opportunity presented itself to study not only Permian-aged Gondwana vitrinite but also inertinite. It was expected that these coals would differ from Northern hemisphere Carboniferous coals. It was concluded from various structural data that both coals, although different in maceral composition and depositional basins, are similar in their base structural composition. The main differences were that the inertinite-rich Highveld coal was more ordered, more aromatic, and had less hydrogen than the vitrinite-rich Waterberg coal. Analytical data were used to construct large-scale advanced molecular representations for vitrinite-rich Waterberg and inertinite-rich Highveld coals. The three-dimensional models were structurally diverse with a molecular weight range of 78 to 1900 amu. The vitrinite-rich coal model consisted of 18,572 atoms and 191 individual molecules and the inertinite-rich coal model consisted of 14,242 atoms and 158 individual molecules. This largescale modeling effort was enabled by the development of various PERL scripts to automate various visualization and analytical aspects. Coal swelling studies were conducted using the traditional pack-bed swelling method and a new novel single-particle stop-motion videography swelling method with NMP and CS2/NMP solvents. The pack-bed swelling showed that vitrinite-rich coal had a greater swelling extent and that swelling extent for both coals was greater in CS2/NMP binary solvent than for NMP. Single-particle swelling experiments showed that both coals, for both solvents, exhibit overshoot-type and climbing-type swelling behaviors. Inertinite-coal had a faster swelling rate, in both solvents, than the vitrinite-rich coal. The single-particle swelling data was used to calculate the kinetic parameters and it was found that the swelling was governed by relaxation of the coal structure (super-Case II swelling). X-ray computed tomography was conducted confirming anisotropic swelling. The petrographic transitions (maceral-group composition and reflectance) with solvent swelling and extraction were quantified. No changes in the maceral compositions were found, but changes in some coal particles were observed. Random reflectance analysis showed that, for both vitrinite and inertinite, there is a decrease in reflectance values with solvent treatment. Vitrinite reflectograms showed a shift from the dominant reflecting V-types to lower V-types. The inertinite reflectograms exhibited an increase in number of I-types (broadening of reflectrograms). Molecular simulation and visualization approaches to solvent swelling and extraction were performed on the proposed molecular models of vitrinite-rich and inertinite-rich coals. A theoretical extraction yield was determined using solubility parameters and showed agreement with experimental extraction yield trends. Statistical Associating Fluid Theory (SAFT) modeling was explored to test whether this method could predict swelling extent. The predicted swelling trends of SAFT were comparable to that of the experimental swelling results. SAFT was found to be a promising tool for solvent-coal interaction predictions. Partially solvent swollen structures were constructed by the addition of solvent molecules to the original coal molecules using a amorphous building approach. This method showed that coal-coal non-bonding interaction changed with the introduction of solvent. A disruption in the van der Waals interaction energies and a change in hydrogen bond distributions were observed in the swollen coal models and quantified. It was concluded that small changes in coal structure translates to significant changes in solvent interaction behavior. These changes were successfully visualized and simulated using atomistic molecular representations.

Macromolecular 'size' and 'hardness' drives structure in solvent-swollen blends of linear, cyclic, and star polymers.

PubMed

Gartner, Thomas E; Jayaraman, Arthi

2018-01-17

In this paper, we apply molecular simulation and liquid state theory to uncover the structure and thermodynamics of homopolymer blends of the same chemistry and varying chain architecture in the presence of explicit solvent species. We use hybrid Monte Carlo (MC)/molecular dynamics (MD) simulations in the Gibbs ensemble to study the swelling of ∼12 000 g mol -1 linear, cyclic, and 4-arm star polystyrene chains in toluene. Our simulations show that the macroscopic swelling response is indistinguishable between the various architectures and matches published experimental data for the solvent annealing of linear polystyrene by toluene vapor. We then use standard MD simulations in the NPT ensemble along with polymer reference interaction site model (PRISM) theory to calculate effective polymer-solvent and polymer-polymer Flory-Huggins interaction parameters (χ eff ) in these systems. As seen in the macroscopic swelling results, there are no significant differences in the polymer-solvent and polymer-polymer χ eff between the various architectures. Despite similar macroscopic swelling and effective interaction parameters between various architectures, the pair correlation function between chain centers-of-mass indicates stronger correlations between cyclic or star chains in the linear-cyclic blends and linear-star blends, compared to linear chain-linear chain correlations. Furthermore, we note striking similarities in the chain-level correlations and the radius of gyration of cyclic and 4-arm star architectures of identical molecular weight. Our results indicate that the cyclic and star chains are 'smaller' and 'harder' than their linear counterparts, and through comparison with MD simulations of blends of soft spheres with varying hardness and size we suggest that these macromolecular characteristics are the source of the stronger cyclic-cyclic and star-star correlations.

40 CFR 63.5749 - How do I calculate the organic HAP content of aluminum wipedown solvents?

Code of Federal Regulations, 2011 CFR

2011-07-01

... the past 12 months, liters. Dj= density of aluminum wipedown solvent j, kilograms per liter. Wj= mass fraction of organic HAP in aluminum wipedown solvent j. m = number of different aluminum surface coatings...

Solubility and surface thermodynamics of conducting polymers by inverse gas chromatography. III: polypyrrole chloride.

PubMed

Duaij, Omar K; Alghamdi, Ali; Al-Saigh, Zeki Y

2013-05-24

Inverse gas chromatography, IGC, was applied to characterize conducting polypyrrole chloride (PPyCl) using twenty three solvents. IGC is able to reveal the change in the morphology, the strength of solvent-PPyCl interactions, thermodynamics parameters (χ12, Ω1(∞)), solvent and polymer solubility parameters, and molar heats of sorption, mixing and evaporation (ΔH1(s), ΔH1(∞), ΔH1(v)). The following solvents showed stronger interactions than others; yet, none of these solvents are good solvents for PPyCl: dodecane among the alkane family, tetrahydrofuran and methyl ethyl ketone among the oxy and keto group, dichloromethane among the chlorinated group up to 120°C and chloroform at 180°C, and toluene among the cyclic and aromatic group. Overall, the groups showed higher affinities to PPyCl are: acetates, oxy and cyclic, and chlorinated groups. Comprehensive solvents and PPyCl solubility parameters are obtained. The latter showed that PPyCl is not soluble in any solvent used. Copyright © 2013 Elsevier B.V. All rights reserved.

Tuning structure and mobility of solvation shells surrounding tracer additives

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carmer, James; Jain, Avni; Bollinger, Jonathan A.

2015-03-28

Molecular dynamics simulations and a stochastic Fokker-Planck equation based approach are used to illuminate how position-dependent solvent mobility near one or more tracer particle(s) is affected when tracer-solvent interactions are rationally modified to affect corresponding solvation structure. For tracers in a dense hard-sphere fluid, we compare two types of tracer-solvent interactions: (1) a hard-sphere-like interaction, and (2) a soft repulsion extending beyond the hard core designed via statistical mechanical theory to enhance tracer mobility at infinite dilution by suppressing coordination-shell structure [Carmer et al., Soft Matter 8, 4083–4089 (2012)]. For the latter case, we show that the mobility of surroundingmore » solvent particles is also increased by addition of the soft repulsive interaction, which helps to rationalize the mechanism underlying the tracer’s enhanced diffusivity. However, if multiple tracer surfaces are in closer proximity (as at higher tracer concentrations), similar interactions that disrupt local solvation structure instead suppress the position-dependent solvent dynamics.« less

Tuning structure and mobility of solvation shells surrounding tracer additives.

PubMed

Carmer, James; Jain, Avni; Bollinger, Jonathan A; van Swol, Frank; Truskett, Thomas M

2015-03-28

Molecular dynamics simulations and a stochastic Fokker-Planck equation based approach are used to illuminate how position-dependent solvent mobility near one or more tracer particle(s) is affected when tracer-solvent interactions are rationally modified to affect corresponding solvation structure. For tracers in a dense hard-sphere fluid, we compare two types of tracer-solvent interactions: (1) a hard-sphere-like interaction, and (2) a soft repulsion extending beyond the hard core designed via statistical mechanical theory to enhance tracer mobility at infinite dilution by suppressing coordination-shell structure [Carmer et al., Soft Matter 8, 4083-4089 (2012)]. For the latter case, we show that the mobility of surrounding solvent particles is also increased by addition of the soft repulsive interaction, which helps to rationalize the mechanism underlying the tracer's enhanced diffusivity. However, if multiple tracer surfaces are in closer proximity (as at higher tracer concentrations), similar interactions that disrupt local solvation structure instead suppress the position-dependent solvent dynamics.

Insecticide solvents: interference with insecticidal action.

PubMed

Brattsten, L B; Wilkinson, C F

1977-06-10

Several commercial solvent mixtures commonly used as insecticide carriers in spray formulations increase by more than threefold the microsomal N-demethylation of p-chloro N-methylaniline in midgut preparations of southern army-worm (Spodoptera eridania) larvae exposed orally to the test solvents. Under laboratory conditions, the same solvent mixtures exhibit a protective action against the in vivo toxicity of the insecticide carbaryl to the larvae. The data are discussed with respect to possible solvent-insecticide interactions occurring under field conditions and, more broadly, to potential toxicological hazards of these solvents to humans.

The Influence of Solvent on the Structural Properties of trans-(NHC)PtI2Py Complex: A Platinum-Based Anticancer Drug

NASA Astrophysics Data System (ADS)

Sadigh Vishkaee, Teherh; Fazaeli, Reza

2018-06-01

Quantum chemical calculations using MPW1PW91 method were applied to analyze the solvent effect on the structural, spectral, and thermochemical parameters for a platinum-based anticancer drug trans-(NHC)PtI2Py complex. The solvent effects were examined by the self-consistent reaction field theory (SCRF) based on Polarizable Continuum Model (PCM). The linear correlations between the solvation energies, HOMO-LUMO gaps, IR-active stretching vibration of Pt-N bonds and N-H of NHC ligand with dielectric constants of solvents were studied. The wave numbers of these IR-active stretching vibrations in different solvents were correlated with the Kirkwood-Bauer-Magat equation (KBM). The thermodynamic activation parameter such free energy of solvation, enthalpy of solvation were also calculated.

Brownian motion of a nano-colloidal particle: the role of the solvent.

PubMed

Torres-Carbajal, Alexis; Herrera-Velarde, Salvador; Castañeda-Priego, Ramón

2015-07-15

Brownian motion is a feature of colloidal particles immersed in a liquid-like environment. Usually, it can be described by means of the generalised Langevin equation (GLE) within the framework of the Mori theory. In principle, all quantities that appear in the GLE can be calculated from the molecular information of the whole system, i.e., colloids and solvent molecules. In this work, by means of extensive Molecular Dynamics simulations, we study the effects of the microscopic details and the thermodynamic state of the solvent on the movement of a single nano-colloid. In particular, we consider a two-dimensional model system in which the mass and size of the colloid are two and one orders of magnitude, respectively, larger than the ones associated with the solvent molecules. The latter ones interact via a Lennard-Jones-type potential to tune the nature of the solvent, i.e., it can be either repulsive or attractive. We choose the linear momentum of the Brownian particle as the observable of interest in order to fully describe the Brownian motion within the Mori framework. We particularly focus on the colloid diffusion at different solvent densities and two temperature regimes: high and low (near the critical point) temperatures. To reach our goal, we have rewritten the GLE as a second kind Volterra integral in order to compute the memory kernel in real space. With this kernel, we evaluate the momentum-fluctuating force correlation function, which is of particular relevance since it allows us to establish when the stationarity condition has been reached. Our findings show that even at high temperatures, the details of the attractive interaction potential among solvent molecules induce important changes in the colloid dynamics. Additionally, near the critical point, the dynamical scenario becomes more complex; all the correlation functions decay slowly in an extended time window, however, the memory kernel seems to be only a function of the solvent density. Thus, the explicit inclusion of the solvent in the description of Brownian motion allows us to better understand the behaviour of the memory kernel at those thermodynamic states near the critical region without any further approximation. This information is useful to elaborate more realistic descriptions of Brownian motion that take into account the particular details of the host medium.

Thermodynamic Approach to Boron Nitride Nanotube Solubility and Dispersion

NASA Technical Reports Server (NTRS)

Tiano, A. L.; Gibbons, L.; Tsui, M.; Applin, S. I.; Silva, R.; Park, C.; Fay, C. C.

2016-01-01

Inadequate dispersion of nanomaterials is a critical issue that significantly limits the potential properties of nanocomposites and when overcome, will enable further enhancement of material properties. The most common methods used to improve dispersion include surface functionalization, surfactants, polymer wrapping, and sonication. Although these approaches have proven effective, they often achieve dispersion by altering the surface or structure of the nanomaterial and ultimately, their intrinsic properties. Co-solvents are commonly utilized in the polymer, paint, and art conservation industries to selectively dissolve materials. These co-solvents are utilized based on thermodynamic interaction parameters and are chosen so that the original materials are not affected. The same concept was applied to enhance the dispersion of boron nitride nanotubes (BNNTs) to facilitate the fabrication of BNNT nanocomposites. Of the solvents tested, dimethylacetamide (DMAc) exhibited the most stable, uniform dispersion of BNNTs, followed by N,N-dimethylformamide (DMF), acetone, and N-methyl-2-pyrrolidone (NMP). Utilizing the known Hansen solubility parameters of these solvents in comparison to the BNNT dispersion state, a region of good solubility was proposed. This solubility region was used to identify co-solvent systems that led to improved BNNT dispersion in poor solvents such as toluene, hexane, and ethanol. Incorporating the data from the co-solvent studies further refined the proposed solubility region. From this region, the Hansen solubility parameters for BNNTs are thought to lie at the midpoint of the solubility sphere: 16.8, 10.7, and 9.0 MPa(exp 1/2) for delta d, delta p, and delta h, respectively, with a calculated Hildebrand parameter of 21.8 MPa)exp 1/2).

Thermodynamic approach to boron nitride nanotube solubility and dispersion.

PubMed

Tiano, A L; Gibbons, L; Tsui, M; Applin, S I; Silva, R; Park, C; Fay, C C

2016-02-21

Inadequate dispersion of nanomaterials is a critical issue that significantly limits the potential properties of nanocomposites and when overcome, will enable further enhancement of material properties. The most common methods used to improve dispersion include surface functionalization, surfactants, polymer wrapping, and sonication. Although these approaches have proven effective, they often achieve dispersion by altering the surface or structure of the nanomaterial and ultimately, their intrinsic properties. Co-solvents are commonly utilized in the polymer, paint, and art conservation industries to selectively dissolve materials. These co-solvents are utilized based on thermodynamic interaction parameters and are chosen so that the original materials are not affected. The same concept was applied to enhance the dispersion of boron nitride nanotubes (BNNTs) to facilitate the fabrication of BNNT nanocomposites. Of the solvents tested, dimethylacetamide (DMAc) exhibited the most stable, uniform dispersion of BNNTs, followed by N,N-dimethylformamide (DMF), acetone, and N-methyl-2-pyrrolidone (NMP). Utilizing the known Hansen solubility parameters of these solvents in comparison to the BNNT dispersion state, a region of good solubility was proposed. This solubility region was used to identify co-solvent systems that led to improved BNNT dispersion in poor solvents such as toluene, hexane, and ethanol. Incorporating the data from the co-solvent studies further refined the proposed solubility region. From this region, the Hansen solubility parameters for BNNTs are thought to lie at the midpoint of the solubility sphere: 16.8, 10.7, and 9.0 MPa(1/2) for δd, δp, and δh, respectively, with a calculated Hildebrand parameter of 21.8 MPa(1/2).

Tunable solvation effects on the size-selective fractionation of metal nanoparticles in CO2 gas-expanded solvents.

PubMed

Anand, Madhu; McLeod, M Chandler; Bell, Philip W; Roberts, Christopher B

2005-12-08

This paper presents an environmentally friendly, inexpensive, rapid, and efficient process for size-selective fractionation of polydisperse metal nanoparticle dispersions into multiple narrow size populations. The dispersibility of ligand-stabilized silver and gold nanoparticles is controlled by altering the ligand tails-solvent interaction (solvation) by the addition of carbon dioxide (CO2) gas as an antisolvent, thereby tailoring the bulk solvent strength. This is accomplished by adjusting the CO2 pressure over the liquid, resulting in a simple means to tune the nanoparticle precipitation by size. This study also details the influence of various factors on the size-separation process, such as the types of metal, ligand, and solvent, as well as the use of recursive fractionation and the time allowed for settling during each fractionation step. The pressure range required for the precipitation process is the same for both the silver and gold particles capped with dodecanethiol ligands. A change in ligand or solvent length has an effect on the interaction between the solvent and the ligand tails and therefore the pressure range required for precipitation. Stronger interactions between solvent and ligand tails require greater CO2 pressure to precipitate the particles. Temperature is another variable that impacts the dispersibility of the nanoparticles through changes in the density and the mole fraction of CO2 in the gas-expanded liquids. Recursive fractionation for a given system within a particular pressure range (solvent strength) further reduces the polydispersity of the fraction obtained within that pressure range. Specifically, this work utilizes the highly tunable solvent properties of organic/CO2 solvent mixtures to selectively size-separate dispersions of polydisperse nanoparticles (2 to 12 nm) into more monodisperse fractions (+/-2 nm). In addition to providing efficient separation of the particles, this process also allows all of the solvent and antisolvent to be recovered, thereby rendering it a green solvent process.

Effective interactions between nanoparticles: Creating temperature-independent solvation environments for self-assembly

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yadav, Hari O. S., E-mail: cyz108802@chemistry.iitd.ac.in, E-mail: hariyadav.iitd@gmail.com; Shrivastav, Gourav; Agarwal, Manish

2016-06-28

The extent to which solvent-mediated effective interactions between nanoparticles can be predicted based on structure and associated thermodynamic estimators for bulk solvents and for solvation of single and pairs of nanoparticles is studied here. As a test of the approach, we analyse the strategy for creating temperature-independent solvent environments using a series of homologous chain fluids as solvents, as suggested by an experimental paper [M. I. Bodnarchuk et al., J. Am. Chem. Soc. 132, 11967 (2010)]. Our conclusions are based on molecular dynamics simulations of Au{sub 140}(SC{sub 10}H{sub 21}){sub 62} nanoparticles in n-alkane solvents, specifically hexane, octane, decane and dodecane,more » using the TraPPE-UA potential to model the alkanes and alkylthiols. The 140-atom gold core of the nanocrystal is held rigid in a truncated octahedral geometry and the gold-thiolate interaction is modeled using a Morse potential. The experimental observation was that the structural and rheological properties of n-alkane solvents are constant over a temperature range determined by equivalent solvent vapour pressures. We show that this is a consequence of the fact that long chain alkane liquids behave to a good approximation as simple liquids formed by packing of monomeric methyl/methylene units. Over the corresponding temperature range (233–361 K), the solvation environment is approximately constant at the single and pair nanoparticle levels under good solvent conditions. However, quantitative variations of the order of 10%–20% do exist in various quantities, such as molar volume of solute at infinite dilution, entropy of solvation, and onset distance for soft repulsions. In the opposite limit of a poor solvent, represented by vacuum in this study, the effective interactions between nanoparticles are no longer temperature-independent with attractive interactions increasing by up to 50% on decreasing the temperature from 361 K to 290 K, accompanied by an increase in emergent anisotropy due to correlation of mass dipoles on the two nanoparticles. One expects therefore that during self-assembly using solvent evaporation, temperature can be used as a structure-directing factor as long as good solvent conditions are maintained. It also suggests that disordered configurations may emerge as solvent quality decreases due to increasing role of short-range attractions and ligand fluctuation-driven anisotropy. The possibilities of using structural estimators of various thermodynamic quantities to analyse the interplay of ligand fluctuations and solvent quality in self-assembly as well as to design solvation environments are discussed.« less

High Energy Density in Azobenzene-based Materials for Photo-Thermal Batteries via Controlled Polymer Architecture and Polymer-Solvent Interactions.

PubMed

Jeong, Seung Pyo; Renna, Lawrence A; Boyle, Connor J; Kwak, Hyunwook S; Harder, Edward; Damm, Wolfgang; Venkataraman, Dhandapani

2017-12-19

Energy densities of ~510 J/g (max: 698 J/g) have been achieved in azobenzene-based syndiotactic-rich poly(methacrylate) polymers. The processing solvent and polymer-solvent interactions are important to achieve morphologically optimal structures for high-energy density materials. This work shows that morphological changes of solid-state syndiotactic polymers, driven by different solvent processings play an important role in controlling the activation energy of Z-E isomerization as well as the shape of the DSC exotherm. Thus, this study shows the crucial role of processing solvents and thin film structure in achieving higher energy densities.

The role of molecular conformation and polarizable embedding for one- and two-photon absorption of disperse orange 3 in solution.

PubMed

Silva, Daniel L; Murugan, N Arul; Kongsted, Jacob; Rinkevicius, Zilvinas; Canuto, Sylvio; Ågren, Hans

2012-07-19

Solvent effects on the one- and two-photon absorption (1PA and 2PA) of disperse orange 3 (DO3) in dimethyl sulfoxide (DMSO) are studied using a discrete polarizable embedding (PE) response theory. The scheme comprises a quantum region containing the chromophore and an atomically granulated classical region for the solvent accounting for full interactions within and between the two regions. Either classical molecular dynamics (MD) or hybrid Car-Parrinello (CP) quantum/classical (QM/MM) molecular dynamics simulations are employed to describe the solvation of DO3 in DMSO, allowing for an analysis of the effect of the intermolecular short-range repulsion, long-range attraction, and electrostatic interactions on the conformational changes of the chromophore and also the effect of the solute-solvent polarization. PE linear response calculations are performed to verify the character, solvatochromic shift, and overlap of the two lowest energy transitions responsible for the linear absorption spectrum of DO3 in DMSO in the visible spectral region. Results of the PE linear and quadratic response calculations, performed using uncorrelated solute-solvent configurations sampled from either the classical or hybrid CP QM/MM MD simulations, are used to estimate the width of the line shape function of the two electronic lowest energy excited states, which allow a prediction of the 2PA cross-sections without the use of empirical parameters. Appropriate exchange-correlation functionals have been employed in order to describe the charge-transfer process following the electronic transitions of the chromophore in solution.

Evaluation of the influence of the internal aqueous solvent structure on electrostatic interactions at the protein-solvent interface by nonlocal continuum electrostatic approach.

PubMed

Rubinstein, Alexander; Sherman, Simon

The dielectric properties of the polar solvent on the protein-solvent interface at small intercharge distances are still poorly explored. To deconvolute this problem and to evaluate the pair-wise electrostatic interaction (PEI) energies of the point charges located at the protein-solvent interface we used a nonlocal (NL) electrostatic approach along with a static NL dielectric response function of water. The influence of the aqueous solvent microstructure (determined by a strong nonelectrostatic correlation effect between water dipoles within the orientational Debye polarization mode) on electrostatic interactions at the interface was studied in our work. It was shown that the PEI energies can be significantly higher than the energies evaluated by the classical (local) consideration, treating water molecules as belonging to the bulk solvent with a high dielectric constant. Our analysis points to the existence of a rather extended, effective low-dielectric interfacial water shell on the protein surface. The main dielectric properties of this shell (effective thickness together with distance- and orientation-dependent dielectric permittivity function) were evaluated. The dramatic role of this shell was demonstrated when estimating the protein association rate constants.

Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Drenscko, Mihaela

Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of small membranes using all atomistic and coarse-grained methods. The molecular interaction between common polymer chains used in biomedical applications and the cell membrane is unknown. This interaction may affect the biocompatibility of the polymer chains. Molecular dynamics simulations offer an emerging tool to characterize the interaction between common degradable polymer chains used in biomedical applications, such as polycaprolactone, and model cell membranes. We systematically characterize with long-time all-atomistic molecular dynamics simulations the interaction between single polycaprolactone chains of varying chain lengths with a model phospholipid membrane. We find that the length of polymer chain greatly affects the nature of interaction with the membrane, as well as the membrane properties. Furthermore, we next utilize advanced sampling techniques in molecular dynamics to characterize the two-dimensional free energy surface for the interaction of varying polymer chain lengths (short, intermediate, and long) with model cell membranes. We find that the free energy minimum shifts from the membrane-water interface to the hydrophobic core of the phospholipid membrane as a function of chain length. These results can be used to design polymer chain lengths and chemistries to optimize their interaction with cell membranes at the molecular level.

Strong Solvent Effects on the Nonlinear Optical Properties of Z and E isomers from Azo-Enaminone Derivatives.

PubMed

Machado, Daniel Francisco Scalabrini; Lopes, Thiago O; Lima, Igo Torres; da Silva Filho, Demetrio Antonio; de Oliveira, Heibbe Cristhian Benedito

2016-07-01

We calculated the nonlinear optical properties of 24 azo-enaminone derivatives, incorporating solvent effects on their geometric and elec-tronic structure, to assess the impact of the environment on these properties. Namely, we incorporated chloroform, tetrahydrofuran, acetone, ethanol, methanol, dimethyl sulfoxide on our calculations and compared our results incorporating solvent effects with our gas phase calculations. To account for the electron correlation effects on NLO properties, the calculations were performed at MP2/6-31G(p)//MP2/6-31G(d) level set. The Polarizable Continuum Model (PCM) was used to simulate the presence of the solvent. The exponents of p extra functions added to heavy atoms were obtained, imposing the maximization of the first hyperpolarizability. Two structural configurations (Z and E) of azo-enaminones were investigated to assess the isomeric effects of the electric properties. Our results show that both solvent polarity and relative strength of the donor groups have significant impact on the electric properties, but more strikingly on the first hyperpolarizability β.

The local phase transitions of the solvent in the neighborhood of a solvophobic polymer at high pressures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Budkov, Yu. A., E-mail: urabudkov@rambler.ru; National Research University Higher School of Economics, Moscow; Department of Chemistry, Lomonosov Moscow State University, Moscow

2014-11-28

We investigate local phase transitions of the solvent in the neighborhood of a solvophobic polymer chain which is induced by a change of the polymer-solvent repulsion and the solvent pressure in the bulk solution. We describe the polymer in solution by the Edwards model, where the conditional partition function of the polymer chain at a fixed radius of gyration is described by a mean-field theory. The contributions of the polymer-solvent and the solvent-solvent interactions to the total free energy are described within the mean-field approximation. We obtain the total free energy of the solution as a function of the radiusmore » of gyration and the average solvent number density within the gyration volume. The resulting system of coupled equations is solved varying the polymer-solvent repulsion strength at high solvent pressure in the bulk. We show that the coil-globule (globule-coil) transition occurs accompanied by a local solvent evaporation (condensation) within the gyration volume.« less

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers.

PubMed

Reimers, Jeffrey R; Panduwinata, Dwi; Visser, Johan; Chin, Yiing; Tang, Chunguang; Goerigk, Lars; Ford, Michael J; Sintic, Maxine; Sum, Tze-Jing; Coenen, Michiel J J; Hendriksen, Bas L M; Elemans, Johannes A A W; Hush, Noel S; Crossley, Maxwell J

2015-11-10

Modern quantum chemical electronic structure methods typically applied to localized chemical bonding are developed to predict atomic structures and free energies for meso-tetraalkylporphyrin self-assembled monolayer (SAM) polymorph formation from organic solution on highly ordered pyrolytic graphite surfaces. Large polymorph-dependent dispersion-induced substrate-molecule interactions (e.g., -100 kcal mol(-1) to -150 kcal mol(-1) for tetratrisdecylporphyrin) are found to drive SAM formation, opposed nearly completely by large polymorph-dependent dispersion-induced solvent interactions (70-110 kcal mol(-1)) and entropy effects (25-40 kcal mol(-1) at 298 K) favoring dissolution. Dielectric continuum models of the solvent are used, facilitating consideration of many possible SAM polymorphs, along with quantum mechanical/molecular mechanical and dispersion-corrected density functional theory calculations. These predict and interpret newly measured and existing high-resolution scanning tunnelling microscopy images of SAM structure, rationalizing polymorph formation conditions. A wide range of molecular condensed matter properties at room temperature now appear suitable for prediction and analysis using electronic structure calculations.

Empirical Estimation of Local Dielectric Constants: Toward Atomistic Design of Collagen Mimetic Peptides

PubMed Central

Pike, Douglas H.; Nanda, Vikas

2017-01-01

One of the key challenges in modeling protein energetics is the treatment of solvent interactions. This is particularly important in the case of peptides, where much of the molecule is highly exposed to solvent due to its small size. In this study, we develop an empirical method for estimating the local dielectric constant based on an additive model of atomic polarizabilities. Calculated values match reported apparent dielectric constants for a series of Staphylococcus aureus nuclease mutants. Calculated constants are used to determine screening effects on Coulombic interactions and to determine solvation contributions based on a modified Generalized Born model. These terms are incorporated into the protein modeling platform protCAD, and benchmarked on a data set of collagen mimetic peptides for which experimentally determined stabilities are available. Computing local dielectric constants using atomistic protein models and the assumption of additive atomic polarizabilities is a rapid and potentially useful method for improving electrostatics and solvation calculations that can be applied in the computational design of peptides. PMID:25784456

A recipe for free-energy functionals of polarizable molecular fluids

NASA Astrophysics Data System (ADS)

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Arias, T. A.

2014-04-01

Classical density-functional theory is the most direct approach to equilibrium structures and free energies of inhomogeneous liquids, but requires the construction of an approximate free-energy functional for each liquid of interest. We present a general recipe for constructing functionals for small-molecular liquids based only on bulk experimental properties and ab initio calculations of a single solvent molecule. This recipe combines the exact free energy of the non-interacting system with fundamental measure theory for the repulsive contribution and a weighted density functional for the short-ranged attractive interactions. We add to these ingredients a weighted polarization functional for the long-range correlations in both the rotational and molecular-polarizability contributions to the dielectric response. We also perform molecular dynamics calculations for the free energy of cavity formation and the high-field dielectric response, and show that our free-energy functional adequately describes these properties (which are key for accurate solvation calculations) for all three solvents in our study: water, chloroform, and carbon tetrachloride.

Tuning aggregation of microemulsion droplets and silica nanoparticles using solvent mixtures.

PubMed

Salabat, Alireza; Eastoe, Julian; Mutch, Kevin J; Tabor, Rico F

2008-02-15

The effect of solvent on stability of water-in-oil microemulsions has been studied with AOT (sodium bis(2-ethylhexyl)sulfosuccinate) and different solvent mixtures of n-heptane, toluene and dodecane. Dynamic light scattering DLS was used to monitor the apparent diffusion coefficient D(A) and effective microemulsion droplet diameter on changing composition of the solvent. Interdroplet attractive interactions, as indicated by variations in D(A), can be tuned by formulation of appropriate solvent mixtures using heptane, toluene, and dodecane. In extreme cases, solvent mixtures can be used to induce phase transitions in the microemulsions. Aggregation and stability of model AOT-stabilized silica nanoparticles in different solvents were also investigated to explore further these solvent effects. For both systems the state of aggregation can be correlated with the effective molecular volume of the solvent V(mol)(eff) mixture.

Solvent effect in implicit/explicit model on FT-IR, 1H, 13C and 19F NMR, UV-vis and fluorescence spectra, linear, second- and third-nonlinear optical parameters of 2-(trifluoromethyl)benzoic acid: Experimental and computational study

NASA Astrophysics Data System (ADS)

Avcı, Davut; Altürk, Sümeyye; Tamer, Ömer; Kuşbazoğlu, Mustafa; Atalay, Yusuf

2017-09-01

FT-IR, 1H, 13C and 19F NMR, UV-vis and fluorescence spectra for 2-(trifluoromethyl)benzoic acid (2-TFMBA) were recorded. DFT//B3LYP/6-31++G(d,p) calculations were used to determine the optimized molecular geometry, vibrational frequencies, 1H, 13C and 19F GIAO-NMR chemical shifts of 2-TFMBA. The detailed assignments of vibrational frequencies were carried out on the basis of potential energy distribution (PED) by using VEDA program. TD-DFT/B3LYP/6-31++G(d,p) calculations with the PCM (polarizable continuum model) in ethanol and DMSO solvents based on implicit/explicit model and gas phase in the excited state were employed to investigate UV-vis absorption and fluorescence emission wavelengths. The UV-vis and emission spectra were given in ethanol and DMSO solvents, and the major contributions to the electronic transitions were obtained. In addition, the NLO parameters (β, γ and χ(3)) and frontier molecular orbital energies of 2-TFMBA were calculated by using B3LYP/6-31++G(d,p) level. The NLO parameters of 2-TFMBA were compared with that of para-Nitroaniline (pNA) and urea which are the typical NLO materials. The refractive index (n) is calculated by using the Lorentz-Lorenz equation to observe polarization behavior of 2-TFMBA in DMSO and ethanol solvents. In order to investigate intramolecular and hydrogen bonding interactions, NBO calculations were also performed by the same level. To sum up, considering the well-known biological role, photochemical properties of 2-TFMBA were discussed.

Conformational analysis of some 4‧-substituted 2-(phenylselanyl)- 2-(methoxy)- acetophenones

NASA Astrophysics Data System (ADS)

Traesel, Henrique J.; Olivato, Paulo R.; Valença, J.; Rodrigues, Daniel N. S.; Zukerman-Schpector, Julio; Colle, Maurizio Dal

2018-04-01

A conformational study of some 4‧-substituited 2-(phenylselanyl)-2-(methoxy)-acetophenones (OMe 1, H 2, and Cl 3) was performed using IR carbonyl stretching band analysis supported by NBO and PCM calculations at the B3LYP/6-31 + G (d,p) level for 1-3 and using X-ray diffraction for 1 and 2. The computational results indicated the existence of three stable conformers for the series (c2, c3, and c1 in order of decreasing stability), whose relative abundance changes with solvent permittivity. The experimental trend observed for the components of the triplet carbonyl band in all solvents matches well with computational results and thus allows for their assignment to distinct conformers. The relative population of the c1 conformer increases in more polar solvents, becoming the most stable conformer in the highest permittivity solvent, acetonitrile, as indicated by IR spectra and PCM calculations. These findings are related to the quasi parallel geometry assumed by the Cδ+ = Oδ- and Cδ+-Oδ- dipoles, which favour stronger solvation. NBO analysis shows that the sum of the energies (ΣE) of the relevant orbital interactions stabilizes the c3 conformer of 1-3 slightly, likely due to the minor contribution of the LPO5→σ*C3sbnd Se10 interaction. However, only the c1 conformer is significantly destabilized by the Oδ-(1)CO … Oδ-(5)OMe short contact electrostatic repulsion, which is also responsible for its highest νCO frequency. In addition, the LPO5→ σ*C2sbnd C3 orbital interaction accounts for the lowest νCO frequency of c3 conformer. X-ray single crystal analysis of compounds 1 and 2 indicates that in the solid state they assume the least stable c1 conformation found in the gas phase. Molecules of these compounds are stabilized in the crystal through a series of Csbnd H⋯O and Csbnd H … π intermolecular interactions.

Wetting behavior of nonpolar nanotubes in simple dipolar liquids for varying nanotube diameter and solute-solvent interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rana, Malay Kumar; Chandra, Amalendu, E-mail: amalen@iitk.ac.in

2015-01-21

Atomistic simulations of model nonpolar nanotubes in a Stockmayer liquid are carried out for varying nanotube diameter and nanotube-solvent interactions to investigate solvophobic interactions in generic dipolar solvents. We have considered model armchair type single-walled nonpolar nanotubes with increasing radii from (5,5) to (12,12). The interactions between solute and solvent molecules are modeled by the well-known Lennard-Jones and repulsive Weeks-Chandler-Andersen potentials. We have investigated the density profiles and microscopic arrangement of Stockmayer molecules, orientational profiles of their dipole vectors, time dependence of their occupation, and also the translational and rotational motion of solvent molecules in confined environments of the cylindricalmore » nanopores and also in their external peripheral regions. The present results of structural and dynamical properties of Stockmayer molecules inside and near atomistically rough nonpolar surfaces including their wetting and dewetting behavior for varying interactions provide a more generic picture of solvophobic effects experienced by simple dipolar liquids without any specific interactions such as hydrogen bonds.« less

Solvent Additive-Assisted Anisotropic Assembly and Enhanced Charge Transport of π-Conjugated Polymer Thin Films.

PubMed

Jeong, Jae Won; Jo, Gyounglyul; Choi, Solip; Kim, Yoong Ahm; Yoon, Hyeonseok; Ryu, Sang-Wan; Jung, Jaehan; Chang, Mincheol

2018-05-30

Charge transport in π-conjugated polymer films involves π-π interactions within or between polymer chains. Here, we demonstrate a facile solution processing strategy that provides enhanced intra- and interchain π-π interactions of the resultant polymer films using a good solvent additive with low volatility. These increased interactions result in enhanced charge transport properties. The effect of the good solvent additive on the intra- and intermolecular interactions, morphologies, and charge transport properties of poly(3-hexylthiophene) (P3HT) films is systematically investigated. We found that the good solvent additive facilitates the self-assembly of P3HT chains into crystalline fibrillar nanostructures by extending the solvent drying time during thin-film formation. As compared to the prior approach using a nonsolvent additive with low volatility, the solvent blend system containing a good solvent additive results in enhanced charge transport in P3HT organic field-effect transistor (OFET) devices [from ca. 1.7 × 10 -2 to ca. 8.2 × 10 -2 cm 2 V -1 s -1 for dichlorobenzene (DCB) versus 4.4 × 10 -2 cm 2 V -1 s -1 for acetonitrile]. The mobility appears to be maximized over a broad spectrum of additive concentrations (1-7 vol %), indicative of a wide processing window. Detailed analysis results regarding the charge injection and transport characteristics of the OFET devices reveal that a high-boiling-point solvent additive decreases both the contact resistance ( R c ) and channel resistance ( R ch ), contributing to the mobility enhancement of the devices. Finally, the platform presented here is proven to be applicable to alternative good solvent additives with low volatility, such as chlorobenzene (CB) and trichlorobenzene (TCB). Specifically, the mobility enhancement of the resultant P3HT films increases in the order CB (bp 131 °C) < DCB (bp 180 °C) < TCB (bp 214 °C), suggesting that solvent additives with higher boiling points provide resultant films with preferable molecular ordering and morphologies for efficient charge transport.

Solvophobic and solvophilic contributions in the water-to-aqueous guanidinium chloride transfer free energy of model peptides

NASA Astrophysics Data System (ADS)

Tomar, Dheeraj S.; Ramesh, Niral; Asthagiri, D.

2018-06-01

We study the solvation free energy of two different conformations (helix and extended) of two different peptides (deca-alanine and deca-glycine) in two different solvents (water and aqueous guanidinium chloride, GdmCl). The free energies are obtained using the quasichemical organization of the potential distribution theorem, an approach that naturally provides the repulsive (solvophobic or cavity) and attractive (solvophilic) contributions to solvation. The solvophilic contribution is further parsed into a chemistry contribution arising from solute interaction with the solvent in the first solvation shell and a long-range contribution arising from non-specific interactions between the solute and the solvent beyond the first solvation shell. The cavity contribution is obtained for two different envelopes, ΣS E, which theory helps identify as the solvent excluded volume, and ΣG, a larger envelope beyond which solute-solvent interactions are Gaussian. The ΣS E envelope is independent of the solvent, as expected on the basis of the insensitivity to the solvent type of the distance of closest approach between protein heavy atoms and solvent heavy atoms, but contrary to the intuition based on treating solvent constituents as spheres of some effective radii. For both envelopes, the cavity contribution in water is proportional to the surface area of the envelope. The same does not hold for GdmCl(aq), revealing the limitation of using molecular area to assess solvation energetics. The ΣG-cavity contribution predicts that GdmCl(aq) should favor the more compact state, contrary to the role of GdmCl in unfolding proteins. The chemistry contribution attenuates this effect, but still the net local (chemistry plus ΣG-packing) contribution is inadequate in capturing the role of GdmCl. With the inclusion of the long-range contribution, which is dominated by van der Waals interaction, aqueous GdmCl favors the extended conformation over the compact conformation. Our finding emphasizes the importance of weak, but attractive, long-range dispersion interactions in protein solution thermodynamics.

Solvophobic and solvophilic contributions in the water-to-aqueous guanidinium chloride transfer free energy of model peptides.

PubMed

Tomar, Dheeraj S; Ramesh, Niral; Asthagiri, D

2018-06-14

We study the solvation free energy of two different conformations (helix and extended) of two different peptides (deca-alanine and deca-glycine) in two different solvents (water and aqueous guanidinium chloride, GdmCl). The free energies are obtained using the quasichemical organization of the potential distribution theorem, an approach that naturally provides the repulsive (solvophobic or cavity) and attractive (solvophilic) contributions to solvation. The solvophilic contribution is further parsed into a chemistry contribution arising from solute interaction with the solvent in the first solvation shell and a long-range contribution arising from non-specific interactions between the solute and the solvent beyond the first solvation shell. The cavity contribution is obtained for two different envelopes, Σ SE , which theory helps identify as the solvent excluded volume, and Σ G , a larger envelope beyond which solute-solvent interactions are Gaussian. The Σ SE envelope is independent of the solvent, as expected on the basis of the insensitivity to the solvent type of the distance of closest approach between protein heavy atoms and solvent heavy atoms, but contrary to the intuition based on treating solvent constituents as spheres of some effective radii. For both envelopes, the cavity contribution in water is proportional to the surface area of the envelope. The same does not hold for GdmCl(aq), revealing the limitation of using molecular area to assess solvation energetics. The Σ G -cavity contribution predicts that GdmCl(aq) should favor the more compact state, contrary to the role of GdmCl in unfolding proteins. The chemistry contribution attenuates this effect, but still the net local (chemistry plus Σ G -packing) contribution is inadequate in capturing the role of GdmCl. With the inclusion of the long-range contribution, which is dominated by van der Waals interaction, aqueous GdmCl favors the extended conformation over the compact conformation. Our finding emphasizes the importance of weak, but attractive, long-range dispersion interactions in protein solution thermodynamics.

Behaviour of a solvent trapped in a physical molecular gel

NASA Astrophysics Data System (ADS)

Morfin, I.; Spagnoli, S.; Rambaud, C.; Longeville, S.; Plazanet, M.

2016-03-01

Physical gels formed by amphiphilic molecules, namely in this study Methyl-4,6-O-benzylidene-? -D-mannopyranoside, can be form either in polar and protic liquid-like water or in organic apolar solvent such as toluene. The solvent, that influences the supramolecular organization of the gelators, plays an important role in the stability and formation of the gel phase. Gelator-solvent interactions govern not only the assembly but also the solvent diffusion in the material. We present here measurements of neutron scattering (Time of Flight and Neutron Spin Echo) characterizing this microscopic behaviour. In addition, we show that transient grating spectroscopy provides valuable information through the characterization of the longitudinal acoustic wave propagating in the system. Opposite effects on the speed of sound in the gels are observed for the two solvents investigated, being relevant of the interactions between the gelators and the surrounding liquid.

Main chemical species and molecular structure of deep eutectic solvent studied by experiments with DFT calculation: a case of choline chloride and magnesium chloride hexahydrate.

PubMed

Zhang, Chao; Jia, Yongzhong; Jing, Yan; Wang, Huaiyou; Hong, Kai

2014-08-01

The infrared spectrum of deep eutectic solvent of choline chloride and magnesium chloride hexahydrate was measured by the FTIR spectroscopy and analyzed with the aid of DFT calculations. The main chemical species and molecular structure in deep eutectic solvent of [MgClm(H2O)6-m]2-m and [ChxCly]x+y complexes were mainly identified and the active ion of magnesium complex during the electrochemical process was obtained. The mechanism of the electrochemical process of deep eutectic solvent of choline chloride and magnesium chloride hexahydrate was well explained by combination theoretical calculations and experimental. Besides, based on our results we proposed a new system for the dehydration study of magnesium chloride hexahydrate.

Elucidation of ionic interactions in the protic ionic liquid solutions by isothermal titration calorimetry.

PubMed

Rai, Gitanjali; Kumar, Anil

2014-04-17

The strong hydrogen-bonded network noted in protic ionic liquids (PILs) may lead to stronger interactions of the ionic entities of PILs with solvents (water, methanol, ethylene glycol, dimethylsulfoxide (DMSO), N,N'-dimethylformamide (DMF)) as compared with those of aprotic ionic liquids (APILs). The PILs used in this work are 1-methylimidazolium tetrafluoroborate, 2-methylpyridinium tetrafluoroborate, and N-methylpyrrolodinium tetrafluoroborate in comparison to 1-butyl-3-methylimidazolium tetrafluoroborate, which is classified as an APIL. In this work, the excess partial molar enthalpy, H(E)IL obtained from isothermal calorimetric titrations at 298.15 K is used to probe the nature of interactions of the PIL cations with solvent molecules against those present in APIL-solvent systems. This work also reports interesting flip-flopping in the thermal behavior of these PIL-solvent systems depending upon the structure of the cationic ring of a PIL. In some cases, these flip-flops are the specific fingerprints for specific PILs in a common solvent environment. The excess partial molar enthalpy at infinite dilution, H(E,∞)IL, of these PILs bears a critical dependence on the solvent properties. An analysis of relative apparent molar enthalpies, ϕL, of the PIL solutions by the ion interaction model of Pitzer yields important information on ionic interactions of these systems.

Solvent empirical scales and their importance for the study of intermolecular interactions

NASA Astrophysics Data System (ADS)

Babusca, Daniela; Benchea, Andreea Celia; Morosanu, Ana Cezarina; Dimitriu, Dan Gheorghe; Dorohoi, Dana Ortansa

2017-01-01

The solvent empirical scales were developed in order to classify the solvents regarding their influence on the absorption or fluorescence spectra of different spectrally active molecules. The intermolecular interactions in binary solutions of three molecule having an intramolecular charge transfer visible absorption band are studied in this paper: 5-[2-(1,2,2,4-tetramethyl-1,2,3,4-tetrahydroquinolin-6-yl)-vinyl]-thiophene-2-carbaldehyde (QTC), 1-cyano-2-{5-[2-(1,2,2,4-tetramethyl-1,2,3,4-tetrahydroquinolin-6-yl)-vinyl]-thiophen-2-yl}-vinyl)-phosphonic acid diethyl ester (QTCP) and p-phenyl pyridazinium-p-nitro-phenacylid (PPNP). The solvent empirical scales with a single parameter (Z scale of Kosower, ET (30) or ETN scale of Reichardt and Dimroth) can be used to describe the strength of intermolecular interactions. The contributions of each type of interactions to the total spectral shift are evaluated using the solvent multiple parameters empirical scales defined by Kamlet and Taft and by Catalan et al.

A combined TD-DFT and spectroscopic investigation of the solute-solvent interactions of efavirenz

NASA Astrophysics Data System (ADS)

Jordaan, Maryam A.; Singh, Parvesh; Martincigh, Bice S.

2016-03-01

Efavirenz, commercially known as Sustiva® or Stocrin®, is a first-line antiretroviral treatment for HIV/AIDS. The clinical efficacy of efavirenz is, however, hindered by its solubility. We sought to investigate the solute-solvent effects of efavirenz by means of a combined qualitative study implementing UV-visible spectrophotometry, 1H NMR spectroscopy and time-dependent density functional theory (TD-DFT) calculations. The UV spectrum displayed two main absorbance maxima, band I and band II at 246-260 and 291-295 nm, respectively. A general bathochromic shift was noticed from the non-polar solvent cyclohexane to the most polar solvent DMSO (≈ 13.69 nm) in band I and a smaller bathochromic (≈ 2.17 nm) and hyperchromic shift was observed in band II. We propose that these observations are due to the role of the amino (NH) and carbonyl (CO) functionalities which induce charge-transfer and intra- and inter-molecular hydrogen bonding. The aromatic and amine protons showed the most deshielded effects in the observed chemical shifts (δ) in the more polar DMSO-d6 solvent relative to CDCl3. The 1H NMR chemical shifts observed are due to the increased delocalization of the lone pair electrons of the amino nitrogen with increased polarity of the more polar DMSO solvent. The theoretical reproduction of the UV and 1H NMR spectra by means of TD-DFT is in good agreement with the experimental results.

Nuclear magnetic resonance spectral analysis and molecular properties of berberine

NASA Astrophysics Data System (ADS)

Huang, Ming-Ju; Lee, Ken S.; Hurley, Sharon J.

An extensive theoretical study of berberine has been performed at the ab initio HF/6-31G**, HF/6-311G**, and B3LYP/6-311G** levels with and without solvent effects. The optimized structures are compared with X-ray data. We found that the optimized structures with solvent effects are in slightly better agreement with X-ray data than those without solvent effects. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of berberine were calculated by using the gauge-independent atomic orbital (GIAO) (with and without solvent effects), CSGT, and IGAIM methods. The calculated chemical shifts were compared with the two-dimensional NMR experimental data. Overall, the calculated chemical shifts show very good agreement with the experimental results. The harmonic vibrational frequencies for berberine were calculated at the B3LYP/6-311G** level.

Face-Dependent Solvent Adsorption: A Comparative Study on the Interfaces of HMX Crystal with Three Solvents.

PubMed

Liu, Yingzhe; Lai, Weipeng; Ma, Yiding; Yu, Tao; Kang, Ying; Ge, Zhongxue

2017-07-27

To understand the crystal-solvent interfacial interactions on the molecular scale, the interfaces between three solvents, that is, acetone, γ-butyrolactone, and cyclohexanone, and three growth faces of 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) crystal have been investigated with the aid of theoretical chemistry. The results show that the structural features of crystal faces play a critical role in the energetic, structural, and dynamic properties at the interfaces. For each solvent, the same change trend of some properties among the three faces of HMX crystal is observed, including adsorption affinity, local mass density, and solvent diffusion. For example, the rate of solvent diffusion at the three faces ranks as (011) > (110) > (020) regardless of solvent species. This can be attributed to the similar adsorption sites for solvent incorporation at the same face, which are concentrated at the cavities formed by surficial HMX molecules.

Deactivation of 6-Aminocoumarin Intramolecular Charge Transfer Excited State through Hydrogen Bonding

PubMed Central

Krystkowiak, Ewa; Dobek, Krzysztof; Maciejewski, Andrzej

2014-01-01

This paper presents results of the spectral (absorption and emission) and photophysical study of 6-aminocoumarin (6AC) in various aprotic hydrogen-bond forming solvents. It was established that solvent polarity as well as hydrogen-bonding ability influence solute properties. The hydrogen-bonding interactions between S1-electronic excited solute and solvent molecules were found to facilitate the nonradiative deactivation processes. The energy-gap dependence on radiationless deactivation in aprotic solvents was found to be similar to that in protic solvents. PMID:25244014

Multiple hydrogen-bonded complexes based on 2-ureido-4[1H]-pyrimidinone: a theoretical study.

PubMed

Sun, Hao; Lee, Hui Hui; Blakey, Idriss; Dargaville, Bronwin; Chirila, Traian V; Whittaker, Andrew K; Smith, Sean C

2011-09-29

In the present work, the electronic structures and properties of a series of 2-ureido-4[1H]-pyrimidinone(UPy)-based monomers and dimers in various environments (vacuum, chloroform, and water) are studied by density functional theoretical methods. Most dimers prefer to form a DDAA-AADD (D, H-bond donor; A, H-bond acceptor) array in both vacuum and solvents. Topological analysis proved that intramolecular and intermolecular hydrogen bonds coexist in the dimers. Frequency and NBO calculations show that all the hydrogen bonds exhibit an obvious red shift in their stretching vibrational frequencies. Larger substituents at position 6 of the pyrimidinone ring with stronger electron-donating ability favor the total binding energy and free energy of dimerization. Calculations on the solvent effect show that dimerization is discouraged by the stronger polarity of the solvent. Further computations show that Dimer-1 may be formed in chloroform, but water molecules may interact with the donor or acceptor sites and hence disrupt the hydrogen bonds of Dimer-1. © 2011 American Chemical Society

Force fields for describing the solution-phase synthesis of shape-selective metal nanoparticles

NASA Astrophysics Data System (ADS)

Zhou, Ya; Al-Saidi, Wissam; Fichthorn, Kristen

2013-03-01

Polyvinylpyrrolidone (PVP) and polyethylene oxide (PEO) are structure-directing agents that exhibit different performance in the polyol synthesis of Ag nanostructures. The success of these structure-directing agents in selective nanostructure synthesis is often attributed to their selective binding to Ag(100) facets. We use first-principles, density-functional theory (DFT) calculations in a vacuum environment to show that PVP has a stronger preference to bind to Ag(100) than to Ag(111), whereas PEO exhibits much weaker selectivity. To understand the role of solvent in the surface-sensitive binding, we develop classical force fields to describe the interactions of the structure-directing (PVP and PEO) and solvent (ethylene glycol) molecules with various Ag substrates. We parameterize the force fields through force-and-energy matching to DFT results using simulated annealing. We validate the force fields by comparisons to DFT and experimental binding energies. Our force fields reproduce the surface-sensitive binding predicted by DFT calculations. Molecular dynamics simulations based on these force fields can be used to reveal the role of solvent, polymer chain length, and polymer concentration in the selective synthesis of Ag nanostructures.

Chlorophenol sorption on multi-walled carbon nanotubes: DFT modeling and structure-property relationship analysis.

PubMed

Watkins, Marquita; Sizochenko, Natalia; Moore, Quentarius; Golebiowski, Marek; Leszczynska, Danuta; Leszczynski, Jerzy

2017-02-01

The presence of chlorophenols in drinking water can be hazardous to human health. Understanding the mechanisms of adsorption under specific experimental conditions would be beneficial when developing methods to remove toxic substances from drinking water during water treatment in order to limit human exposure to these contaminants. In this study, we investigated the sorption of chlorophenols on multi-walled carbon nanotubes using a density functional theory (DFT) approach. This was applied to study selected interactions between six solvents, five types of nanotubes, and six chlorophenols. Experimental data were used to construct structure-adsorption relationship (SAR) models that describe the recovery process. Specific interactions between solvents and chlorophenols were taken into account in the calculations by using novel specific mixture descriptors.

Molecular gels in the gas phase? Gelator-gelator and gelator-solvent interactions probed by vibrational spectroscopy.

PubMed

Lozada-Garcia, Rolando; Mu, Dan; Plazanet, Marie; Çarçabal, Pierre

2016-08-10

Benzylidene glucose (BzGlc) is a member of the benzylidene glycoside family. These molecules have the ability to form molecular physical gels. These materials are formed when gelator molecules create a non-covalently bound frame where solvent molecules are trapped. Since the gel formation process and its properties are determined by the subtle balance between non-covalent forces, it is difficult to anticipate them. Quantitative and qualitative understanding of the gelator-gelator and gelator-solvent interactions is needed to better control these materials for important potential applications. We have used gas phase vibrational spectroscopy and theoretical chemistry to study the conformational choices of BzGlc, its dimer and the complexes it forms with water or toluene. To interpret the vibrational spectra we have used the dispersion corrected functional B97D which we have calibrated for the calculation of OH stretching frequencies. Even at the most basic molecular level, it is possible to interrogate a large range of non-covalent interactions ranging from OH → OH hydrogen bonding, to OH → π, and CH → π, all being at the center of gel properties at the macroscopic level.

40 CFR 63.471 - Facility-wide standards.

Code of Federal Regulations, 2014 CFR

2014-07-01

... solvent, recycled solvent, and used solvent that has been cleaned of soiled materials. A fill line must be... section either in electronic or written form for a period of 5 years. For purposes of this paragraph... using the procedure described in paragraph (c)(3) of this section. (3) Calculation sheets showing how...

40 CFR 63.471 - Facility-wide standards.

Code of Federal Regulations, 2013 CFR

2013-07-01

... solvent, recycled solvent, and used solvent that has been cleaned of soiled materials. A fill line must be... section either in electronic or written form for a period of 5 years. For purposes of this paragraph... using the procedure described in paragraph (c)(3) of this section. (3) Calculation sheets showing how...

van der Waals Interactions on the Mesoscale: Open-Science Implementation, Anisotropy, Retardation, and Solvent Effects.

PubMed

Dryden, Daniel M; Hopkins, Jaime C; Denoyer, Lin K; Poudel, Lokendra; Steinmetz, Nicole F; Ching, Wai-Yim; Podgornik, Rudolf; Parsegian, Adrian; French, Roger H

2015-09-22

The self-assembly of heterogeneous mesoscale systems is mediated by long-range interactions, including van der Waals forces. Diverse mesoscale architectures, built of optically and morphologically anisotropic elements such as DNA, collagen, single-walled carbon nanotubes, and inorganic materials, require a tool to calculate the forces, torques, interaction energies, and Hamaker coefficients that govern assembly in such systems. The mesoscale Lifshitz theory of van der Waals interactions can accurately describe solvent and temperature effects, retardation, and optically and morphologically anisotropic materials for cylindrical and planar interaction geometries. The Gecko Hamaker open-science software implementation of this theory enables new and sophisticated insights into the properties of important organic/inorganic systems: interactions show an extended range of magnitudes and retardation rates, DNA interactions show an imprint of base pair composition, certain SWCNT interactions display retardation-dependent nonmonotonicity, and interactions are mapped across a range of material systems in order to facilitate rational mesoscale design.

Carbon Nanotube Dispersion in Solvents and Polymer Solutions: Mechanisms, Assembly, and Preferences.

PubMed

Pramanik, Chandrani; Gissinger, Jacob R; Kumar, Satish; Heinz, Hendrik

2017-12-26

Debundling and dispersion of carbon nanotubes (CNTs) in polymer solutions play a major role in the preparation of carbon nanofibers due to early effects on interfacial ordering and mechanical properties. A roadblock toward ultrastrong fibers is the difficulty to achieve homogeneous dispersions of CNTs in polyacrylonitrile (PAN) and poly(methyl methacrylate) (PMMA) precursor solutions in solvents such as dimethyl sulfoxide (DMSO), N,N-dimethylacetamide (DMAc), and N,N-dimethylformamide (DMF). In this contribution, molecular dynamics simulations with accurate interatomic potentials for graphitic materials that include virtual π electrons are reported to analyze the interaction of pristine single wall CNTs with the solvents and polymer solutions at 25 °C. The results explain the barriers toward dispersion of SWCNTs and quantify CNT-solvent, polymer-solvent, as well as CNT-polymer interactions in atomic detail. Debundling of CNTs is overall endothermic and unfavorable with dispersion energies of +20 to +30 mJ/m 2 in the pure solvents, + 20 to +40 mJ/m 2 in PAN solutions, and +20 to +60 mJ/m 2 in PMMA solutions. Differences arise due to molecular geometry, polar, van der Waals, and CH-π interactions. Among the pure solvents, DMF restricts CNT dispersion less due to the planar geometry and stronger van der Waals interactions. PAN and PMMA interact favorably with the pure solvents with dissolution energies of -0.7 to -1.1 kcal per mole monomer and -1.5 to -2.2 kcal per mole monomer, respectively. Adsorption of PMMA onto CNTs is stronger than that of PAN in all solvents as the molecular geometry enables more van der Waals contacts between alkyl groups and the CNT surface. Polar side groups in both polymers prefer interactions with the polar solvents. Higher polymer concentrations in solution lead to polymer aggregation via alkyl groups and reduce adsorption onto CNTs. PAN and PMMA solutions in DMSO and dilute solutions in DMF support CNT dispersion more than other combinations whereby the polymers significantly adsorb onto CNTs in DMSO solution. The observations by molecular simulations are consistent with available experimental data and solubility parameters and aid in the design of carbon nanofibers. The methods can be applied to other multiphase graphitic materials.

Internal friction controls the speed of protein folding from a compact configuration.

PubMed

Pabit, Suzette A; Roder, Heinrich; Hagen, Stephen J

2004-10-05

Several studies have found millisecond protein folding reactions to be controlled by the viscosity of the solvent: Reducing the viscosity allows folding to accelerate. In the limit of very low solvent viscosity, however, one expects a different behavior. Internal interactions, occurring within the solvent-excluded interior of a compact molecule, should impose a solvent-independent upper limit to folding speed once the bulk diffusional motions become sufficiently rapid. Why has this not been observed? We have studied the effect of solvent viscosity on the folding of cytochrome c from a highly compact, late-stage intermediate configuration. Although the folding rate accelerates as the viscosity declines, it tends toward a finite limiting value approximately 10(5) s(-1) as the viscosity tends toward zero. This limiting rate is independent of the cosolutes used to adjust solvent friction. Therefore, interactions within the interior of a compact denatured polypeptide can limit the folding rate, but the limiting time scale is very fast. It is only observable when the solvent-controlled stages of folding are exceedingly rapid or else absent. Interestingly, we find a very strong temperature dependence in these "internal friction"-controlled dynamics, indicating a large energy scale for the interactions that govern reconfiguration within compact, near-native states of a protein.

Solvation thermodynamics of L-cystine, L-tyrosine, and L-leucine in aqueous-electrolyte media

NASA Astrophysics Data System (ADS)

Roy, Sanjay; Guin, Partha Sarathi; Mahali, Kalachand; Dolui, Bijoy Krishna

2017-12-01

Solubilities of L-cystine, L-tyrosine, and L-leucine in aqueous NaCl media at 298.15 K have been studied. Indispensable and related solvent parameters such as molar mass, molar volume, etc., were also determined. The results are used to evaluate the standard transfer Gibbs free energy, cavity forming enthalpy of transfer, cavity forming transfer Gibbs free energy and dipole-dipole interaction effects during the course of solvation. Various weak interactions involving solute-solvent or solvent-solvent molecules were characterized in order to find their role on the solvation of these amino acids.

The Role of Solvent-Solute Interactions on The Behavior of Low Molecular Mass Organo-Gelators

NASA Astrophysics Data System (ADS)

Cavicchi, Kevin; Feng, Li

2012-02-01

Low molecular mass organo-gelators (LMOGs) are a class of small molecules that can self-assemble in organic solvents to form three-dimensional fibrillar networks. This has a profound effect on the viscoelastic properties of the solution causing physical gelation. These gels have uses in a range of industries including cosmetics, foodstuffs, plastics, petroleum and pharmaceuticals. A fundamental question in this field is: What makes a good LMOG? This talk will discuss the relationships between the viscoelastic properties and thermodynamic phase behavior of LMOG/solvent solutions. The regular solution model was used to fit the liquidus line and sol/gel transition temperature vs. concentration in different solvents to determine LMOG-solvent interaction parameters (χ = A/T). This parameter A was found to scale with the solubility parameter of the solvent, especially for non-polar solvents. This demonstrates that gelation is strongly linked to LMOG solubility and indicates that the bulk thermodynamic parameters of the LMOG (solubility parameter and melting temperature) are useful to predict the solution behavior of LMOGs.

Thermal properties of Bentonite Modified with 3-aminopropyltrimethoxysilane

NASA Astrophysics Data System (ADS)

Pramono, E.; Pratiwi, W.; Wahyuningrum, D.; Radiman, C. L.

2018-03-01

Chemical modifications of Bentonite (BNT) clay have been carried out by using 3-aminoprophyltrimethoxysilane (APS) in various solvent media. The degradation properties of products (BNTAPS) were characterized by thermogravimetric analysis (TGA). Samples were heated at 30 to 700°C with a heating rate 10 deg/min, and the total silane-grafted amount was determined by calculating the weight loss at 200 – 600°C. The thermogram of TGA showed that there were three main decomposition regions which are attributed to the elimination of physically adsorbed water, decomposition of silane and dehydroxylation of Bentonite. High weight loss attributed to the thermal decomposition of silane was observed between 200 to 550°C. Quantitative analysis of grafted silane results high silane loaded using a solvent with high surface energy, which indicates the type of solvent affected interaction and adsorption of APS in BNT platelets.

A molecular dynamics simulation of solvent effects on the crystal morphology of HMX.

PubMed

Duan, Xiaohui; Wei, Chunxue; Liu, Yonggang; Pei, Chonghua

2010-02-15

The solvent has a large effect on the crystal morphology of the organic explosive compound octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX, C(4)H(8)N(8)O(8)). The attachment energy calculations predict a growth morphology in vacuum dominated by (020), (011), (102 ), (111 ) and (100) crystal forms. Molecular dynamics simulations are performed for these crystal faces of HMX in contact with acetone solvent. A corrected attachment energy model, accounting for the surface chemistry and the associated topography (step structure) of the habit crystal plane, is applied to predict the morphological importance of a crystal surface in solvent. From the solvent-effected attachment energy calculations it follows that the (100) face becomes morphologically more important compared with that in vacuum, while the (020) and (102 ) are not visible at all. This agrees well with the observed experimental HMX morphology grown from the acetone solution.

Features of the adsorption of naproxen enantiomers on weak chiral anion-exchangers in nonlinear chromatography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Asnin, Leonid; Kaczmarski, Krzysztof; Guiochon, Georges A

The retention mechanism of the enantiomers of naproxen on a Pirkle-type chiral stationary phase (CSP) was studied. This CSP is made of a porous silica grafted with quinidine carbamate. It can interact with the weak organic electrolyte naproxen either by adsorbing it or by ion-exchange. Using frontal chromatography, we explored the adsorption equilibrium under such experimental conditions that naproxen dissociates or cannot dissociate. Under conditions preventing ionic dissociation, the adsorption isotherms were measured, the adsorption energy distributions determined, and the chromatographic profiles calculated. Three different types of the adsorption sites were found for both enantiomers. The density and the bindingmore » energy of these sites depend on the nature of the organic modifier. Different solute species, anions, neutral molecules, solvent-ion associates, and solute dimers can coexist in solution, giving rise to different forms of adsorption. This study showed the unexpected occurrence of secondary steps in the breakthrough profiles of S-naproxen in the adsorption mode at high concentrations. Being enantioselective, this phenomenon was assumed to result from the association of solute molecules involving a chiral selector moiety. A multisite Langmuir adsorption model was used to calculate band profiles. Although this model accounts excellently for the experimental adsorption isotherms, it does not explain all the features of the breakthrough profiles. A comparison between the calculated and experimental profiles allowed useful conclusions concerning the effects of the adsorbate-adsorbate and adsorbate-solvent interactions on the adsorption mechanism.« less

Solvent dependence of the activation energy of attachment determined by single molecule observations of surfactant adsorption.

PubMed

Honciuc, Andrei; Baptiste, Denver Jn; Campbell, Ian P; Schwartz, Daniel K

2009-07-07

Single-molecule total internal reflection fluorescence microscopy was used to obtain real-time images of fluorescently labeled hexadecanoic (palmitic) acid molecules as they adsorbed at the interface between fused silica and three different solvents: hexadecane (HD), tetrahydrofuran (THF), and water. These solvents were chosen to explore the effect of solvent polarity on the activation energy associated with the attachment rate, i.e., the rate at which molecules were transferred to the surface from the near-surface layer. Direct counting of single-molecule events, made under steady-state conditions at extremely low coverage, provided direct, model-independent measurements of this attachment rate, in contrast with conventional ensemble-averaged methods, which are influenced by bulk transport and competing detachment processes. We found that the attachment rate increased with increasing temperature for all solvents. Arrhenius analyses gave activation energies of 5+/-2 kJ/mol for adsorption from HD, 10+/-2 kJ/mol for adsorption from THF, and 19+/-2 kJ/mol for adsorption from water. These energies increased systematically with the solvent polarity and, therefore, with the expected strength of the solvent-substrate interaction. We hypothesize that the adsorption of amphiphilic solute molecules from solution can be regarded as a competitive exchange between solute molecules and surface-bound solvent. In this scenario, adsorption is an activated process, and the activation energy for attachment is associated with the solvent-substrate interaction energy.

Molecular dynamics analysis of the aggregation propensity of polyglutamine segments

PubMed Central

Wen, Jingran; Scoles, Daniel R.

2017-01-01

Protein misfolding and aggregation is a pathogenic feature shared among at least ten polyglutamine (polyQ) neurodegenerative diseases. While solvent-solution interaction is a key factor driving protein folding and aggregation, the solvation properties of expanded polyQ tracts are not well understood. By using GPU-enabled all-atom molecular dynamics simulations of polyQ monomers in an explicit solvent environment, this study shows that solvent-polyQ interaction propensity decreases as the lengths of polyQ tract increases. This study finds a predominance in long-distance interactions between residues far apart in polyQ sequences with longer polyQ segments, that leads to significant conformational differences. This study also indicates that large loops, comprised of parallel β-structures, appear in long polyQ tracts and present new aggregation building blocks with aggregation driven by long-distance intra-polyQ interactions. Finally, consistent with previous observations using coarse-grain simulations, this study demonstrates that there is a gain in the aggregation propensity with increased polyQ length, and that this gain is correlated with decreasing ability of solvent-polyQ interaction. These results suggest the modulation of solvent-polyQ interactions as a possible therapeutic strategy for treating polyQ diseases. PMID:28542401

Electrostatic Interactions and Self-Assembly in Polymeric Systems

NASA Astrophysics Data System (ADS)

Dobrynin, Andrey

Electrostatic interactions between macroions play an important role in different areas ranging from materials science to biophysics. They are main driving forces behind layer-by-layer assembly technique that allows self-assembly of multilayer films from synthetic polyelectrolytes, DNA, proteins and nanoparticles. They are responsible for complexation and reversible gelation between polyelectrolytes and proteins. In this talk, using results of the molecular dynamics simulations and analytical calculations, I will demonstrate what effect electrostatic interactions, counterion condensation and polymer solvent affinity have on a collapse of polyelectrolyte chain in a poor solvent conditions for the polymer backbone, on complexations and reversible gelation between polyelectrolytes and polyamholytes (unstructured proteins), on microphase separation transitions in spherical and planar charged brushes, and on a layer-by-layer assembly of charged nanoparticles and linear polyelectrolytes on charged surfaces. NSF DMR-1004576 DMR-1409710.

Contribution of Charged Groups to the Enthalpic Stabilization of the Folded States of Globular Proteins

PubMed Central

Dadarlat, Voichita M.; Post, Carol Beth

2016-01-01

In this paper we use the results from all atom MD simulations of proteins and peptides to assess individual contribution of charged atomic groups to the enthalpic stability of the native state of globular proteins and investigate how the distribution of charged atomic groups in terms of solvent accessibility relates to protein enthalpic stability. The contributions of charged groups is calculated using a comparison of nonbonded interaction energy terms from equilibrium simulations of charged amino acid dipeptides in water (the “unfolded state”) and charged amino acids in globular proteins (the “folded state”). Contrary to expectation, the analysis shows that many buried, charged atomic groups contribute favorably to protein enthalpic stability. The strongest enthalpic contributions favoring the folded state come from the carboxylate (COO−) groups of either Glu or Asp. The contributions from Arg guanidinium groups are generally somewhat stabilizing, while NH3+ groups from Lys contribute little toward stabilizing the folded state. The average enthalpic gain due to the transfer of a methyl group in an apolar amino acid from solution to the protein interior is described for comparison. Notably, charged groups that are less exposed to solvent contribute more favorably to protein native-state enthalpic stability than charged groups that are solvent exposed. While solvent reorganization/release has favorable contributions to folding for all charged atomic groups, the variation in folded state stability among proteins comes mainly from the change in the nonbonded interaction energy of charged groups between the unfolded and folded states. A key outcome is that the calculated enthalpic stabilization is found to be inversely proportional to the excess charge density on the surface, in support of an hypothesis proposed previously. PMID:18303881

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carpenter, Barry K.; Harvey, Jeremy N.; Glowacki, David R.

Classical molecular dynamics simulations are reported for the deazetisation and ring opening of meso-2,3-difluoro-2,3-dimethyldiazocyclopropane in three solvents: CHCl 3, CHFClBr and CH 3CH(OH)CF 3 (TFIPA). In this study, the achiral reactant leads to enantiomeric allene products, and the question addressed in the study is whether either of the chiral, enantiomerically pure solvents can induce significant enantiomeric excess in the products. The direct dynamics calculations use an empirical valence bond potential for the solute, with empirical parameters optimised against M06-2X/cc-pVTZ density functional results. The results reveal that the exothermic N 2 loss and ring opening promote transient strong solvent–solute interactions withinmore » the first ~100 fs of the reaction. Because of the bifurcating reaction path, these interactions occur at time when the “decision” about which enantiomer of the product to form has yet to be made (at least for many of the trajectories). Hence, it is possible in principle that the solvent could exert a larger-than-normal influence on the course of the reaction. In fact, the results reveal no such effect for CHFClBr but do predict that TFIPA should induce 15.2 ± 2.1% enantiomeric excess. This is roughly an order of magnitude larger than solvent-induced enantiomeric excesses found experimentally in reactions where the conversion of reactant(s) to enantiomeric products occur over separate transition states.« less

PBEQ-Solver for online visualization of electrostatic potential of biomolecules.

PubMed

Jo, Sunhwan; Vargyas, Miklos; Vasko-Szedlar, Judit; Roux, Benoît; Im, Wonpil

2008-07-01

PBEQ-Solver provides a web-based graphical user interface to read biomolecular structures, solve the Poisson-Boltzmann (PB) equations and interactively visualize the electrostatic potential. PBEQ-Solver calculates (i) electrostatic potential and solvation free energy, (ii) protein-protein (DNA or RNA) electrostatic interaction energy and (iii) pKa of a selected titratable residue. All the calculations can be performed in both aqueous solvent and membrane environments (with a cylindrical pore in the case of membrane). PBEQ-Solver uses the PBEQ module in the biomolecular simulation program CHARMM to solve the finite-difference PB equation of molecules specified by users. Users can interactively inspect the calculated electrostatic potential on the solvent-accessible surface as well as iso-electrostatic potential contours using a novel online visualization tool based on MarvinSpace molecular visualization software, a Java applet integrated within CHARMM-GUI (http://www.charmm-gui.org). To reduce the computational time on the server, and to increase the efficiency in visualization, all the PB calculations are performed with coarse grid spacing (1.5 A before and 1 A after focusing). PBEQ-Solver suggests various physical parameters for PB calculations and users can modify them if necessary. PBEQ-Solver is available at http://www.charmm-gui.org/input/pbeqsolver.

Theoretical evidence of charge transfer interaction between SO₂ and deep eutectic solvents formed by choline chloride and glycerol.

PubMed

Li, Hongping; Chang, Yonghui; Zhu, Wenshuai; Wang, Changwei; Wang, Chao; Yin, Sheng; Zhang, Ming; Li, Huaming

2015-11-21

The nature of the interaction between deep eutectic solvents (DESs), formed by ChCl and glycerol, and SO2 has been systematically investigated using the M06-2X density functional combined with cluster models. Block-localized wave function energy decomposition (BLW-ED) analysis shows that the interaction between SO2 and DESs is dominated by a charge transfer interaction. After this interaction, the SO2 molecule becomes negatively charged, whereas the ChCl-glycerol molecule is positively charged, which is the result of Lewis acid-base interaction. The current result affords a theoretical proof that it is highly useful and efficient to manipulate the Lewis acidity of absorbents for SO2 capture. Moreover, hydrogen bonding as well as electrostatic interactions may also contribute to the stability of the complex. Structure analysis shows that solvent molecules will adjust their geometries to interact with SO2. In addition, the structure of SO2 is barely changed after interaction. The interaction energy between different cluster models and SO2 ranges from -6.8 to -14.4 kcal mol(-1). It is found that the interaction energy is very sensitive to the solvent structure. The moderate interaction between ChCl-glycerol and SO2 is consistent with the concept that highly efficient solvents for SO2 absorption should not only be solvable but also regenerable.

FTIR Imaging Coupled with Multivariate Analysis for Study of Initial Diffusion of Different Solvents in Cellulose Acetate Butyrate Films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lindblad, M.S.; Keyes, B.; Gedvilas, L.

Fourier transform infrared (FTIR) spectroscopic imaging was used to study the initial diffusion of different solvents in cellulose acetate butyrate (CAB) films containing different amounts of acetyl and butyryl substituents. Different solvents and solvent/non-solvent mixtures were also studied. The FTIR imaging system allowed acquisition of sequential images of the CAB films as solvent penetration proceeded without disturbing the system. The interface between the non-swollen polymer and the initial swelling front could be identified using multivariate data analysis tools. For a series of ketone solvents the initial diffusion coefficients and diffusion rates could be quantified and were found to be relatedmore » to the polar and hydrogen interaction parameters in the Hansen solubility parameters of the solvents. For the solvent/non-solvent system the initial diffusion rate decreased less than linearly with the weight-percent of non-solvent present in the solution, which probably was due to the swelling characteristic of the non-solvent. For a given solvent, increasing the butyryl content of the CAB increased the initial diffusion rate. Increasing the butyryl content from 17 wt.% butyryl to 37 wt.% butyryl produced a considerably larger increase in initial diffusion rate compared to an increase in butyryl content from 37 wt.% to 50 wt.% butyryl.« less

Interactions between Biological and Abiotic Pathways in the Reduction of Chlorinated Solvents

EPA Science Inventory

While biologically mediated reductive dechlorination continues to be a significant focus of chlorinated solvent remediation, there has been an increased interest in abiotic reductive processes for the remediation of chlorinated solvents. In situ chemical reduction (ISCR) uses zer...

Unravelling the mechanisms of vibrational relaxation in solution† †All experimental data are archived in the University of Bristol's Research Data Storage Facility (DOI: 10.5523/bris.2vk036f35m5aq2dnlb79c0wcsh). ‡ ‡Electronic supplementary information (ESI) available: Further discussion of spectral lineshapes, concentration dependence of transient absorption data, theoretical calculations, IR-pump IR-probe spectra, transient absorption spectra including animation of spectra. See DOI: 10.1039/c6sc05234g Click here for additional data file. Click here for additional data file.

PubMed Central

Grubb, Michael P.; Coulter, Philip M.; Marroux, Hugo J. B.

2017-01-01

We present a systematic study of the mode-specific vibrational relaxation of NO2 in six weakly-interacting solvents (perfluorohexane, perfluoromethylcyclohexane, perfluorodecalin, carbon tetrachloride, chloroform, and d-chloroform), chosen to elucidate the dominant energy transfer mechanisms in the solution phase. Broadband transient vibrational absorption spectroscopy has allowed us to extract quantum state-resolved relaxation dynamics of the two distinct NO2 fragments produced from the 340 nm photolysis of N2O4 → NO2(X) + NO2(A) and their separate paths to thermal equilibrium. Distinct relaxation pathways are observed for the NO2 bending and stretching modes, even at energies as high as 7000 cm–1 above the potential minimum. Vibrational energy transfer is governed by different interaction mechanisms in the various solvent environments, and proceeds with timescales ranging from 20–1100 ps. NO2 relaxation rates in the perfluorocarbon solvents are identical despite differences in acceptor mode state densities, infrared absorption cross sections, and local solvent structure. Vibrational energy is shown to be transferred to non-vibrational solvent degrees of freedom (V-T) through impulsive collisions with the perfluorocarbon molecules. Conversely, NO2 relaxation in chlorinated solvents is reliant on vibrational resonances (V-V) while V-T energy transfer is inefficient and thermal excitation of the surrounding solvent molecules inhibits faster vibrational relaxation through direct complexation. Intramolecular vibrational redistribution allows the symmetric stretch of NO2 to act as a gateway for antisymmetric stretch energy to exit the molecule. This study establishes an unprecedented level of detail for the cooling dynamics of a solvated small molecule, and provides a benchmark system for future theoretical studies of vibrational relaxation processes in solution. PMID:28451375

Sorption and solubility of ofloxacin and norfloxacin in water-methanol cosolvent.

PubMed

Peng, Hongbo; Li, Hao; Wang, Chi; Zhang, Di; Pan, Bo; Xing, Baoshan

2014-05-01

Prediction of the properties and behavior of antibiotics is important for their risk assessment and pollution control. Theoretical calculation was incorporated in our experimental study to investigate the sorption of ofloxacin (OFL) and norfloxacin (NOR) on carbon nanotubes and their solubilities in water, methanol, and their mixture. Sorption for OFL and NOR decreased as methanol volume fractions (fc) increased. But the log-linear cosolvency model could not be applied as a general model to describe the cosolvent effect on OFL and NOR sorption. We computed the bond lengths of possible hydrogen bonds between solute and solvent and the corresponding interaction energies using Density Functional Theory. The decreased OFL solubility with increased fc could be attributed to the generally stronger hydrogen bond between OFL and H2O than that between OFL and CH3OH. Solubility of NOR varied nonmonotonically with increasing fc, which may be understood from the stronger hydrogen bond of NOR-CH3OH than NOR-H2O at two important sites (-O18 and -O21). The interaction energies were also calculated for the solute surrounded by solvent molecules at all the possible hydrogen bond sites, but it did not match the solubility variations with fc for both chemicals. The difference between the simulated and real systems was discussed. Similar sorption but different solubility of NOR and OFL from water-methanol cosolvent suggested that sorbate-solvent interaction seems not control their sorption. Copyright © 2013 Elsevier Ltd. All rights reserved.

40 CFR 63.5753 - How do I calculate the combined organic HAP content of aluminum wipedown solvents and aluminum...

Code of Federal Regulations, 2010 CFR

2010-07-01

... HAP content of aluminum wipedown solvents and aluminum recreational boat surface coatings? 63.5753... Standards for Hazardous Air Pollutants for Boat Manufacturing Standards for Aluminum Recreational Boat... wipedown solvents and aluminum recreational boat surface coatings? (a) Use equation 1 of this section to...

40 CFR 63.5753 - How do I calculate the combined organic HAP content of aluminum wipedown solvents and aluminum...

Code of Federal Regulations, 2011 CFR

2011-07-01

... HAP content of aluminum wipedown solvents and aluminum recreational boat surface coatings? 63.5753... Standards for Hazardous Air Pollutants for Boat Manufacturing Standards for Aluminum Recreational Boat... wipedown solvents and aluminum recreational boat surface coatings? (a) Use equation 1 of this section to...

Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations.

PubMed

Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

2015-06-15

In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and interpretations of hydrophobicity in terms of alternative but parallel signatures such as interfacial fluctuations, dewetting transitions, and enhanced fluctuation probabilities at interfaces. © 2015 Wiley Periodicals, Inc.

Interaction-component analysis of the hydration and urea effects on cytochrome c

NASA Astrophysics Data System (ADS)

Yamamori, Yu; Ishizuka, Ryosuke; Karino, Yasuhito; Sakuraba, Shun; Matubayasi, Nobuyuki

2016-02-01

Energetics was analyzed for cytochrome c in pure-water solvent and in a urea-water mixed solvent to elucidate the solvation effect in the structural variation of the protein. The solvation free energy was computed through all-atom molecular dynamics simulation combined with the solution theory in the energy representation, and its correlations were examined over sets of protein structures against the electrostatic and van der Waals components in the average interaction energy of the protein with the solvent and the excluded-volume component in the solvation free energy. It was observed in pure-water solvent that the solvation free energy varies in parallel to the electrostatic component with minor roles played by the van der Waals and excluded-volume components. The effect of urea on protein structure was then investigated in terms of the free-energy change upon transfer of the protein solute from pure-water solvent to the urea-water mixed solvent. The decomposition of the transfer free energy into the contributions from urea and water showed that the urea contribution is partially canceled by the water contribution and governs the total free energy of transfer. When correlated against the change in the solute-solvent interaction energy upon transfer and the corresponding changes in the electrostatic, van der Waals, and excluded-volume components, the transfer free energy exhibited strong correlations with the total change in the solute-solvent energy and its van der Waals component. The solute-solvent energy was decomposed into the contributions from the protein backbone and side chain, furthermore, and neither of the contributions was seen to be decisive in the correlation to the transfer free energy.

Quantum-Chemical Simulation of the Solvent Effect on Spontaneous Emission of Singlet Oxygen

NASA Astrophysics Data System (ADS)

Ivashin, N. V.; Shchupak, E. E.

2018-01-01

A molecular simulation of the solvent effect on radiative rate constant k r of singlet oxygen is carried out. This study included a search for the most probable conformations of the complexes of molecules of singlet oxygen and ten solvents and calculation of dipole moments M of transitions a 1Δ g -b1Σ g + ( M a-b ) and a 1Δ g - X 3Σ g - ( M a-X ) of the oxygen molecule for them. Averaging of M a-b by conformations, taking into account the probability of their formation for complexes without atoms with a large atomic number (Cl, S), yields values that, as a rule, correlate well with the behavior of k r in the experiment. Taking into account the possibility of decreasing the distance (compared to equilibrium) between molecules in a collision complex at room temperature made it possible to achieve satisfactory agreement of the calculated and experimental data also for complexes with CCl4, C2Cl4, and CS2. The obtained data indicate that a number of factors affect k r . The correlation of k r with molecular polarizability in a number of cases is due, on the one hand, to its effect on the strength of dispersion interactions in the complex and, on the other hand, to the fact that it to some extent reflects the position of the upper filled orbitals of the solvent molecule. Both factors affect the degree of mixing of the π orbitals of the singlet oxygen molecule with the orbitals of the solvent molecule, which, as was found earlier, facilitates the activation of the a 1Δ g -b1Σ g + transition and the borrowing of its intensity by the a 1Δ g - X 3Σ g - transition.

In silico prediction of medium effects on esterification equilibrium using the COSMO-RS method.

PubMed

Fermeglia, Maurizio; Braiuca, Paolo; Gardossi, Lucia; Pricl, Sabrina; Halling, Peter J

2006-01-01

This paper presents a new approach for predicting solvent effects on esterification reactions of industrial importance in the field of biocatalysis. The COSMO-RS method has been used to calculate the activity coefficients of the chemical species involved in various reactions, carried out in different solvents. For comparison we also used the traditional UNIFAC method. Three lipase-catalyzed esterifications were considered: (1) 1-dodecanoic acid with menthol in n-hexane, n-heptane, cyclohexane, 2,2,4-trimethylpentane, toluene, acetonitrile, and 2-methyl-2-butanol; (2) 1-dodecanoic acid and 1-dodecanol in n-hexane, n-heptane, cyclohexane, 2,2,4-trimethylpentane, and toluene; and (3) glycerol and n-octanoic acid in acetonitrile, benzene, and toluene and in the neat reaction mixture (without any solvent). Predicted activities were used to calculate the thermodynamic equilibrium ratio. This should be independent of medium, and the variation in COSMO-RS values is at most 9-fold (corresponding to a DeltaG degrees of about 5.5 kJ/mol, which would still be a very useful prediction) and often only 2-fold (corresponding to less than 2 kJ/mol or 0.5 kcal/mol, therefore comparable with experimental error). UNIFAC is weaker, especially when important roles are played by conformational freedom, intramolecular interactions, strong polar effects, and charge distribution of molecules in the mixture. The relative percent deviations from the mean of equilibrium constants in different solvents range between 17 and 49 for COSMO-RS versus 32 to 65 for UNIFAC. The COSMO-RS method opens up new perspectives for the development of theoretical models for solvent selection with general applicability.

DIFFUSED SOLUTE-SOLVENT INTERFACE WITH POISSON-BOLTZMANN ELECTROSTATICS: FREE-ENERGY VARIATION AND SHARP-INTERFACE LIMIT.

PubMed

Li, B O; Liu, Yuan

A phase-field free-energy functional for the solvation of charged molecules (e.g., proteins) in aqueous solvent (i.e., water or salted water) is constructed. The functional consists of the solute volumetric and solute-solvent interfacial energies, the solute-solvent van der Waals interaction energy, and the continuum electrostatic free energy described by the Poisson-Boltzmann theory. All these are expressed in terms of phase fields that, for low free-energy conformations, are close to one value in the solute phase and another in the solvent phase. A key property of the model is that the phase-field interpolation of dielectric coefficient has the vanishing derivative at both solute and solvent phases. The first variation of such an effective free-energy functional is derived. Matched asymptotic analysis is carried out for the resulting relaxation dynamics of the diffused solute-solvent interface. It is shown that the sharp-interface limit is exactly the variational implicit-solvent model that has successfully captured capillary evaporation in hydrophobic confinement and corresponding multiple equilibrium states of underlying biomolecular systems as found in experiment and molecular dynamics simulations. Our phase-field approach and analysis can be used to possibly couple the description of interfacial fluctuations for efficient numerical computations of biomolecular interactions.

Stability-limit "Ouzo region" boundaries for poly(lactide-co-glycolide) nanoparticles prepared by nanoprecipitation.

PubMed

Beck-Broichsitter, Moritz

2016-09-10

The introduction of "Ouzo diagrams" has enhanced the applicability of the basic nanoprecipitation process for drug delivery research. The current study investigated the interaction of two relevant polymer/solvent systems, which is thought to impact the location of the stability-limit "Ouzo boundary". Viscosity measurements (Kurata-Stockmayer-Fixman approach) and static light scattering (Debye method) underlined a distinct interplay of the employed polymer (poly(lactide-co-glycolide)) with the utilized organic solvents (acetone and tetrahydrofuran). Both methods indicated that tetrahydrofuran was the "better" solvent for poly(lactide-co-glycolide). Thus, nanoprecipitation of this polymer/solvent composition resulted in larger nanoparticles. This observation can be attributed to the chain configuration of poly(lactide-co-glycolide) in the organic solvent, which influenced the extent of the break-up of the injected solvent layer. Accordingly, the stability-limit curve of the "Ouzo region" was shifted to lower poly(lactide-co-glycolide) fractions for tetrahydrofuran. Overall, the location of the "Ouzo region", which is an essential tool for drug delivery research, is influenced by the employed organic solvent. The current study described two distinct methods suitable to identify relevant polymer-solvent interactions, which dictate the stability-limit "Ouzo boundary" for relevant poly(lactide-co-glycolide). Copyright © 2016 Elsevier B.V. All rights reserved.

Effects of Solvent Composition on Liquid Range, Glass Transition, and Conductivity of Electrolytes of a (Li, Cs)PF 6 Salt in EC-PC-EMC Solvents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ding, Michael S.; Li, Qiuyan; Li, Xing

Electrolytes of 1 M LiPF 6 (lithium hexafluorophosphate) and 0.05 M CsPF 6 (cesium hexafluorophosphate) in EC-PC-EMC (ethylene carbonate-propylene carbonate-ethyl methyl carbonate) solvents of varying solvent compositions were studied for the effects of solvent composition on the lower limit of liquid range, viscosity (as reflected by the glass transition temperature), and electrolytic conductivity. In addition, a ternary phase diagram of EC-PC-EMC was constructed and crystallization temperatures of EC and EMC were calculated to assist the interpretation and understanding of the change of liquid range with solvent composition. A function based on Vogel-Fulcher-Tammann equation was fitted to the conductivity data inmore » their entirety and plotted as conductivity surfaces in solvent composition space for more direct and clear comparisons and discussions. Changes of viscosity and dielectric constant of the solvents with their composition, in relation to those of the solvent components, were found to be underlying many of the processes studied.« less

Thermodynamics of solvent interaction with the metal-organic framework MOF-5.

PubMed

Akimbekov, Zamirbek; Wu, Di; Brozek, Carl K; Dincă, Mircea; Navrotsky, Alexandra

2016-01-14

The inclusion of solvent in metal-organic framework (MOF) materials is a highly specific form of guest-host interaction. In this work, the energetics of solvent MOF-5 interactions has been investigated by solution calorimetry in 5 M sodium hydroxide (NaOH) at room temperature. Solution calorimetric measurement of enthalpy of formation (ΔH(f)) of Zn4O(C8H4O4)3·C3H7NO (MOF-5·DMF) and Zn4O(C8H4O4)3·0.60C5H11NO (MOF-5·0.60DEF) from the dense components zinc oxide (ZnO), 1,4-benzenedicarboxylic acid (H2BDC), N,N-dimethylformamide (DMF) and N,N-diethylformamide (DEF) gives values of 16.69 ± 1.21 and 45.90 ± 1.46 kJ (mol Zn4O)(-1), respectively. The enthalpies of interaction (ΔH(int)) for DMF and DEF with MOF-5 are -82.78 ± 4.84 kJ (mol DMF)(-1) and -89.28 ± 3.05 kJ (mol DEF)(-1), respectively. These exothermic interaction energies suggest that, at low guest loading, Lewis base solvents interact more strongly with electron accepting Zn4O clusters in the MOF than at high solvent loading. These data provide a quantitative thermodynamic basis to investigate transmetallation and solvent assisted linker exchange (SALE) methods and to synthesize new MOFs.

Lithiated imines: solvent-dependent aggregate structures and mechanisms of alkylation.

PubMed

Zuend, Stephan J; Ramirez, Antonio; Lobkovsky, Emil; Collum, David B

2006-05-03

We describe efforts to understand the structure and reactivity of lithiated cyclohexanone N-cyclohexylimine. The lithioimine affords complex solvent-dependent distributions of monomers, dimers, and trimers in a number of ethereal solvents. Careful selection of solvent provides exclusively monosolvated dimers. Rate studies on the C-alkylations reveal chronic mixtures of monomer- and dimer-based pathways. We explore the factors influencing reactants and alkylation transition structures and the marked differences between lithioimines and isostructural lithium dialkylamides with the aid of density functional theory calculations.

Understanding Solvent Manipulation of Morphology in Bulk-Heterojunction Organic Solar Cells.

PubMed

Chen, Yuxia; Zhan, Chuanlang; Yao, Jiannian

2016-10-06

Film morphology greatly influences the performance of bulk-heterojunction (BHJ)-structure-based solar cells. It is known that an interpenetrating bicontinuous network with nanoscale-separated donor and acceptor phases for charge transfer, an ordered molecular packing for exciton diffusion and charge transport, and a vertical compositionally graded structure for charge collection are prerequisites for achieving highly efficient BHJ organic solar cells (OSCs). Therefore, control of the morphology to obtain an ideal structure is a key problem. For this solution-processing BHJ system, the solvent participates fully in film processing. Its involvement is critical in modifying the nanostructure of BHJ films. In this review, we discuss the effects of solvent-related methods on the morphology of BHJ films, including selection of the casting solvent, solvent mixture, solvent vapor annealing, and solvent soaking. On the basis of a discussion on interaction strength and time between solvent and active materials, we believe that the solvent-morphology-performance relationship will be clearer and that solvent selection as a means to manipulate the morphology of BHJ films will be more rational. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Solvent, temperature and concentration effects on the optical rotatory dispersion of (R)-3-methylcyclohexanone

NASA Astrophysics Data System (ADS)

Alenaizan, Asem; Al-Basheer, Watheq; Musa, Musa M.

2017-02-01

Optical rotatory dispersion (ORD) spectra are reported for isolated and solvated (R)-3-methylcyclohexanone (R-3MCH) in 10 solvents, of wide polarity range, and over the spectral range 350-650 nm. Sample concentration effects on ORD spectra of R-3MCH were also recorded and investigated over widely varying concentrations from 2.5 × 10-3 to 2.5 × 10-1 g/mL where an observed sensitivity of optical rotation (OR) to incident light wavelength at low concentrations is correlated to solvent effects. Temperature effects were also studied by recording ORD spectra over the temperature range 0-65 °C in toluene. Recorded specific OR was plotted against various solvent parameters, namely, dipole moment, polarity, refractive index and polarizability to probe solvent effects. Furthermore, solvent effects were studied by incorporating Kamlet's and Taft's solvent parameters in the multi-parametric linear fitting. Theoretically, ORD spectra and populations of optimized geometries of equatorial and axial conformers of R-3MCH were calculated in the gas and solvated phases. All theoretical calculations were performed employing the polarizable continuum model using density functional theoretical and composite scheme (G4) methods with aug-cc-pVTZ and aug-cc-pVDZ basis sets. Net ORD spectra of R-3MCH were generated by the Boltzmann-weighted sum of the contributions of the dominant conformers. Upon comparing theoretical and experimental ORD spectra, a very good agreement is observed for the ORD spectra in the gas phase and high polarity solvents compared to relatively lesser agreement in low polarity solvents.

Weighted-density functionals for cavity formation and dispersion energies in continuum solvation models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sundararaman, Ravishankar; Gunceler, Deniz; Arias, T. A.

2014-10-07

Continuum solvation models enable efficient first principles calculations of chemical reactions in solution, but require extensive parametrization and fitting for each solvent and class of solute systems. Here, we examine the assumptions of continuum solvation models in detail and replace empirical terms with physical models in order to construct a minimally-empirical solvation model. Specifically, we derive solvent radii from the nonlocal dielectric response of the solvent from ab initio calculations, construct a closed-form and parameter-free weighted-density approximation for the free energy of the cavity formation, and employ a pair-potential approximation for the dispersion energy. We show that the resulting modelmore » with a single solvent-independent parameter: the electron density threshold (n c), and a single solvent-dependent parameter: the dispersion scale factor (s 6), reproduces solvation energies of organic molecules in water, chloroform, and carbon tetrachloride with RMS errors of 1.1, 0.6 and 0.5 kcal/mol, respectively. We additionally show that fitting the solvent-dependent s 6 parameter to the solvation energy of a single non-polar molecule does not substantially increase these errors. Parametrization of this model for other solvents, therefore, requires minimal effort and is possible without extensive databases of experimental solvation free energies.« less

Weighted-density functionals for cavity formation and dispersion energies in continuum solvation models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sundararaman, Ravishankar; Gunceler, Deniz; Arias, T. A.

2014-10-07

Continuum solvation models enable efficient first principles calculations of chemical reactions in solution, but require extensive parametrization and fitting for each solvent and class of solute systems. Here, we examine the assumptions of continuum solvation models in detail and replace empirical terms with physical models in order to construct a minimally-empirical solvation model. Specifically, we derive solvent radii from the nonlocal dielectric response of the solvent from ab initio calculations, construct a closed-form and parameter-free weighted-density approximation for the free energy of the cavity formation, and employ a pair-potential approximation for the dispersion energy. We show that the resulting modelmore » with a single solvent-independent parameter: the electron density threshold (n{sub c}), and a single solvent-dependent parameter: the dispersion scale factor (s{sub 6}), reproduces solvation energies of organic molecules in water, chloroform, and carbon tetrachloride with RMS errors of 1.1, 0.6 and 0.5 kcal/mol, respectively. We additionally show that fitting the solvent-dependent s{sub 6} parameter to the solvation energy of a single non-polar molecule does not substantially increase these errors. Parametrization of this model for other solvents, therefore, requires minimal effort and is possible without extensive databases of experimental solvation free energies.« less

Bench-Scale Silicone Process for Low-Cost CO{sub 2} Capture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vipperla, Ravikumar; Yee, Michael; Steele, Ray

This report presents system and economic analysis for a carbon capture unit which uses an amino-silicone solvent for CO{sub 2} capture and sequestration (CCS) in a pulverized coal (PC) boiler. The amino-silicone solvent is based on GAP-1 with Tri-Ethylene Glycol (TEG) as a co-solvent. The report also shows results for a CCS unit based on a conventional approach using mono-ethanol amine (MEA). Models were developed for both processes and used to calculate mass and energy balances. Capital costs and energy penalty were calculated for both systems, as well as the increase in cost of electricity. The amino-silicone solvent based systemmore » demonstrates significant advantages compared to the MEA system.« less

Variational Implicit Solvation with Solute Molecular Mechanics: From Diffuse-Interface to Sharp-Interface Models.

PubMed

Li, Bo; Zhao, Yanxiang

2013-01-01

Central in a variational implicit-solvent description of biomolecular solvation is an effective free-energy functional of the solute atomic positions and the solute-solvent interface (i.e., the dielectric boundary). The free-energy functional couples together the solute molecular mechanical interaction energy, the solute-solvent interfacial energy, the solute-solvent van der Waals interaction energy, and the electrostatic energy. In recent years, the sharp-interface version of the variational implicit-solvent model has been developed and used for numerical computations of molecular solvation. In this work, we propose a diffuse-interface version of the variational implicit-solvent model with solute molecular mechanics. We also analyze both the sharp-interface and diffuse-interface models. We prove the existence of free-energy minimizers and obtain their bounds. We also prove the convergence of the diffuse-interface model to the sharp-interface model in the sense of Γ-convergence. We further discuss properties of sharp-interface free-energy minimizers, the boundary conditions and the coupling of the Poisson-Boltzmann equation in the diffuse-interface model, and the convergence of forces from diffuse-interface to sharp-interface descriptions. Our analysis relies on the previous works on the problem of minimizing surface areas and on our observations on the coupling between solute molecular mechanical interactions with the continuum solvent. Our studies justify rigorously the self consistency of the proposed diffuse-interface variational models of implicit solvation.

Solvent and substituent effects on aggregation constants of perylene bisimide π-stacks--a linear free energy relationship analysis.

PubMed

Chen, Zhijian; Fimmel, Benjamin; Würthner, Frank

2012-08-14

A series of six perylene bisimides (PBIs) with hydrophilic and hydrophobic side chains at the imide nitrogens were applied for a comparative study of the solvent and structural effects on the aggregation behaviour of this class of dyes. A comparison of the binding constants in tetrachloromethane at room temperature revealed the highest binding constant of about 10(5) M(-1) for a PBI bearing 3,4,5-tridodecyloxyphenyl substituents at the imide nitrogens, followed by 3,4,5-tridodecylphenyl and alkyl-substituted PBIs, whereas no aggregation could be observed in the accessible concentration range for PBIs equipped with bulky 2,6-diisopropylphenyl substituents at the imide nitrogens. The aggregation behaviour of three properly soluble compounds was investigated in 17 different solvents covering a broad polarity range from nonpolar n-hexane to highly polar DMSO and water. Linear free energy relationships (LFER) revealed a biphasic behaviour between Gibbs free energies of aggregation and common empirical solvent polarity scales indicating particularly strong π-π stacking interactions in nonpolar aliphatic and polar alcoholic solvents whilst the weakest binding is observed in dichloromethane and chloroform. Accordingly, PBI aggregation is dominated by electrostatic interactions in nonpolar solvents and by solvophobic interactions in protic solvents. In water, the aggregation constant is increased far beyond LFER expectations pointing at a pronounced hydrophobic effect.

A simple method for the fast calculation of charge redistribution of solutes in an implicit solvent model

NASA Astrophysics Data System (ADS)

Dias, L. G.; Shimizu, K.; Farah, J. P. S.; Chaimovich, H.

2002-09-01

We propose and demonstrate the usefulness of a method, defined as generalized Born electronegativity equalization method (GBEEM) to estimate solvent-induced charge redistribution. The charges obtained by GBEEM, in a representative series of small organic molecules, were compared to PM3-CM1 charges in vacuum and in water. Linear regressions with appropriate correlation coefficients and standard deviations between GBEEM and PM3-CM1 methods were obtained ( R=0.94,SD=0.15, Ftest=234, N=32, in vacuum; R=0.94,SD=0.16, Ftest=218, N=29, in water). In order to test the GBEEM response when intermolecular interactions are involved we calculated a water dimer in dielectric water using both GBEEM and PM3-CM1 and the results were similar. Hence, the method developed here is comparable to established calculation methods.

Influence of the hydrogen-bond interactions on the excited-state dynamics of a push-pull azobenzene dye: the case of Methyl Orange.

PubMed

Nançoz, Christoph; Licari, Giuseppe; Beckwith, Joseph S; Soederberg, Magnus; Dereka, Bogdan; Rosspeintner, Arnulf; Yushchenko, Oleksandr; Letrun, Romain; Richert, Sabine; Lang, Bernhard; Vauthey, Eric

2018-03-07

The excited-state dynamics of the push-pull azobenzene Methyl Orange (MO) were investigated in several solvents and water/glycerol mixtures using a combination of ultrafast time-resolved fluorescence and transient absorption in both the UV-visible and the IR regions, as well as quantum chemical calculations. Optical excitation of MO in its trans form results in the population of the S 2 ππ* state and is followed by internal conversion to the S 1 nπ* state in ∼50 fs. The population of this state decays on the sub-picosecond timescale by both internal conversion to the trans ground state and isomerisation to the cis ground state. Finally, the cis form converts thermally to the trans form on a timescale ranging from less than 50 ms to several minutes. Significant differences depending on the hydrogen-bond donor strength of the solvents, quantified by the Kamlet Taft parameter α, were observed: compared to the other solvents, in highly protic solvents (α > 1), (i) the viscosity dependence of the S 1 state lifetime is less pronounced, (ii) the S 1 state lifetime is shorter by a factor of ≈1.5 for the same viscosity, (iii) the trans-to-cis photoisomerisation efficiency is smaller, and (iv) the thermal cis-to-trans isomerisation is faster by a factor of ≥10 3 . These differences are explained in terms of hydrogen-bond interactions between the solvent and the azo nitrogen atoms of MO, which not only change the nature of the S 1 state but also have an impact on the shape of ground- and excited-state potentials, and, thus, affect the deactivation pathways from the excited state.

Solvation behavior of carbonate-based electrolytes in sodium ion batteries.

PubMed

Cresce, Arthur V; Russell, Selena M; Borodin, Oleg; Allen, Joshua A; Schroeder, Marshall A; Dai, Michael; Peng, Jing; Gobet, Mallory P; Greenbaum, Steven G; Rogers, Reginald E; Xu, Kang

2016-12-21

Sodium ion batteries are on the cusp of being a commercially available technology. Compared to lithium ion batteries, sodium ion batteries can potentially offer an attractive dollar-per-kilowatt-hour value, though at the penalty of reduced energy density. As a materials system, sodium ion batteries present a unique opportunity to apply lessons learned in the study of electrolytes for lithium ion batteries; specifically, the behavior of the sodium ion in an organic carbonate solution and the relationship of ion solvation with electrode surface passivation. In this work the Li + and Na + -based solvates were characterized using electrospray mass spectrometry, infrared and Raman spectroscopy, 17 O, 23 Na and pulse field gradient double-stimulated-echo pulse sequence nuclear magnetic resonance (NMR), and conductivity measurements. Spectroscopic evidence demonstrate that the Li + and Na + cations share a number of similar ion-solvent interaction trends, such as a preference in the gas and liquid phase for a solvation shell rich in cyclic carbonates over linear carbonates and fluorinated carbonates. However, quite different IR spectra due to the PF 6 - anion interactions with the Na + and Li + cations were observed and were rationalized with the help of density functional theory (DFT) calculations that were also used to examine the relative free energies of solvates using cluster - continuum models. Ion-solvent distances for Na + were longer than Li + , and Na + had a greater tendency towards forming contact pairs compared to Li + in linear carbonate solvents. In tests of hard carbon Na-ion batteries, performance was not well correlated to Na + solvent preference, leading to the possibility that Na + solvent preference may play a reduced role in the passivation of anode surfaces and overall Na-ion battery performance.

An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions

NASA Astrophysics Data System (ADS)

Lin, Yuchun; Baumketner, Andrij; Deng, Shaozhong; Xu, Zhenli; Jacobs, Donald; Cai, Wei

2009-10-01

In this paper, a new solvation model is proposed for simulations of biomolecules in aqueous solutions that combines the strengths of explicit and implicit solvent representations. Solute molecules are placed in a spherical cavity filled with explicit water, thus providing microscopic detail where it is most needed. Solvent outside of the cavity is modeled as a dielectric continuum whose effect on the solute is treated through the reaction field corrections. With this explicit/implicit model, the electrostatic potential represents a solute molecule in an infinite bath of solvent, thus avoiding unphysical interactions between periodic images of the solute commonly used in the lattice-sum explicit solvent simulations. For improved computational efficiency, our model employs an accurate and efficient multiple-image charge method to compute reaction fields together with the fast multipole method for the direct Coulomb interactions. To minimize the surface effects, periodic boundary conditions are employed for nonelectrostatic interactions. The proposed model is applied to study liquid water. The effect of model parameters, which include the size of the cavity, the number of image charges used to compute reaction field, and the thickness of the buffer layer, is investigated in comparison with the particle-mesh Ewald simulations as a reference. An optimal set of parameters is obtained that allows for a faithful representation of many structural, dielectric, and dynamic properties of the simulated water, while maintaining manageable computational cost. With controlled and adjustable accuracy of the multiple-image charge representation of the reaction field, it is concluded that the employed model achieves convergence with only one image charge in the case of pure water. Future applications to pKa calculations, conformational sampling of solvated biomolecules and electrolyte solutions are briefly discussed.

Solvent effects on the relative stability of radicals derived from artemisinin: DFT study using the PCM/COSMO approach

NASA Astrophysics Data System (ADS)

Araujo, M. T. De; Carneiro, J. W. De M.; Taranto, A. G.

The PCM/COSMO approach was employed to calculate the relative stability of radicals derived from the antimalarial artemisinin. The calculations were performed in polar (water) and apolar (THF) solvent at the density functional level [B3LYP/6-31g(d)]. Relative stabilities were calculated by means of isodesmic equations using artemisinin as reference. Replacement of oxygen atoms by CH2 unities was found to decrease the relative stability of the anionic radical intermediates. The degree of destabilization is reduced in the presence of solvent, being less in water than in THF. The dipole moment and the corresponding solvation free energies of these species modulate this effect. Derivatives with inverted stereochemistry are more stable than those with the artemisinin-like stereochemistry, although the solvent attenuates this stabilization effect. As was found in the in vacuo calculations, the radicals centered on carbon are always more stable than the corresponding radicals centered on oxygen.

What factors control dimerization of coniferyl alcohol?

Treesearch

Carl J. Houtman

1999-01-01

Data suggest that the dimerization of coniferyl alcohol is not under thermodynamic control. In this study, molecular dynamics calculations were used to estimate the effect of the solvent environment. In water, the coniferyl alcohol radicals were forced to associate by the formation of a solvent cage. In glycerol, the solvent cage effect appeared to be absent. These...

Ferutinin as a Ca(2+) complexone: lipid bilayers, conductometry, FT-IR, NMR studies and DFT-B3LYP calculations.

PubMed

Dubis, A; Zamaraeva, M V; Siergiejczyk, L; Charishnikova, O; Shlyonsky, V

2015-10-07

Calcium ionophoretic properties of ferutinin were re-evaluated in solvent-containing bilayer lipid membranes. The slopes of conductance-concentration curves suggest that in the presence of a solvent in the membrane the majority of complexes appear to consist of a single terpenoid molecule bound to one Ca ion. By contrast, the stoichiometry of ferutinin-Ca(2+) complexes in acetone determined using the conductometric method was 2 : 1. While the cation-cation selectivity of ferutinin did not change, the cation-anion selectivity slightly decreased in solvent containing membranes. FT-IR and NMR data together with DFT calculations at the B3LYP/6-31G(d) level of theory indicate that in the absence of Ca ions ferutinin molecules are hydrogen-bonded at the phenol hydroxyl groups. The variations of absorption assigned to -OH and -C-O stretching mode suggest that ferutinin interacts strongly with Ca ions via the hydroxyl group of ferutinol and carboxyl oxygen of the complex ether bond. The coordination through the carbonyl group of ferutinin was demonstrated by theoretical calculations. Taken together, ferutinin molecules form H-bonded dimers, while complexation of Ca(2+) by ferutinin ruptures this hydrogen bond due to spatial re-orientation of the ferutinin molecules from parallel to antiparallel alignment.

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics.

PubMed

Azuara, Cyril; Lindahl, Erik; Koehl, Patrice; Orland, Henri; Delarue, Marc

2006-07-01

We describe a new way to calculate the electrostatic properties of macromolecules which eliminates the assumption of a constant dielectric value in the solvent region, resulting in a Generalized Poisson-Boltzmann-Langevin equation (GPBLE). We have implemented a web server (http://lorentz.immstr.pasteur.fr/pdb_hydro.php) that both numerically solves this equation and uses the resulting water density profiles to place water molecules at preferred sites of hydration. Surface atoms with high or low hydration preference can be easily displayed using a simple PyMol script, allowing for the tentative prediction of the dimerization interface in homodimeric proteins, or lipid binding regions in membrane proteins. The web site includes options that permit mutations in the sequence as well as reconstruction of missing side chain and/or main chain atoms. These tools are accessible independently from the electrostatics calculation, and can be used for other modeling purposes. We expect this web server to be useful to structural biologists, as the knowledge of solvent density should prove useful to get better fits at low resolution for X-ray diffraction data and to computational biologists, for whom these profiles could improve the calculation of interaction energies in water between ligands and receptors in docking simulations.

Reference interaction site model with hydrophobicity induced density inhomogeneity: An analytical theory to compute solvation properties of large hydrophobic solutes in the mixture of polyatomic solvent molecules.

PubMed

Cao, Siqin; Sheong, Fu Kit; Huang, Xuhui

2015-08-07

Reference interaction site model (RISM) has recently become a popular approach in the study of thermodynamical and structural properties of the solvent around macromolecules. On the other hand, it was widely suggested that there exists water density depletion around large hydrophobic solutes (>1 nm), and this may pose a great challenge to the RISM theory. In this paper, we develop a new analytical theory, the Reference Interaction Site Model with Hydrophobicity induced density Inhomogeneity (RISM-HI), to compute solvent radial distribution function (RDF) around large hydrophobic solute in water as well as its mixture with other polyatomic organic solvents. To achieve this, we have explicitly considered the density inhomogeneity at the solute-solvent interface using the framework of the Yvon-Born-Green hierarchy, and the RISM theory is used to obtain the solute-solvent pair correlation. In order to efficiently solve the relevant equations while maintaining reasonable accuracy, we have also developed a new closure called the D2 closure. With this new theory, the solvent RDFs around a large hydrophobic particle in water and different water-acetonitrile mixtures could be computed, which agree well with the results of the molecular dynamics simulations. Furthermore, we show that our RISM-HI theory can also efficiently compute the solvation free energy of solute with a wide range of hydrophobicity in various water-acetonitrile solvent mixtures with a reasonable accuracy. We anticipate that our theory could be widely applied to compute the thermodynamic and structural properties for the solvation of hydrophobic solute.

Analysis of the complex formation, interaction and electron transfer pathway between the "open" conformation of NADPH-cytochrome P450 reductase and aromatase.

PubMed

Dai, Yuejie; Zhen, Jing; Zhang, Xiuli; Zhong, Yonghui; Liu, Shaodan; Sun, Ziyue; Guo, Yue; Wu, Qingli

2015-09-01

The complex structure of human aromatase (CYP19) and the open form of ΔTGEE mutant NADPH-cytochrome P450 reductase (mCPR) was constructed using template-based protein alignment method. Dynamic simulation of formed complex was performed on NAMD 2.9, in which CHARMm all 27_prot_lipid_na force field and an explicit TIP3P water solvent model were applied. The result showed mCPR in its open conformation could steadily combine with aromatase from the proximal face. Data analysis indicates hydrogen bonds and four salt bridges on the binding surface enhance the interaction between the two protein molecules. Amino acid, Lys108 plays a key role in aromatase activity through the formation of a salt bridge with Asp147 and two hydrogen bonds with Asp147 and Gln150 in mCPR. The optimal pathway for the first electron transfer from CPR to aromatase was revealed and calculated using HARLEM software. The rates for solvent mediated and non-solvent mediated electron transfer from FMNH2 to heme were determined as 1.04×10(6)s(-)(1) and 4.86×10(5)s(-)(1) respectively, which indicates the solvent water can facilitate the electron transfer from FMNH2 to heme. This study presents a novel strategy for the study of the protein-protein interactions based on the template-based protein alignment, which may help new aromtase development targeting the electron transfer between mCPR and aromatase. Copyright © 2015 Elsevier Inc. All rights reserved.

Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (Phi, Psi) energy maps and conformers in the gas phase, ether, and water.

PubMed

Wang, Zhi-Xiang; Duan, Yong

2004-11-15

The effects of solvation on the conformations and energies of alanine dipeptide (AD) have been studied by ab initio calculations up to MP2/cc-pVTZ//MP2/6-31G**, utilizing the polarizable continuum model (PCM) to mimic solvation effects. The energy surfaces in the gas phase, ether, and water bear similar topological features carved by the steric hindrance, but the details differ significantly due to the solvent effects. The gas-phase energy map is qualitatively consistent with the Ramachandran plot showing seven energy minima. With respect to the gas-phase map, the significant changes of the aqueous map include (1) the expanded low-energy regions, (2) the emergence of an energy barrier between C5-beta and alpha(R)-beta(2) regions, (3) a clearly pronounced alpha(R) minimum, a new beta-conformer, and the disappearance of the gas-phase global minimum, and (4) the shift of the dominant region in LEII from the gas-phase C7(ax) region to the alpha(L) region. These changes bring the map in water to be much closer to the Ramachandran plot than the gas-phase map. The solvent effects on the geometries include the elongation of the exposed N-H and C=O bonds, the shortening of the buried HN--CO peptide bonds, and the enhanced planarity of the peptide bonds. The energy surface in ether has features similar to those both in the gas phase and in water. The free energy order computed in the gas phase and in ether is in good agreement with experimental studies that concluded that C5 and C7(eq) are the dominant species in both the gas phase and nonpolar solvents. The free energy order in water is consistent with the experimental observation that the dominant C7(eq) in the nonpolar solvent was largely replaced by P(II)-like (i.e., beta) and alpha(R) in the strong polar solvents. Based on calculations on AD + 4H(2)O and other AD-water clusters, we suggest that explicit water-AD interactions may distort C5 and beta (or alpha(R) and beta) to an intermediate conformation. Our analysis also shows that the PCM calculations at the MP2/cc-pVTZ//MP2/6-31G** level give good descriptions to the bulk solvent polarization effect. The results presented in this article should be of sufficient quality to characterize the peptide bonds in the gas phase and solvents. The energy surfaces may serve as the basis for developing of strategies enabling the inclusion of solvent polarization in the force field.

The solvation of the ground and transition states in the reaction of ortho-palladized acetanilide with styrene in organic solvents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sakodynskaya, I.K.; Neverov, A.A; Ryabov, A.D.

1986-07-01

The rate of the reaction of di-mu-chlorobis(acetanilidato-2C, 0) dipalladium(II) with styrene leading to 2-acetaminostilbene was found in 11 organic solvents. In all media, the reaction has second-order kinetics. The free energy, enthalpy and entropy of activation were determined in each solvent. The data for the solubility of the starting Pd(II) complex were used to determine the free energy for the transfer of the ground state of this reaction from a standard solvent (heptane) to the other solvents. The analogous transfer functions were calculated for the transition state. The correlation of the transfer functions of the starting and transition states ofmore » this reaction with empirical solvent parameters was examined.« less

New methods for the analysis of the protein-solvent interface

NASA Astrophysics Data System (ADS)

Goodfellow, Julia M.; Pitt, William R.; Smart, Oliver S.; Williams, Mark A.

1995-09-01

The protein-solvent interface is complex and may include solvent channels and cavities as well as the normal surface water molecules. We describe several algorithms for investigating the intra- and inter-molecular interactions of proteins in general but with the aim of developing methods to accurately and definitively characterise the interactions of water and other small ligands with proteins. Specifically, we present the methods which underlie three programs (AQUARIUS2, HOLE and PRO_ACT) which can be used to to look at different aspects of these interactions.

The effect of intermolecular hydrogen bonding on the fluorescence of a bimetallic platinum complex.

PubMed

Zhao, Guang-Jiu; Northrop, Brian H; Han, Ke-Li; Stang, Peter J

2010-09-02

The bimetallic platinum complexes are known as unique building blocks and arewidely utilized in the coordination-driven self-assembly of functionalized supramolecular metallacycles. Hence, photophysical study of the bimetallic platinum complexes will be very helpful for the understanding on the optical properties and further applications of coordination-driven self-assembled supramolecular metallacycles. Herein, we report steady-state and time-resolved spectroscopic experiments as well as quantum chemistry calculations to investigate the significant intermolecular hydrogen bonding effects on the intramolecular charge transfer (ICT) fluorescence of a bimetallic platinum compound 4,4'-bis(trans-Pt(PEt(3))(2)OTf)benzophenone 3 in solution. We demonstrated that the fluorescent state of compound 3 can be assigned as a metal-to-ligand charge transfer (MLCT) state. Moreover, it was observed that the formation of intermolecular hydrogen bonds can effectively lengthen the fluorescence lifetime of 3 in alcoholic solvents compared with that in hexane solvent. At the same time, the electronically excited states of 3 in solution are definitely changed by intermolecular hydrogen bonding interactions. As a consequence, we propose a new fluorescence modulation mechanism by hydrogen bonding to explain different fluorescence emissions of 3 in hydrogen-bonding solvents and nonhydrogen-bonding solvents.

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers

PubMed Central

Reimers, Jeffrey R.; Panduwinata, Dwi; Visser, Johan; Chin, Yiing; Tang, Chunguang; Goerigk, Lars; Ford, Michael J.; Sintic, Maxine; Sum, Tze-Jing; Coenen, Michiel J. J.; Hendriksen, Bas L. M.; Elemans, Johannes A. A. W.; Hush, Noel S.; Crossley, Maxwell J.

2015-01-01

Modern quantum chemical electronic structure methods typically applied to localized chemical bonding are developed to predict atomic structures and free energies for meso-tetraalkylporphyrin self-assembled monolayer (SAM) polymorph formation from organic solution on highly ordered pyrolytic graphite surfaces. Large polymorph-dependent dispersion-induced substrate−molecule interactions (e.g., −100 kcal mol−1 to −150 kcal mol−1 for tetratrisdecylporphyrin) are found to drive SAM formation, opposed nearly completely by large polymorph-dependent dispersion-induced solvent interactions (70–110 kcal mol−1) and entropy effects (25–40 kcal mol−1 at 298 K) favoring dissolution. Dielectric continuum models of the solvent are used, facilitating consideration of many possible SAM polymorphs, along with quantum mechanical/molecular mechanical and dispersion-corrected density functional theory calculations. These predict and interpret newly measured and existing high-resolution scanning tunnelling microscopy images of SAM structure, rationalizing polymorph formation conditions. A wide range of molecular condensed matter properties at room temperature now appear suitable for prediction and analysis using electronic structure calculations. PMID:26512115

Hydration property of globular proteins: An analysis of solvation free energy by energy representation method

NASA Astrophysics Data System (ADS)

Saito, Hiroaki; Matubayasi, Nobuyuki; Nishikawa, Kiyoshi; Nagao, Hidemi

2010-09-01

Molecular dynamics simulations and solvation free energy calculations of five globular proteins (BPTI, RNase A, Lysozyme, β-lactoglobulin A, and α-chymotrypsinogen A) have been carried out to elucidate the hydration properties. Solvation free energies of the proteins with explicit solvent were estimated by energy representation (ER) method. The calculated solvation free energies were correlated with the solvent accessible surface area of hydrophilic portion, being consistent with the hydrophilic property of the proteins. These results showed that the ER method should be a powerful tool for estimating the hydration property of proteins, showing a progress of the free energy calculation with explicit solvent.

Classification of Solvents according to Interaction Mechanisms.

ERIC Educational Resources Information Center

Ahmed, Wasi

1979-01-01

Presented is a model for solvent effects based on the observation that the excitation energy of all-trans-N-Retinylidenmethyl-n-butylammonium iodide is directly related to the dielectric constant of a series of aromatic and aliphatic solvents as the dielectric constant (e) ranges from 2 to 10.5. (BT)

Investigation of attractive and repulsive interactions associated with ketones in supercritical CO2, based on Raman spectroscopy and theoretical calculations.

PubMed

Kajiya, Daisuke; Saitow, Ken-ichi

2013-08-07

Carbonyl compounds are solutes that are highly soluble in supercritical CO2 (scCO2). Their solubility governs the efficiency of chemical reactions, and is significantly increased by changing a chromophore. To effectively use scCO2 as solvent, it is crucial to understand the high solubility of carbonyl compounds, the solvation structure, and the solute-solvent intermolecular interactions. We report Raman spectroscopic data, for three prototypical ketones dissolved in scCO2, and four theoretical analyses. The vibrational Raman spectra of the C=O stretching modes of ketones (acetone, acetophenone, and benzophenone) were measured in scCO2 along the reduced temperature Tr = T∕Tc = 1.02 isotherm as a function of the reduced density ρr = ρ∕ρc in the range 0.05-1.5. The peak frequencies of the C=O stretching modes shifted toward lower energies as the fluid density increased. The density dependence was analyzed by using perturbed hard-sphere theory, and the shift was decomposed into attractive and repulsive energy components. The attractive energy between the ketones and CO2 was up to nine times higher than the repulsive energy, and its magnitude increased in the following order: acetone < acetophenone < benzophenone. The Mulliken charges of the three solutes and CO2 molecules obtained by using quantum chemistry calculations described the order of the magnitude of the attractive energy and optimized the relative configuration between each solute and CO2. According to theoretical calculations for the dispersion energy, the dipole-induced-dipole interaction energy, and the frequency shift due to their interactions, the experimentally determined attractive energy differences in the three solutes were attributed to the dispersion energies that depended on a chromophore attached to the carbonyl groups. It was found that the major intermolecular interaction with the attractive shift varied from dipole-induced dipole to dispersion depending on the chromophore in the ketones in scCO2. As the common conclusion for the Raman spectral measurements and the four theoretical calculations, solute polarizability, modified by the chromophore, was at the core of the solute-solvent interactions of the ketones in scCO2.

Long Dynamics Simulations of Proteins Using Atomistic Force Fields and a Continuum Representation of Solvent Effects: Calculation of Structural and Dynamic Properties

PubMed Central

Li, Xianfeng; Hassan, Sergio A.; Mehler, Ernest L.

2006-01-01

Long dynamics simulations were carried out on the B1 immunoglobulin-binding domain of streptococcal protein G (ProtG) and bovine pancreatic trypsin inhibitor (BPTI) using atomistic descriptions of the proteins and a continuum representation of solvent effects. To mimic frictional and random collision effects, Langevin dynamics (LD) were used. The main goal of the calculations was to explore the stability of tens-of-nanosecond trajectories as generated by this molecular mechanics approximation and to analyze in detail structural and dynamical properties. Conformational fluctuations, order parameters, cross correlation matrices, residue solvent accessibilities, pKa values of titratable groups, and hydrogen-bonding (HB) patterns were calculated from all of the trajectories and compared with available experimental data. The simulations comprised over 40 ns per trajectory for ProtG and over 30 ns per trajectory for BPTI. For comparison, explicit water molecular dynamics simulations (EW/MD) of 3 ns and 4 ns, respectively, were also carried out. Two continuum simulations were performed on each protein using the CHARMM program, one with the all-atom PAR22 representation of the protein force field (here referred to as PAR22/LD simulations) and the other with the modifications introduced by the recently developed CMAP potential (CMAP/LD simulations). The explicit solvent simulations were performed with PAR22 only. Solvent effects are described by a continuum model based on screened Coulomb potentials (SCP) reported earlier, i.e., the SCP-based implicit solvent model (SCP–ISM). For ProtG, both the PAR22/LD and the CMAP/LD 40-ns trajectories were stable, yielding Cα root mean square deviations (RMSD) of about 1.0 and 0.8 Å respectively along the entire simulation time, compared to 0.8 Å for the EW/MD simulation. For BPTI, only the CMAP/LD trajectory was stable for the entire 30-ns simulation, with a Cα RMSD of ≈ 1.4 Å, while the PAR22/LD trajectory became unstable early in the simulation, reaching a Cα RMSD of about 2.7 Å and remaining at this value until the end of the simulation; the Cα RMSD of the EW/MD simulation was about 1.5 Å. The source of the instabilities of the BPTI trajectories in the PAR22/LD simulations was explored by an analysis of the backbone torsion angles. To further validate the findings from this analysis of BPTI, a 35-ns SCP–ISM simulation of Ubiquitin (Ubq) was carried out. For this protein, the CMAP/LD simulation was stable for the entire simulation time (Cα RMSD of ≈1.0 Å), while the PAR22/LD trajectory showed a trend similar to that in BPTI, reaching a Cα RMSD of ≈1.5 Å at 7 ns. All the calculated properties were found to be in agreement with the corresponding experimental values, although local deviations were also observed. HB patterns were also well reproduced by all the continuum solvent simulations with the exception of solvent-exposed side chain–side chain (sc–sc) HB in ProtG, where several of the HB interactions observed in the crystal structure and in the EW/MD simulation were lost. The overall analysis reported in this work suggests that the combination of an atomistic representation of a protein with a CMAP/CHARMM force field and a continuum representation of solvent effects such as the SCP–ISM provides a good description of structural and dynamic properties obtained from long computer simulations. Although the SCP–ISM simulations (CMAP/LD) reported here were shown to be stable and the properties well reproduced, further refinement is needed to attain a level of accuracy suitable for more challenging biological applications, particularly the study of protein–protein interactions. PMID:15959866

Molecular microenvironments: Solvent interactions with nucleic acid bases and ions

NASA Technical Reports Server (NTRS)

Macelroy, R. D.; Pohorille, A.

1986-01-01

The possibility of reconstructing plausible sequences of events in prebiotic molecular evolution is limited by the lack of fossil remains. However, with hindsight, one goal of molecular evolution was obvious: the development of molecular systems that became constituents of living systems. By understanding the interactions among molecules that are likely to have been present in the prebiotic environment, and that could have served as components in protobiotic molecular systems, plausible evolutionary sequences can be suggested. When stable aggregations of molecules form, a net decrease in free energy is observed in the system. Such changes occur when solvent molecules interact among themselves, as well as when they interact with organic species. A significant decrease in free energy, in systems of solvent and organic molecules, is due to entropy changes in the solvent. Entropy-driven interactioins played a major role in the organization of prebiotic systems, and understanding the energetics of them is essential to understanding molecular evolution.

Experimental and Molecular Modeling Evaluation of the Physicochemical Properties of Proline-Based Deep Eutectic Solvents.

PubMed

van den Bruinhorst, Adriaan; Spyriouni, Theodora; Hill, Jörg-Rüdiger; Kroon, Maaike C

2018-01-11

The liquid range and applicability of deep eutectic solvents (DESs) are determined by their physicochemical properties. In this work, the physicochemical properties of glycolic acid:proline and malic acid:proline were evaluated experimentally and with MD simulations at five different ratios. Both DESs exhibited esterification upon preparation, which affected the viscosity in particular. In order to minimize oligomer formation and water release, three different experimental preparation methods were explored, but none could prevent esterification. The experimental and calculated densities of the DESs were found to be in good agreement. The measured and modeled glass transition temperature showed similar trends with composition, as did the experimental viscosity and the calculated diffusivities. The MD simulations provided additional insight at the atomistic level, showing that at acid-rich compositions, the acid-acid hydrogen bonding (HB) interactions prevail. Malic acid-based DESs show stronger acid-acid HB interactions than glycolic acid-based ones, possibly explaining its extreme viscosity. Upon the addition of proline, the interspecies interactions become predominant, confirming the formation of the widely assumed HB network between the DESs constituents in the liquid phase.

Study of intermolecular interactions in binary mixtures of 2'-chloro-4-methoxy-3-nitro benzil in various solvents and at different concentrations by the measurement of acoustic properties.

PubMed

Nithya, G; Thanuja, B; Kanagam, Charles C

2013-01-01

Density (ρ), ultrasonic velocity (u), adiabatic compressibility (β), apparent molar volume (Ø), acoustic impedance (Z), intermolecular free length (L(f)), relative association (RA) of binary mixtures of 2'-chloro-4-methoxy-3-nitro benzil (abbreviated as 2CBe) in ethanol, acetonitrile, chloroform, dioxane and benzene were measured at different concentrations at 298 K. Several useful parameters such as excess density, excess ultrasonic velocity, excess adiabatic compressibility, excess apparent molar volume, excess acoustic impedance and excess intermolecular free length have been calculated. These parameters are used to explain the nature of intermolecular interactions taking place in the binary mixture. The above study is useful in understanding the solute--solvent interactions occurring in different concentrations at room temperature. Copyright © 2012 Elsevier B.V. All rights reserved.

Determination of thermodynamic properties of isotactic poly(1-butene) at infinite dilution using density and inverse gas chromatography.

PubMed

Kozłowska, Marta Karolina; Domańska, Urszula; Lempert, Małgorzata; Rogalski, Marek

2005-03-18

The partial molar volumes, V1(M), and the molar volume of isotactic crystalline low-molecular-weight poly(1-butene), iPBu-1, V1, have been calculated from the measured density of {iPBu-1 + solvent (n-hexane, n-heptane, n-nonane, n-decane, p-xylene, cyclohexane and chloroform)} systems. Some of the thermodynamic quantities were also obtained for the iPBu-1 with eight hydrocarbons (n-octane, n-decane, n-undecane, n-dodecane, n-tridecane, o-xylene, m-xylene, p-xylene) by the method of inverse gas chromatography at various temperatures. The weight fraction activity coefficients of the solvent at infinite dilution, omega2(infinity) and the Flory-Huggins thermodynamic interaction parameters, chi21(infinity), between polymer and solvents were determined. The partial molar free energy, deltaG2(infinity), the partial molar heat of mixing, deltaH2(infinity), at infinite dilution and the polymer solubility parameter, delta1, were calculated. Additionally, the (solid + liquid) binary mixtures equilibria, SLE, of iPBu-1 with three hydrocarbons (n-octane, n-decane and m-xylene) were studied by a dynamic method. By performing these experiments over a large concentration range, the T-x phase diagrams of the polymer-solvent systems were constructed. The excess Gibbs energy models were used to describe the nonideal behaviour of the liquid phase. The omega2(infinity) were determined from the solubility measurements and were predicted by using the UNIFAC FV model.

Phenolic Polymer Solvation in Water and Ethylene Glycol, I: Molecular Dynamics Simulations

NASA Technical Reports Server (NTRS)

Bucholz, Eric W.; Haskins, Justin B.; Monk, Joshua D.; Bauschlicher, Charles W.; Lawson, John W.

2017-01-01

Interactions between pre-cured phenolic polymer chains and a solvent have a significant impact on the structure and properties of the final post-cured phenolic resin. Developing an understanding of the nature of these interactions is important and will aid in the selection of the proper solvent that will lead to the desired final product. Here, we investigate the role of phenolic chain structure and solvent type on the overall solvation performance of the system through molecular dynamics simulations. Two types of solvents are considered, ethylene glycol (EGL) and H2O. In addition, three phenolic chain structures were considered including two novolac-type chains with either an ortho-ortho (OON) or ortho-para (OPN) backbone network and a resole-type (RES) chain with an ortho-ortho network. Each system is characterized through structural analysis of the solvation shell and hydrogen bonding environment as well as through quantification of the solvation free energy along with partitioned interaction energies between specific molecular species. The combination of the simulations and analyses indicate that EGL provides a larger solvation free energy than H2O due to more energetically favorable hydrophilic interactions as well as favorable hydrophobic interactions between CH element groups. In addition, phenolic chain structure significantly impacts solvation performance with OON having limited intermolecular hydrogen bond formations while OPN and RES interact more favorably with the solvent molecules. The results suggest that a resole-type phenolic chain with an ortho-para network should have the best solvation performance in EGL, H2O, and other similar solvents.

Phenolic Polymer Solvation in Water and Ethylene Glycol, I: Molecular Dynamics Simulations.

PubMed

Bucholz, Eric W; Haskins, Justin B; Monk, Joshua D; Bauschlicher, Charles W; Lawson, John W

2017-04-06

Interactions between pre-cured phenolic polymer chains and a solvent have a significant impact on the structure and properties of the final postcured phenolic resin. Developing an understanding of the nature of these interactions is important and will aid in the selection of the proper solvent that will lead to the desired final product. Here, we investigate the role of the phenolic chain structure and the solvent type on the overall solvation performance of the system through molecular dynamics simulations. Two types of solvents are considered: ethylene glycol (EGL) and H 2 O. In addition, three phenolic chain structures are considered, including two novolac-type chains with either an ortho-ortho (OON) or an ortho-para (OPN) backbone network and a resole-type (RES) chain with an ortho-ortho network. Each system is characterized through a structural analysis of the solvation shell and the hydrogen-bonding environment as well as through a quantification of the solvation free energy along with partitioned interaction energies between specific molecular species. The combination of simulations and the analyses indicate that EGL provides a higher solvation free energy than H 2 O due to more energetically favorable hydrophilic interactions as well as favorable hydrophobic interactions between CH element groups. In addition, the phenolic chain structure significantly affects the solvation performance, with OON having limited intermolecular hydrogen-bond formations, while OPN and RES interact more favorably with the solvent molecules. The results suggest that a resole-type phenolic chain with an ortho-para network should have the best solvation performance in EGL, H 2 O, and other similar solvents.

Solubility enhancement of simvastatin by arginine: thermodynamics, solute-solvent interactions, and spectral analysis.

PubMed

Meor Mohd Affandi, M M R; Tripathy, Minaketan; Shah, Syed Adnan Ali; Majeed, A B A

2016-01-01

We examined the solubility of simvastatin in water in 0.01 mol·dm(-3), 0.02 mol·dm(-3), 0.04 mol·dm(-3), 0.09 mol·dm(-3), 0.18 mol·dm(-3), 0.36 mol·dm(-3), and 0.73 mol·dm(-3) arginine (ARG) solutions. The investigated drug is termed the solute, whereas ARG the cosolute. Phase solubility studies illustrated a higher extent of solubility enhancement for simvastatin. The aforementioned system was subjected to conductometric and volumetric measurements at temperatures (T) of 298.15 K, 303.15 K, 308.15 K, and 313.15 K to illustrate the thermodynamics involved and related solute-solvent interactions. The conductance values were used to evaluate the limiting molar conductance and association constants. Thermodynamic parameters (ΔG (0), ΔH (0), ΔS (0), and E s) for the association process of the solute in the aqueous solutions of ARG were calculated. Limiting partial molar volumes and expansibilities were evaluated from the density values. These values are discussed in terms of the solute-solvent and solute-cosolute interactions. Further, these systems were analyzed using ultraviolet-visible analysis, Fourier-transform infrared spectroscopy, and (13)C, (1)H, and two-dimensional nuclear overhauser effect spectroscopy nuclear magnetic resonance to complement thermophysical explanation.

Solubility enhancement of simvastatin by arginine: thermodynamics, solute–solvent interactions, and spectral analysis

PubMed Central

Meor Mohd Affandi, MMR; Tripathy, Minaketan; Shah, Syed Adnan Ali; Majeed, ABA

2016-01-01

We examined the solubility of simvastatin in water in 0.01 mol·dm−3, 0.02 mol·dm−3, 0.04 mol·dm−3, 0.09 mol·dm−3, 0.18 mol·dm−3, 0.36 mol·dm−3, and 0.73 mol·dm−3 arginine (ARG) solutions. The investigated drug is termed the solute, whereas ARG the cosolute. Phase solubility studies illustrated a higher extent of solubility enhancement for simvastatin. The aforementioned system was subjected to conductometric and volumetric measurements at temperatures (T) of 298.15 K, 303.15 K, 308.15 K, and 313.15 K to illustrate the thermodynamics involved and related solute–solvent interactions. The conductance values were used to evaluate the limiting molar conductance and association constants. Thermodynamic parameters (ΔG0, ΔH0, ΔS0, and Es) for the association process of the solute in the aqueous solutions of ARG were calculated. Limiting partial molar volumes and expansibilities were evaluated from the density values. These values are discussed in terms of the solute–solvent and solute–cosolute interactions. Further, these systems were analyzed using ultraviolet–visible analysis, Fourier-transform infrared spectroscopy, and 13C, 1H, and two-dimensional nuclear overhauser effect spectroscopy nuclear magnetic resonance to complement thermophysical explanation. PMID:27041998

Molecular dynamics simulation on adsorption of pyrene-polyethylene onto ultrathin single-walled carbon nanotube

NASA Astrophysics Data System (ADS)

Cai, Lu; Lv, Wenzhen; Zhu, Hong; Xu, Qun

2016-07-01

The mechanism of the adsorption of pyrene-polyethylene (Py-PE) onto ultrathin single-walled carbon nanotube (SWNT) was studied by using all-atom molecular dynamics (MD) simulations. We found that solvent polarity and pyrene group are two critical factors in the Py-PE decoration on ultrathin SWNT. Combined MD simulations with free energy calculations, our results indicate that larger solvent polarity can decrease the contribution of conformation entropy, but contributes little to the interaction energy, moreover, larger SWNT diameter can decrease the contribution of conformation entropy but lead to the increasing of the interaction energy. In polar organic solvent (N, N-Dimethylacetamide), the pyrene group plays a key role in the adsorption of Py-PE onto ultrathin SWNT, not only facilitates the spontaneous adsorption of Py-PE onto ultrathin SWNT, but also helps to form compact structure between themselves in the final adsorption states. While in aqueous solution, pyrene group no longer works as an anchor, but still affects a lot to the final adsorption conformation. Our present work provides detailed theoretical clue to understand the noncovalent interaction between aromatic segment appended polymer and ultrathin SWNT, and helps to explore the potential application of ultrathin SWNT in the fields of hybrid material, biomedical and electronic materials.

Regimes of electrostatic collapse of a highly charged polyelectrolyte in a poor solvent.

PubMed

Tom, Anvy Moly; Vemparala, Satyavani; Rajesh, R; Brilliantov, Nikolai V

2017-03-01

We perform extensive molecular dynamics simulations of a highly charged, collapsed, flexible polyelectrolyte chain in a poor solvent for the case when the electrostatic interactions, characterized by the reduced Bjerrum length l B , are strong. We find the existence of several sub-regimes in the dependence of the gyration radius of the chain R g on l B characterized by R g ∼ l. In contrast to a good solvent, the exponent γ for a poor solvent crucially depends on the size and valency of the counterions. To explain the different sub-regimes, we generalize the existing counterion fluctuation theory by including a more complete account of all possible volume interactions in the free energy of the polyelectrolyte chain. We also show that the presence of condensed counterions modifies the effective attraction among the chain monomers and modulates the sign of the second virial coefficient under poor solvent conditions.

Photoinduced intramolecular charge transfer (ICT) reaction in trans-methyl p-(dimethylamino) cinnamate: A combined fluorescence measurement and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Chakraborty, Amrita; Kar, Samiran; Guchhait, Nikhil

2006-01-01

The photophysical behaviour of trans-methyl p-(dimethylamino) cinnamate ( t-MDMAC) donor-acceptor system has been investigated by steady-state absorption and emission spectroscopy and quantum chemical calculations. The molecule t-MDMAC shows an emission from the locally excited state in non-polar solvents. In addition to weak local emission, a strong solvent dependent red shifted fluorescence in polar aprotic solvents is attributed to highly polar intramolecular charge transfer state. However, the formation of hydrogen-bonded clusters with polar protic solvents has been suggested from a linear correlation between the observed red shifted fluorescence band maxima with hydrogen bonding parameters ( α). Calculations by ab initio and density functional theory show that the lone pair electron at nitrogen center is out of plane of the benzene ring in the global minimum ground state structure. In the gas phase, a potential energy surface along the twist coordinate at the donor (-NMe 2) and acceptor (-CH = CHCOOMe) sites shows stabilization of S 1 state and destabilization S 2 and S 0 states. A similar potential energy calculation along the twist coordinate in acetonitrile solvent using non-equilibrium polarized continuum model also shows more stabilization of S 1 state relative to other states and supports solvent dependent red shifted emission properties. In all types of calculations it is found that the nitrogen lone pair is delocalized over the benzene ring in the global minimum ground state and is localized on the nitrogen centre at the 90° twisted configuration. The S 1 energy state stabilization along the twist coordinate at the donor site and localized nitrogen lone pair at the perpendicular configuration support well the observed dual fluorescence in terms of proposed twisted intramolecular charge transfer (TICT) model.

Exploring Hamiltonian dielectric solvent molecular dynamics

NASA Astrophysics Data System (ADS)

Bauer, Sebastian; Tavan, Paul; Mathias, Gerald

2014-09-01

Hamiltonian dielectric solvent (HADES) is a recent method [7,25], which enables Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric continua. Sample simulations of an α-helical decapeptide with and without explicit solvent demonstrate the high efficiency of HADES-MD. Addressing the folding of this peptide by replica exchange MD we study the properties of HADES by comparing melting curves, secondary structure motifs and salt bridges with explicit solvent results. Despite the unoptimized ad hoc parametrization of HADES, calculated reaction field energies correlate well with numerical grid solutions of the dielectric Poisson equation.

Solvent effects on the properties of hyperbranched polythiophenes.

PubMed

Torras, Juan; Zanuy, David; Aradilla, David; Alemán, Carlos

2016-09-21

The structural and electronic properties of all-thiophene dendrimers and dendrons in solution have been evaluated using very different theoretical approaches based on quantum mechanical (QM) and hybrid QM/molecular mechanics (MM) methodologies: (i) calculations on minimum energy conformations using an implicit solvation model in combination with density functional theory (DFT) or time-dependent DFT (TD-DFT) methods; (ii) hybrid QM/MM calculations, in which the solute and solvent molecules are represented at the DFT level as point charges, respectively, on snapshots extracted from classical molecular dynamics (MD) simulations using explicit solvent molecules, and (iii) QM/MM-MD trajectories in which the solute is described at the DFT or TD-DFT level and the explicit solvent molecules are represented using classical force-fields. Calculations have been performed in dichloromethane, tetrahydrofuran and dimethylformamide. A comparison of the results obtained using the different approaches with the available experimental data indicates that the incorporation of effects associated with both the conformational dynamics of the dendrimer and the explicit solvent molecules is strictly necessary to satisfactorily reproduce the properties of the investigated systems. Accordingly, QM/MM-MD simulations are able to capture such effects providing a reliable description of electronic properties-conformational flexibility relationships in all-Th dendrimers.

Processing Solvent Dependent Morphology of Diketopyrrolopyrrole (DPP) based Low Band Gap Polymer and PCBM Blends

NASA Astrophysics Data System (ADS)

Ferdous, Sunzida; Liu, Feng; Russell, Thomas

2013-03-01

Solution processing of polymer semiconductors is widely used for fabrication of low cost organic solar cells. Recently, mixed solvent systems or additive based systems for fabricating polymer solar cells have proven to be beneficial for obtaining high performance devices with multi-length scale morphologies. To control the morphology during the processing step, one needs to understand the effect of solvent as it evaporates to form the final thin film structure. In this study, we used diketopyrrolopyrrole (DPP) based low band gap polymer and phenyl-C71-butyric acid methyl ester (PCBM) blend in a series of mixed solvent systems consisting of a good solvent for both of the active material components, as well as different solvents that are good solvents for PCBM, but poor solvents for the polymer. Different evaporation times of the poor solvents during the drying process, and different solubility of the polymer in these poor solvents as well as their interaction with the substrate play an important role in the final morphology. In-situ GIWAXS studies were performed to observe the evolution of the structure as the solvent evaporates. The final morphologies of the thin film devices were also characterized by AFM, TEM, and various x-ray scattering techniques to correlate the morphology with the obtained device performances.

First-Principles Molecular Dynamics Studies of Organometallic Complexes and Homogeneous Catalytic Processes.

PubMed

Vidossich, Pietro; Lledós, Agustí; Ujaque, Gregori

2016-06-21

Computational chemistry is a valuable aid to complement experimental studies of organometallic systems and their reactivity. It allows probing mechanistic hypotheses and investigating molecular structures, shedding light on the behavior and properties of molecular assemblies at the atomic scale. When approaching a chemical problem, the computational chemist has to decide on the theoretical approach needed to describe electron/nuclear interactions and the composition of the model used to approximate the actual system. Both factors determine the reliability of the modeling study. The community dedicated much effort to developing and improving the performance and accuracy of theoretical approaches for electronic structure calculations, on which the description of (inter)atomic interactions rely. Here, the importance of the model system used in computational studies is highlighted through examples from our recent research focused on organometallic systems and homogeneous catalytic processes. We show how the inclusion of explicit solvent allows the characterization of molecular events that would otherwise not be accessible in reduced model systems (clusters). These include the stabilization of nascent charged fragments via microscopic solvation (notably, hydrogen bonding), transfer of charge (protons) between distant fragments mediated by solvent molecules, and solvent coordination to unsaturated metal centers. Furthermore, when weak interactions are involved, we show how conformational and solvation properties of organometallic complexes are also affected by the explicit inclusion of solvent molecules. Such extended model systems may be treated under periodic boundary conditions, thus removing the cluster/continuum (or vacuum) boundary, and require a statistical mechanics simulation technique to sample the accessible configurational space. First-principles molecular dynamics, in which atomic forces are computed from electronic structure calculations (namely, density functional theory), is certainly the technique of choice to investigate chemical events in solution. This methodology is well established and thanks to advances in both algorithms and computational resources simulation times required for the modeling of chemical events are nowadays accessible, though the computational requirements use to be high. Specific applications reviewed here include mechanistic studies of the Shilov and Wacker processes, speciation in Pd chemistry, hydrogen bonding to metal centers, and the dynamics of agostic interactions.

Solute-solvent interactions in 2,4-dihydroxyacetophenone isonicotinoylhydrazone solutions in N, N-dimethylformamide and dimethyl sulfoxide at 298-313 K on ultrasonic and viscometric data

NASA Astrophysics Data System (ADS)

Dikkar, A. B.; Pethe, G. B.; Aswar, A. S.

2016-02-01

The speed of sound ( u), density (ρ), and viscosity (η) of 2,4-dihydroxyacetophenone isonicotinoylhydrazone (DHAIH) have been measured in N, N-dimethyl formamide and dimethyl sulfoxide at equidistance temperatures 298.15, 303.15, 308.15, and 313.15 K. These data were used to calculate some important ultrasonic and thermodynamic parameters such as apparent molar volume ( V ϕ s st ), apparent molar compressibility ( K ϕ), partial molar volume ( V ϕ 0 ) and partial molar compressibility ( K ϕ 0 ), were estimated by using the values of ( V ϕ 0 ) and ( K ϕ), at infinite dilution. Partial molar expansion at infinite dilution, (ϕ E 0 ) has also been calculated from temperature dependence of partial molar volume V ϕ 0 . The viscosity data have been analyzed using the Jones-Dole equation, and the viscosity, B coefficients are calculated. The activation free energy has been calculated from B coefficients and partial molar volume data. The results have been discussed in the term of solute-solvent interaction occurring in solutions and it was found that DHAIH acts as a structure maker in present systems.

Substitution of carcinogenic solvent dichloromethane for the extraction of volatile compounds in a fat-free model food system.

PubMed

Cayot, Nathalie; Lafarge, Céline; Bou-Maroun, Elias; Cayot, Philippe

2016-07-22

Dichloromethane is known as a very efficient solvent, but, as other halogenated solvents, is recognized as a hazardous product (CMR substance). The objective of the present work is to propose substitution solvent for the extraction of volatile compounds. The most important physico-chemical parameters in the choice of an appropriate extraction solvent of volatile compounds are reviewed. Various solvents are selected on this basis and on their hazard characteristics. The selected solvents, safer than dichloromethane, are compared using the extraction efficiency of volatile compounds from a model food product able to interact with volatile compounds. Volatile compounds with different hydrophobicity are used. High extraction yields were positively correlated with high boiling points and high Log Kow values of volatile compounds. Mixtures of solvents such as azeotrope propan-2-one/cyclopentane, azeotrope ethyl acetate/ethanol, and mixture ethyl acetate/ethanol (3:1, v/v) gave higher extraction yields than those obtained with dichloromethane. Copyright © 2016 Elsevier B.V. All rights reserved.

A thermodynamic study of complexation process between N, N'-dipyridoxylidene(1,4-butanediamine) and Cd2+ in some binary mixed solvents using conductometry

NASA Astrophysics Data System (ADS)

Ebrahimpoor, Sonia; Khoshnood, Razieh Sanavi; Beyramabadi, S. Ali

2016-12-01

Complexation of the Cd2+ ion with N, N'-dipyridoxylidene(1,4-butanediamine) Schiff base was studied in pure solvents including acetonitrile (AN), ethanol (EtOH), methanol (MeOH), tetrahydrofuran (THF), dimethylformamide (DMF), water (H2O), and various binary solvent mixtures of acetonitrile-ethanol (AN-EtOH), acetonitrile-methanol (AN-MeOH), acetonitrile-tetrahydrofuran (AN-THF), acetonitrile-dimethylformamide (AN-DMF), and acetonitrile-water (AN-H2O) systems at different temperatures using the conductometric method. The conductance data show that the stoichiometry of complex is 1: 1 [ML] in all solvent systems. A non-linear behavior was observed for changes of log K f of [Cd( N, N'-dipyridoxylidene(1,4-butanediamine)] complex versus the composition of the binary mixed solvents, which was explained in terms of solvent-solvent interactions. The results show that the thermodynamics of complexation reaction is affected by the nature and composition of the mixed solvents.

Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis.

PubMed

Mao, Yuezhi; Shao, Yihan; Dziedzic, Jacek; Skylaris, Chris-Kriton; Head-Gordon, Teresa; Head-Gordon, Martin

2017-05-09

The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized with respect to both the QM electronic density and the MM induced dipoles. This QM/AMOEBA model is implemented through the Q-Chem/LibEFP code interface and then applied to the evaluation of solute-solvent interaction energies for various systems ranging from the water dimer to neutral and ionic solutes (NH 3 , NH 4 + , CN - ) surrounded by increasing numbers of water molecules (up to 100). In order to analyze the resulting interaction energies, we also utilize an energy decomposition analysis (EDA) scheme which identifies contributions from permanent electrostatics, polarization, and van der Waals (vdW) interaction for the interaction between the QM solute and the solvent molecules described by AMOEBA. This facilitates a component-wise comparison against full QM calculations where the corresponding energy components are obtained via a modified version of the absolutely localized molecular orbitals (ALMO)-EDA. The results show that the present QM/AMOEBA model can yield reasonable solute-solvent interaction energies for neutral and cationic species, while further scrutiny reveals that this accuracy highly relies on the delicate balance between insufficiently favorable permanent electrostatics and softened vdW interaction. For anionic solutes where the charge penetration effect becomes more pronounced, the QM/MM interface turns out to be unbalanced. These results are consistent with and further elucidate our findings in a previous study using a slightly different QM/AMOEBA model ( Dziedzic et al. J. Chem. Phys. 2016 , 145 , 124106 ). The implications of these results for further refinement of this model are also discussed.

Connecting Free Energy Surfaces in Implicit and Explicit Solvent: an Efficient Method to Compute Conformational and Solvation Free Energies

PubMed Central

Deng, Nanjie; Zhang, Bin W.; Levy, Ronald M.

2015-01-01

The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions and protein-ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibration on rugged landscapes containing multiple basins separated by barriers. In many cases, implicit solvent models can be used to significantly speed up the conformational sampling; however, implicit solvent simulations do not fully capture the effects of a molecular solvent, and this can lead to loss of accuracy in the estimated free energies. Here we introduce a new approach to compute free energy changes in which the molecular details of explicit solvent simulations are retained while also taking advantage of the speed of the implicit solvent simulations. In this approach, the slow equilibration in explicit solvent, due to the long waiting times before barrier crossing, is avoided by using a thermodynamic cycle which connects the free energy basins in implicit solvent and explicit solvent using a localized decoupling scheme. We test this method by computing conformational free energy differences and solvation free energies of the model system alanine dipeptide in water. The free energy changes between basins in explicit solvent calculated using fully explicit solvent paths agree with the corresponding free energy differences obtained using the implicit/explicit thermodynamic cycle to within 0.3 kcal/mol out of ~3 kcal/mol at only ~8 % of the computational cost. We note that WHAM methods can be used to further improve the efficiency and accuracy of the explicit/implicit thermodynamic cycle. PMID:26236174

Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.

PubMed

Deng, Nanjie; Zhang, Bin W; Levy, Ronald M

2015-06-09

The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions, and protein–ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibration on rugged landscapes containing multiple basins separated by barriers. In many cases, implicit solvent models can be used to significantly speed up the conformational sampling; however, implicit solvent simulations do not fully capture the effects of a molecular solvent, and this can lead to loss of accuracy in the estimated free energies. Here we introduce a new approach to compute free energy changes in which the molecular details of explicit solvent simulations are retained while also taking advantage of the speed of the implicit solvent simulations. In this approach, the slow equilibration in explicit solvent, due to the long waiting times before barrier crossing, is avoided by using a thermodynamic cycle which connects the free energy basins in implicit solvent and explicit solvent using a localized decoupling scheme. We test this method by computing conformational free energy differences and solvation free energies of the model system alanine dipeptide in water. The free energy changes between basins in explicit solvent calculated using fully explicit solvent paths agree with the corresponding free energy differences obtained using the implicit/explicit thermodynamic cycle to within 0.3 kcal/mol out of ∼3 kcal/mol at only ∼8% of the computational cost. We note that WHAM methods can be used to further improve the efficiency and accuracy of the implicit/explicit thermodynamic cycle.

Influence of Polar Organic Solvents in an Ionic Liquid Containing Lithium Bis(fluorosulfonyl)amide: Effect on the Cation-Anion Interaction, Lithium Ion Battery Performance, and Solid Electrolyte Interphase.

PubMed

Lahiri, Abhishek; Li, Guozhu; Olschewski, Mark; Endres, Frank

2016-12-14

Ionic liquid-organic solvent mixtures have recently been investigated as potential battery electrolytes. However, contradictory results with these mixtures have been shown for battery performance. In this manuscript, we studied the influence of the addition of polar organic solvents into the ionic liquid electrolyte 1 M lithium bis(fluorosulfonyl)amide (LiFSI)-1-butyl-1-methylpyrrolidinium bis(fluorosulfonyl)amide ([Py 1,4 ]FSI) and tested it for lithium ion battery applications. From infrared and Raman spectroscopy, clear changes in the lithium solvation and cation-anion interactions in the ionic liquid were observed on addition of organic solvents. From the lithiation/delithiation studies on electrodeposited Ge, the storage capacity for the ionic liquid-highly polar organic solvent (acetonitrile) mixture was found to be the highest at low C-rates (0.425 C) compared to using an ionic liquid alone and ionic liquid-less polar solvent (dimethyl carbonate) mixtures. Furthermore, XPS and AFM were used to evaluate the solid electrolyte interphase (SEI) and to correlate its stability with Li storage capacity.

Probing the Hofmeister series beyond water: Specific-ion effects in non-aqueous solvents

NASA Astrophysics Data System (ADS)

Mazzini, Virginia; Liu, Guangming; Craig, Vincent S. J.

2018-06-01

We present an experimental investigation of specific-ion effects in non-aqueous solvents, with the aim of elucidating the role of the solvent in perturbing the fundamental ion-specific trend. The focus is on the anions: CH3COO->F->Cl->Br->I->ClO4 ->SCN- in the solvents water, methanol, formamide, dimethyl sulfoxide (DMSO), and propylene carbonate (PC). Two types of experiments are presented. The first experiment employs the technique of size exclusion chromatography to evaluate the elution times of electrolytes in the different solvents. We observe that the fundamental (Hofmeister) series is observed in water and methanol, whilst the series is reversed in DMSO and PC. No clear series is observed for formamide. The second experiment uses the quartz crystal microbalance technique to follow the ion-induced swelling and collapse of a polyelectrolyte brush. Here the fundamental series is observed in the protic solvents water, methanol, and formamide, and the series is once again reversed in DMSO and PC. These behaviours are not attributed to the protic/aprotic nature of the solvents, but rather to the polarisability of the solvents and are due to the competition between the interaction of ions with the solvent and the surface. A rule of thumb is proposed for ion specificity in non-aqueous solvents. In weakly polarisable solvents, the trends in specific-ion effects will follow those in water, whereas in strongly polarisable solvents the reverse trend will be observed. Solvents of intermediate polarisability will give weak specific-ion effects.

Probing the Hofmeister series beyond water: Specific-ion effects in non-aqueous solvents.

PubMed

Mazzini, Virginia; Liu, Guangming; Craig, Vincent S J

2018-06-14

We present an experimental investigation of specific-ion effects in non-aqueous solvents, with the aim of elucidating the role of the solvent in perturbing the fundamental ion-specific trend. The focus is on the anions: CH 3 COO - >F - >Cl - >Br - >I - >ClO 4 - >SCN - in the solvents water, methanol, formamide, dimethyl sulfoxide (DMSO), and propylene carbonate (PC). Two types of experiments are presented. The first experiment employs the technique of size exclusion chromatography to evaluate the elution times of electrolytes in the different solvents. We observe that the fundamental (Hofmeister) series is observed in water and methanol, whilst the series is reversed in DMSO and PC. No clear series is observed for formamide. The second experiment uses the quartz crystal microbalance technique to follow the ion-induced swelling and collapse of a polyelectrolyte brush. Here the fundamental series is observed in the protic solvents water, methanol, and formamide, and the series is once again reversed in DMSO and PC. These behaviours are not attributed to the protic/aprotic nature of the solvents, but rather to the polarisability of the solvents and are due to the competition between the interaction of ions with the solvent and the surface. A rule of thumb is proposed for ion specificity in non-aqueous solvents. In weakly polarisable solvents, the trends in specific-ion effects will follow those in water, whereas in strongly polarisable solvents the reverse trend will be observed. Solvents of intermediate polarisability will give weak specific-ion effects.

A Novel Mechanism for Chemical Sensing Based on Solvent-Fluorophore-Substrate Interaction: Highly Selective Alcohol and Water Sensor with Large Fluorescence Signal Contrast.

PubMed

Chung, Kyeongwoon; Yang, Da Seul; Jung, Jaehun; Seo, Deokwon; Kwon, Min Sang; Kim, Jinsang

2016-10-06

Differentiation of solvents having similar physicochemical properties, such as ethanol and methanol, is an important issue of interest. However, without performing chemical analyses, discrimination between methanol and ethanol is highly challenging due to their similarity in chemical structure as well as properties. Here, we present a novel type of alcohol and water sensor based on the subtle differences in interaction among solvent analytes, fluorescent organic molecules, and a mesoporous silica gel substrate. A gradual change in the chemical structure of the fluorescent diketopyrrolopyrrole (DPP) derivatives alters their interaction with the substrate and solvent analyte, which creates a distinct intermolecular aggregation of the DPP derivatives on the silica gel substrate depending on the solvent environment and produces a change in the fluorescence color and intensity as a sensory signal. The devised sensor device, which is fabricated with simple drop-casting of the DPP derivative solutions onto a silica gel substrate, exhibited a completely reversible fluorescence signal change with large fluorescence signal contrast, which allows selective solvent detection by simple optical observation with the naked eye under UV light. Superior selectivity of the alcohol and water sensor system, which can clearly distinguish among ethanol, methanol, ethylene glycol, and water, is demonstrated.

Reconstructing Solvent Density of Myoglobin Unit Cell from Proximal Radial Distribution Functions of Amino Acids

NASA Astrophysics Data System (ADS)

Galbraith, Madeline; Lynch, Gc; Pettitt, Bm

Understanding the solvent density around a protein crystal structure is an important step for refining accurate crystal structures for use in dynamics simulations or in free energy calculations. The free energy of solvation has typically been approximated using an implicit continuum solvent model or an all atom MD simulation, with a trade-off between accuracy and computation time. For proteins, using precomputed proximal radial distribution functions (pRDFs) of the solvent to reconstruct solvent density on a grid is much faster than all atom MD simulations and more accurate than using implicit solvent models. MD simulations were run for the 20 common amino acids and pRDFs were calculated for several atom type data sets with and without hydrogens, using atom types representative of amino acid side chain atoms. Preliminary results from reconstructions suggest using a data set with 15 heavy atoms and 3 hydrogen yields results with the lowest error without a tradeoff on time. The results of using precomputed pRDFs to reconstruct the solvent density of water for the myoglobin (pdb ID 2mgk) unit cell quantifies the accuracy of the method in comparison with the crystallographic data. Funding Acknowledgement: This research was funded by the CPRIT Summer Undergraduate Program in Computational Cancer Biology, training Grant award RP 140113 from the Cancer Prevention & Research Institute of Texas (CPRIT).

Volumetric, rheological, and optical properties of hydroxylamine hydrochloride aqueous solutions containing NaCl, KCl, and NH4Cl at 30°C

NASA Astrophysics Data System (ADS)

Deosarkar, S. D.; Puyad, A. L.; Shaikh, U. B.; Solanke, S. S.

2014-04-01

Densities, viscosities, and refractive indices of aqueous solutions of hydroxylamine hydrochloride containing 0.05, 0.10, and 0.15 mol/dm3 NaCl, KCl, and NH4Cl were measured at different concentrations of hydroxylamine hydrochloride at 30°C. Viscosity coefficients A and B representing ion-ion and ion-solvent interactions were determined from Jones-Dole equation. Experimental properties and viscosity coefficients have been interpreted in terms of ion-ion and ion-solvent interactions. Ion-solvent interactions were found to be dominating over the ion-ion interactions in studied systems.

Mutual influence between triel bond and cation-π interactions: an ab initio study

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.; Mousavian, Parisasadat

2017-12-01

Using ab initio calculations, the cooperative and solvent effects on cation-π and B...N interactions are studied in some model ternary complexes, where these interactions coexist. The nature of the interactions and the mechanism of cooperativity are investigated by means of quantum theory of atoms in molecules (QTAIM), noncovalent interaction (NCI) index and natural bond orbital analysis. The results indicate that all cation-π and B...N binding distances in the ternary complexes are shorter than those of corresponding binary systems. The QTAIM analysis reveals that ternary complexes have higher electron density at their bond critical points relative to the corresponding binary complexes. In addition, according to the QTAIM analysis, the formation of cation-π interaction increases covalency of B...N bonds. The NCI analysis indicates that the cooperative effects in the ternary complexes make a shift in the location of the spike associated with each interaction, which can be regarded as an evidence for the reinforcement of both cation-π and B...N interactions in these systems. Solvent effects on the cooperativity of cation-π and B...N interactions are also investigated.

Photo-physical and interactional behavior of two members of group B vitamins in different solvent media

NASA Astrophysics Data System (ADS)

Zakerhamidi, M. S.; Zare Haghighi, L.; Seyed Ahmadian, S. M.

2017-09-01

In this paper, absorption and fluorescence spectra of vitamin B12 (cyanocobalamin) and vitamin B6 (pyridoxine) were recorded in solvents with different polarity, at room temperature. These vitamins' photo-physical behavior depends strongly on the solvent's nature along with different attached groups in their structures. In order to investigate the solvent-solute interactions and environmental effect on spectral variations, linear solvation energy relationships concept, suggested by Kamlet and Taft was used. Solvatochromic method was also used for measuring the ground and excited state dipole moments of these vitamins. According to our experimental results, dipole moment of these groups of vitamins in excited state is larger than ground state. Furthermore, obtained photo-physical and interactional properties of used vitamins can give important information on how this group of vitamins behaves in biological systems.

Protein-style dynamical transition in a non-biological polymer and a non-aqueous solvent

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mamontov, E.; Sharma, V. K.; Borreguero, J. M.

Using neutron scattering and molecular dynamics simulation, techniques most often associated with protein dynamical transition studies, we have investigated the microscopic dynamics of one of the most common polymers, polystyrene, which was exposed to toluene vapor, mimicking the process of protein hydration from water vapor. Polystyrene with adsorbed toluene is an example of a solvent-solute system, which, unlike biopolymers, is anhydrous and lacks hydrogen bonding. Nevertheless, it exhibits the essential traits of the dynamical transition in biomolecules, such as a specific dependence of the microscopic dynamics of both solvent and host on the temperature and the amount of solvent adsorbed.more » Ultimately, we conclude that the protein dynamical transition is a manifestation of a universal solvent-solute dynamical relationship, which is not specific to either biomolecules as solute, or aqueous media as solvent, or even a particular type of interactions between solvent and solute.« less

Protein-style dynamical transition in a non-biological polymer and a non-aqueous solvent

DOE PAGES

Mamontov, E.; Sharma, V. K.; Borreguero, J. M.; ...

2016-03-15

Using neutron scattering and molecular dynamics simulation, techniques most often associated with protein dynamical transition studies, we have investigated the microscopic dynamics of one of the most common polymers, polystyrene, which was exposed to toluene vapor, mimicking the process of protein hydration from water vapor. Polystyrene with adsorbed toluene is an example of a solvent-solute system, which, unlike biopolymers, is anhydrous and lacks hydrogen bonding. Nevertheless, it exhibits the essential traits of the dynamical transition in biomolecules, such as a specific dependence of the microscopic dynamics of both solvent and host on the temperature and the amount of solvent adsorbed.more » Ultimately, we conclude that the protein dynamical transition is a manifestation of a universal solvent-solute dynamical relationship, which is not specific to either biomolecules as solute, or aqueous media as solvent, or even a particular type of interactions between solvent and solute.« less

Lid opening and conformational stability of T1 Lipase is mediated by increasing chain length polar solvents

PubMed Central

Mohamad Ali, Mohd Shukuri; Salleh, Abu Bakar; Rahman, Raja Noor Zaliha Raja Abd; Normi, Yahaya M.; Mohd Shariff, Fairolniza

2017-01-01

The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD) of a thermostable Geobacillus zalihae T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol) and water mixture systems to a concentration of 50%. On the basis of the MD results, the structural deviations of the backbone atoms elucidated the dynamic effects of water/organic solvent mixtures on the equilibrium state of the protein simulations in decreasing solvent polarity. The results show that the solvent mixture gives rise to deviations in enzyme structure from the native one simulated in water. The drop in the flexibility in H2O, MtOH, EtOH and PrOH simulation mixtures shows that greater motions of residues were influenced in BtOH and PtOH simulation mixtures. Comparing the root mean square fluctuations value with the accessible solvent area (SASA) for every residue showed an almost correspondingly high SASA value of residues to high flexibility and low SASA value to low flexibility. The study further revealed that the organic solvents influenced the formation of more hydrogen bonds in MtOH, EtOH and PrOH and thus, it is assumed that increased intraprotein hydrogen bonding is ultimately correlated to the stability of the protein. However, the solvent accessibility analysis showed that in all solvent systems, hydrophobic residues were exposed and polar residues tended to be buried away from the solvent. Distance variation of the tetrahedral intermediate packing of the active pocket was not conserved in organic solvent systems, which could lead to weaknesses in the catalytic H-bond network and most likely a drop in catalytic activity. The conformational variation of the lid domain caused by the solvent molecules influenced its gradual opening. Formation of additional hydrogen bonds and hydrophobic interactions indicates that the contribution of the cooperative network of interactions could retain the stability of the protein in some solvent systems. Time-correlated atomic motions were used to characterize the correlations between the motions of the atoms from atomic coordinates. The resulting cross-correlation map revealed that the organic solvent mixtures performed functional, concerted, correlated motions in regions of residues of the lid domain to other residues. These observations suggest that varying lengths of polar organic solvents play a significant role in introducing dynamic conformational diversity in proteins in a decreasing order of polarity. PMID:28533982

Using polarizable POSSIM force field and fuzzy-border continuum solvent model to calculate pK(a) shifts of protein residues.

PubMed

Sharma, Ity; Kaminski, George A

2017-01-15

Our Fuzzy-Border (FB) continuum solvent model has been extended and modified to produce hydration parameters for small molecules using POlarizable Simulations Second-order Interaction Model (POSSIM) framework with an average error of 0.136 kcal/mol. It was then used to compute pK a shifts for carboxylic and basic residues of the turkey ovomucoid third domain (OMTKY3) protein. The average unsigned errors in the acid and base pK a values were 0.37 and 0.4 pH units, respectively, versus 0.58 and 0.7 pH units as calculated with a previous version of polarizable protein force field and Poisson Boltzmann continuum solvent. This POSSIM/FB result is produced with explicit refitting of the hydration parameters to the pK a values of the carboxylic and basic residues of the OMTKY3 protein; thus, the values of the acidity constants can be viewed as additional fitting target data. In addition to calculating pK a shifts for the OMTKY3 residues, we have studied aspartic acid residues of Rnase Sa. This was done without any further refitting of the parameters and agreement with the experimental pK a values is within an average unsigned error of 0.65 pH units. This result included the Asp79 residue that is buried and thus has a high experimental pK a value of 7.37 units. Thus, the presented model is capable or reproducing pK a results for residues in an environment that is significantly different from the solvated protein surface used in the fitting. Therefore, the POSSIM force field and the FB continuum solvent parameters have been demonstrated to be sufficiently robust and transferable. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Acidity in DMSO from the embedded cluster integral equation quantum solvation model.

PubMed

Heil, Jochen; Tomazic, Daniel; Egbers, Simon; Kast, Stefan M

2014-04-01

The embedded cluster reference interaction site model (EC-RISM) is applied to the prediction of acidity constants of organic molecules in dimethyl sulfoxide (DMSO) solution. EC-RISM is based on a self-consistent treatment of the solute's electronic structure and the solvent's structure by coupling quantum-chemical calculations with three-dimensional (3D) RISM integral equation theory. We compare available DMSO force fields with reference calculations obtained using the polarizable continuum model (PCM). The results are evaluated statistically using two different approaches to eliminating the proton contribution: a linear regression model and an analysis of pK(a) shifts for compound pairs. Suitable levels of theory for the integral equation methodology are benchmarked. The results are further analyzed and illustrated by visualizing solvent site distribution functions and comparing them with an aqueous environment.

Exploring the role of ionic liquids to tune the polymorphic outcome of organic compounds.

PubMed

Zeng, Qingying; Mukherjee, Arijit; Müller, Peter; Rogers, Robin D; Myerson, Allan S

2018-02-14

While molecular solvents are commonly used in the screening of polymorphs, the choices are often restricted. Ionic liquids (ILs) - also referred as designer solvents - have immense possibility in this regard because of their wide flexibility of tunability. More importantly, the interactions among the IL components are completely unique compared to those present in the molecular solvents. In this context, we have chosen tetrolic acid (TA) and isonicotinamide (INA), which showed solution-structure link in molecular solvents in the past, as probes to investigate the role of imidazolium based ionic liquids in the polymorphism of these two systems and whether the different solute-solvent interactions in ILs affect the polymorphic outcome. It is observed that the selected imidazolium-based ILs, with varying anion basicity have influenced the crystallization outcome by the interaction between ILs and model compounds. Later, we have utilized the concept of double salt ionic liquids (DSIL) for INA, a penta-morphic system, to investigate the variation in the polymorphic outcome. This approach helped to obtain the forms that were otherwise inaccessible in ILs.

A chromophoric study of 2-ethylhexyl p-methoxycinnamate

NASA Astrophysics Data System (ADS)

Alves, Leonardo F.; Gargano, Ricardo; Alcanfor, Silvia K. B.; Romeiro, Luiz A. S.; Martins, João B. L.

2011-11-01

Ultraviolet absorption spectra of 2-ethylhexyl p-methoxycinnamate have been recorded in different solvents and calculated using the time dependent density functional theory. The calculations were performed with the aid of B3LYP, PBE1PBE, M06, and PBEPBE functionals and 6-31+G(2d) basis set. The geometries were initially optimized using PM5 semiempirical method for the conformational search. The calculations of excited states were carried out using the time dependent with IEF-PCM solvent reaction field method. The experimental data were obtained in the wavelength range from 200 to 400 nm using 10 different solvents. The TD-PBE1PBE method shows the best agreement to the experimental results.

Vibrational energy transfer between carbon nanotubes and nonaqueous solvents: a molecular dynamics study.

PubMed

Nelson, Tammie R; Chaban, Vitaly V; Prezhdo, Victor V; Prezhdo, Oleg V

2011-05-12

We report molecular dynamics (MD) simulation of energy exchange between single-walled carbon nanotubes (CNTs) and two aprotic solvents, acetonitrile and cyclohexane. Following our earlier study of hydrated CNTs, we find that the time scales and molecular mechanisms of the energy transfer are largely independent of the nature of the surrounding medium, and therefore, should hold for other media including polymer matrices and DNA. The vibrational energy exchange between CNT and solvents exhibits two time-scales. Over half of the energy is transferred in less than one picosecond, indicating that the dominant exchange mechanism is inertial relaxation. It occurs by collisions of solvent molecules with CNT walls, facilitated by the short-range Lennard-Jones interaction. Additional several picoseconds are required for the remainder of the vibrational energy exchange, corresponding to the diffusive relaxation mechanism and involving collective molecular motions. The faster stage of the CNT-solvent energy exchange occurs on the same time-scale, and therefore, competes with the vibrational energy relaxation inside CNTs. The energy exchange time-scales are significantly influenced by the arrangement of solvent molecules inside CNTs. Generally, the effects of confinement on the dynamics can be rationalized by analysis of the solvent structure. For the same CNT diameter, the extent of the confinement effect strongly depends on the size of the solvent molecules. Icelike properties in water seen in small CNTs disappear in CNTs with intermediate diameters. In acetonitrile and cyclohexane, medium size CNTs still show strong confinement effects. Rotational motions of acetonitrile molecules are inhibited, and the cyclohexane density is dramatically decreased. The disbalance between the local temperatures of the inside and outside regions of the solvent equilibrates through a tube-mediated interaction, rather than by a direct coupling between the two solvent subsystems. In all cases, the CNT-solvent energy transfer is mediated by slow motions in the frequency range of CNT radial breathing modes.

Unified interpretation of exciplex formation and marcus electron transfer on the basis of two-dimensional free energy surfaces.

PubMed

Murata, Shigeo; Tachiya, M

2007-09-27

The mechanism of exciplex formation proposed in a previous paper has been refined to show how exciplex formation and Marcus electron transfer (ET) in fluorescence quenching are related to each other. This was done by making simple calculations of the free energies of the initial (DA*) and final (D+A-) states of ET. First it was shown that the decrease in D-A distance can induce intermolecular ET even in nonpolar solvents where solvent orientational polarization is absent, and that it leads to exciplex formation. This is consistent with experimental results that exciplex is most often observed in nonpolar solvents. The calculation was then extended to ET in polar solvents where the free energies are functions of both D-A distance and solvent orientational polarization. This enabled us to discuss both exciplex formation and Marcus ET in the same D-A pair and solvent on the basis of 2-dimensional free energy surfaces. The surfaces contain more information about the rates of these reactions, the mechanism of fluorescence quenching by ET, etc., than simple reaction schemes. By changing the parameters such as the free energy change of reaction, solvent dielectric constants, etc., one can construct the free energy surfaces for various systems. The effects of free energy change of reaction and of solvent polarity on the mechanism and relative importance of exciplex formation and Marcus ET in fluorescence quenching can be well explained. The free energy surface will also be useful for discussion of other phenomena related to ET reactions.

Functionalization of Cadmium Selenide Quantum Dots with Poly(ethylene glycol): Ligand Exchange, Surface Coverage, and Dispersion Stability.

PubMed

Wenger, Whitney Nowak; Bates, Frank S; Aydil, Eray S

2017-08-22

Semiconductor quantum dots synthesized using rapid mixing of precursors by injection into a hot solution of solvents and surfactants have surface ligands that sterically stabilize the dispersions in nonpolar solvents. Often, these ligands are exchanged to disperse the quantum dots in polar solvents, but quantitative studies of quantum dot surfaces before and after ligand exchange are scarce. We studied exchanging trioctylphosphine (TOP) and trioctylphosphine oxide (TOPO) ligands on as-synthesized CdSe quantum dots dispersed in hexane with a 2000 g/mol thiolated poly(ethylene glycol) (PEG) polymer. Using infrared spectroscopy we quantify the absolute surface concentration of TOP/TOPO and PEG ligands per unit area before and after ligand exchange. While 50-85% of the TOP/TOPO ligands are removed upon ligand exchange, only a few are replaced with PEG. Surprisingly, the remaining TOP/TOPO ligands outnumber the PEG ligands, but these few PEG ligands are sufficient to disperse the quantum dots in polar solvents such as chloroform, tetrahydrofuran, and water. Moreover, as-synthesized quantum dots once easily dispersed in hexane are no longer dispersible in nonpolar solvents after ligand exchange. A subtle coverage-dependent balance between attractive PEG-solvent interactions and repulsive TOP/TOPO-solvent interactions determines the dispersion stability.

Conformation of repaglinide: A solvent dependent structure

NASA Astrophysics Data System (ADS)

Chashmniam, Saeed; Tafazzoli, Mohsen

2017-09-01

Experimental and theoretical conformational study of repaglinide in chloroform and dimethyl sulfoxide was investigated. By applying potential energy scanning (PES) at B3LYP/6-311++g** and B3LYP-D3/6-311++g** level of theory on rotatable single bonds, four stable conformers (R1-R4) were identified. Spin-spin coupling constant values were obtained from a set of 2D NMR spectra (Hsbnd H COSY, Hsbnd C HMQC and Hsbnd C HMBC) and compared to its calculated values. Interestingly, from 1HNMR and 2D-NOESY NMR, it has been found that repaglinide structure is folded in CDCl3 and cause all single bonds to rotate at an extremely slow rate. On the other hand, in DMSO-d6, with strong solvent-solute intermolecular interactions, the single bonds rotate freely. Also, energy barrier and thermodynamic parameters for chair to chair interconversion was measured (13.04 kcal mol-1) in CDCl3 solvent by using temperature dynamic NMR.

Temperature-Dependent Implicit-Solvent Model of Polyethylene Glycol in Aqueous Solution.

PubMed

Chudoba, Richard; Heyda, Jan; Dzubiella, Joachim

2017-12-12

A temperature (T)-dependent coarse-grained (CG) Hamiltonian of polyethylene glycol/oxide (PEG/PEO) in aqueous solution is reported to be used in implicit-solvent material models in a wide temperature (i.e., solvent quality) range. The T-dependent nonbonded CG interactions are derived from a combined "bottom-up" and "top-down" approach. The pair potentials calculated from atomistic replica-exchange molecular dynamics simulations in combination with the iterative Boltzmann inversion are postrefined by benchmarking to experimental data of the radius of gyration. For better handling and a fully continuous transferability in T-space, the pair potentials are conveniently truncated and mapped to an analytic formula with three structural parameters expressed as explicit continuous functions of T. It is then demonstrated that this model without further adjustments successfully reproduces other experimentally known key thermodynamic properties of semidilute PEG solutions such as the full equation of state (i.e., T-dependent osmotic pressure) for various chain lengths as well as their cloud point (or collapse) temperature.

Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection

NASA Astrophysics Data System (ADS)

Cox, Courtney E.; Phifer, Jeremy R.; Ferreira da Silva, Larissa; Gonçalves Nogueira, Gabriel; Ley, Ryan T.; O'Loughlin, Elizabeth J.; Pereira Barbosa, Ana Karolyne; Rygelski, Brett T.; Paluch, Andrew S.

2017-02-01

Solubility parameter based methods have long been a valuable tool for solvent formulation and selection. Of these methods, the MOdified Separation of Cohesive Energy Density (MOSCED) has recently been shown to correlate well the equilibrium solubility of multifunctional non-electrolyte solids. However, before it can be applied to a novel solute, a limited amount of reference solubility data is required to regress the necessary MOSCED parameters. Here we demonstrate for the solutes methylparaben, ethylparaben, propylparaben, butylparaben, lidocaine and ephedrine how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here the SMD or SM8 solvation model, can instead be used to generate the necessary reference data, resulting in a predictive flavor of MOSCED. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. We find the method is able to well correlate the (mole fraction) equilibrium solubility in non-aqueous solvents over four orders of magnitude with good quantitative agreement.

Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection.

PubMed

Cox, Courtney E; Phifer, Jeremy R; Ferreira da Silva, Larissa; Gonçalves Nogueira, Gabriel; Ley, Ryan T; O'Loughlin, Elizabeth J; Pereira Barbosa, Ana Karolyne; Rygelski, Brett T; Paluch, Andrew S

2017-02-01

Solubility parameter based methods have long been a valuable tool for solvent formulation and selection. Of these methods, the MOdified Separation of Cohesive Energy Density (MOSCED) has recently been shown to correlate well the equilibrium solubility of multifunctional non-electrolyte solids. However, before it can be applied to a novel solute, a limited amount of reference solubility data is required to regress the necessary MOSCED parameters. Here we demonstrate for the solutes methylparaben, ethylparaben, propylparaben, butylparaben, lidocaine and ephedrine how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here the SMD or SM8 solvation model, can instead be used to generate the necessary reference data, resulting in a predictive flavor of MOSCED. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. We find the method is able to well correlate the (mole fraction) equilibrium solubility in non-aqueous solvents over four orders of magnitude with good quantitative agreement.

A comparative study of spray-dried and freeze-dried hydrocortisone/polyvinyl pyrrolidone solid dispersions.

PubMed

Dontireddy, Rakesh; Crean, Abina M

2011-10-01

Poor water solubility of new chemical entities (NCEs) is one of the major challenges the pharmaceutical industry currently faces. The purpose of this study was to investigate the feasibility of freeze-drying as an alternative technique to spray-drying to produce solid dispersions of poorly water-soluble drugs. Also investigated was the use of aqueous solvent mixtures in place of pure solvent for the production of solid dispersions. Aqueous solvent systems would reduce the environmental impact of pure organic solvent systems. Spray-dried and freeze-dried hydrocortisone/polyvinyl pyrrolidone solid dispersions exhibited differences in dissolution behavior. Freeze-dried dispersions exhibited faster dissolution rates than the corresponding spray-dried dispersions. Spray-dried systems prepared using both solvent systems (20% v/v and 96% v/v ethanol) displayed similar dissolution performance despite displaying differences in glass transition temperatures (T(g)) and surface areas. All dispersions showed drug/polymer interactions indicated by positive deviations in T(g) from the predicted values calculated using the Couchman-Karasz equation. Fourier transform infrared (FTIR) spectroscopic results confirmed the conversion of crystalline drug to the amorphous in the dispersions. Stability studies were preformed at 40°C and 75% relative humidity to investigate the physical stability of prepared dispersions. Recrystallization was observed after a month and the resultant dispersions were tested for their dissolution performance to compare with the dissolution performance of the dispersions prior to the stability study. The dissolution rate of the freeze-dried dispersions remained higher than both spray-dried dispersions after storage.

NMR shielding and a thermodynamic study of the effect of environmental exposure to petrochemical solvent on DPPC, an important component of lung surfactant

NASA Astrophysics Data System (ADS)

Monajjemi, M.; Afsharnezhad, S.; Jaafari, M. R.; Abdolahi, T.; Nikosade, A.; Monajemi, H.

2007-12-01

The chemical and petrochemical industries are the major air polluters. Millions of workers are exposed to toxic chemicals on the job, and it is becoming more toxic, causing much damage to respiratory system, today. One of the main components of lung alveoli is a surfactant. DPPC (Dipalmitolphosphatidylcholine) is the predominant lipid component in the lung surfactant, which is responsible for lowering surface tension in alveoli. In this article, we used an approximate model and ab initio computations to describe interactions between DPPC and some chemical solvents, such as benzene, toluene, heptane, acetone, chloroform, ether, and ethanol, which cause lung injuries and lead to respiratory distress such as ARDS. The effect of these solvents on the conformation and disordering of the DPPC head group was investigated by calculations at the Hatree-Fock level using the 6-31G basis set with the Onsager continuum solvation, GAIO, and frequency models. The simulation model was confirmed by accurate NMR measurements as concerns conformational energy. Water can be the most suitable solvent for DPPC. Furthermore, this study shows that ethanol has the most destructive effect on the conformation and lipid disorder of the DPPC head group of the lung surfactant in our model. Our finding will be useful for detecting the dysfunction of DPPC in the lung surfactant caused by acute or chronic exposures to air toxics from petrochemical organic solvent emission source and chronic alcohol consumption, which may lead to ARDS.

Assessment of the impact of the next generation solvent on DWPF melter off-gas flammability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daniel, W. E.

2013-02-13

An assessment has been made to evaluate the impact on the DWPF melter off-gas flammability of replacing the current solvent used in the Modular Caustic-Side Solvent Extraction Process Unit (MCU) process with the Next Generation Solvent (NGS-MCU) and blended solvent. The results of this study showed that the concentrations of nonvolatile carbon and hydrogen of the current solvent in the Slurry Mix Evaporator (SME) product would both be about 29% higher than their counterparts of the NGS-MCU and blended solvent in the absence of guanidine partitioning. When 6 ppm of guanidine (TiDG) was added to the effluent transfer to DWPFmore » to simulate partitioning for the NGS-MCU and blended solvent cases and the concentration of Isopar{reg_sign} L in the effluent transfer was controlled below 87 ppm, the concentrations of nonvolatile carbon and hydrogen of the NGS-MCU and blended solvent were still about 12% and 4% lower, respectively, than those of the current solvent. It is, therefore, concluded that as long as the volume of MCU effluent transfer to DWPF is limited to 15,000 gallons per Sludge Receipt and Adjustment Tank (SRAT)/SME cycle and the concentration of Isopar{reg_sign} L in the effluent transfer is controlled below 87 ppm, using the current solvent assumption of 105 ppm Isopar{reg_sign} L or 150 ppm solvent in lieu of NGS-MCU or blended solvent in the DWPF melter off-gas flammability assessment is conservative for up to an additional 6 ppm of TiDG in the effluent due to guanidine partitioning. This report documents the calculations performed to reach this conclusion.« less

HF in clusters of molecular hydrogen. I. Size evolution of quantum solvation by parahydrogen molecules.

PubMed

Jiang, Hao; Bacić, Zlatko

2005-06-22

We present a theoretical study of the quantum solvation of the HF molecule by a small number of parahydrogen molecules, having n = 1-13 solvent particles. The minimum-energy cluster structures determined for n = 1-12 have all of the H(2) molecules in the first solvent shell. The first solvent shell closes at n = 12 and its geometry is icosahedral, with the HF molecule at the center. The quantum-mechanical ground-state properties of the clusters are calculated exactly using the diffusion Monte Carlo method. The zero-point energy of (p-H(2))(n)HF clusters is unusually large, amounting to 86% of the potential well depth for n > 7. The radial probability distribution functions (PDFs) confirm that the first solvent shell is complete for n = 12, and that the 13th p-H(2) molecule begins to fill the second solvent shell. The p-H(2) molecules execute large-amplitude motions and are highly mobile, making the solvent cage exceptionally fluxional. The anisotropy of the solvent, very pronounced for small clusters, decreases rapidly with increasing n, so that for n approximately 8-9 the solvent environment is practically isotropic. The analysis of the pair angular PDF reveals that for a given n, the parahydrogen solvent density around the HF is modulated in a pattern which clearly reflects the lowest-energy cluster configuration. The rigidity of the solvent clusters displays an interesting size dependence, increasing from n = 6 to 9, becoming floppier for n = 10, and increasing again up to n = 12, as the solvent shell is filled. The rigidity of the solvent cage appears to reach its maximum for n = 12, the point at which the first solvent shell is closed.

Theoretical investigation on functional monomer and solvent selection for molecular imprinting of tramadol

NASA Astrophysics Data System (ADS)

Fonseca, Matheus C.; Nascimento, Clebio S.; Borges, Keyller B.

2016-02-01

The purpose of this Letter was to study for the first time the interaction process of tramadol (TRM) with distinct functional monomers (FM) in the formation of molecular imprinted polymer (MIP), using density functional theory (DFT) calculations at B3LYP/6-31G(d,p). As result we were able to establish that the best MIP synthesis conditions are obtained with acrylic acid as FM in 1:3 molar ratio and with chloroform as solvent. This condition presented the lowest stabilization energy for the pre-polymerization complexes. Besides, the intermolecular hydrogen bonds found between the template molecule and functional monomers play a primary role to the complex stability.

Mass Transport through Nanostructured Membranes: Towards a Predictive Tool

PubMed Central

Darvishmanesh, Siavash; Van der Bruggen, Bart

2016-01-01

This study proposes a new mechanism to understand the transport of solvents through nanostructured membranes from a fundamental point of view. The findings are used to develop readily applicable mathematical models to predict solvent fluxes and solute rejections through solvent resistant membranes used for nanofiltration. The new model was developed based on a pore-flow type of transport. New parameters found to be of fundamental importance were introduced to the equation, i.e., the affinity of the solute and the solvent for the membrane expressed as the hydrogen-bonding contribution of the solubility parameter for the solute, solvent and membrane. A graphical map was constructed to predict the solute rejection based on the hydrogen-bonding contribution of the solubility parameter. The model was evaluated with performance data from the literature. Both the solvent flux and the solute rejection calculated with the new approach were similar to values reported in the literature. PMID:27918434

Effects of monohydric alcohols and polyols on the thermal stability of a protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murakami, Shota; Kinoshita, Masahiro, E-mail: kinoshit@iae.kyoto-u.ac.jp

2016-03-28

The thermal stability of a protein is lowered by the addition of a monohydric alcohol, and this effect becomes larger as the size of hydrophobic group in an alcohol molecule increases. By contrast, it is enhanced by the addition of a polyol possessing two or more hydroxyl groups per molecule, and this effect becomes larger as the number of hydroxyl groups increases. Here, we show that all of these experimental observations can be reproduced even in a quantitative sense by rigid-body models focused on the entropic effect originating from the translational displacement of solvent molecules. The solvent is either puremore » water or water-cosolvent solution. Three monohydric alcohols and five polyols are considered as cosolvents. In the rigid-body models, a protein is a fused hard spheres accounting for the polyatomic structure in the atomic detail, and the solvent is formed by hard spheres or a binary mixture of hard spheres with different diameters. The effective diameter of cosolvent molecules and the packing fractions of water and cosolvent, which are crucially important parameters, are carefully estimated using the experimental data of properties such as the density of solid crystal of cosolvent, parameters in the pertinent cosolvent-cosolvent interaction potential, and density of water-cosolvent solution. We employ the morphometric approach combined with the integral equation theory, which is best suited to the physical interpretation of the calculation result. It is argued that the degree of solvent crowding in the bulk is the key factor. When it is made more serious by the cosolvent addition, the solvent-entropy gain upon protein folding is magnified, leading to the enhanced thermal stability. When it is made less serious, the opposite is true. The mechanism of the effects of monohydric alcohols and polyols is physically the same as that of sugars. However, when the rigid-body models are employed for the effect of urea, its addition is predicted to enhance the thermal stability, which conflicts with the experimental fact. We then propose, as two essential factors, not only the solvent-entropy gain but also the loss of protein-solvent interaction energy upon protein folding. The competition of changes in these two factors induced by the cosolvent addition determines the thermal-stability change.« less

Effects of monohydric alcohols and polyols on the thermal stability of a protein

NASA Astrophysics Data System (ADS)

Murakami, Shota; Kinoshita, Masahiro

2016-03-01

The thermal stability of a protein is lowered by the addition of a monohydric alcohol, and this effect becomes larger as the size of hydrophobic group in an alcohol molecule increases. By contrast, it is enhanced by the addition of a polyol possessing two or more hydroxyl groups per molecule, and this effect becomes larger as the number of hydroxyl groups increases. Here, we show that all of these experimental observations can be reproduced even in a quantitative sense by rigid-body models focused on the entropic effect originating from the translational displacement of solvent molecules. The solvent is either pure water or water-cosolvent solution. Three monohydric alcohols and five polyols are considered as cosolvents. In the rigid-body models, a protein is a fused hard spheres accounting for the polyatomic structure in the atomic detail, and the solvent is formed by hard spheres or a binary mixture of hard spheres with different diameters. The effective diameter of cosolvent molecules and the packing fractions of water and cosolvent, which are crucially important parameters, are carefully estimated using the experimental data of properties such as the density of solid crystal of cosolvent, parameters in the pertinent cosolvent-cosolvent interaction potential, and density of water-cosolvent solution. We employ the morphometric approach combined with the integral equation theory, which is best suited to the physical interpretation of the calculation result. It is argued that the degree of solvent crowding in the bulk is the key factor. When it is made more serious by the cosolvent addition, the solvent-entropy gain upon protein folding is magnified, leading to the enhanced thermal stability. When it is made less serious, the opposite is true. The mechanism of the effects of monohydric alcohols and polyols is physically the same as that of sugars. However, when the rigid-body models are employed for the effect of urea, its addition is predicted to enhance the thermal stability, which conflicts with the experimental fact. We then propose, as two essential factors, not only the solvent-entropy gain but also the loss of protein-solvent interaction energy upon protein folding. The competition of changes in these two factors induced by the cosolvent addition determines the thermal-stability change.

Comprehensive Experimental and Computational Spectroscopic Study of Hexacyanoferrate Complexes in Water: From Infrared to X-ray Wavelengths.

PubMed

Ross, Matthew; Andersen, Amity; Fox, Zachary W; Zhang, Yu; Hong, Kiryong; Lee, Jae-Hyuk; Cordones, Amy; March, Anne Marie; Doumy, Gilles; Southworth, Stephen H; Marcus, Matthew A; Schoenlein, Robert W; Mukamel, Shaul; Govind, Niranjan; Khalil, Munira

2018-05-17

We present a joint experimental and computational study of the hexacyanoferrate aqueous complexes at equilibrium in the 250 meV to 7.15 keV regime. The experiments and the computations include the vibrational spectroscopy of the cyanide ligands, the valence electronic absorption spectra, and Fe 1s core hole spectra using element-specific-resonant X-ray absorption and emission techniques. Density functional theory-based quantum mechanics/molecular mechanics molecular dynamics simulations are performed to generate explicit solute-solvent configurations, which serve as inputs for the spectroscopy calculations of the experiments spanning the IR to X-ray wavelengths. The spectroscopy simulations are performed at the same level of theory across this large energy window, which allows for a systematic comparison of the effects of explicit solute-solvent interactions in the vibrational, valence electronic, and core-level spectra of hexacyanoferrate complexes in water. Although the spectroscopy of hexacyanoferrate complexes in solution has been the subject of several studies, most of the previous works have focused on a narrow energy window and have not accounted for explicit solute-solvent interactions in their spectroscopy simulations. In this work, we focus our analysis on identifying how the local solvation environment around the hexacyanoferrate complexes influences the intensity and line shape of specific spectroscopic features in the UV/vis, X-ray absorption, and valence-to-core X-ray emission spectra. The identification of these features and their relationship to solute-solvent interactions is important because hexacyanoferrate complexes serve as model systems for understanding the photochemistry and photophysics of a large class of Fe(II) and Fe(III) complexes in solution.

Dielectric relaxation of ethylene carbonate and propylene carbonate from molecular dynamics simulations

DOE PAGES

Chaudhari, Mangesh I.; You, Xinli; Pratt, Lawrence R.; ...

2015-11-24

Ethylene carbonate (EC) and propylene carbonate (PC) are widely used solvents in lithium (Li)-ion batteries and supercapacitors. Ion dissolution and diffusion in those media are correlated with solvent dielectric responses. Here, we use all-atom molecular dynamics simulations of the pure solvents to calculate dielectric constants and relaxation times, and molecular mobilities. The computed results are compared with limited available experiments to assist more exhaustive studies of these important characteristics. As a result, the observed agreement is encouraging and provides guidance for further validation of force-field simulation models for EC and PC solvents.

Predicting the Activity Coefficients of Free-Solvent for Concentrated Globular Protein Solutions Using Independently Determined Physical Parameters

PubMed Central

McBride, Devin W.; Rodgers, Victor G. J.

2013-01-01

The activity coefficient is largely considered an empirical parameter that was traditionally introduced to correct the non-ideality observed in thermodynamic systems such as osmotic pressure. Here, the activity coefficient of free-solvent is related to physically realistic parameters and a mathematical expression is developed to directly predict the activity coefficients of free-solvent, for aqueous protein solutions up to near-saturation concentrations. The model is based on the free-solvent model, which has previously been shown to provide excellent prediction of the osmotic pressure of concentrated and crowded globular proteins in aqueous solutions up to near-saturation concentrations. Thus, this model uses only the independently determined, physically realizable quantities: mole fraction, solvent accessible surface area, and ion binding, in its prediction. Predictions are presented for the activity coefficients of free-solvent for near-saturated protein solutions containing either bovine serum albumin or hemoglobin. As a verification step, the predictability of the model for the activity coefficient of sucrose solutions was evaluated. The predicted activity coefficients of free-solvent are compared to the calculated activity coefficients of free-solvent based on osmotic pressure data. It is observed that the predicted activity coefficients are increasingly dependent on the solute-solvent parameters as the protein concentration increases to near-saturation concentrations. PMID:24324733

Experimental and theoretical investigation of the molecular, electronic structure and solvatochromism of phenyl salicylate: External electric field effect on the electronic structure

NASA Astrophysics Data System (ADS)

Sıdır, İsa; Sıdır, Yadigar Gülseven

2017-11-01

The UV-vis absorption and steady state fluorescence spectra of phenyl salicylate (abbreviated as PS) have been recorded in a series of non-polar, polar protic and polar aprotic solvents at room temperature and the obtained spectral data are used to determine the solvatochromic behavior and the ground and excited state dipole moments. Basis set sensitive molecular structure along with X-ray crystal data are evaluated. The ground state and excited state dipole moments are determined by using Lippert-Mataga, Bakhshiev, Bilot-Kawski and Reichardt solvatochromic shift methods as a function of dielectric constant (ε) and refractive index (n) of the solvents. The larger excited state dipole moment value indicates the more polar PS in the excited state. The rate of μe/μg is found as 2.4239. Solvatochromic behavior of PS is enlightened by using Kamlet-Taft and Catalan models. Kamlet-Taft solvatochromic model indicates that non-specific solute solvent interactions are controlled by solvent dispersion-induction forces and specific interactions are directed by hydrogen-bond donor capacity of solvent. Catalan solvatochromic model designates that solute-solvent interactions are governed by solvent polarizability. Ground and excited state dipole moments are found theoretically by using DFT/B3LYP/6-311++G(d, p) and TDDFT/B3LYP/6-31++G(d, p) methods. External electric field effect on LUMO-HOMO band gap and dipole moment have been investigated by using B3LYP/6-311++G(d, p) method.

Peptide chain dynamics in light and heavy water: zooming in on internal friction.

PubMed

Schulz, Julius C F; Schmidt, Lennart; Best, Robert B; Dzubiella, Joachim; Netz, Roland R

2012-04-11

Frictional effects due to the chain itself, rather than the solvent, may have a significant effect on protein dynamics. Experimentally, such "internal friction" has been investigated by studying folding or binding kinetics at varying solvent viscosity; however, the molecular origin of these effects is hard to pinpoint. We consider the kinetics of disordered glycine-serine and α-helix forming alanine peptides and a coarse-grained protein folding model in explicit-solvent molecular dynamics simulations. By varying the solvent mass over more than two orders of magnitude, we alter only the solvent viscosity and not the folding free energy. Folding dynamics at the near-vanishing solvent viscosities accessible by this approach suggests that solvent and internal friction effects are intrinsically entangled. This finding is rationalized by calculation of the polymer end-to-end distance dynamics from a Rouse model that includes internal friction. An analysis of the friction profile along different reaction coordinates, extracted from the simulation data, demonstrates that internal as well as solvent friction varies substantially along the folding pathways and furthermore suggests a connection between friction and the formation of hydrogen bonds upon folding. © 2012 American Chemical Society

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics

NASA Astrophysics Data System (ADS)

Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J. Andrew

2015-12-01

Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson-Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum-Chandler-Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods.

Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid.

PubMed

Xiao, Li; Luo, Ray

2017-12-07

We explored a multi-scale algorithm for the Poisson-Boltzmann continuum solvent model for more robust simulations of biomolecules. In this method, the continuum solvent/solute interface is explicitly simulated with a numerical fluid dynamics procedure, which is tightly coupled to the solute molecular dynamics simulation. There are multiple benefits to adopt such a strategy as presented below. At this stage of the development, only nonelectrostatic interactions, i.e., van der Waals and hydrophobic interactions, are included in the algorithm to assess the quality of the solvent-solute interface generated by the new method. Nevertheless, numerical challenges exist in accurately interpolating the highly nonlinear van der Waals term when solving the finite-difference fluid dynamics equations. We were able to bypass the challenge rigorously by merging the van der Waals potential and pressure together when solving the fluid dynamics equations and by considering its contribution in the free-boundary condition analytically. The multi-scale simulation method was first validated by reproducing the solute-solvent interface of a single atom with analytical solution. Next, we performed the relaxation simulation of a restrained symmetrical monomer and observed a symmetrical solvent interface at equilibrium with detailed surface features resembling those found on the solvent excluded surface. Four typical small molecular complexes were then tested, both volume and force balancing analyses showing that these simple complexes can reach equilibrium within the simulation time window. Finally, we studied the quality of the multi-scale solute-solvent interfaces for the four tested dimer complexes and found that they agree well with the boundaries as sampled in the explicit water simulations.

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics.

PubMed

Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J Andrew

2015-12-28

Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson-Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum-Chandler-Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods.

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson–Boltzmann electrostatics

PubMed Central

Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J. Andrew

2015-01-01

Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson–Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum–Chandler–Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods. PMID:26723595

The theoretical investigation of solvent effects on the relative stability and 15N NMR shielding of antidepressant heterocyclic drug

NASA Astrophysics Data System (ADS)

Tahan, Arezoo; Khojandi, Mahya; Salari, Ali Akbar

2016-01-01

The density functional theory (DFT) and Tomasi's polarized continuum model (PCM) were used for the investigation of solvent polarity and its dielectric constant effects on the relative stability and NMR shielding tensors of antidepressant mirtazapine (MIR). The obtained results indicated that the relative stability in the polar solvents is higher than that in non-polar solvents and the most stable structure was observed in the water at the B3LYP/6-311++G ( d, p) level of theory. Also, natural bond orbital (NBO) interpretation demonstrated that by increase of solvent dielectric constant, negative charge on nitrogen atoms of heterocycles and resonance energy for LP(N10) → σ* and π* delocalization of the structure's azepine ring increase and the highest values of them were observed in water. On the other hand, NMR calculations showed that with an increase in negative charge of nitrogen atoms, isotropic chemical shielding (σiso) around them increase and nitrogen of piperazine ring (N19) has the highest values of negative charge and σiso among nitrogen atoms. NMR calculations also represented that direct solvent effect on nitrogen of pyridine ring (N15) is more than other nitrogens, while its effect on N19 is less than other ones. Based on NMR data and NBO interpretation, it can be deduced that with a decrease in the negative charge on nitrogen atoms, the intramolecular effects on them decrease, while direct solvent effect increases.

A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields

NASA Astrophysics Data System (ADS)

Eichinger, M.; Tavan, P.; Hutter, J.; Parrinello, M.

1999-06-01

We present a hybrid method for molecular dynamics simulations of solutes in complex solvents as represented, for example, by substrates within enzymes. The method combines a quantum mechanical (QM) description of the solute with a molecular mechanics (MM) approach for the solvent. The QM fragment of a simulation system is treated by ab initio density functional theory (DFT) based on plane-wave expansions. Long-range Coulomb interactions within the MM fragment and between the QM and the MM fragment are treated by a computationally efficient fast multipole method. For the description of covalent bonds between the two fragments, we introduce the scaled position link atom method (SPLAM), which removes the shortcomings of related procedures. The various aspects of the hybrid method are scrutinized through test calculations on liquid water, the water dimer, ethane and a small molecule related to the retinal Schiff base. In particular, the extent to which vibrational spectra obtained by DFT for the solute can be spoiled by the lower quality force field of the solvent is checked, including cases in which the two fragments are covalently joined. The results demonstrate that our QM/MM hybrid method is especially well suited for the vibrational analysis of molecules in condensed phase.

Potential of mean force for ion pairs in non-aqueous solvents. Comparison of polarizable and non-polarizable MD simulations

NASA Astrophysics Data System (ADS)

Odinokov, A. V.; Leontyev, I. V.; Basilevsky, M. V.; Petrov, N. Ch.

2011-01-01

Potentials of mean force (PMF) are calculated for two model ion pairs in two non-aqueous solvents. Standard non-polarizable molecular dynamics simulation (NPMD) and approximate polarizable simulation (PMD) are implemented and compared as tools for monitoring PMF profiles. For the polar solvent (dimethylsulfoxide, DMSO) the PMF generated in terms of the NPMD reproduces fairly well the refined PMD-PMF profile. For the non-polar solvent (benzene) the conventional NPMD computation proves to be deficient. The validity of the correction found in terms of the approximate PMD approach is verified by its comparison with the result of the explicit PMD computation in benzene. The shapes of the PMF profiles in DMSO and in benzene are quite different. In DMSO, owing to dielectric screening, the PMF presents a flat plot with a shallow minimum positioned in the vicinity of the van der Waals contact of the ion pair. For the benzene case, the observed minimum proves to be unexpectedly deep, which manifests the formation of a tightly-binded contact ion pair. This remarkable effect arises owing to the strong electrostatic interaction that is incompletely screened by a non-polar medium. The PMFs for the binary benzene/DMSO mixtures display intermediate behaviour depending on the DMSO content.

How High Pressure Unifies Solvation Processes in Liquid Chromatography.

PubMed

Bocian, Szymon; Škrinjar, Tea; Bolanca, Tomislav; Buszewski, Bogusław

2017-11-01

A series of core-shell-based stationary phases of varying surface chemistry were subjected to solvent adsorption investigation under ultra-HPLC conditions. Acetonitrile and water excess isotherms were measured using a minor disturbance method. It was observed that adsorption of organic solvent is unified under high pressure. Preferential solvation due to specific interactions between the stationary phases and solvent molecules was limited. The obtained results showed that the solvation process is almost independent of surface chemistry, in contrast to HPLC conditions in which specific interactions differentiate solvation processes.

Solvent-driven reductive activation of carbon dioxide by gold anions.

PubMed

Knurr, Benjamin J; Weber, J Mathias

2012-11-14

Catalytic activation and electrochemical reduction of CO(2) for the formation of chemically usable feedstock and fuel are central goals for establishing a carbon neutral fuel cycle. The role of solvent molecules in catalytic processes is little understood, although solvent-solute interactions can strongly influence activated intermediate species. We use vibrational spectroscopy of mass-selected Au(CO(2))(n)(-) cluster ions to probe the solvation of AuCO(2)(-) as a model for a reactive intermediate in the reductive activation of a CO(2) ligand by a single-atom catalyst. For the first few solvent molecules, solvation of the complex preferentially occurs at the CO(2) moiety, enhancing reductive activation through polarization of the excess charge onto the partially reduced ligand. At higher levels of solvation, direct interaction of additional solvent molecules with the Au atom diminishes reduction. The results show how the solvation environment can enhance or diminish the effects of a catalyst, offering design criteria for single-atom catalyst engineering.

Effect of Aprotic Solvents on the Dynamics of a Room Temperature Ionic Liquid

NASA Astrophysics Data System (ADS)

Osti, Naresh; van Aken, Katherine; Thompson, Matthew; Tiet, Felix; Jiang, De-En; Cummings, Peter; Gogotsi, Yury; Mamontov, Eugene

Room temperature ionic liquids (RTILs) have attracted much attention as electrolytes in energy storage devices because of their peculiar physical and chemical characteristics. However, their remarkably high viscosity, which results in low conductivity and diffusivity, may adversely affect the charging and discharging rates. Despite changing molecular configurations, use of aprotic solvent allows to enhance the transport properties of ionic liquids by disrupting the cation-anion interactions. We explore the impact of dipole moment of aprotic solvents on the cation-anion interaction and transport in 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [BMIM +][Tf2N-], RTIL using molecular dynamics (MD) simulations and quasi-elastic neutrons scattering (QENS) measurements. We observed an increase in cation diffusivity with the increasing dipole moment of the solvent. This effect is due to a decrease in the solvation free energy induced by the increasing solvent polarity. A clear nano-phase separation into ionic liquid-rich and ionic liquid-poor phases as observed by QENS will be also discussed.

40 CFR 63.5753 - How do I calculate the combined organic HAP content of aluminum wipedown solvents and aluminum...

Code of Federal Regulations, 2012 CFR

2012-07-01

... organic HAP content of aluminum wipedown solvents and aluminum recreational boat surface coatings? 63.5753...) National Emission Standards for Hazardous Air Pollutants for Boat Manufacturing Standards for Aluminum Recreational Boat Surface Coating Operations § 63.5753 How do I calculate the combined organic HAP content of...

40 CFR 63.5753 - How do I calculate the combined organic HAP content of aluminum wipedown solvents and aluminum...

Code of Federal Regulations, 2014 CFR

2014-07-01

... organic HAP content of aluminum wipedown solvents and aluminum recreational boat surface coatings? 63.5753...) National Emission Standards for Hazardous Air Pollutants for Boat Manufacturing Standards for Aluminum Recreational Boat Surface Coating Operations § 63.5753 How do I calculate the combined organic HAP content of...

40 CFR 63.5753 - How do I calculate the combined organic HAP content of aluminum wipedown solvents and aluminum...

Code of Federal Regulations, 2013 CFR

2013-07-01

... HAP content of aluminum wipedown solvents and aluminum recreational boat surface coatings? 63.5753...) National Emission Standards for Hazardous Air Pollutants for Boat Manufacturing Standards for Aluminum Recreational Boat Surface Coating Operations § 63.5753 How do I calculate the combined organic HAP content of...

Solvent decompositions and physical properties of decomposition compounds in Li-ion battery electrolytes studied by DFT calculations and molecular dynamics simulations.

PubMed

Tasaki, Ken

2005-02-24

The density functional theory (DFT) calculations have been performed for the reduction decompositions of solvents widely used in Li-ion secondary battery electrolytes, ethylene carbonate (EC), propylene carbonate (PC), dimethyl carbonates (DMC), ethyl methyl carbonate (EMC), and diethyl carbonate (DEC), including a typical electrolyte additive, vinylene carbonate (VC), at the level of B3LYP/6-311+G(2d,p), both in the gas phase and solution using the polarizable conductor calculation model. In the gas phase, the first electron reduction for the cyclic carbonates and for the linear carbonates is found to be exothermic and endothermic, respectively, while the second electron reduction is endothermic for all the compounds examined. On the contrary, in solution both first and second electron reductions are exothermic for all the compounds. Among the solvents and the additive examined, the likelihood of undergoing the first electron reduction in solution was found in the order of EC > PC > VC > DMC > EMC > DEC with EC being the most likely reduced. VC, on the other hand, is most likely to undergo the second electron reduction among the compounds, in the order of VC > EC > PC. Based on the results, the experimentally demonstrated effectiveness of VC as an excellent electrolyte additive was discussed. The bulk thermodynamic properties of two dilithium alkylene glycol dicarbonates, dilithium ethylene glycol dicarbonate (Li-EDC) and dilithium 1,2-propylene glycol dicarbonate (Li-PDC), as the major component of solid-electrolyte interface (SEI) films were also examined through molecular dynamics (MD) simulations in order to understand the stability of the SEI film. It was found that film produced from a decomposition of EC, modeled by Li-EDC, has a higher density, more cohesive energy, and less solubility to the solvent than the film produced from decomposition of PC, Li-PDC. Further, MD simulations of the interface between the decomposition compound and graphite suggested that Li-EDC has more favorable interactions with the graphite surface than Li-PDC. The difference in the SEI film stability and the behavior of Li-ion battery cycling among the solvents were discussed in terms of the molecular structures.

Molecular Level Structure and Dynamics of Electrolytes Using 17O Nuclear Magnetic Resonance Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murugesan, Vijayakumar; Han, Kee Sung; Hu, Jianzhi

2017-03-19

Electrolytes help harness the energy from electrochemical processes by serving as solvents and transport media for redox-active ions. Molecular-level interactions between ionic solutes and solvent molecules – commonly referred to as solvation phenomena – give rise to many functional properties of electrolytes such as ionic conductivity, viscosity, and stability. It is critical to understand the evolution of solvation phenomena as a function of competing counterions and solvent mixtures to predict and design the optimal electrolyte for a target application. Probing oxygen environments is of great interest as oxygens are located at strategic molecular sites in battery solvents and are directlymore » involved in inter- and intramolecular solvation interactions. NMR signals from 17O nuclei in battery electrolytes offer nondestructive bulk measurements of isotropic shielding, electric field gradient tensors, and transverse and longitudinal relaxation rates, which are excellent means for probing structure, bonding, and dynamics of both solute and solvent molecules. This article describes the use of 17O NMR spectroscopy in probing the solvation structures of various electrolyte systems ranging from transition metal ions in aqueous solution to lithium cations in organic solvent mixtures.« less

The reorganization energy of electron transfer in nonpolar solvents: Molecular level treatment of the solvent

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leontyev, I.V.; Tachiya, M.

The intermolecular electron transfer in a solute pair consisting of pyrene and dimethylaniline is investigated in a nonpolar solvent, n-hexane. The earlier elaborated approach [M. Tachiya, J. Phys Chem. 97, 5911 (1993)] is used; this method provides a physically relevant background for separating inertial and inertialess polarization responses for both nonpolarizable and polarizable molecular level simulations. The molecular-dynamics technique was implemented for obtaining the equilibrium ensemble of solvent configurations. The nonpolar solvent, n-hexane, was treated in terms of OPLS-AA parametrization. Solute Lennard-Jones parameters were taken from the same parametrization. Solute charge distributions of the initial and final states were determinedmore » using ab initio level [HF/6-31G(d,p)] quantum-chemical calculations. Configuration analysis was performed explicitly taking into account the anisotropic polarizability of n-hexane. It is shown that the Gaussian law well describes calculated distribution functions of the solvent coordinate, therefore, the rate constant of the ET reaction can be characterized by the reorganization energy. Evaluated values of the reorganization energies are in a range of 0.03-0.11 eV and significant contribution (more then 40% of magnitude) comes from anisotropic polarizability. Investigation of the reorganization energy {lambda} dependence on the solute pair separation distance d revealed unexpected behavior. The dependence has a very sharp peak at the distance d=7 A where solvent molecules are able to penetrate into the intermediate space between the solute pair. The reason for such behavior is clarified. This new effect has a purely molecular origin and cannot be described within conventional continuum solvent models.« less

Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms

PubMed Central

Wagoner, Jason A.; Baker, Nathan A.

2006-01-01

Continuum solvation models provide appealing alternatives to explicit solvent methods because of their ability to reproduce solvation effects while alleviating the need for expensive sampling. Our previous work has demonstrated that Poisson-Boltzmann methods are capable of faithfully reproducing polar explicit solvent forces for dilute protein systems; however, the popular solvent-accessible surface area model was shown to be incapable of accurately describing nonpolar solvation forces at atomic-length scales. Therefore, alternate continuum methods are needed to reproduce nonpolar interactions at the atomic scale. In the present work, we address this issue by supplementing the solvent-accessible surface area model with additional volume and dispersion integral terms suggested by scaled particle models and Weeks–Chandler–Andersen theory, respectively. This more complete nonpolar implicit solvent model shows very good agreement with explicit solvent results and suggests that, although often overlooked, the inclusion of appropriate dispersion and volume terms are essential for an accurate implicit solvent description of atomic-scale nonpolar forces. PMID:16709675

Aqueous or solvent based surface modification: The influence of the combination solvent - organic functional group on the surface characteristics of titanium dioxide grafted with organophosphonic acids

NASA Astrophysics Data System (ADS)

Roevens, Annelore; Van Dijck, Jeroen G.; Geldof, Davy; Blockhuys, Frank; Prelot, Benedicte; Zajac, Jerzy; Meynen, Vera

2017-09-01

To alter the versatility of interactions at its surface, TiO2 is modified with organophosphonic acids (PA). A thorough understanding of the role of all synthesis conditions is necessary to achieve controlled functionalization. This study reports on the effect of using water, toluene and their mixtures when performing the modification of TiO2 with PA. Sorption and calorimetry measurements of surface interactions with various probing species clearly indicate that, by grafting PA in water, clear differences appear in the distribution of organic groups on the surface. Also the functional group of the PA determines the impact of using water as solvent. Modification in toluene results in a higher modification degree for propylphosphonic acid (3PA), as the solvent-solute interaction may hinder the grafting with phenylphosphonic acid (PhPA) in toluene. Water is preferred as solvent for PhPA modification as stabilizing π-OH interactions enhance surface grafting overcoming the competitive interaction of water at the surface as observed with 3PA. By using water in toluene mixtures for the functionalization of TiO2 with 3PA, the degree of functionalization is higher than when only water or toluene is used. Furthermore, adding small amounts of water leads to the formation of titanium propylphosphonates, next to surface grafting.

Qualitative and quantitative evaluation of solvent systems for countercurrent separation.

PubMed

Friesen, J Brent; Ahmed, Sana; Pauli, Guido F

2015-01-16

Rational solvent system selection for countercurrent chromatography and centrifugal partition chromatography technology (collectively known as countercurrent separation) studies continues to be a scientific challenge as the fundamental questions of comparing polarity range and selectivity within a solvent system family and between putative orthogonal solvent systems remain unanswered. The current emphasis on metabolomic investigations and analysis of complex mixtures necessitates the use of successive orthogonal countercurrent separation (CS) steps as part of complex fractionation protocols. Addressing the broad range of metabolite polarities demands development of new CS solvent systems with appropriate composition, polarity (π), selectivity (σ), and suitability. In this study, a mixture of twenty commercially available natural products, called the GUESSmix, was utilized to evaluate both solvent system polarity and selectively characteristics. Comparisons of GUESSmix analyte partition coefficient (K) values give rise to a measure of solvent system polarity range called the GUESSmix polarity index (GUPI). Solvatochromic dye and electrical permittivity measurements were also evaluated in quantitatively assessing solvent system polarity. The relative selectivity of solvent systems were evaluated with the GUESSmix by calculating the pairwise resolution (αip), the number of analytes found in the sweet spot (Nsw), and the pairwise resolution of those sweet spot analytes (αsw). The combination of these parameters allowed for both intra- and inter-family comparison of solvent system selectivity. Finally, 2-dimensional reciprocal shifted symmetry plots (ReSS(2)) were created to visually compare both the polarities and selectivities of solvent system pairs. This study helps to pave the way to the development of new solvent systems that are amenable to successive orthogonal CS protocols employed in metabolomic studies. Copyright © 2014 Elsevier B.V. All rights reserved.

The solvation of ions in acetonitrile and acetone. II. Monte Carlo simulations using polarizable solvent models

NASA Astrophysics Data System (ADS)

Fischer, R.; Richardi, J.; Fries, P. H.; Krienke, H.

2002-11-01

Structural properties and energies of solvation are simulated for alkali and halide ions. The solvation structure is discussed in terms of various site-site distribution functions, of solvation numbers, and of orientational correlation functions of the solvent molecules around the ions. The solvent polarizability has notable effects which cannot be intuitively predicted. In particular, it is necessary to reproduce the experimental solvation numbers of small ions. The changes of solvation properties are investigated along the alkali and halide series. By comparing the solvation of ions in acetone to that in acetonitrile, it is shown that the spatial correlations among the solvent molecules around an ion result in a strong screening of the ion-solvent direct intermolecular potential and are essential to understand the changes in the solvation structures and energies between different solvents. The solvation properties derived from the simulations are compared to earlier predictions of the hypernetted chain (HNC) approximation of the molecular Ornstein-Zernike (MOZ) theory [J. Richardi, P. H. Fries, and H. Krienke, J. Chem. Phys. 108, 4079 (1998)]. The MOZ(HNC) formalism gives an overall qualitatively correct picture of the solvation and its various unexpected findings are corroborated. For the larger ions, its predictions become quantitative. The MOZ approach allows to calculate solvent-solvent and ion-solvent potentials of mean force, which shed light on the 3D labile molecular and ionic architectures in the solution. These potentials of mean force convey a unique information which is necessary to fully interpret the angle-averaged structural functions computed from the simulations. Finally, simulations of solutions at finite concentrations show that the solvent-solvent and ion-solvent spatial correlations at infinite dilution are marginally altered by the introduction of fair amounts of ions.

Persistent Self-Association of Solute Molecules in Solution.

PubMed

Tang, Weiwei; Mo, Huaping; Zhang, Mingtao; Parkin, Sean; Gong, Junbo; Wang, Jingkang; Li, Tonglei

2017-11-02

The structural evolvement of a solute determines the crystallization outcome. The self-association mechanism leading to nucleation, however, remains poorly understood. Our current study explored the solution chemistry of a model compound, tolfenamic acid (TFA), in three different solvents mainly by solution NMR. It was found that hydrogen-bonded pairs of solute-solute or solute-solvent stack with each through forming a much weaker π-π interaction as the concentration increases. Depending on the solvent, configurations of the solution species may be retained in the resultant crystal structure or undergo rearrangement. Yet, the π-π stacking is always retained in the crystal regardless of the solvent used for the crystallization. The finding suggests that nucleation not only involves the primary intermolecular interaction (hydrogen bonding) but also engages the secondary forces in the self-assembly process.

Rational Design of Molecular Gelator - Solvent Systems Guided by Solubility Parameters

NASA Astrophysics Data System (ADS)

Lan, Yaqi

Self-assembled architectures, such as molecular gels, have attracted wide interest among chemists, physicists and engineers during the past decade. However, the mechanism behind self-assembly remains largely unknown and no capability exists to predict a priori whether a small molecule will gelate a specific solvent or not. The process of self-assembly, in molecular gels, is intricate and must balance parameters influencing solubility and those contrasting forces that govern epitaxial growth into axially symmetric elongated aggregates. Although the gelator-gelator interactions are of paramount importance in understanding gelation, the solvent-gelator specific (i.e., H-bonding) and nonspecific (dipole-dipole, dipole-induced and instantaneous dipole induced forces) intermolecular interactions are equally important. Solvent properties mediate the self-assembly of molecular gelators into their self-assembled fibrillar networks. Herein, solubility parameters of solvents, ranging from partition coefficients (logP), to Henry's law constants (HLC), to solvatochromic ET(30) parameters, to Kamlet-Taft parameters (beta, alpha and pi), to Hansen solubility parameters (deltap, deltad, deltah), etc., are correlated with the gelation ability of numerous classes of molecular gelators. Advanced solvent clustering techniques have led to the development of a priori tools that can identify the solvents that will be gelled and not gelled by molecular gelators. These tools will greatly aid in the development of novel gelators without solely relying on serendipitous discoveries.

Organosolv extraction of lignin from hydrolyzed almond shells and application of the delta-value theory.

PubMed

Quesada-Medina, Joaquín; López-Cremades, Francisco Javier; Olivares-Carrillo, Pilar

2010-11-01

The solubility of lignin from hydrolyzed almond (Prunus amygdalus) shells in different acetone, ethanol and dioxane-water mixtures and conditions (extraction time and temperature) was studied. The concept of the solubility parameter (delta-value) was applied to explain the effect of organic solvent concentration on lignin solubility. The organic solvent-water mixture that led to the highest lignin extraction was composed of a 75% vol. of organic solvent for all the solvent series investigated (acetone, ethanol and dioxane). Moreover, the best lignin extraction conditions were a temperature of 210 degrees C and an extraction time of 40 min for the acetone and ethanol series, and 25 min for the dioxane series. The delta-value of the hydrolyzed almond shell lignin [14.60 (cal/cm(3))(1/2)] and that of the organic solvent-water mixtures was calculated. The experimental delignification capacity of the aqueous organic solvents clearly reflected the proximity of their delta-value to that of lignin. The hydrogen-bonding capacity of the solvent-water mixtures was also taken into account. Copyright 2010 Elsevier Ltd. All rights reserved.

Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions.

PubMed

Arcon, Juan Pablo; Defelipe, Lucas A; Modenutti, Carlos P; López, Elias D; Alvarez-Garcia, Daniel; Barril, Xavier; Turjanski, Adrián G; Martí, Marcelo A

2017-04-24

One of the most important biological processes at the molecular level is the formation of protein-ligand complexes. Therefore, determining their structure and underlying key interactions is of paramount relevance and has direct applications in drug development. Because of its low cost relative to its experimental sibling, molecular dynamics (MD) simulations in the presence of different solvent probes mimicking specific types of interactions have been increasingly used to analyze protein binding sites and reveal protein-ligand interaction hot spots. However, a systematic comparison of different probes and their real predictive power from a quantitative and thermodynamic point of view is still missing. In the present work, we have performed MD simulations of 18 different proteins in pure water as well as water mixtures of ethanol, acetamide, acetonitrile and methylammonium acetate, leading to a total of 5.4 μs simulation time. For each system, we determined the corresponding solvent sites, defined as space regions adjacent to the protein surface where the probability of finding a probe atom is higher than that in the bulk solvent. Finally, we compared the identified solvent sites with 121 different protein-ligand complexes and used them to perform molecular docking and ligand binding free energy estimates. Our results show that combining solely water and ethanol sites allows sampling over 70% of all possible protein-ligand interactions, especially those that coincide with ligand-based pharmacophoric points. Most important, we also show how the solvent sites can be used to significantly improve ligand docking in terms of both accuracy and precision, and that accurate predictions of ligand binding free energies, along with relative ranking of ligand affinity, can be performed.

UV-Vis spectroscopy and solvatochromism of the tyrosine kinase inhibitor AG-1478

NASA Astrophysics Data System (ADS)

Khattab, Muhammad; Wang, Feng; Clayton, Andrew H. A.

2016-07-01

The effect of twenty-one solvents on the UV-Vis spectrum of the tyrosine kinase inhibitor AG-1478 was investigated. The absorption spectrum in the range 300-360 nm consisted of two partially overlapping bands at approximately 340 nm and 330 nm. The higher energy absorption band was more sensitive to solvent and exhibited a peak position that varied from 327 nm to 336 nm, while the lower energy absorption band demonstrated a change in peak position from 340 nm to 346 nm in non-chlorinated solvents. The fluorescence spectrum of AG-1478 was particularly sensitive to solvent. The wavelength of peak intensity varied from 409 nm to 495 nm with the corresponding Stokes shift in the range of 64 nm to 155 nm (4536 cm- 1 to 9210 cm- 1). We used a number of methods to assess the relationship between spectroscopic properties and solvent properties. The detailed analysis revealed that for aprotic solvents, the peak position of the emission spectrum in wavenumber scale correlated with the polarity (dielectric constant or ET(30)) of the solvent. In protic solvents, a better correlation was observed between the hydrogen bonding power of the solvent and the position of the emission spectrum. Moreover, the fluorescence quantum yields were larger in aprotic solvents as compared to protic solvents. This analysis underscores the importance of polarity and hydrogen-bonding environment on the spectroscopic properties of AG-1478. These studies will assume relevance in understanding the interaction of AG-1478 in vitro and in vivo.

Impact of solvent granularity and layering on tracer hydrodynamics in confinement.

PubMed

Bollinger, Jonathan A; Carmer, James; Jain, Avni; Truskett, Thomas M

2016-11-28

Classic hydrodynamic arguments establish that when a spherical tracer particle is suspended between parallel walls, tracer-wall coupling mediated by the solvent will cause the tracer to exhibit position-dependent diffusivity. We investigate how the diffusivity profiles of confined tracers are impacted by the diameter size-ratio of the tracer to solvent: starting from the classic limit of infinite size-ratio (i.e., continuum solvent), we consider size-ratios of four or less to examine how hydrodynamic predictions are disrupted for systems where the tracer and solvent are of similar scale. We use computer simulations and techniques based on the Fokker-Planck formalism to calculate the diffusivity profiles of hard-sphere tracer particles in hard-sphere solvents, focusing on the dynamics perpendicular to the walls. Given wall separations of several tracer diameters, we first consider confinement between hard walls, where anisotropic structuring at the solvent lengthscale generates inhomogeneity in the tracer free-energy landscape and undermines hydrodynamic predictions locally. We then introduce confining planes that we term transparent walls, which restrict tracer and solvent center-accessibilities while completely eliminating static anisotropy, and reveal position-dependent signatures in tracer diffusivity solely attributable to confinement. With or without suppressing static heterogeneity, we find that tracer diffusivity increasingly deviates on a local basis from hydrodynamic predictions at smaller size-ratios. However, hydrodynamic theory still approximately captures spatially-averaged dynamics across the pores even for very small tracer-solvent size-ratios over a wide range of solvent densities and wall separations.

Ab initio studies on the solvation, electronic structures and intracluster reactions in M(+)L(n), with M(+)=magnesium and calcium singly-charged ions, L=water, methanol, ammonia, and n=1-6, and the elimination of a hydrogen atom in H atom in hydrated sodium clusters

NASA Astrophysics Data System (ADS)

Chan, Ka Wai

The solvation and electronic structures of M+Ln, with M+ = Mg+ and Cat, L = H2O, CH 3OH and NH3, n=1-6 were investigated by ab initio calculations using G03 package and density functional theory based ab initio molecular dynamics (AIMD) simulations with projector augmented-wave (PAW) method and a planewave basis set using Vienna Ab initio Simulation Package (VASP). Furthermore, ab initio studies on the intracluster reactions of Mg+ and Ca+ ions with different solvent molecules, H2O, CH3OH and NH3, were also done using G03 package. Finally, the elimination of a H atom in Na(H2O)n was studied. Such studies on the interactions and reactivity in gas clusters can provide insights into their analogies existing in condense phase. Interactions of Mg+ and Ca+ ions in different solvent molecules, H2O, CH3OH and NH3, were calculated with B3LYP and MP2 methods with basis sets 6-31+g** and 6-311+g**. A systematic comparison on the structures and reactivities of these clusters should provide a better understanding on the interplay of the ion-solvent, solvent-solvent, and electron-solvent interactions. It can provide a better understanding on the structures and bonding of complexes having analogies to those existing in condense phase. For Mg+(CH3OH)n and Ca+(CH 3OH)n, both H-elimination from OH/CH bond and CH3-elimination were investigated. H-elimination from O---H bond becomes more accessible for large cluster due to the diffusion of electron density to O---H bond. Studies on the H-elimination in Mg+(NH3)n and H-elimination from C---H bond in Mg+(CH3OH) n show that the reaction barriers flatten above 20 kcal/mol as n reaches 4 and above. These calculation results prove that the source of loss of H atom in ground state Mg+(CH3OH)n should be through the O---H bond rather than through the C---H bond. Compared to Mg+(CH3OH)n, the reaction barriers for H-elimination in Mg+(NH3)n is much larger, which is in consistent with the experimental observation of little H-elimination for Mg+(NH3)n unless it's photo-excited. The examination of neutral Na(H2O)n clusters, n=4~15 for H-elimination was carried out. The reaction profile for H-elimination was obtained by energy minimization at constrained O---H distance which was successively increased. There was a general trend of decreasing reaction barrier, as the cluster size grows. In contrast to Mg+(H 2O)n, the expected switch-off of H-elimination as in Mg +(H2O)n cannot be observed.

Efficient encapsulation of chloroform with cryptophane-M and the formation of exciplex studied by fluorescence spectroscopy.

PubMed

Shi, Yanqi; Li, Xueming; Yang, Jianchun; Gao, Fang; Tao, Chuanyi

2011-03-01

Efficient encapsulation of small molecules with supermolecules is one of significantly important subjects due to strong application potentials. This article presents the interaction between cryptophane-M and chloroform by fluorescence spectroscopy. The sonicated cryptophane-M solution exhibits light green color in chloroform, and the solid obtained from the evaporation of chloroform also has different color from that of cryptophane-M. In contrast, the sonicated cryptophane-M solutions in other solvents are colorless, and the solid obtained from the evaporation of these solvents has the same color as that of cryptophane-M. Furthermore, the freshly prepared cryptophane-M solution in different solvents is almost colorless, and the solid obtained from the evaporation of these solvents displays the same color as that of cryptophane-M. Although the sonicated cryptophane-M solutions in different solvents have very similar absorption spectra, they exhibit quite different emission spectra in chloroform. In contrast, the freshly-prepared cryptophane-M solutions show similar absorption and emission spectroscopy in various solvents. The variation of the fluorescence spectroscopy in binary solvents with the increasing chloroform ratio suggests that cryptophane-M and chloroform form a 1:1 exciplex, and the binding constant is estimated to be 292.95 M(-1). Although all solvents are able to enter into the cavity of cryptophane-M, only chloroform can stay in the cavity of cryptophane-M for a while, which is mostly due to the strong intermolecular interaction between cryptophane-M and chloroform, and this results in the formation of the exciplex between them. © Springer Science+Business Media, LLC 2010

Structure and properties of polycaprolactone/chitosan nonwovens tailored by solvent systems.

PubMed

Urbanek, Olga; Sajkiewicz, Paweł; Pierini, Filippo; Czerkies, Maciej; Kołbuk, Dorota

2017-02-03

Electrospinning of chitosan blends is a reasonable idea to prepare fibre mats for biomedical applications. Synthetic and natural components provide, for example, appropriate mechanical strength and biocompatibility, respectively. However, solvent characteristics and the polyelectrolyte nature of chitosan influence the spinnability of these blends. In order to compare the effect of solvent on polycaprolactone/chitosan fibres, two types of the most commonly used solvent systems were chosen, namely 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) and acetic acid (AA)/formic acid (FA). Results obtained by various experimental methods clearly indicated the effect of the solvent system on the structure and properties of electrospun polycaprolactone/chitosan fibres. Viscosity measurements confirmed different polymer-solvent interactions. Various molecular interactions resulting in different macromolecular conformations of chitosan influenced its spinnability and properties. HFIP enabled fibres to be obtained whose average diameter was less than 250 nm while maintaining the brittle and hydrophilic character of the nonwoven, typical for the chitosan component. Spectroscopy studies revealed the formation of chitosan salts in the case of the AA/FA solvent system. Chitosan salts visibly influenced the structure and properties of the prepared fibre mats. The use of AA/FA caused a reduction of Young's modulus and wettability of the proposed blends. It was confirmed that wettability, mechanical properties and the antibacterial effect of polycaprolactone/chitosan fibres may be tailored by selecting an appropriate solvent system. The MTT cell proliferation assay revealed an increase of cytotoxicity to mouse fibroblasts in the case of 25% w/w of chitosan in electrospun nonwovens.

Towards ultra-fast solvent evaporation, the development of a computer controlled solvent vapor annealing chamber

NASA Astrophysics Data System (ADS)

Nelson, Gunnar; Wong, J.; Drapes, C.; Grant, M.; Baruth, A.

Despite the promise of cheap and fast nanoscale ordering of block polymer thin films via solvent vapor annealing, a standardized, scalable production scheme remains elusive. Solvent vapor annealing exposes a nano-thin film to the vapors of one or more solvents with the goal of forming a swollen and mobile state to direct the self-assembly process by tuning surface energies and mediating unfavorable chain interactions. We have shown that optimized annealing conditions, where kinetic and thermal properties for crystal growth are extremely fast (<1s), exist at solvent concentrations just below the order-disorder transition of the film. However, when investigating the propagation of a given morphology into the bulk of a film during drying, the role of solvent evaporation comes under great scrutiny. During this process, the film undergoes a competition between two fronts; phase separation and kinetic trapping. Recent results in both theory and experiment point toward this critical element in controlling the resultant morphologies; however, no current method includes a controllable solvent evaporation rate at ultra-fast time scales. We report on a computer-controlled, pneumatically actuated chamber that provides control over solvent evaporation down to 15 ms. Furthermore, in situ spectral reflectance monitors solvent concentration with 10 ms temporal resolution and reveals several possible evaporation trajectories, ranging from linear to exponential to logarithmic. Funded by Dr. Randolph Ferlic Summer Research Scholarship and NASA Nebraska Space Grant.

The Denaturation Transition of DNA in Mixed Solvents

PubMed Central

Hammouda, Boualem; Worcester, David

2006-01-01

The helix-to-coil denaturation transition in DNA has been investigated in mixed solvents at high concentration using ultraviolet light absorption spectroscopy and small-angle neutron scattering. Two solvents have been used: water and ethylene glycol. The “melting” transition temperature was found to be 94°C for 4% mass fraction DNA/d-water and 38°C for 4% mass fraction DNA/d-ethylene glycol. The DNA melting transition temperature was found to vary linearly with the solvent fraction in the mixed solvents case. Deuterated solvents (d-water and d-ethylene glycol) were used to enhance the small-angle neutron scattering signal and 0.1M NaCl (or 0.0058 g/g mass fraction) salt concentration was added to screen charge interactions in all cases. DNA structural information was obtained by small-angle neutron scattering, including a correlation length characteristic of the inter-distance between the hydrogen-containing (desoxyribose sugar-amine base) groups. This correlation length was found to increase from 8.5 to 12.3 Å across the melting transition. Ethylene glycol and water mixed solvents were found to mix randomly in the solvation region in the helix phase, but nonideal solvent mixing was found in the melted coil phase. In the coil phase, solvent mixtures are more effective solvating agents than either of the individual solvents. Once melted, DNA coils behave like swollen water-soluble synthetic polymer chains. PMID:16815902

Molecular dynamics investigation of the ionic liquid/enzyme interface: application to engineering enzyme surface charge.

PubMed

Burney, Patrick R; Nordwald, Erik M; Hickman, Katie; Kaar, Joel L; Pfaendtner, Jim

2015-04-01

Molecular simulations of the enzymes Candida rugosa lipase and Bos taurus α-chymotrypsin in aqueous ionic liquids 1-butyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium ethyl sulfate were used to study the change in enzyme-solvent interactions induced by modification of the enzyme surface charge. The enzymes were altered by randomly mutating lysine surface residues to glutamate, effectively decreasing the net surface charge by two for each mutation. These mutations resemble succinylation of the enzyme by chemical modification, which has been shown to enhance the stability of both enzymes in ILs. After establishing that the enzymes were stable on the simulated time scales, we focused the analysis on the organization of the ionic liquid substituents about the enzyme surface. Calculated solvent charge densities show that for both enzymes and in both solvents that changing positively charged residues to negative charge does indeed increase the charge density of the solvent near the enzyme surface. The radial distribution of IL constituents with respect to the enzyme reveals decreased interactions with the anion are prevalent in the modified systems when compared to the wild type, which is largely accompanied by an increase in cation contact. Additionally, the radial dependence of the charge density and ion distribution indicates that the effect of altering enzyme charge is confined to short range (≤1 nm) ordering of the IL. Ultimately, these results, which are consistent with that from prior experiments, provide molecular insight into the effect of enzyme surface charge on enzyme stability in ILs. © 2015 Wiley Periodicals, Inc.

Simulations of fluorescence solvatochromism in substituted PPV oligomers from excited state molecular dynamics with implicit solvent

DOE PAGES

Bjorgaard, J. A.; Nelson, T.; Kalinin, K.; ...

2015-04-28

In this study, an efficient method of treating solvent effects in excited state molecular dynamics (ESMD) is implemented and tested by exploring the solvatochromic effects in substituted p-phenylene vinylene oligomers. A continuum solvent model is used which has very little computational overhead. This allows simulations of ESMD with solvent effects on the scale of hundreds of picoseconds for systems of up to hundreds of atoms. At these time scales, solvatochromic shifts in fluoresence spectra can be described. Solvatochromic shifts in absorption and fluorescence spectra from ESMD are compared with time-dependent density functional theory calculations and experiments.

Theoretical study of solvent effects on the electronic coupling matrix elements in rigidly linked donor-acceptor systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cave, R.J.; Newton, M.D.; Kumar, K.

1995-12-07

The recently developed generalized Mulliken-Hush approach for the calculation of the electronic coupling matrix element for electron-transfer processes is applied to two rigidly linked donor-bridge-acceptor systems having dimethoxyanthracene as the donor and a dicarbomethoxycyclobutene unit as the acceptor. The dependence of the electronic coupling matrix element as a function of bridge type is examined with and without solvent molecules present. For clamp-shaped bridge structures solvent can have a dramatic effect on the electronic coupling matrix element. The behavior with variation of solvent is in good agreement with that observed experimentally for these systems. 23 refs., 2 tabs.

Spectral regression and correlation coefficients of some benzaldimines and salicylaldimines in different solvents

NASA Astrophysics Data System (ADS)

Hammud, Hassan H.; Ghannoum, Amer; Masoud, Mamdouh S.

2006-02-01

Sixteen Schiff bases obtained from the condensation of benzaldehyde or salicylaldehyde with various amines (aniline, 4-carboxyaniline, phenylhydrazine, 2,4-dinitrophenylhydrazine, ethylenediamine, hydrazine, o-phenylenediamine and 2,6-pyridinediamine) are studied with UV-vis spectroscopy to observe the effect of solvents, substituents and other structural factors on the spectra. The bands involving different electronic transitions are interpreted. Computerized analysis and multiple regression techniques were applied to calculate the regression and correlation coefficients based on the equation that relates peak position λmax to the solvent parameters that depend on the H-bonding ability, refractive index and dielectric constant of solvents.

The electrostatics of solvent and membrane interfaces and the role of electronic polarizability

NASA Astrophysics Data System (ADS)

Vorobyov, Igor; Allen, Toby W.

2010-05-01

The electrostatics of solvent and lipid bilayer interfaces are investigated with the aim of understanding the interaction of ions and charged peptides with biological membranes. We overcome the lacking dielectric response of hydrocarbon by carrying out atomistic molecular dynamics simulations using a polarizable model. For air-solvent or solvent-solvent interfaces, the effect of polarizability itself is small, yet changes in the fixed atomic charge distribution are responsible for substantial changes in the potential. However, when electrostatics is probed by finite solutes, a cancellation of dominant quadrupolar terms from the macroscopic and microscopic (solute-solvent) interfaces eliminates this dependence and leads to small net contributions to partitioning thermodynamics. In contrast, the membrane dipole potential exhibits considerable dependence on lipid electronic polarizability, due to its dominant dipolar contribution. We report the dipole potential for a polarizable lipid hydrocarbon membrane model of 480-610 mV, in better accord with experimental measurements.

Adsorption behavior of acetone solvent at the HMX crystal faces: A molecular dynamics study.

PubMed

Liu, Yingzhe; Yu, Tao; Lai, Weipeng; Ma, Yiding; Kang, Ying; Ge, Zhongxue

2017-06-01

Molecular dynamics simulations have been performed to understand the adsorption behavior of acetone (AC) solvent at the three surfaces of 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctan (HMX) crystal, i.e. (011), (110), and (020) faces. The simulation results show that the structural features and electrostatic potentials of crystal faces are determined by the HMX molecular packing, inducing distinct mass density distribution, dipole orientation, and diffusion of solvent molecules in the interfacial regions. The solvent adsorption is mainly governed by the van der Waals forces, and the crystal-solvent interaction energies among three systems are ranked as (020)≈(110)>(011). The adsorption sites for solvent incorporation at the crystal surface were found and visualized with the aid of occupancy analysis. A uniform arrangement of adsorption sites is observed at the rough (020) surface as a result of ordered adsorption motif. Copyright © 2017 Elsevier Inc. All rights reserved.

Excited state properties of peridinin: Observation of a solvent dependence of the lowest excited singlet state lifetime and spectral behavior unique among carotenoids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bautista, J.A.; Connors, R.E.; Raju, B.B.

1999-10-14

The spectroscopic properties and dynamic behavior of peridinin in several different solvents were studied by steady-state absorption, fluorescence, and transient optical spectroscopy. The lifetime of the lowest excited singlet state of peridinin is found to be strongly dependent on solvent polarity and ranges from 7 ps in the strongly polar solvent trifluoroethanol to 172 ps in the nonpolar solvents cyclohexane and benzene. The lifetimes show no obvious correlation with solvent polarizability, and hydrogen bonding of the solvent molecules to peridinin is not an important factor in determining the dynamic behavior of the lowest excited singlet state. The wavelengths of emissionmore » maxima, the quantum yields of fluorescence, and the transient absorption spectra are also affected by the solvent environment. A model consistent with the data and supported by preliminary semiempirical calculations invokes the presence of a charge transfer state in the excited state manifold of peridinin to account for the observations. The charge transfer state most probably results from the presence of the lactone ring in the {pi}-electron conjugation of peridinin analogous to previous findings on aminocoumarins and related compounds. The behavior of peridinin reported here is highly unusual for carotenoids, which generally show little dependence of the spectral properties and lifetimes of the lowest excited singlet state on the solvent environment.« less

Computational insights into the photocyclization of diclofenac in solution: effects of halogen and hydrogen bonding.

PubMed

Bani-Yaseen, Abdulilah Dawoud

2016-08-21

The effects of noncovalent interactions, namely halogen and hydrogen bonding, on the photochemical conversion of the photosensitizing drug diclofenac (DCF) in solution were investigated computationally. Both explicit and implicit solvent effects were qualitatively and quantitatively assessed employing the DFT/6-31+G(d) and SQM(PM7) levels of theory. Full geometry optimizations were performed in solution for the reactant DCF, hypothesized radical-based intermediates, and the main product at both levels of theories. Notably, in good agreement with previous experimental results concerning the intermolecular halogen bonding of DCF, the SQM(PM7) method revealed different values for d(ClO, Å) and ∠(C-ClO, °) for the two chlorine-substituents of DCF, with values of 2.63 Å/162° and 3.13 Å/142° for the trans and cis orientations, respectively. Employing the DFT/6-31+G(d) method with implicit solvent effects was not conclusive; however, explicit solvent effects confirmed the key contribution of hydrogen and halogen bonding in stabilizing/destabilizing the reactant and hypothesized intermediates. Interestingly, the obtained results revealed that a protic solvent such as water can increase the rate of photocyclization of DCF not only through hydrogen bonding effects, but also through halogen bonding. Furthermore, the atomic charges of atoms majorly involved in the photocyclization of DCF were calculated using different methods, namely Mulliken, Hirshfeld, and natural bond orbital (NBO). The obtained results revealed that in all cases there is a notable nonequivalency in the noncovalent intermolecular interactions of the two chlorine substituents of DCF and the radical intermediates with the solvent, which in turn may account for the discrepancy of their reactivity in different media. These computational results provide insight into the importance of halogen and hydrogen bonding throughout the progression of the photochemical conversion of DCF in solution.

Evaluation of the detachment energy of hydrated phosphate anion over a wide range of cluster size and revisiting solvent-berg model: a theoretical study

NASA Astrophysics Data System (ADS)

Pathak, Arup Kumar

2014-12-01

An explicit analytical expression has been obtained for vertical detachment energy (VDE) that can be used to calculate the same over a wide range (both stable and unstable regions) of cluster sizes including the bulk from the knowledge of VDE for a finite number of stable clusters (n = 16-23). The calculated VDE for the bulk is found to be very good in agreement (within 1%) with the available experimental result and the domain of instability lies between n = 0 and n = 15 for the hydrated clusters, PO3 -4 . nH2O. The minimum number (n0) of water molecules needed to stabilise the phosphate anion is 16. We are able to explain the origin of solvent-berg model and anomalous conductivity from the knowledge of first stable cluster. We have also provided a scheme to calculate the radius of the solvent-berg for phosphate anion. The calculated conductivity using Stokes-Einstein relation and the radius of solvent-berg is found to be very good in agreement (within 4%) with the available experimental results.

Lid dynamics of porcine pancreatic lipase in non-aqueous solvents.

PubMed

Haque, Neshatul; Prabhu, N Prakash

2016-10-01

Understanding the dynamics of enzymes in organic solvents has wider implications on their industrial applications. Pancreatic lipases, which show activity in their lid open-state, demonstrate enhanced activity in organic solvents at higher temperatures. However, the lid dynamics of pancreatic lipases in non-aqueous environment is yet to be clearly understood. Dynamics of porcine pancreatic lipase (PPL) in open and closed conformations was followed in ethanol, toluene, and octanol using molecular simulation methods. In silico double mutant D250V and E254L of PPL (PPLmut-Cl) was created and its lid opening dynamics in water and in octanol was analyzed. PPL showed increase in solvent accessible surface area and decrease in packing density as the polarity of the surrounded solvent decreased. Breaking the interactions between D250-Y115, and D250-E254 in PPLmut-Cl directed the lid to attain open-state conformation. Major energy barriers during the lid movement in water and in octanol were identified. Also, the trajectories of lid movement were found to be different in these solvents. Only the double mutant at higher temperature showed lid opening movement suggesting the essential role of the three residues in holding the lid in closed conformation. The lid opening dynamics was faster in octanol than water suggesting that non-polar solvents favor open conformation of the lid. This study identifies important interactions between the lid and the residues in domain 1 which possibly keeps the lid in closed conformation. Also, it explains the rearrangements of residue-residue interactions during lid opening movement in water and in octanol. Copyright © 2016 Elsevier B.V. All rights reserved.

Tautomerism and spectroscopic properties of the immunosuppressant azathioprine.

PubMed

Makhyoun, Mohamed A; Massoud, Raghdaa A; Soliman, Saied M

2013-10-01

The molecular structure and the relative stabilities of the four possible tautomers of the immunosuppressant azathioprine (AZA) are calculated by DFT/B3LYP method using different basis sets. The results of the energy analysis and thermodynamic treatment of the obtained data are used to predict the relative stabilities of the AZA tautomers. The effect of solvents such as DMSO and water on the stability of the AZA tautomers was studied using the polarized continuum method (PCM) at the same level of theory. The calculation predicted that, the total energies of all tautomers are decreased indicating that all tautomers are more or less stabilized by the solvent effect. The vibrational spectra of AZA are calculated using the same level of theory and the results are compared with the experimentally measured FTIR spectra. Good correlation is obtained between the experimental and calculated vibrational frequencies (R(2)=0.997). The electronic spectra of AZA in gas phase and in methanol as solvent are calculated using the TD-DFT method. The calculations predicted bathochromic shift in all the spectral bands in presence of solvent compared to the gas phase. Also the NMR spectra of all tautomers are calculated and the results are correlated with the experimental NMR chemical shifts where the most stable tautomer gives the best correlation coefficient (R(2)=0.996). Copyright © 2013 Elsevier B.V. All rights reserved.

Development and application of QM/MM methods to study the solvation effects and surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dibya, Pooja Arora

2010-01-01

Quantum mechanical (QM) calculations have the advantage of attaining high-level accuracy, however QM calculations become computationally inefficient as the size of the system grows. Solving complex molecular problems on large systems and ensembles by using quantum mechanics still poses a challenge in terms of the computational cost. Methods that are based on classical mechanics are an inexpensive alternative, but they lack accuracy. A good trade off between accuracy and efficiency is achieved by combining QM methods with molecular mechanics (MM) methods to use the robustness of the QM methods in terms of accuracy and the MM methods to minimize themore » computational cost. Two types of QM combined with MM (QM/MM) methods are the main focus of the present dissertation: the application and development of QM/MM methods for solvation studies and reactions on the Si(100) surface. The solvation studies were performed using a discreet solvation model that is largely based on first principles called the effective fragment potential method (EFP). The main idea of combining the EFP method with quantum mechanics is to accurately treat the solute-solvent and solvent-solvent interactions, such as electrostatic, polarization, dispersion and charge transfer, that are important in correctly calculating solvent effects on systems of interest. A second QM/MM method called SIMOMM (surface integrated molecular orbital molecular mechanics) is a hybrid QM/MM embedded cluster model that mimics the real surface.3 This method was employed to calculate the potential energy surfaces for reactions of atomic O on the Si(100) surface. The hybrid QM/MM method is a computationally inexpensive approach for studying reactions on larger surfaces in a reasonably accurate and efficient manner. This thesis is comprised of four chapters: Chapter 1 describes the general overview and motivation of the dissertation and gives a broad background of the computational methods that have been employed in this work. Chapter 2 illustrates the methodology of the interface of the EFP method with the configuration interaction with single excitations (CIS) method to study solvent effects in excited states. Chapter 3 discusses the study of the adiabatic electron affinity of the hydroxyl radical in aqueous solution and in micro-solvated clusters using a QM/EFP method. Chapter 4 describes the study of etching and diffusion of oxygen atom on a reconstructed Si(100)-2 x 1 surface using a hybrid QM/MM embedded cluster model (SIMOMM). Chapter 4 elucidates the application of the EFP method towards the understanding of the aqueous ionization potential of Na atom. Finally, a general conclusion of this dissertation work and prospective future direction are presented in Chapter 6.« less

Using tethered triblock copolymers to mediate the interaction between substrates

NASA Astrophysics Data System (ADS)

Chern, Shyh-Shi; Zhulina, Ekaterina B.; Pickett, Galen T.; Balazs, Anna C.

1998-04-01

Using scaling analysis and a self-consistent field (SCF) theory, we compress two copolymer-coated surfaces and isolate conditions that yield multiple, distinct minima in the interaction profile. We focus on planar surfaces that are coated with ABC triblock copolymers. Tethered to the surface by the last monomer in the C block, the copolymers are grafted at relatively low densities. The surrounding solution is a poor solvent for both the A and C blocks, and is a good solvent for the B blocks. Through scaling theory, we pinpoint the parameters that yield two minima in the interaction profile. The SCF calculations reveal the changes in the morphology of the polymers as the layers are compressed. Through both studies, we determine how the morphological changes give rise to the observed surface interactions. The results provide guidelines for creating polymer-coated colloidal systems that can form two stable crystal structures. Such systems could be used for bistable, optical switches. The findings also yield a prescription for creating systems that exhibit additional minima in the free energy of interaction.

Application of liquid-liquid interactions with single-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Wang, Randy Kai-Wei

This study covers three important research topics related to the application of liquid-liquid interaction with single-walled carbon nanotubes (SWNTs). The first topic describes the removal of SWNT bundles from liquid suspensions of nanotubes. The key to this work includes the use of liquid-liquid interfaces to trap the SWNT bundles due to the free energy change of the system during the process. SWNTs pack into crystalline ropes that form bundles due to strong van der Waals attraction. Bundling diminishes mechanical and electronic properties because it could interrupt the electronic structure of the nanotubes. Also, the electronic devices based on as-grown nanotubes, which contains a mixture of individual nanotubes and nanotube bundles, make the electrical response unpredictable. We developed a new simple process to remove bundles by liquid-liquid interaction. SWNTs bundles are trapped at the interface because bundles stabilize the emulsions. Eliminating the use of ultracentrifugation to remove SWNT bundles enables large-scale production with reduced production costs and time savings. The second topic presented the swelling effect of the surfactant layer surrounding SWNTs with nonpolar solvents. Solvatochromic shifts in the absorbance and fluorescence spectra are observed when surfactant-stabilized aqueous SWNT suspensions are mixed with immiscible organic solvents. When aqueous surfactant-suspended SWNTs are mixed with certain solvents, the spectra closely match the peaks for SWNTs dispersed in only that solvent. These spectral changes suggest the hydrophobic region of the micelle surrounding SWNTs swells with the organic solvent when mixed. The solvatochromic shifts of the aqueous SWNT suspensions are reversible once the solvent evaporates. However, some surfactant-solvent systems show permanent changes to the fluorescence emission intensity after exposure to the organic solvent. The intensity of some large diameter SWNT (n, m) types increase by more than 175%. These differences are attributed to surfactant reorganization, which can improve nanotube coverage, resulting in decreased exposure to quenching mechanisms from the aqueous phase. The third topic describes the further study of the solvatochromism of the SWNTs. Since SWNTs are encapsulated with microenvironments of nonpolar solvents, it provides a new method to measure the photophysical properties of nanotubes in environments with known properties. Fluorescence and absorbance spectra of SWNTs show solvatochromic shifts in 16 nonpolar solvents, which are proportional to the solvent induction polarization. The photophysical properties of SWNTs were used to determine the relationship between the longitudinal polarizability and other nanotube properties, alpha11,|| ∝ 1/(R2E11 3). (Full text of this dissertation may be available via the University of Florida Libraries web site. Please check http://www.uflib.ufl.edu/etd.html)

Conformational analysis of glutamic acid: a density functional approach using implicit continuum solvent model.

PubMed

Turan, Başak; Selçuki, Cenk

2014-09-01

Amino acids are constituents of proteins and enzymes which take part almost in all metabolic reactions. Glutamic acid, with an ability to form a negatively charged side chain, plays a major role in intra and intermolecular interactions of proteins, peptides, and enzymes. An exhaustive conformational analysis has been performed for all eight possible forms at B3LYP/cc-pVTZ level. All possible neutral, zwitterionic, protonated, and deprotonated forms of glutamic acid structures have been investigated in solution by using polarizable continuum model mimicking water as the solvent. Nine families based on the dihedral angles have been classified for eight glutamic acid forms. The electrostatic effects included in the solvent model usually stabilize the charged forms more. However, the stability of the zwitterionic form has been underestimated due to the lack of hydrogen bonding between the solute and solvent; therefore, it is observed that compact neutral glutamic acid structures are more stable in solution than they are in vacuum. Our calculations have shown that among all eight possible forms, some are not stable in solution and are immediately converted to other more stable forms. Comparison of isoelectronic glutamic acid forms indicated that one of the structures among possible zwitterionic and anionic forms may dominate over the other possible forms. Additional investigations using explicit solvent models are necessary to determine the stability of charged forms of glutamic acid in solution as our results clearly indicate that hydrogen bonding and its type have a major role in the structure and energy of conformers.

Level-Set Variational Implicit-Solvent Modeling of Biomolecules with the Coulomb-Field Approximation

PubMed Central

2011-01-01

Central in the variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett.2006, 96, 087802 and J. Chem. Phys.2006, 124, 084905] of molecular solvation is a mean-field free-energy functional of all possible solute–solvent interfaces or dielectric boundaries. Such a functional can be minimized numerically by a level-set method to determine stable equilibrium conformations and solvation free energies. Applications to nonpolar systems have shown that the level-set VISM is efficient and leads to qualitatively and often quantitatively correct results. In particular, it is capable of capturing capillary evaporation in hydrophobic confinement and corresponding multiple equilibrium states as found in molecular dynamics (MD) simulations. In this work, we introduce into the VISM the Coulomb-field approximation of the electrostatic free energy. Such an approximation is a volume integral over an arbitrary shaped solvent region, requiring no solutions to any partial differential equations. With this approximation, we obtain the effective boundary force and use it as the “normal velocity” in the level-set relaxation. We test the new approach by calculating solvation free energies and potentials of mean force for small and large molecules, including the two-domain protein BphC. Our results reveal the importance of coupling polar and nonpolar interactions in the underlying molecular systems. In particular, dehydration near the domain interface of BphC subunits is found to be highly sensitive to local electrostatic potentials as seen in previous MD simulations. This is a first step toward capturing the complex protein dehydration process by an implicit-solvent approach. PMID:22346739

First-principles calculation of electronic energy level alignment at electrochemical interfaces

NASA Astrophysics Data System (ADS)

Azar, Yavar T.; Payami, Mahmoud

2017-08-01

Energy level alignment at solid-solvent interfaces is an important step in determining the properties of electrochemical systems. The positions of conduction and valence band edges of a semiconductor are affected by its environment. In this study, using first-principles DFT calculation, we have determined the level shifts of the semiconductors TiO2 and ZnO at the interfaces with MeCN and DMF solvent molecules. The level shifts of semiconductor are obtained using the potential difference between the clean and exposed surfaces of asymmetric slabs. In this work, neglecting the effects of present ions in the electrolyte solution, we have shown that the solvent molecules give rise to an up-shift for the levels, and the amount of this shift varies with coverage. It is also shown that the shapes of density of states do not change sensibly near the gap. Molecular dynamics simulations of the interface have shown that at room temperatures the semiconductor surface is not fully covered by the solvent molecules, and one must use intermediate values in an static calculations.

Photo-physics study of a styrylquinoline as inhibitor of Pim-1 kinase: Solvent and concentration effects

NASA Astrophysics Data System (ADS)

Lamhasni, Taibi; Barbache, Sara; Ait Lyazidi, Saadia; Haddad, Mustapha; Hnach, Mohamed; Desmaële, Didier

2018-03-01

7-Nicotinoyl-styrylquinoline (MB96) displays an antiviral activity on HIV-1 infected CEM cell lines and is a promising inhibitor of the serine/threonine-protein Pim-1 kinase. By means of UV-vis spectroscopy supported by theoretical calculations this styrylquinoline is shown to exist in different conformations: the s-trans planar conformation along with other twisted ones with respect to the torsion around the single bond between the quinoline and the phenylethenyl appendage. Hydrogen bonding interactions with the solvent shift the skeleton of the MB96 towards the planar form, enhancing conjugation of π-electrons between the quinoline and the catechol parts, while self-association process seems furthering this planar conformation.

Assessment of spectroscopic parameters of solvated Eu(dmh)3 phen organometallic complex in various basic and acidic solvents.

PubMed

Chitnis, Dipti; Kalyani, N Thejo; Dhoble, Sanjay

2018-05-31

We report on the comprehension of novel europium activated hybrid organic Eu(dmh) 3 phen (Eu: europium, dmh: 2,6-dimethyl-3,5-heptanedione, phen: 1,10 phenanthroline) organo-metallic complexes, synthesized at different pH values by the solution technique. Photo physical properties of these complexes in various basic and acidic solvents were probed by UV-vis optical absorption and photoluminescence (PL) spectra. Minute differences in optical absorption peaks with variable optical densities were encountered with the variation in solvent from basic (chloroform, toluene, tetrahydrofuran) to acidic (acetic acid) media, revealing bathochromic shift in the absorption peaks. The PL spectra of the complex in various acidic and basic organic solvents revealed the position of the emission peak at 613 nm irrespective of the changes in solvents whereas the excitation spectrum almost matched with that of the UV-vis absorption data. The optical density was found to be maximum for the complex with pH 7.0 whereas it gradually decreased when pH was lowered to 6.0 or raised to 8.0 at an interval of 0.5, demonstrating its pH sensitive nature. Several spectroscopic parameters related to probability of transition such as absorbance A(λ), Napierian absorption coefficient α(λ), molecular absorption cross-section σ(λ), radiative lifetime (τ 0 ) and oscillator strength (f) were calculated from UV-vis spectra. The relative intensity ratio (R-ratio), calculated from the emission spectra was found to be almost the same in all the organic solvents. The optical energy gap, calculated for the designed complexes were found to be well in accordance with the ideal acceptance value of energy gap of the emissive materials used for fabrication of red organic light-emitting diode (OLED). The relation between Stoke's shift and solvent polarity function was established by Lippert-Mataga plot. This remarkable independence of the electronic absorption spectra of Eu complexes on the nature of the solvent with unique emission wavelength furnishes its potential to serve as a red light emitter for solution processed OLEDs, display panels and solid-state lighting. Copyright © 2018 John Wiley & Sons, Ltd.

Effect of solvent quality on aggregate structures of common surfactants.

PubMed

Hollamby, Martin J; Tabor, Rico; Mutch, Kevin J; Trickett, Kieran; Eastoe, Julian; Heenan, Richard K; Grillo, Isabelle

2008-11-04

Aggregate structures of two model surfactants, AOT and C12E5 are studied in pure solvents D2O, dioxane-d8 (d-diox) and cyclohexane-d12 (C6D12) as well as in formulated D2O/d-diox and d-diox/C6D12 mixtures. As such these solvents and mixtures span a wide and continuous range of polarities. Small-angle neutron scattering (SANS) has been employed to follow an evolution of the preferred aggregate curvature, from normal micelles in high polarity solvents, through to reversed micelles in low polarity media. SANS has also been used to elucidate the micellar size, shape as well as to highlight intermicellar interactions. The results shed new light on the nature of aggregation structures in intermediate polarity solvents, and point to a region of solvent quality (as characterized by Hildebrand Solubility Parameter, Snyder polarity parameter or dielectric constant) in which aggregation is not favored. Finally these observed trends in aggregation as a function of solvent quality are successfully used to predict the self-assembly behavior of C12E5 in a different solvent, hexane-d14 (C6D14).

Vegetable Oils as Alternative Solvents for Green Oleo-Extraction, Purification and Formulation of Food and Natural Products.

PubMed

Yara-Varón, Edinson; Li, Ying; Balcells, Mercè; Canela-Garayoa, Ramon; Fabiano-Tixier, Anne-Sylvie; Chemat, Farid

2017-09-05

Since solvents of petroleum origin are now strictly regulated worldwide, there is a growing demand for using greener, bio-based and renewable solvents for extraction, purification and formulation of natural and food products. The ideal alternative solvents are non-volatile organic compounds (VOCs) that have high dissolving power and flash point, together with low toxicity and less environmental impact. They should be obtained from renewable resources at a reasonable price and be easy to recycle. Based on the principles of Green Chemistry and Green Engineering, vegetable oils could become an ideal alternative solvent to extract compounds for purification, enrichment, or even pollution remediation. This review presents an overview of vegetable oils as solvents enriched with various bioactive compounds from natural resources, as well as the relationship between dissolving power of non-polar and polar bioactive components with the function of fatty acids and/or lipid classes in vegetable oils, and other minor components. A focus on simulation of solvent-solute interactions and a discussion of polar paradox theory propose a mechanism explaining the phenomena of dissolving polar and non-polar bioactive components in vegetable oils as green solvents with variable polarity.

Contact angle studies on anodic porous alumina.

PubMed

Redón, Rocío; Vázquez-Olmos, A; Mata-Zamora, M E; Ordóñez-Medrano, A; Rivera-Torres, F; Saniger, J M

2005-07-15

The preparation of nanostructures using porous anodic aluminum oxide (AAO) as templates involves the introduction of dissolved materials into the pores of the membranes; one way to determine which materials are preferred to fill the pores involves the measurement of the contact angles (theta) of different solvents or test liquids on the AAOs. Thus, we present measurements of contact angles of nine solvents on four different AAO sheets by tensiometric and goniometric methods. From the solvents tested, we found dimethyl sulfoxide (DMSO) and N,N(')-dimethylformamide (DMF) to interact with the AAOs, the polarity of the solvents and the surfaces being the driving force.

Capping the calix: How toluene completes cesium(i) coordination with calix[4]pyrrole

DOE PAGES

Ellis, Ross J.; Reinhart, Benjamin; Williams, Neil J.; ...

2017-05-04

The role of solvent in molecular recognition systems is under-researched and often ignored, especially when the solvent is considered “non-interacting”. This study concerns the role of toluene solvent in cesium(I) recognition by calix[4]pyrrole. We show that π-donor interactions bind toluene molecules onto the open face of the cation-receptor complex, thus “capping the calix.” As a result, by characterizing this unusual aromatically-saturated complex, we show how “non-interacting” aromatic solvents can directly coordinate receptor-bound cations and thus influence recognition.

Capping the calix: How toluene completes cesium(i) coordination with calix[4]pyrrole

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ellis, Ross J.; Reinhart, Benjamin; Williams, Neil J.

The role of solvent in molecular recognition systems is under-researched and often ignored, especially when the solvent is considered “non-interacting”. This study concerns the role of toluene solvent in cesium(I) recognition by calix[4]pyrrole. We show that π-donor interactions bind toluene molecules onto the open face of the cation-receptor complex, thus “capping the calix.” As a result, by characterizing this unusual aromatically-saturated complex, we show how “non-interacting” aromatic solvents can directly coordinate receptor-bound cations and thus influence recognition.

Solvent effect on the vibrational spectra of Carvedilol.

PubMed

Billes, Ferenc; Pataki, Hajnalka; Unsalan, Ozan; Mikosch, Hans; Vajna, Balázs; Marosi, György

2012-09-01

Carvedilol (CRV) is an important medicament for heart arrhythmia. The aim of this work was the interpretation of its vibrational spectra with consideration on the solvent effect. Infrared and Raman spectra were recorded in solid state as well in solution. The experimental spectra were evaluated using DFT quantum chemical calculations computing the optimized structure, atomic net charges, vibrational frequencies and force constants. The same calculations were done for the molecule in DMSO and aqueous solutions applying the PCM method. The calculated force constants were scaled to the experimentally observed solid state frequencies. The characters of the vibrational modes were determined by their potential energy distributions. Solvent effects on the molecular properties were interpreted. Based on these results vibrational spectra were simulated. Copyright © 2012 Elsevier B.V. All rights reserved.

The molecular structure and absorption spectrum of hydroxy substituted dibenzoylmethanatoboron difluoride in solution: A theoretical and experimental study

NASA Astrophysics Data System (ADS)

Gelfand, Natalia; Freidzon, Alexandra; Fedorenko, Elena

2018-01-01

Electronic spectroscopy and quantum chemistry are used to study the structure and absorption spectra of the hydroxy substituted dibenzoylmethanatoboron difluoride (OHDBMBF2) in solutions. Introducing a hydroxy group in the diketonate moiety allows the dye to form intermolecular complexes with proton acceptors, such as solvents or analytes, thus making it a promising chemical sensor. Our calculations show that donor oxygen-containing solvents break the intramolecular hydrogen bond Osbnd H···Odik and form an intermolecular Osbnd H···Osolv bond thus disrupting the coplanarity of the dye and affecting the position and shape of its absorption bands. The spectra calculated with explicit solvent combined with polarizable continuum model (PCM) better agree with the experiment than those calculated only within PCM.

Aromatic Rings Commonly Used in Medicinal Chemistry: Force Fields Comparison and Interactions With Water Toward the Design of New Chemical Entities.

PubMed

Polêto, Marcelo D; Rusu, Victor H; Grisci, Bruno I; Dorn, Marcio; Lins, Roberto D; Verli, Hugo

2018-01-01

The identification of lead compounds usually includes a step of chemical diversity generation. Its rationale may be supported by both qualitative (SAR) and quantitative (QSAR) approaches, offering models of the putative ligand-receptor interactions. In both scenarios, our understanding of which interactions functional groups can perform is mostly based on their chemical nature (such as electronegativity, volume, melting point, lipophilicity etc.) instead of their dynamics in aqueous, biological solutions (solvent accessibility, lifetime of hydrogen bonds, solvent structure etc.). As a consequence, it is challenging to predict from 2D structures which functional groups will be able to perform interactions with the target receptor, at which intensity and relative abundance in the biological environment, all of which will contribute to ligand potency and intrinsic activity. With this in mind, the aim of this work is to assess properties of aromatic rings, commonly used for drug design, in aqueous solution through molecular dynamics simulations in order to characterize their chemical features and infer their impact in complexation dynamics. For this, common aromatic and heteroaromatic rings were selected and received new atomic charge set based on the direction and module of the dipole moment from MP2/6-31G * calculations, while other topological terms were taken from GROMOS53A6 force field. Afterwards, liquid physicochemical properties were simulated for a calibration set composed by nearly 40 molecules and compared to their respective experimental data, in order to validate each topology. Based on the reliance of the employed strategy, we expanded the dataset to more than 100 aromatic rings. Properties in aqueous solution such as solvent accessible surface area, H-bonds availability, H-bonds residence time, and water structure around heteroatoms were calculated for each ring, creating a database of potential interactions, shedding light on features of drugs in biological solutions, on the structural basis for bioisosterism and on the enthalpic/entropic costs for ligand-receptor complexation dynamics.

Influence of polarity of solvents on IR absorption and Raman spectra of ascorbic acid

NASA Astrophysics Data System (ADS)

Kutsenko, S. A.; Danyaeva, Y. S.; Maximova, S. V.

2018-04-01

The results of numerical calculations of IR absorption and Raman spectra of ascorbic acid in polar and nonpolar solutions are presented. The dependence of the change in the total energy and the dipole moment of the molecule on the characteristics of the solvents was investigated using the two solvation models. Spectral bands and the corresponding structural groups of the molecule are found, the characteristics of which are most vulnerable to solvents.

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations

NASA Astrophysics Data System (ADS)

Misini Ignjatović, Majda; Caldararu, Octav; Dong, Geng; Muñoz-Gutierrez, Camila; Adasme-Carreño, Francisco; Ryde, Ulf

2016-09-01

We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.

PubMed

Misini Ignjatović, Majda; Caldararu, Octav; Dong, Geng; Muñoz-Gutierrez, Camila; Adasme-Carreño, Francisco; Ryde, Ulf

2016-09-01

We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

PubMed Central

Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.; Hünenberger, Philippe H.

2013-01-01

The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges −5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol−1) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol−1). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning. PMID:24320250

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects.

PubMed

Rocklin, Gabriel J; Mobley, David L; Dill, Ken A; Hünenberger, Philippe H

2013-11-14

The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges -5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol(-1)) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol(-1)). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

NASA Astrophysics Data System (ADS)

Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.; Hünenberger, Philippe H.

2013-11-01

The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges -5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol-1) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol-1). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

Preparation of Some Novel Copper(I) Complexes and their Molar Conductances in Organic Solvents

NASA Astrophysics Data System (ADS)

Gill, Dip Singh; Rana, Dilbag

2009-04-01

Attempts have been made to prepare some novel copper(I) nitrate, sulfate, and perchlorate complexes. Molar conductances of these complexes have been measured in organic solvents like acetonitrile (AN), acetone (AC), methanol (MeOH), N,N-dimethylformamide (DMF), N,Ndimethylacetamide (DMA), and dimethylsulfoxide (DMSO) at 298 K. The molar conductance data have been analyzed to obtain limiting molar conductances (λ0) and ion association constants (KA) of the electrolytes. The results showed that all these complexes are strong electrolytes in all organic solvents. The limiting ionic molar conductances (λo± ) for various ions have been calculated using Bu4NBPh4 as reference electrolyte. The actual radii for copper(I) complex ions are very large and different in different solvents and indicate some solvation effects in each solvent system

X-Ray Fluorescence Solvent Detection at the Substrate-Adhesive Interface

NASA Technical Reports Server (NTRS)

Wurth, Laura; Evans, Kurt; Weber, Bart; Headrick, Sarah

2005-01-01

With environmental regulations limiting the use of volatile organic compounds, low-vapor pressure solvents have replaced traditional degreasing solvents for bond substrate preparation. When used to clean and prepare porous bond substrates such as phenolic composites, low vapor pressure solvents can penetrate deep into substrate pore networks and remain there for extended periods. Trapped solvents can interact with applied adhesives either prior to or during cure, potentially compromising bond properties. Currently, methods for characterizing solvent time-depth profiles in bond substrates are limited to bulk gravimetric or sectioning techniques. While sectioning techniques such as microtome allow construction of solvent depth profiles, their depth resolution and reliability are limited by substrate type. Sectioning techniques are particularly limited near the adhesive-substrate interface where depth resolution is further limited by adhesive-substrate hardness and, in the case of a partially cured adhesive, mechanical properties differences. Additionally, sectioning techniques cannot provide information about lateral solvent diffusion. Cross-section component mapping is an alternative method for measuring solvent migration in porous substrates that eliminates the issues associated with sectioning techniques. With cross-section mapping, the solvent-wiped substrate is sectioned perpendicular rather than parallel to the wiped surface, and the sectioned surface is analyzed for the solvent or solvent components of interest using a two-dimensional mapping or imaging technique. Solvent mapping can be performed using either direct or indirect methods. With a direct method, one or more solvent components are mapped using red or Raman spectroscopy together with a moveable sample stage and/or focal plane array detector. With an indirect method, an elemental "tag" not present in the substrate is added to the solvent before the substrate is wiped. Following cross sectioning, the tag element can then be mapped by its characteristic x-ray emission using either x-ray fluorescence, or electron-beam energy-and wavelength-dispersive x-ray spectrometry. The direct mapping techniques avoid issues of different diffusion or migration rates of solvents and elemental tags, while the indirect techniques avoid spectral resolution issues in cases where solvents and substrates have adjacent or overlapping peaks. In this study, cross-section component indirect mapping is being evaluated as a method for measuring migration of d-limonene based solvents in glass-cloth phenolic composite (GCP) prior to and during subsequent bonding and epoxy adhesive cure.

Sample Results From The Extraction, Scrub, And Strip Test For The Blended NGS Solvent

DOE Office of Scientific and Technical Information (OSTI.GOV)

Washington, A. L. II; Peters, T. B.

This report summarizes the results of the extraction, scrub, and strip testing for the September 2013 sampling of the Next Generation Solvent (NGS) Blended solvent from the Modular Caustic Side-Solvent Extraction Unit (MCU) Solvent Hold Tank. MCU is in the process of transitioning from the BOBCalixC6 solvent to the NGS Blend solvent. As part of that transition, MCU has intentionally created a blended solvent to be processed using the Salt Batch program. This sample represents the first sample received from that blended solvent. There were two ESS tests performed where NGS blended solvent performance was assessed using either the Tankmore » 21 material utilized in the Salt Batch 7 analyses or a simulant waste material used in the V-5/V-10 contactor testing. This report tabulates the temperature corrected cesium distribution, or D Cs values, step recovery percentage, and actual temperatures recorded during the experiment. This report also identifies the sample receipt date, preparation method, and analysis performed in the accumulation of the listed values. The calculated extraction D Cs values using the Tank 21H material and simulant are 59.4 and 53.8, respectively. The DCs values for two scrub and three strip processes for the Tank 21 material are 4.58, 2.91, 0.00184, 0.0252, and 0.00575, respectively. The D-values for two scrub and three strip processes for the simulant are 3.47, 2.18, 0.00468, 0.00057, and 0.00572, respectively. These values are similar to previous measurements of Salt Batch 7 feed with lab-prepared blended solvent. These numbers are considered compatible to allow simulant testing to be completed in place of actual waste due to the limited availability of feed material.« less

Carbonyl Activation by Borane Lewis Acid Complexation: Transition States of H2 Splitting at the Activated Carbonyl Carbon Atom in a Lewis Basic Solvent and the Proton-Transfer Dynamics of the Boroalkoxide Intermediate.

PubMed

Heshmat, Mojgan; Privalov, Timofei

2017-07-06

By using transition-state (TS) calculations, we examined how Lewis acid (LA) complexation activates carbonyl compounds in the context of hydrogenation of carbonyl compounds by H 2 in Lewis basic (ethereal) solvents containing borane LAs of the type (C 6 F 5 ) 3 B. According to our calculations, LA complexation does not activate a ketone sufficiently enough for the direct addition of H 2 to the O=C unsaturated bond; but, calculations indicate a possibly facile heterolytic cleavage of H 2 at the activated and thus sufficiently Lewis acidic carbonyl carbon atom with the assistance of the Lewis basic solvent (i.e., 1,4-dioxane or THF). For the solvent-assisted H 2 splitting at the carbonyl carbon atom of (C 6 F 5 ) 3 B adducts with different ketones, a number of TSs are computed and the obtained results are related to insights from experiment. By using the Born-Oppenheimer molecular dynamics with the DFT for electronic structure calculations, the evolution of the (C 6 F 5 ) 3 B-alkoxide ionic intermediate and the proton transfer to the alkoxide oxygen atom were investigated. The results indicate a plausible hydrogenation mechanism with a LA, that is, (C 6 F 5 ) 3 B, as a catalyst, namely, 1) the step of H 2 cleavage that involves a Lewis basic solvent molecule plus the carbonyl carbon atom of thermodynamically stable and experimentally identifiable (C 6 F 5 ) 3 B-ketone adducts in which (C 6 F 5 ) 3 B is the "Lewis acid promoter", 2) the transfer of the solvent-bound proton to the oxygen atom of the (C 6 F 5 ) 3 B-alkoxide intermediate giving the (C 6 F 5 ) 3 B-alcohol adduct, and 3) the S N 2-style displacement of the alcohol by a ketone or a Lewis basic solvent molecule. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multi-scale dynamics and relaxation of a tethered membrane in a solvent by Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Pandey, Ras; Anderson, Kelly; Farmer, Barry

2006-03-01

A tethered membrane modeled by a flexible sheet dissipates entropy as it wrinkles and crumples. Nodes of a coarse grained membrane are connected via multiple pathways for dynamical modes to propagate. We consider a sheet with nodes connected by fluctuating bonds on a cubic lattice. The empty lattice sites constitute an effective solvent medium via node-solvent interaction. Each node execute its stochastic motion with the Metropolis algorithm subject to bond fluctuations, excluded volume constraints, and interaction energy. Dynamics and conformation of the sheet are examined at a low and a high temperature with attractive and repulsive node-node interactions for the contrast in an attractive solvent medium. Variations of the mean square displacement of the center node of the sheet and that of its center of mass with the time steps are examined in detail which show different power-law motion from short to long time regimes. Relaxation of the gyration radius and scaling of its asymptotic value with the molecular weight are examined.

The effect of solvent interactions on alpha-, beta-, and gamma-cyclodextrin/flavor molecular inclusion complexes.

PubMed

Reineccius, Teresa A; Reineccius, Gary A; Peppard, Terry L

2005-01-26

Three commonly used flavor industry solvents (propylene glycol, triacetin, and triethyl citrate) were tested for their capacity to interfere with the ability of alpha-, beta-, and gamma-cyclodextrin to form molecular inclusion complexes with flavors. Six flavor compounds (ethyl butyrate, ethyl heptanoate, l-menthol, methyl anthranilate, neral, and geranial) were measured by headspace gas chromatography above 2:1 water/ethanol containing appropriate additions of cyclodextrin and flavor solvent. The smallest and most polar solvent molecule represented by propylene glycol had the least effect on cyclodextrin/flavorant complex formation. In contrast, triacetin, intermediate in size among the three flavor diluents studied, had the greatest effect, even though, based on at least some computed molecular parameters, it appears to be more polar than triethyl citrate. The explanation for this apparent anomaly may lie in differences in the extent to which triacetin and triethyl citrate are able to interact with cyclodextrins by means of partial interaction with the hydrophobic cavities of the latter.

Atomistic Simulations of Hydrodynamic and Interaction Forces on Functionalized Silica Nanoparticles

NASA Astrophysics Data System (ADS)

Lane, J. Matthew D.; Ismail, Ahmed E.; Chandross, Michael; Lorenz, Christian D.; Grest, Gary S.

2009-03-01

It is often desired to prevent the flocculation and phase separation of nanoparticles in solution. This can be accomplished either by manipulating the solvent or by tailoring the surface chemistry of the nanoparticles through functionalization with a monolayer of oligomer chains. Since it is not known how these functionalized coatings affect the interactions between nanoparticles and with the surrounding solvent, we present results from a series of molecular dynamics simulations of polyethylene oxide (PEO) coated silica nanoparticles of varying size (5 to 20 nm diameter) in water. For a single nanoparticle we determined the Stokes drag on the nanoparticle as it moves through the solvent and as it approaches a wall. Due to hydrodynamic interactions there are large finite size effects which we estimate by varying the size of the simulation cell. We also determined both solvent-mediated (velocity-independent) and lubrication (velocity-dependent) forces between two nanoparticles as a function of the coverage and chain length of the PEO chains.

Protein-solvent preferential interactions, protein hydration, and the modulation of biochemical reactions by solvent components.

PubMed

Timasheff, Serge N

2002-07-23

Solvent additives (cosolvents, osmolytes) modulate biochemical reactions if, during the course of the reaction, there is a change in preferential interactions of solvent components with the reacting system. Preferential interactions can be expressed in terms of preferential binding of the cosolvent or its preferential exclusion (preferential hydration). The driving force is the perturbation by the protein of the chemical potential of the cosolvent. It is shown that the measured change of the amount of water in contact with protein during the course of the reaction modulated by an osmolyte is a change in preferential hydration that is strictly a measure of the cosolvent chemical potential perturbation by the protein in the ternary water-protein-cosolvent system. It is not equal to the change in water of hydration, because water of hydration is a reflection strictly of protein-water forces in a binary system. There is no direct relation between water of preferential hydration and water of hydration.

An Experimental and Computational Investigation into the Gas-Phase Acidities of Tyrosine and Phenylalanine: Three Structures for Deprotonated Tyrosine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bokatzian, Samantha S.; Stover, Michele L.; Plummer, Chelsea E.

Using mass spectrometry and correlated molecular orbital theory, three deprotonated structures were revealed for the amino acid tyrosine. The structures were distinguished experimentally by ion/molecule reactions involving proton transfer and trimethylsilyl azide. Gas-phase acidities from proton transfer reactions and from G3(MP2) calculations generally agree well. The lowest energy structure, which was only observed experimentally using electrospray ionization from aprotic solvents, is deprotonated at the carboxylic acid group and is predicted to be highly folded. A second unfolded carboxylate structure is several kcal/mol higher in energy and primarily forms from protic solvents. Protic solvents also yield a structure deprotonated at themore » phenolic side chain, which experiments find to be intermediate in energy to the two carboxylate forms. G3(MP2) calculations indicate that the three structures differ in energy by only 2.5 kcal/mol, yet they are readily distinguished experimentally. Structural abundance ratios are dependent upon experimental conditions, including the solvent and accumulation time of ions in a hexapole. Under some conditions, carboxylate ions may convert to phenolate ions. For phenylalanine, which lacks a phenolic group, only one deprotonated structure was observed experimentally when electrosprayed from protic solvent. This agrees with G3(MP2) calculations that find the folded and unfolded carboxylate forms to differ by 0.3 kcal/mol.« less

Lipase in aqueous-polar organic solvents: Activity, structure, and stability

PubMed Central

Kamal, Md Zahid; Yedavalli, Poornima; Deshmukh, Mandar V; Rao, Nalam Madhusudhana

2013-01-01

Studying alterations in biophysical and biochemical behavior of enzymes in the presence of organic solvents and the underlying cause(s) has important implications in biotechnology. We investigated the effects of aqueous solutions of polar organic solvents on ester hydrolytic activity, structure and stability of a lipase. Relative activity of the lipase monotonically decreased with increasing concentration of acetone, acetonitrile, and DMF but increased at lower concentrations (upto ∼20% v/v) of dimethylsulfoxide, isopropanol, and methanol. None of the organic solvents caused any appreciable structural change as evident from circular dichorism and NMR studies, thus do not support any significant role of enzyme denaturation in activity change. Change in 2D [15N, 1H]-HSQC chemical shifts suggested that all the organic solvents preferentially localize to a hydrophobic patch in the active-site vicinity and no chemical shift perturbation was observed for residues present in protein's core. This suggests that activity alteration might be directly linked to change in active site environment only. All organic solvents decreased the apparent binding of substrate to the enzyme (increased Km); however significantly enhanced the kcat. Melting temperature (Tm) of lipase, measured by circular dichroism and differential scanning calorimetry, altered in all solvents, albeit to a variable extent. Interestingly, although the effect of all organic solvents on various properties on lipase is qualitatively similar, our study suggest that magnitudes of effects do not appear to follow bulk solvent properties like polarity and the solvent effects are apparently dictated by specific and local interactions of solvent molecule(s) with the protein. PMID:23625694

UV-Vis spectroscopy and solvatochromism of the tyrosine kinase inhibitor AG-1478.

PubMed

Khattab, Muhammad; Wang, Feng; Clayton, Andrew H A

2016-07-05

The effect of twenty-one solvents on the UV-Vis spectrum of the tyrosine kinase inhibitor AG-1478 was investigated. The absorption spectrum in the range 300-360nm consisted of two partially overlapping bands at approximately 340nm and 330nm. The higher energy absorption band was more sensitive to solvent and exhibited a peak position that varied from 327nm to 336nm, while the lower energy absorption band demonstrated a change in peak position from 340nm to 346nm in non-chlorinated solvents. The fluorescence spectrum of AG-1478 was particularly sensitive to solvent. The wavelength of peak intensity varied from 409nm to 495nm with the corresponding Stokes shift in the range of 64nm to 155nm (4536cm(-1) to 9210cm(-1)). We used a number of methods to assess the relationship between spectroscopic properties and solvent properties. The detailed analysis revealed that for aprotic solvents, the peak position of the emission spectrum in wavenumber scale correlated with the polarity (dielectric constant or ET(30)) of the solvent. In protic solvents, a better correlation was observed between the hydrogen bonding power of the solvent and the position of the emission spectrum. Moreover, the fluorescence quantum yields were larger in aprotic solvents as compared to protic solvents. This analysis underscores the importance of polarity and hydrogen-bonding environment on the spectroscopic properties of AG-1478. These studies will assume relevance in understanding the interaction of AG-1478 in vitro and in vivo. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantitative real-time monitoring of dryer effluent using fiber optic near-infrared spectroscopy.

PubMed

Harris, S C; Walker, D S

2000-09-01

This paper describes a method for real-time quantitation of the solvents evaporating from a dryer. The vapor stream in the vacuum line of a dryer was monitored in real time using a fiber optic-coupled acousto-optic tunable filter near-infrared (AOTF-NIR) spectrometer. A balance was placed in the dryer, and mass readings were recorded for every scan of the AOTF-NIR. A partial least-squares (PLS) calibration was subsequently built based on change in mass over change in time for solvents typically used in a chemical manufacturing plant. Controlling software for the AOTF-NIR was developed. The software collects spectra, builds the PLS calibration model, and continuously fits subsequently collected spectra to the calibration, allowing the operator to follow the mass loss of solvent from the dryer. The results indicate that solvent loss can be monitored and quantitated in real time using NIR for the optimization of drying times. These time-based mass loss values have also been used to calculate "dynamic" vapor density values for the solvents. The values calculated are in agreement with values determined from the ideal gas law and could prove valuable as tools to measure temperature or pressure indirectly.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Siqin; Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon; Sheong, Fu Kit

Reference interaction site model (RISM) has recently become a popular approach in the study of thermodynamical and structural properties of the solvent around macromolecules. On the other hand, it was widely suggested that there exists water density depletion around large hydrophobic solutes (>1 nm), and this may pose a great challenge to the RISM theory. In this paper, we develop a new analytical theory, the Reference Interaction Site Model with Hydrophobicity induced density Inhomogeneity (RISM-HI), to compute solvent radial distribution function (RDF) around large hydrophobic solute in water as well as its mixture with other polyatomic organic solvents. To achievemore » this, we have explicitly considered the density inhomogeneity at the solute-solvent interface using the framework of the Yvon-Born-Green hierarchy, and the RISM theory is used to obtain the solute-solvent pair correlation. In order to efficiently solve the relevant equations while maintaining reasonable accuracy, we have also developed a new closure called the D2 closure. With this new theory, the solvent RDFs around a large hydrophobic particle in water and different water-acetonitrile mixtures could be computed, which agree well with the results of the molecular dynamics simulations. Furthermore, we show that our RISM-HI theory can also efficiently compute the solvation free energy of solute with a wide range of hydrophobicity in various water-acetonitrile solvent mixtures with a reasonable accuracy. We anticipate that our theory could be widely applied to compute the thermodynamic and structural properties for the solvation of hydrophobic solute.« less

Separation of Gadolinium (Gd) using Synergic Solvent Mixed Topo-D2EHPA with Extraction Method.

NASA Astrophysics Data System (ADS)

Effendy, N.; Basuki, K. T.; Biyantoro, D.; Perwira, N. K.

2018-04-01

The main problem to obtain Gd with high purity is the similarity of chemical properties and physical properties with the other rare earth elements (REE) such as Y and Dy, it is necessary to do separation by the extraction process. The purpose of this research to determine the best solvent type, amount of solvent, feed and solvent ratio in the Gd extraction process, to determine the rate order and the value of the rate constant of Gd concentration based on experimental data of aqueous phase concentration as a function of time and to know the effect of temperature on the reaction speed constant. This research was conducted on variation of solvent, amount of solvent, feed and solvent ratio in the extraction process of Gd separation, extraction time to determine the order value and the rate constant of Gd concentration in extraction process based on the aqueous phase concentration data as a function of time, to the rate constant of decreasing concentration of Gd. Based on the calculation results, the solvent composition was obtained with the best feed to separate the rare earth elements Gd in the extraction process is 1 : 4 with 15% concentration of TOPO and 10% concentration of D2EHPA. The separation process of Gd using extraction method by solvent TOPO-D2EHPA 2 : 1 comparison is better than single solvent D2EHPA / TOPO because of the synergistic effect. The rate order of separation process of Gd follows order 1. The Arrhenius Gd equation becomes k = 1.46 x 10-7 exp (-6.96 kcal / mol / RT).

Modeling solvent evaporation during thin film formation in phase separating polymer mixtures

DOE PAGES

Cummings, John; Lowengrub, John S.; Sumpter, Bobby G.; ...

2018-02-09

Preparation of thin films by dissolving polymers in a common solvent followed by evaporation of the solvent has become a routine processing procedure. However, modeling of thin film formation in an evaporating solvent has been challenging due to a need to simulate processes at multiple length and time scales. In this paper, we present a methodology based on the principles of linear non-equilibrium thermodynamics, which allows systematic study of various effects such as the changes in the solvent properties due to phase transformation from liquid to vapor and polymer thermodynamics resulting from such solvent transformations. The methodology allows for themore » derivation of evaporative flux and boundary conditions near each surface for simulations of systems close to the equilibrium. We apply it to study thin film microstructural evolution in phase segregating polymer blends dissolved in a common volatile solvent and deposited on a planar substrate. Finally, effects of the evaporation rates, interactions of the polymers with the underlying substrate and concentration dependent mobilities on the kinetics of thin film formation are studied.« less

Modeling solvent evaporation during thin film formation in phase separating polymer mixtures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cummings, John; Lowengrub, John S.; Sumpter, Bobby G.

Preparation of thin films by dissolving polymers in a common solvent followed by evaporation of the solvent has become a routine processing procedure. However, modeling of thin film formation in an evaporating solvent has been challenging due to a need to simulate processes at multiple length and time scales. In this paper, we present a methodology based on the principles of linear non-equilibrium thermodynamics, which allows systematic study of various effects such as the changes in the solvent properties due to phase transformation from liquid to vapor and polymer thermodynamics resulting from such solvent transformations. The methodology allows for themore » derivation of evaporative flux and boundary conditions near each surface for simulations of systems close to the equilibrium. We apply it to study thin film microstructural evolution in phase segregating polymer blends dissolved in a common volatile solvent and deposited on a planar substrate. Finally, effects of the evaporation rates, interactions of the polymers with the underlying substrate and concentration dependent mobilities on the kinetics of thin film formation are studied.« less

Effect of degree of sulfonation and casting solvent on sulfonated poly(ether ether ketone) membrane for vanadium redox flow battery

NASA Astrophysics Data System (ADS)

Xi, Jingyu; Li, Zhaohua; Yu, Lihong; Yin, Bibo; Wang, Lei; Liu, Le; Qiu, Xinping; Chen, Liquan

2015-07-01

The properties of sulfonated poly(ether ether ketone) (SPEEK) membranes with various degree of sulfonation (DS) and casting solvent are investigated for vanadium redox flow battery (VRFB). The optimum DS of SPEEK membrane is firstly confirmed by various characterizations such as physicochemical properties, ion selectivity, and VRFB single-cell performance. Subsequently the optimum casting solvent is selected for the optimum DS SPEEK membrane within N,N‧-dimethylformamide (DMF), N,N‧-dimethylacetamide (DMAc), N-methyl-2-pyrrolidone (NMP), and dimethylsulfoxide (DMSO). The different performance of SPEEK membranes prepared with various casting solvents can be attributed to the different interaction between solvent and -SO3H group of SPEEK. In the VRFB single-cell test, the optimum SPEEK membrane with DS of 67% and casting solvent of DMF (S67-DMF membrane) exhibits higher VRFB efficiencies and better cycle-life performance at 80 mA cm-2. The investigation of various DS and casting solvent will be effective guidance on the selection and modification of SPEEK membrane towards VRFB application.

Protein-Style Dynamical Transition in a Non-Biological Polymer and a Non-Aqueous Solvent.

PubMed

Mamontov, E; Sharma, V K; Borreguero, J M; Tyagi, M

2016-03-31

Temperature-dependent onset of apparent anharmonicity in the microscopic dynamics of hydrated proteins and other biomolecules has been known as protein dynamical transition for the last quarter of a century. Using neutron scattering and molecular dynamics simulation, techniques most often associated with protein dynamical transition studies, we have investigated the microscopic dynamics of one of the most common polymers, polystyrene, which was exposed to toluene vapor, mimicking the process of protein hydration from water vapor. Polystyrene with adsorbed toluene is an example of a solvent-solute system, which, unlike biopolymers, is anhydrous and lacks hydrogen bonding. Nevertheless, it exhibits the essential traits of the dynamical transition in biomolecules, such as a specific dependence of the microscopic dynamics of both solvent and host on the temperature and the amount of solvent adsorbed. We conclude that the protein dynamical transition is a manifestation of a universal solvent-solute dynamical relationship, which is not specific to either biomolecules as solute, or aqueous media as solvent, or even a particular type of interactions between solvent and solute.

Solvent signal suppression for high-resolution MAS-DNP

NASA Astrophysics Data System (ADS)

Lee, Daniel; Chaudhari, Sachin R.; De Paëpe, Gaël

2017-05-01

Dynamic nuclear polarization (DNP) has become a powerful tool to substantially increase the sensitivity of high-field magic angle spinning (MAS) solid-state NMR experiments. The addition of dissolved hyperpolarizing agents usually results in the presence of solvent signals that can overlap and obscure those of interest from the analyte. Here, two methods are proposed to suppress DNP solvent signals: a Forced Echo Dephasing experiment (FEDex) and TRAnsfer of Populations in DOuble Resonance Echo Dephasing (TRAPDORED) NMR. These methods reintroduce a heteronuclear dipolar interaction that is specific to the solvent, thereby forcing a dephasing of recoupled solvent spins and leaving acquired NMR spectra free of associated resonance overlap with the analyte. The potency of these methods is demonstrated on sample types common to MAS-DNP experiments, namely a frozen solution (of L-proline) and a powdered solid (progesterone), both containing deuterated glycerol as a DNP solvent. The proposed methods are efficient, simple to implement, compatible with other NMR experiments, and extendable past spectral editing for just DNP solvents. The sensitivity gains from MAS-DNP in conjunction with FEDex or TRAPDORED then permits rapid and uninterrupted sample analysis.

Colloidal Asphaltene Deposition and Aggregation in Capillary Flow: Experiments and Mesoscopic Simulation

NASA Astrophysics Data System (ADS)

Boek, Edo S.; Ladva, Hemant K.; Crawshaw, John P.; Padding, Johan T.

2008-07-01

The aggregation and deposition of colloidal asphaltene in reservoir rock is a significant problem in the oil industry. To obtain a fundamental understanding of this phenomenon, we have studied the deposition and aggregation of colloidal asphaltene in capillary flow by experiment and simulation. For the simulation, we have used the stochastic rotation dynamics (SRD) method, in which the solvent hydrodynamic emerges from the collisions between the solvent particles, while the Brownian motion emerges naturally from the interactions between the colloidal asphaltene particles and the solvent. The asphaltene colloids interact through a screened Coulomb potential. We vary the well depth ɛ∝ and the flow rate v to obtain Peflow≫1 (hydrodynamic interactions dominate) and Re≪1 (Stokes flow). In the simulations, we impose a pressure drop over the capillary length and measure the corresponding solvent flow rate. We observe that the transient solvent flow rate decreases when the asphaltene particles become more "sticky". For a well depth ɛ∝ = 2kBT, a monolayer deposits on the capillary wall. With an increasing well depth, the capillary becomes totally blocked. The clogging is transient for ɛ∝ = 5kBT, but appears to be permanent for ɛ∝ = 10-20 kBT. We compare our simulation results with flow experiments in glass capillaries, where we use extracted asphaltenes in toluene, reprecipitated with n-heptane. In the experiments, the dynamics of asphaltene precipitation and deposition were monitored in a slot capillary using optical microscopy under flow conditions similar to those used in the simulation. Maintaining a constant flow rate of 5 μL min-1, we found that the pressure drop across the capillary first increased slowly, followed by a sharp increase, corresponding to a complete local blockage of the capillary. Doubling the flow rate to 10 μL min-1, we observe that the initial deposition occurs faster but the deposits are subsequently entrained by the flow. We calculate the change in the dimensionless permeability as a function of time for both experiment and simulation. By matching the experimental and simulation results, we obtain information about (1) the interaction potential well depth for the particular asphaltenes used in the experiments and (2) the flow conditions associated with the asphaltene deposition process.

Determination of the solubility parameter of ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate by inverse gas chromatography.

PubMed

Ma, Xiaohong; Wang, Qiang; Li, Xiaoping; Tang, Jun; Zhang, Zhengfang

2015-11-01

Thermodynamic properties of ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM] BF4) were determined via inverse gas chromatography (IGC). Two groups of solvents with different chemical natures and polarities were used to obtain information about [BMIM] BF4-solvent interactions. The specific retention volume, molar heat of sorption, weight fraction activity coefficient, Flory-Huggins interaction parameter as well as solubility parameter were also determined in a temperature range of 333 - 373 K. The results showed that the selected solvents n-C10 to n-C12, carbon tetrachloride, cyclohexane and toluene were poor solvents for [BMIM] BF4, while dichloromethane, acetone, chloroform, methyl acetate, ethanol and methanol were favorite solvents for [BMIM] BF4. In addition, the solubility parameter of [ BMIM] BF4 was determined as 23.39 (J/cm3)0.5 by the extrapolation at 298 K. The experiment proved that IGC was a simple and accurate method to obtain the thermodynamic properties of ionic liquids. This study could be used as a reference to the application and research of the ionic liquids.

Simulating chemical reactions in ionic liquids using QM/MM methodology.

PubMed

Acevedo, Orlando

2014-12-18

The use of ionic liquids as a reaction medium for chemical reactions has dramatically increased in recent years due in large part to the numerous reported advances in catalysis and organic synthesis. In some extreme cases, ionic liquids have been shown to induce mechanistic changes relative to conventional solvents. Despite the large interest in the solvents, a clear understanding of the molecular factors behind their chemical impact is largely unknown. This feature article reviews our efforts developing and applying mixed quantum and molecular mechanical (QM/MM) methodology to elucidate the microscopic details of how these solvents operate to enhance rates and alter mechanisms for industrially and academically important reactions, e.g., Diels-Alder, Kemp eliminations, nucleophilic aromatic substitutions, and β-eliminations. Explicit solvent representation provided the medium dependence of the activation barriers and atomic-level characterization of the solute-solvent interactions responsible for the experimentally observed "ionic liquid effects". Technical advances are also discussed, including a linear-scaling pairwise electrostatic interaction alternative to Ewald sums, an efficient polynomial fitting method for modeling proton transfers, and the development of a custom ionic liquid OPLS-AA force field.

Characteristics of Lithium Ions and Superoxide Anions in EMI-TFSI and Dimethyl Sulfoxide.

PubMed

Jung, Sun-ho; Federici Canova, Filippo; Akagi, Kazuto

2016-01-28

To clarify the microscopic effects of solvents on the formation of the Li(+)-O2(–) process of a Li–O2 battery, we studied the kinetics and thermodynamics of these ions in dimethyl sulfoxide (DMSO) and 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EMI-TFSI) using classical molecular dynamics simulation. The force field for ions–solvents interactions was parametrized by force matching first-principles calculations. Despite the solvation energies of the ions are similar in both solvents, their mobility is much higher in DMSO. The free-energy profiles also confirm that the formation and decomposition rates of Li(+)-O2(–) pairs are greater in DMSO than in EMI-TFSI. Our atomistic simulations point out that the strong structuring of EMI-TFSI around the ions is responsible for these differences, and it explains why the LiO2 clusters formed in DMSO during the battery discharge are larger than those in EMI-TFSI. Understanding the origin of such properties is crucial to aid the optimization of electrolytes for Li–O2 batteries.

Substituent and solvent effects on the UV/Vis absorption spectra of 5-(4-substituted arylazo)-6-hydroxy-4-methyl-3-cyano-2-pyridones

NASA Astrophysics Data System (ADS)

Ušćumlić, Gordana S.; Mijin, Dusanˇ Z. ˇ; Valentić, Nataša V.; Vajs, Vlatka V.; Sušić, Biljana M.

2004-10-01

Absorption spectra of ten 5-(4-substituted arylazo)-6-hydroxy-4-methyl-3-cyano-2-pyridones have been recorded in fifteen solvents in the range 200-600 nm. The substituents at the phenyl nucleus are as follows: OH, OCH 3, CH 3, C 2H 5, H, Cl, Br, I, COOH and NO 2. The effects of substituents on the absorption spectra of investigated compounds are interpreted by correlation of absorption frequencies with simple Hammett equation. The effects of solvent polarity and solvent/solute hydrogen bonding interactions are analyzed by means of linear solvation energy relationships concept proposed by Kamlet and Taft. The azo-hydrazone tuatomeric equilibration is found to depend upon substituents as well as on solvents.

Computational solvent system screening for the separation of tocopherols with centrifugal partition chromatography using deep eutectic solvent-based biphasic systems.

PubMed

Bezold, Franziska; Weinberger, Maria E; Minceva, Mirjana

2017-03-31

Tocopherols are a class of molecules with vitamin E activity. Among those, α-tocopherol is the most important vitamin E source in the human diet. The purification of tocopherols involving biphasic liquid systems can be challenging since these vitamins are poorly soluble in water. Deep eutectic solvents (DES) can be used to form water-free biphasic systems and have already proven applicable for centrifugal partition chromatography separations. In this work, a computational solvent system screening was performed using the predictive thermodynamic model COSMO-RS. Liquid-liquid equilibria of solvent systems composed of alkanes, alcohols and DES, as well as partition coefficients of α-tocopherol, β-tocopherol, γ-tocopherol, and σ-tocopherol in these biphasic solvent systems were calculated. From the results the best suited biphasic solvent system, namely heptane/ethanol/choline chloride-1,4-butanediol, was chosen and a batch injection of a tocopherol mixture, mainly consisting of α- and γ-tocopherol, was performed using a centrifugal partition chromatography set up (SCPE 250-BIO). A separation factor of 1.74 was achieved for α- and γ-tocopherol. Copyright © 2017 Elsevier B.V. All rights reserved.

Theoretical design of the cyclic lipopeptide nanotube as a molecular channel in the lipid bilayer, molecular dynamics and quantum mechanics approach.

PubMed

Khavani, Mohammad; Izadyar, Mohammad; Housaindokht, Mohammad Reza

2015-10-14

In this article, cyclic peptides (CP) with lipid substituents were theoretically designed. The dynamical behavior of the CP dimers and the cyclic peptide nanotube (CPNT) without lipid substituents in the solution (water and chloroform) during the 50 ns molecular dynamic (MD) simulations has been investigated. As a result, the CP dimers and CPNT in a non-polar solvent are more stable than in a polar solvent and CPNT is a good container for non-polar small molecules such as chloroform. The effect of the lipid substituents on the CP dimers and CPNT has been investigated in the next stage of our studies. Accordingly, these substituents increase the stability of the CP dimers and CPNT, significantly, in polar solvents. MM-PBSA and MM-GBSA calculations confirm that substitution has an important effect on the stability of the CP dimers and CPNT. Finally, the dynamical behavior of CPNT with lipid substituents in a fully hydrated DMPC bilayer shows the high ability of this structure for molecule transmission across the lipid membrane. This structure is stable enough to be used as a molecular channel. DFT calculations on the CP dimers in the gas phase, water and chloroform, indicate that H-bond formation is the driving force for dimerization. CP dimers are more stable in the gas phase in comparison to in solution. HOMO-LUMO orbital analysis indicates that the interaction of the CP units in the dimer structures is due to the molecular orbital interactions between the NH and CO groups.

Solubility of 3-Caffeoylquinic Acid in Different Solvents at 291-340 K

NASA Astrophysics Data System (ADS)

Wang, Y. T.; Zhang, C. L.; Cheng, X. L.; Zhao, J. H.; Wang, L. C.

2017-12-01

Using a laser monitoring observation technique the solubilities of 3-caffeoylquinic acid in pure solvents, water, methanol, ethanol, 1-propanol, 1-butanol, and two mixed solvents, methanol + water, ethanol + water have been determined at temperature range from 291-340 K. The experimental data were correlated by the modified Apelblat equation, λ h equation, and ideal model. The calculated solubilities were turned out very consistent with the experimental results, and the modified Apelblat equation shows the best agreement.

Scaling Atomic Partial Charges of Carbonate Solvents for Lithium Ion Solvation and Diffusion

DOE PAGES

Chaudhari, Mangesh I.; Nair, Jijeesh R.; Pratt, Lawrence R.; ...

2016-10-21

Lithium-ion solvation and diffusion properties in ethylene carbonate (EC) and propylene carbonate (PC) were studied by molecular simulation, experiments, and electronic structure calculations. Studies carried out in water provide a reference for interpretation. Classical molecular dynamics simulation results are compared to ab initio molecular dynamics to assess nonpolarizable force field parameters for solvation structure of the carbonate solvents. Quasi-chemical theory (QCT) was adapted to take advantage of fourfold occupancy of the near-neighbor solvation structure observed in simulations and used to calculate solvation free energies. The computed free energy for transfer of Li + to PC from water, based on electronicmore » structure calculations with cluster-QCT, agrees with the experimental value. The simulation-based direct-QCT results with scaled partial charges agree with the electronic structure-based QCT values. The computed Li +/PF 6 - transference numbers of 0.35/0.65 (EC) and 0.31/0.69 (PC) agree well with NMR experimental values of 0.31/0.69 (EC) and 0.34/0.66 (PC) and similar values obtained here with impedance spectroscopy. These combined results demonstrate that solvent partial charges can be scaled in systems dominated by strong electrostatic interactions to achieve trends in ion solvation and transport properties that are comparable to ab initio and experimental results. Thus, the results support the use of scaled partial charges in simple, nonpolarizable force fields in future studies of these electrolyte solutions.« less

Exploring the role of ionic liquids to tune the polymorphic outcome of organic compounds† †Electronic supplementary information (ESI) available: CCDC 1577981. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc04353h

PubMed Central

Zeng, Qingying; Mukherjee, Arijit; Müller, Peter; Rogers, Robin D.

2017-01-01

While molecular solvents are commonly used in the screening of polymorphs, the choices are often restricted. Ionic liquids (ILs) – also referred as designer solvents – have immense possibility in this regard because of their wide flexibility of tunability. More importantly, the interactions among the IL components are completely unique compared to those present in the molecular solvents. In this context, we have chosen tetrolic acid (TA) and isonicotinamide (INA), which showed solution-structure link in molecular solvents in the past, as probes to investigate the role of imidazolium based ionic liquids in the polymorphism of these two systems and whether the different solute–solvent interactions in ILs affect the polymorphic outcome. It is observed that the selected imidazolium-based ILs, with varying anion basicity have influenced the crystallization outcome by the interaction between ILs and model compounds. Later, we have utilized the concept of double salt ionic liquids (DSIL) for INA, a penta-morphic system, to investigate the variation in the polymorphic outcome. This approach helped to obtain the forms that were otherwise inaccessible in ILs. PMID:29675194

Effects of the dielectric properties of the ceramic-solvent interface on the binding of proteins to oxide ceramics: a non-local electrostatic approach.

PubMed

Rubinstein, Alexander I; Sabirianov, Renat F; Namavar, Fereydoon

2016-10-14

The rapid development of nanoscience and nanotechnology has raised many fundamental questions that significantly impede progress in these fields. In particular, understanding the physicochemical processes at the interface in aqueous solvents requires the development and application of efficient and accurate methods. In the present work we evaluate the electrostatic contribution to the energy of model protein-ceramic complex formation in an aqueous solvent. We apply a non-local (NL) electrostatic approach that accounts for the effects of the short-range structure of the solvent on the electrostatic interactions of the interfacial systems. In this approach the aqueous solvent is considered as a non-ionic liquid, with the rigid and strongly correlated dipoles of the water molecules. We have found that an ordered interfacial aqueous solvent layer at the protein- and ceramic-solvent interfaces reduces the charging energy of both the ceramic and the protein in the solvent, and significantly increases the electrostatic contribution to their association into a complex. This contribution in the presented NL approach was found to be significantly shifted with respect to the classical model at any dielectric constant value of the ceramics. This implies a significant increase of the adsorption energy in the protein-ceramic complex formation for any ceramic material. We show that for several biocompatible ceramics (for example HfO2, ZrO2, and Ta2O5) the above effect predicts electrostatically induced protein-ceramic complex formation. However, in the framework of the classical continuum electrostatic model (the aqueous solvent as a uniform dielectric medium with a high dielectric constant ∼80) the above ceramics cannot be considered as suitable for electrostatically induced complex formation. Our results also show that the protein-ceramic electrostatic interactions can be strong enough to compensate for the unfavorable desolvation effect in the process of protein-ceramic complex formation.

Effects of the dielectric properties of the ceramic-solvent interface on the binding of proteins to oxide ceramics: a non-local electrostatic approach

NASA Astrophysics Data System (ADS)

Rubinstein, Alexander I.; Sabirianov, Renat F.; Namavar, Fereydoon

2016-10-01

The rapid development of nanoscience and nanotechnology has raised many fundamental questions that significantly impede progress in these fields. In particular, understanding the physicochemical processes at the interface in aqueous solvents requires the development and application of efficient and accurate methods. In the present work we evaluate the electrostatic contribution to the energy of model protein-ceramic complex formation in an aqueous solvent. We apply a non-local (NL) electrostatic approach that accounts for the effects of the short-range structure of the solvent on the electrostatic interactions of the interfacial systems. In this approach the aqueous solvent is considered as a non-ionic liquid, with the rigid and strongly correlated dipoles of the water molecules. We have found that an ordered interfacial aqueous solvent layer at the protein- and ceramic-solvent interfaces reduces the charging energy of both the ceramic and the protein in the solvent, and significantly increases the electrostatic contribution to their association into a complex. This contribution in the presented NL approach was found to be significantly shifted with respect to the classical model at any dielectric constant value of the ceramics. This implies a significant increase of the adsorption energy in the protein-ceramic complex formation for any ceramic material. We show that for several biocompatible ceramics (for example HfO2, ZrO2, and Ta2O5) the above effect predicts electrostatically induced protein-ceramic complex formation. However, in the framework of the classical continuum electrostatic model (the aqueous solvent as a uniform dielectric medium with a high dielectric constant ˜80) the above ceramics cannot be considered as suitable for electrostatically induced complex formation. Our results also show that the protein-ceramic electrostatic interactions can be strong enough to compensate for the unfavorable desolvation effect in the process of protein-ceramic complex formation.

Physicochemical and catalytic properties of Au nanorods micro-assembled in solvents of varying dipole moment and refractive index

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaur, Rupinder; Pal, Bonamali, E-mail: bpal@thapar.edu

2015-02-15

Highlights: • Physicochemical activities of Au nanorods in water largely differ from organic solvents. • Au nanorods agglomeration increased with dipole moments of different polar solvents. • Refractive indexes of Au nanorods dispersion in various polar solvents are enhanced. • Electrokinetics significantly altered depending on agglomerated size of Au nanorods. • Catalysis or co-catalysis activity is varied as per the extent of Au nanorods coagulation. - Abstract: This paper deals with the impact of dipole moment (1.66–3.96 D) and refractive index (1.333–1.422) of the dispersion solvent on the plasmon absorption, surface charge, zeta potential, and adsorption properties of Au nanorodsmore » (AuNRs). AuNRs (length ≈ 53 nm and width ≈ 20 nm) undergo agglomeration (size 50–180 nm) with increase in the dipole moment of solvent (iPrOH < MeOH < DMF < DMSO). Whereas, no such coagulation occurs in H{sub 2}O and CCl{sub 4} suspension as confirmed by DLS and TEM size distribution. The electrostatic interaction of AuNRs with its surface adsorbed solvent dipoles leads to alteration of the their ionic state, absolute electronic charge and zeta potential (+49.79 mV in H{sub 2}O, +8.99 mV in DMF and −4.65 mV in MeOH dispersion) to a greater extent. This interaction distinctly modifies the adsorption behavior of polar molecules like p-nitrophenol and salicylic acid on AuNRs surface, as evidenced by the measured changes in their electro-kinetic parameters. As a result, we observe a substantial difference in catalytic and co-catalytic activities of AuNRs dispersed in various solvents as mentioned above because the catalytic properties of AuNRs are strongly dependent on the type of solvent in which they are dispersed.« less

Aqueous alternatives for metal and composite cleaning

NASA Technical Reports Server (NTRS)

Quitmeyer, Joann

1994-01-01

For many years the metalworking industry has cleaned metal and composite substrates with chlorinated solvents. Recently, however, health and disposal related environmental concerns have increased regarding chlorinated solvents, including 1,1,1-trichloroethane, trichloroethylene, methylene chloride, or Freon'. World leaders have instituted a production ban of certain ozone depleting chlorofluorocarbons (CFC's) by 1996. The Occupational Safety and Health Administration (OSHA) has instituted worker vapor exposure limitations for virtually all of the solvents used in solvent-based cleaners. In addition, the United States Environmental Protection Agency (EPA) has defined nearly all solvent-based cleaners as 'hazardous'. Cradle to grave waste responsibility is another reason manufacturers are trying to replace chlorinated solvents in their cleaning processes. Because of these factors, there now is a world wide effort to reduce and/or eliminate the use of chlorinated solvents for industrial cleaning. Waterbased cleaners are among the alternatives being offered to the industry. New technology alkaline cleaners are now available that can be used instead of chlorinated solvents in many cleaning processes. These waterbased cleaners reduce the release of volatile organic compounds (VOC's) by as much as 99 percent. (The definition and method of calculation of VOC's now varies from region to region.) Hazardous waste generation can also be significantly reduced or eliminated with new aqueous technology. This in turn can ease worker exposure restrictions and positively impact the environment. This paper compares the chemical and physical properties of this aqueous cleaners versus chlorinated solvents.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mo, Alan K; Brown, Victoria L.; Rugg, Brandon K.

The adhesion of 100 nm thick electron-beam deposited Au and Pt and magnetron sputtered Au thin films onto poly(methyl methacrylate) (PMMA) substrates can be significantly enhanced to over 90% adhesion by either spin-casting or vapor-exposure to hydrohalocarbon solvents prior to metal deposition compared to samples that are either cleaned in isopropyl alcohol or pre-treated with a remote O2 plasma. X-ray photoelectron spectroscopy (XPS) and evolved gas Fourier transform infrared spectroscopy (EGA-FTIR) reveal the presence of residual halogenated solvent molecules at the PMMA surface which chemically activates the surface to produce a stable chemical interaction between the noble metal film andmore » the PMMA. Density functional theory (DFT) calculations show that the halogenated solvent molecules preferentially form a Lewis acid-base adduct with the oxygen atoms in the ester group in PMMA which is consistent with the measured enthalpy of desorption of chloroform (CHCl3) on PMMA determined by EGA-FTIR to be 36 kJ mol-1. The DFT model also supports the experimentally observed change in the high resolution XPS O 1s peak at 533.77 eV after metallization attributed to a change in the local bonding environment of the bridging O in the PMMA ester group. DFT also predicts that the deposited metal atom (M) inserts into the C-X bond where X is the halogen atom on either CHCl3 or bromoform (CHBr3) to form a O M X interaction that is observed by a M-X bond in the high resolution XPS Cl 2p3/2 peak at 198.03 eV and Br 3p3/2 peak at 182.06 eV. A range of solvents with differing polarities for PMMA pre-treatment have been used and it is proposed that non-complexing solvents result in significant metal adhesion improvement. The Gutmann acceptor number can be used to predict the effectiveness of solvent treatment for noble metal adhesion. A model is proposed in which the bond energy of the C-X bond of the solvent must be sufficiently low so that the C-X bond can be cleaved to form the M-X bond. Supporting this model, a negative control of vapor phase exposure to fluoroform (CHF3) is shown to have no effect on noble metal adhesion due to the higher bond dissociation energy of the C-F bond compared to the C-Cl and C-Br bond energy. The surface activation of vapor-phase exposed PMMA surfaces is technologically significant for the fabrication of polymer microdevices requiring Au or Pt metallization.« less

Ionic association and solvation of the ionic liquid 1-hexyl-3-methylimidazolium chloride in molecular solvents revealed by vapor pressure osmometry, conductometry, volumetry, and acoustic measurements.

PubMed

Sadeghi, Rahmat; Ebrahimi, Nosaibah

2011-11-17

A systematic study of osmotic coefficient, conductivity, volumetric and acoustic properties of solutions of ionic liquid 1-hexyl-3-methylimidazolium chloride ([C(6)mim][Cl]) in various molecular solvents has been made at different temperatures in order to study of ionic association and solvation behavior of [C(6)mim][Cl] in different solutions. Precise measurements on electrical conductances of solutions of [C(6)mim][Cl] in water, methanol, ethanol, 1-propanol, 2-propanol, 1-butanol, and acetonitrile at 293.15, 298.15, and 303.15 K are reported and analyzed with Barthel's low-concentration chemical model (lcCM) to obtain the limiting molar conductivities and association constants of this ionic liquid in the investigated solvents. Strong ion pairing was found for the ionic liquid in 2-propanol, 1-butanol, and 1-propanol, whereas ion association in acetonitrile, methanol and ethanol is rather weak and in water the ionic liquid is fully dissociated. In the second part of this work, the apparent molar volumes and isentropic compressibilities of [C(6)mim][Cl] in water, methanol, ethanol, acetonitrile, 1-propanol, 2-propanol, and 1-butanol are obtained at the 288.15-313.15 K temperature range at 5 K intervals at atmospheric pressure from the precise measurements of density and sound velocity. The infinite dilution apparent molar volume and isentropic compressibility values of the free ions and ion pairs of [C(6)mim][Cl] in the investigated solvents as well as the excess molar volume of the investigated solutions are determined and their variations with temperature and type of solvents are also studied. Finally, the experimental measurements of osmotic coefficient at 318.15 K for binary solutions of [C(6)mim][Cl] in water, methanol, ethanol, 2-propanol, and acetonitrile are taken using the vapor pressure osmometry (VPO) method and from which the values of the solvent activity, vapor pressure, activity coefficients, and Gibbs free energies are calculated. The results are interpreted in terms of ion association, ion-dipole interactions, and structural factors of the ionic liquid and investigated organic solvents. The ionic liquid is solvated to a different extent by the molecular solvents, and ionic association is affected significantly by ionic solvation.

A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers.

PubMed

Cooper, Christopher D; Bardhan, Jaydeep P; Barba, L A

2014-03-01

The continuum theory applied to biomolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like solvent-filled cavities or ion-exclusion (Stern) layers, due to the added difficulty of treating multiple boundary surfaces. This has hindered meaningful comparisons with volume-based methods, and the effects on accuracy of including these features has remained unknown. This work presents a solver called PyGBe that uses a boundary-element formulation and can handle multiple interacting surfaces. It was used to study the effects of solvent-filled cavities and Stern layers on the accuracy of calculating solvation energy and binding energy of proteins, using the well-known apbs finite-difference code for comparison. The results suggest that if required accuracy for an application allows errors larger than about 2% in solvation energy, then the simpler, single-surface model can be used. When calculating binding energies, the need for a multi-surface model is problem-dependent, becoming more critical when ligand and receptor are of comparable size. Comparing with the apbs solver, the boundary-element solver is faster when the accuracy requirements are higher. The cross-over point for the PyGBe code is in the order of 1-2% error, when running on one gpu card (nvidia Tesla C2075), compared with apbs running on six Intel Xeon cpu cores. PyGBe achieves algorithmic acceleration of the boundary element method using a treecode, and hardware acceleration using gpus via PyCuda from a user-visible code that is all Python. The code is open-source under MIT license.

A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers

NASA Astrophysics Data System (ADS)

Cooper, Christopher D.; Bardhan, Jaydeep P.; Barba, L. A.

2014-03-01

The continuum theory applied to biomolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like solvent-filled cavities or ion-exclusion (Stern) layers, due to the added difficulty of treating multiple boundary surfaces. This has hindered meaningful comparisons with volume-based methods, and the effects on accuracy of including these features has remained unknown. This work presents a solver called PyGBe that uses a boundary-element formulation and can handle multiple interacting surfaces. It was used to study the effects of solvent-filled cavities and Stern layers on the accuracy of calculating solvation energy and binding energy of proteins, using the well-known APBS finite-difference code for comparison. The results suggest that if required accuracy for an application allows errors larger than about 2% in solvation energy, then the simpler, single-surface model can be used. When calculating binding energies, the need for a multi-surface model is problem-dependent, becoming more critical when ligand and receptor are of comparable size. Comparing with the APBS solver, the boundary-element solver is faster when the accuracy requirements are higher. The cross-over point for the PyGBe code is on the order of 1-2% error, when running on one GPU card (NVIDIA Tesla C2075), compared with APBS running on six Intel Xeon CPU cores. PyGBe achieves algorithmic acceleration of the boundary element method using a treecode, and hardware acceleration using GPUs via PyCuda from a user-visible code that is all Python. The code is open-source under MIT license.

Self-assembly of a chiral lipid gelator controlled by solvent and speed of gelation.

PubMed

Xue, Pengchong; Lu, Ran; Yang, Xinchun; Zhao, Li; Xu, Defang; Liu, Yan; Zhang, Hanzhuang; Nomoto, Hiroyuki; Takafuji, Makoto; Ihara, Hirotaka

2009-09-28

Glutamine derivative 1 with two-photon absorbing units has been synthesized and was found to show gelation ability in some solvents. Its self-assembly in the gel phase could be controlled by the solvent and speed of gelation. For example, in DMSO the organogelator self-assembled into H-aggregates with weak exciton coupling between the aromatic moieties. On the other hand, in DMSO/diphenyl ether (1:9, v/v) the molecules formed 1D aggregates, but with strong exciton coupling due to the small distance between the chromophores. Moreover, the formation of these two kinds of aggregates could be adjusted by the ratio of DMSO to diphenyl ether. In DMSO/toluene, DMSO/butanol, DMSO/butyl acetate, and DMSO/acetic acid systems similar results were observed. Therefore, conversion of the packing model occurs irrespective of the nature of the solvent. Notably, a unique sign inversion in the CD spectra could be realized by controlling the speed of gelation in the DMSO/diphenyl ether (1:9, v/v) system. It was found that a low speed of gelation induces the gelator to adopt a packing model with strong pi-pi interactions between the aromatic units. Moreover, the gels, when excited at 800 nm, emit strong green fluorescence and the quantum chemical calculations suggest that intramolecular charge transfer leads to two-photon absorption of the gelator molecule.

1H NMR spectra part 31: 1H chemical shifts of amides in DMSO solvent.

PubMed

Abraham, Raymond J; Griffiths, Lee; Perez, Manuel

2014-07-01

The (1)H chemical shifts of 48 amides in DMSO solvent are assigned and presented. The solvent shifts Δδ (DMSO-CDCl3 ) are large (1-2 ppm) for the NH protons but smaller and negative (-0.1 to -0.2 ppm) for close range protons. A selection of the observed solvent shifts is compared with calculated shifts from the present model and from GIAO calculations. Those for the NH protons agree with both calculations, but other solvent shifts such as Δδ(CHO) are not well reproduced by the GIAO calculations. The (1)H chemical shifts of the amides in DMSO were analysed using a functional approach for near ( ≤ 3 bonds removed) protons and the electric field, magnetic anisotropy and steric effect of the amide group for more distant protons. The chemical shifts of the NH protons of acetanilide and benzamide vary linearly with the π density on the αN and βC atoms, respectively. The C=O anisotropy and steric effect are in general little changed from the values in CDCl3. The effects of substituents F, Cl, Me on the NH proton shifts are reproduced. The electric field coefficient for the protons in DMSO is 90% of that in CDCl3. There is no steric effect of the C=O oxygen on the NH proton in an NH…O=C hydrogen bond. The observed deshielding is due to the electric field effect. The calculated chemical shifts agree well with the observed shifts (RMS error of 0.106 ppm for the data set of 257 entries). Copyright © 2014 John Wiley & Sons, Ltd.

Solvatochromism and linear solvation energy relationship of the kinase inhibitor SKF86002

NASA Astrophysics Data System (ADS)

Khattab, Muhammad; Van Dongen, Madeline; Wang, Feng; Clayton, Andrew H. A.

2017-01-01

We studied the spectroscopic characteristics of SKF86002, an anti-inflammatory and tyrosine kinase inhibitor drug candidate. Two conformers SKF86002A and SKF86002B are separated by energy barriers of 19.68 kJ·mol- 1 and 6.65 kJ·mol- 1 due to H-bonds, and produce the three major UV-Vis absorption bands at 325 nm, 260 nm and 210 nm in cyclohexane solutions. This environment-sensitive fluorophore exhibited emission in the 400-500 nm range with a marked response to changes in environment polarity. By using twenty-two solvents for the solvatochromism study, it was noticed that solvent polarity, represented by dielectric constant, was well correlated with the emission wavelength maxima of SKF86002. Thus, the SKF86002 fluorescence peak red shifted in aprotic solvents from 397.5 nm in cyclohexane to 436 nm in DMSO. While the emission maximum in hydrogen donating solvents ranged from 420 nm in t-butanol to 446 nm in N-methylformamide. Employing Lippert-Mataga, Bakhshiev and Kawski models, we found that one linear correlation provided a satisfactory description of polarity effect of 18 solvents on the spectral changes of SKF86002 with R2 values 0.78, 0.80 and 0.80, respectively. Additionally, the multicomponent linear regression analysis of Kamlet-Taft (R2 = 0.94) revealed that solvent acidity, basicity and polarity accounted for 31%, 24% and 45% of solvent effects on SKF86002 emission, respectively. While Catalán correlation (R2 = 0.92) revealed that solvatochromic change of SKF86002 emission was attributed to changes in solvent dipolarity (71%), solvent polarity (12%), solvent acidity (11%) and solvent basicity (6%). Plot of Reichardt transition energies and emission energies of SKF86002 in 18 solvents showed also a linear correlation with R2 = 0.90. The dipole moment difference between excited and ground state was calculated to be 3.4-3.5 debye.

Solvatochromism and linear solvation energy relationship of the kinase inhibitor SKF86002.

PubMed

Khattab, Muhammad; Van Dongen, Madeline; Wang, Feng; Clayton, Andrew H A

2017-01-05

We studied the spectroscopic characteristics of SKF86002, an anti-inflammatory and tyrosine kinase inhibitor drug candidate. Two conformers SKF86002A and SKF86002B are separated by energy barriers of 19.68kJ·mol(-1) and 6.65kJ·mol(-1) due to H-bonds, and produce the three major UV-Vis absorption bands at 325nm, 260nm and 210nm in cyclohexane solutions. This environment-sensitive fluorophore exhibited emission in the 400-500nm range with a marked response to changes in environment polarity. By using twenty-two solvents for the solvatochromism study, it was noticed that solvent polarity, represented by dielectric constant, was well correlated with the emission wavelength maxima of SKF86002. Thus, the SKF86002 fluorescence peak red shifted in aprotic solvents from 397.5nm in cyclohexane to 436nm in DMSO. While the emission maximum in hydrogen donating solvents ranged from 420nm in t-butanol to 446nm in N-methylformamide. Employing Lippert-Mataga, Bakhshiev and Kawski models, we found that one linear correlation provided a satisfactory description of polarity effect of 18 solvents on the spectral changes of SKF86002 with R(2) values 0.78, 0.80 and 0.80, respectively. Additionally, the multicomponent linear regression analysis of Kamlet-Taft (R(2)=0.94) revealed that solvent acidity, basicity and polarity accounted for 31%, 24% and 45% of solvent effects on SKF86002 emission, respectively. While Catalán correlation (R(2)=0.92) revealed that solvatochromic change of SKF86002 emission was attributed to changes in solvent dipolarity (71%), solvent polarity (12%), solvent acidity (11%) and solvent basicity (6%). Plot of Reichardt transition energies and emission energies of SKF86002 in 18 solvents showed also a linear correlation with R(2)=0.90. The dipole moment difference between excited and ground state was calculated to be 3.4-3.5debye. Copyright © 2016 Elsevier B.V. All rights reserved.

Interaction of Simple Ions with Water: Theoretical Models for the Study of Ion Hydration

ERIC Educational Resources Information Center

Gancheff, Jorge S.; Kremer, Carlos; Ventura, Oscar N.

2009-01-01

A computational experiment aimed to create and systematically analyze models of simple cation hydrates is presented. The changes in the structure (bond distances and angles) and the electronic density distribution of the solvent and the thermodynamic parameters of the hydration process are calculated and compared with the experimental data. The…

Comparison of extraction techniques and modeling of accelerated solvent extraction for the authentication of natural vanilla flavors.

PubMed

Cicchetti, Esmeralda; Chaintreau, Alain

2009-06-01

Accelerated solvent extraction (ASE) of vanilla beans has been optimized using ethanol as a solvent. A theoretical model is proposed to account for this multistep extraction. This allows the determination, for the first time, of the total amount of analytes initially present in the beans and thus the calculation of recoveries using ASE or any other extraction technique. As a result, ASE and Soxhlet extractions have been determined to be efficient methods, whereas recoveries are modest for maceration techniques and depend on the solvent used. Because industrial extracts are obtained by many different procedures, including maceration in various solvents, authenticating vanilla extracts using quantitative ratios between the amounts of vanilla flavor constituents appears to be unreliable. When authentication techniques based on isotopic ratios are used, ASE is a valid sample preparation technique because it does not induce isotopic fractionation.

Modeling and simulations of carbon nanotube (CNT) dispersion in water/surfactant/polymer systems

NASA Astrophysics Data System (ADS)

Uddin, Nasir Mohammad

An innovative multiscale (atomistic to mesoscale) model capable of predicting carbon nanotube (CNT) interactions and dispersion in water/surfactant/polymer systems was developed. The model was verified qualitatively with available experimental data in the literature. It can be used to computationally screen potential surfactants, solvents, polymers, and CNT with appropriate diameter and length to obtain improved CNT dispersion in aqueous medium. Thus the model would facilitate the reduction of time and cost required to produce CNT dispersed homogeneous solutions and CNT reinforced materials. CNT dispersion in any water/surfactant/polymer system depends on interactions between CNTs and surrounding molecules. Central to the study was the atomistic scale model which used the atomic structure of the surfactant, solvent, polymer, and CNT. The model was capable of predicting the CNT interactions in terms of potential of mean force (PMF) between CNTs under the influence of surrounding molecules in an aqueous solution. On the atomistic scale, molecular dynamics method was used to compute the PMF as a function of CNT separation and CNT alignment. An adaptive biasing force (ABF) method was used to speed up the calculations. Correlations were developed to determine the effective interactions between CNTs as a function of their any inter-atomic distance and orientation angle in water as well as in water/surfactant by fitting the calculated PMF data. On the mesoscale, the fitted PMF correlations were used as input in the Monte Carlo simulations to determine the degree of dispersion of CNTs in water and water/surfactant system. The distribution of CNT cluster size was determined for the CNTs dispersed in water with and without surfactant addition. The entropie and enthalpie contributions to the CNT interactions in water were determined to understand the dispersion mechanism of CNTs in water. The effects of CNT orientation, length, diameter, chirality and surfactant concentrations and structures on CNT interactions in water were investigated at room conditions. CNT interactions in polymer solution were also investigated with polyethylene oxide (PEO) polymer and water as a solvent. In all cases, the atomic arrangement of molecules was discussed in detailed. Simulations revealed that CNT orientation, length, diameter, and addition of surfactant and its structures can significantly affect CNT interactions (i.e., PMFs varied significantly) and in-turn the degree of CNT dispersion in aqueous solution. For all simulation cases, a uniform sampling was achieved by using the ABF method to calculate the governing PMF between CNTs indicating the effectiveness and convergence of the adaptive sampling scheme. The surfactant molecules were shown to adsorb at the CNT surface and contribute to weaker interactions between CNTs which resulted less CNT aggregate size at the mesoscale. Surfactant consisting with a benzene ring contributed much weaker interactions between CNTs as compared with that of without benzene ring. The increase in CNT length contributed the stronger CNT interactions where the increase in CNT diameter caused weaker CNT interactions in water. The interfacial characteristics between the CNT, surfactant and the polymer were also predicted and discussed. The model can be expanded for more solvents, surfactants, and polymers.

Balancing size exclusion and adsorption of polymers in nanopores

NASA Astrophysics Data System (ADS)

Kim, Won; Ryu, Chang Y.

2006-03-01

The liquid chromatography at critical condition (LCCC) presents the condition, at which the size exclusion and adsorption of polymer chains are balanced upon interactions with nanoporous substrates. In this study, we investigate how the polymer interactions with nanopores are affected by the solvent quality and nanopore size. Specifically, we measure the retention times of monodisperse polystyrenes in C18-bonded nanoporous silica column as a function of molecular weight, when a mixed solvent of methylene chloride and acetonitrile are used as elutent. C18-bonded silica particles with 70, 100, and 250 A pore size are used as a stationary phase to study how the transition from SEC-like to IC-like retention behavior depends on the condition of temperature and solvent composition. To locate the LCCC at various nanopore sizes, the temperature and solvent composition have been varied from 0 to 60 C and from 51 to 62 v/v% of methylene chloride, respectively.

Unraveling cellulose microfibrils: a twisted tale.

PubMed

Hadden, Jodi A; French, Alfred D; Woods, Robert J

2013-10-01

Molecular dynamics (MD) simulations of cellulose microfibrils are pertinent to the paper, textile, and biofuels industries for their unique capacity to characterize dynamic behavior and atomic-level interactions with solvent molecules and cellulase enzymes. While high-resolution crystallographic data have established a solid basis for computational analysis of cellulose, previous work has demonstrated a tendency for modeled microfibrils to diverge from the linear experimental structure and adopt a twisted conformation. Here, we investigate the dependence of this twisting behavior on computational approximations and establish the theoretical basis for its occurrence. We examine the role of solvent, the effect of nonbonded force field parameters [partial charges and van der Waals (vdW) contributions], and the use of explicitly modeled oxygen lone pairs in both the solute and solvent. Findings suggest that microfibril twisting is favored by vdW interactions, and counteracted by both intrachain hydrogen bonds and solvent effects at the microfibril surface. Copyright © 2013 Wiley Periodicals, Inc.

Unraveling Cellulose Microfibrils: A Twisted Tale

PubMed Central

Hadden, Jodi A.; French, Alfred D.; Woods, Robert J.

2014-01-01

Molecular dynamics (MD) simulations of cellulose microfibrils are pertinent to the paper, textile, and biofuels industries for their unique capacity to characterize dynamic behavior and atomic-level interactions with solvent molecules and cellulase enzymes. While high-resolution crystallographic data have established a solid basis for computational analysis of cellulose, previous work has demonstrated a tendency for modeled microfibrils to diverge from the linear experimental structure and adopt a twisted conformation. Here, we investigate the dependence of this twisting behavior on computational approximations and establish the theoretical basis for its occurrence. We examine the role of solvent, the effect of nonbonded force field parameters [partial charges and van der Waals (vdW) contributions], and the use of explicitly modeled oxygen lone pairs in both the solute and solvent. Findings suggest that microfibril twisting is favored by vdW interactions, and counteracted by both intrachain hydrogen bonds and solvent effects at the microfibril surface. PMID:23681971

MP2, DFT-D, and PCM study of the HMB-TCNE complex: Thermodynamics, electric properties, and solvent effects

NASA Astrophysics Data System (ADS)

Kysel, Ondrej; Budzák, Scaronimon; Medveď, Miroslav; Mach, Pavel

Geometry, thermodynamic, and electric properties of the pi-EDA complex between hexamethylbenzene (HMB) and tetracyanoethylene (TCNE) are investigated at the MP2/6-31G* and, partly, DFT-D/6-31G* levels. Solvent effects on the properties are evaluated using the PCM model. Fully optimized HMB-TCNE geometry in gas phase is a stacking complex with an interplanar distance 2.87 × 10-10 m and the corresponding BSSE corrected interaction energy is -51.3 kJ mol-1. As expected, the interplanar distance is much shorter in comparison with HF and DFT results. However the crystal structures of both (HMB)2-TCNE and HMB-TCNE complexes have interplanar distances somewhat larger (3.18 and 3.28 × 10-10 m, respectively) than our MP2 gas phase value. Our estimate of the distance in CCl4 on the basis of PCM solvent effect study is also larger (3.06-3.16 × 10-10 m). The calculated enthalpy, entropy, Gibbs energy, and equilibrium constant of HMB-TCNE complex formation in gas phase are: DeltaH0 = -61.59 kJ mol-1, DeltaSc0 = -143 J mol-1 K-1, DeltaG0 = -18.97 kJ mol-1, and K = 2,100 dm3 mol-1. Experimental data, however, measured in CCl4 are significantly lower: DeltaH0 = -34 kJ mol-1, DeltaSc0 = -70.4 J mol-1 K-1, DeltaG0 = -13.01 kJ mol-1, and K = 190 dm3 mol-1. The differences are caused by solvation effects which stabilize more the isolated components than the complex. The total solvent destabilization of Gibbs energy of the complex relatively to that of components is equal to 5.9 kJ mol-1 which is very close to our PCM value 6.5 kJ mol-1. MP2/6-31G* dipole moment and polarizabilities are in reasonable agreement with experiment (3.56 D versus 2.8 D for dipole moment). The difference here is due to solvent effect which enlarges interplanar distance and thus decreases dipole moment value. The MP2/6-31G* study supplemented by DFT-D parameterization for enthalpy calculation, and by the PCM approach to include solvent effect seems to be proper tools to elucidate the properties of pi-EDA complexes.

Synergism and antagonism in extracting local anesthetics from aqueous media with mixtures of solvents

NASA Astrophysics Data System (ADS)

Sukhanov, P. T.; Chibisova, T. V.; Korenman, Ya. I.

2014-12-01

The extraction of local anesthetics from aqueous media with mixtures of solvent is examined and its synergistic and antagonistic effects are determined. Synergism parameters, separation factors, constants for the formation of anesthetic complexes, and solvate numbers are calculated.

Substituent and solvent effects on the UV/vis absorption spectra of 5-(3- and 4-substituted arylazo)-4,6-dimethyl-3-cyano-2-pyridones

NASA Astrophysics Data System (ADS)

Mijin, Dušan Ž.; Ušćumlić, Gordana S.; Perišić-Janjić, Nada U.; Valentić, Nataša V.

2006-01-01

Absorption spectra of seventeen 5-(3- and 4-substituted arylazo)-4,6-dimethyl-3-cyano-2-pyridones have been recorded in 12 protic and aprotic solvents in the range 200-600 nm. The effects of substituents on the absorption spectra of these new azo dyes are interpreted by correlation of absorption frequencies with Hammett equation. The solute-solvent interactions were clarified on the basis of linear solvation energy relationships concept proposed by Kamlet and Taft. The 2-pyridone/2-hydroxypiridine tautomeric equilibration is found to depend upon substituents as well as on solvents.

An investigation into dispersion upon switching between solvents within a microfluidic system using a chemically resistant integrated optical refractive index sensor.

PubMed

Parker, Richard M; Gates, James C; Wales, Dominic J; Smith, Peter G R; Grossel, Martin C

2013-02-07

A planar Bragg grating device has been developed that is capable of detecting changes in the refractive index of a wide range of fluids including solvents, acids and bases. The integration of this high precision refractive index sensor within a chemically resistant microfluidic flow system has enabled the investigation of diverse fluid interactions. By cycling between different solvents, both miscible and immiscible, within the microfluidic system it is shown that the previous solvent determines the nature of the refractive index profile across the transition in composition. This solvent dispersion effect is investigated with particular attention to the methanol-water transition, where transients in refractive index are observed that are an order of magnitude larger in amplitude than the difference between the bulk fluids. The potential complications of such phenomenon are discussed together with an example of a device that exploits this effect for the unambiguous composition measurement of a binary solvent system.

Enzymatic synthesis of esculin ester in ionic liquids buffered with organic solvents.

PubMed

Hu, Yifan; Guo, Zheng; Lue, Bena-Marie; Xu, Xuebing

2009-05-13

The enzymatic esterification of esculin catalyzed by Candida antarctica lipase B (Novozym 435) was carried out in ionic liquid (IL)-organic solvent mixed systems in comparison with individual systems. The reaction behaviors in IL-organic solvents were systemically evaluated using acetone as a model solvent. With organic solvents as media, the esterification rates of esculin depended mainly on its solubility in solvents; for the reactions in ILs, the reaction rates were generally low, and the anion part of the IL played a critical role in enzyme activity. Therefore, the esterification of esculin in IL-acetone mixtures made it possible to improve the solubility of esculin while the effects of ILs on lipase activity were minimized. Following the benignity of ILs to lipase activity, the anions of ILs were ranked in the order as [Tf(2)N](-) > [PF(6)](-) > [BF(4)](-) > [CF(3)SO(3)](-) > [C(4)F(9)SO(3)](-) > [TAF](-) > [MDEGSO(4)](-) > [OctSO(4)](-) > [ES](-) = [DMP](-) = [OTs](- )= Cl(-). The reaction behaviors differed in different systems and largely depended on the properties of the ILs and organic solvents. In general, improvements were observed in terms of both solubility and reaction efficiency. The knowledge acquired in this work gives a better understanding of multiple interactions in IL-organic solvent systems, which provide guidance for system design and optimization.

Existence of a new emitting singlet state of proflavine: femtosecond dynamics of the excited state processes and quantum chemical studies in different solvents.

PubMed

Kumar, Karuppannan Senthil; Selvaraju, Chellappan; Malar, Ezekiel Joy Padma; Natarajan, Paramasivam

2012-01-12

Proflavine (3,6-diaminoacridine) shows fluorescence emission with lifetime, 4.6 ± 0.2 ns, in all the solvents irrespective of the solvent polarity. To understand this unusual photophysical property, investigations were carried out using steady state and time-resolved fluorescence spectroscopy in the pico- and femtosecond time domain. Molecular geometries in the ground and low-lying excited states of proflavine were examined by complete structural optimization using ab initio quantum chemical computations at HF/6-311++G** and CIS/6-311++G** levels. Time dependent density functional theory (TDDFT) calculations were performed to study the excitation energies in the low-lying excited states. The steady state absorption and emission spectral details of proflavine are found to be influenced by solvents. The femtosecond fluorescence decay of the proflavine in all the solvents follows triexponential function with two ultrafast decay components (τ(1) and τ(2)) in addition to the nanosecond component. The ultrafast decay component, τ(1), is attributed to the solvation dynamics of the particular solvent used. The second ultrafast decay component, τ(2), is found to vary from 50 to 215 ps depending upon the solvent. The amplitudes of the ultrafast decay components vary with the wavelength and show time dependent spectral shift in the emission maximum. The observation is interpreted that the time dependent spectral shift is not only due to solvation dynamics but also due to the existence of more than one emitting state of proflavine in the solvent used. Time resolved area normalized emission spectral (TRANES) analysis shows an isoemissive point, indicating the presence of two emitting states in homogeneous solution. Detailed femtosecond fluorescence decay analysis allows us to isolate the two independent emitting components of the close lying singlet states. The CIS and TDDFT calculations also support the existence of the close lying emitting states. The near constant lifetime observed for proflavine in different solvents is suggested to be due to the similar dipole moments of the ground and the evolved emitting singlet state of the dye from the Franck-Condon excited state.

In Vitro Antiplasmodial Activities and Synergistic Combinations of Differential Solvent Extracts of the Polyherbal Product, Nefang

PubMed Central

Arrey Tarkang, Protus; Franzoi, Kathrin Diehl; Lee, Eunyoung; Freitas-Junior, Lucio; Liuzzi, Michel; Nolé, Tsabang; Ayong, Lawrence S.; Agbor, Gabriel A.; Okalebo, Faith A.; Guantai, Anastasia N.

2014-01-01

Nefang, a polyherbal product composed of Mangifera indica (bark and leaf), Psidium guajava, Carica papaya, Cymbopogon citratus, Citrus sinensis, and Ocimum gratissimum (leaves), is a potential therapy against P. falciparum malaria. In vitro antiplasmodial activities of its constituent solvent extracts were analyzed on CQ-sensitive (3D7) and multidrug resistant (Dd2) P. falciparum strains. The interactions involving the differential solvent extracts were further analyzed using a variable potency ratio drug combination approach. Effective concentration 50 (EC50) values were determined by nonlinear regression curve-fitting of the dose-response data and used in calculating the fractional inhibitory concentration 50 (FIC50) and combination indices (CI) for each pair. The derived EC50 values (3D7/Dd2, μg/mL) are Nefang-96.96/55.08, MiB-65.33/34.58, MiL-82.56/40.04, Pg-47.02/25.79, Cp-1188/317.5, Cc-723.3/141, Cs-184.4/105.1, and Og-778.5/118.9. Synergism was obtained with MiB/Pg (CI = 0.351), MiL/Pg (0.358), MiB/Cs (0.366), MiL/Cs (0.482), Pg/Cs (0.483), and Cs/Og (0.414) when analyzed at equipotency ratios. Cytotoxicity testing of Nefang and the solvent extracts on two human cell lines (Hep G2 and U2OS) revealed no significant toxicity relative to their antiplasmodial activities (SI > 20). Taken together, our data confirm the antimalarial activities of Nefang and its constituent plant extracts and identified extract pairs with promising synergistic interactions for exploitation towards a rational phytotherapeutic and evidence-based antimalarial drug discovery. PMID:24877138

Relaxation pathways of photoexcited iodide-methanol clusters: a computational investigation.

PubMed

Mak, Chun C; Peslherbe, Gilles H

2014-06-26

Upon photoexcitation of iodide-methanol clusters, I(-)(CH3OH)n, to a charge-transfer-to-solvent (CTTS) excited state, extensive relaxation was found to occur, accompanied by a convoluted modulation of the stability of the excited electron, which ultimately decreases substantially. In order to develop a molecular-level understanding of the relaxation processes of CTTS excited I(-)(CH3OH)n, high-level quantum chemical calculations are first used to investigate the ground, excited, and ionized states of I(-)(CH3OH)n (n = 2). Because of the relatively small size of I(-)(CH3OH)2, it was possible to characterize the contributions of solvent-solvent interactions to the stability of the CTTS excited cluster relative to dissociation into methanol, iodine, and a free electron, which exhibits a substantial dependence on the cluster geometric configuration. Ab initio molecular dynamics simulations of CTTS excited I(-)(CH3OH)3 are then performed to shed some light onto the nature of the relaxation pathways involved in the modulation of the stability of the excited electron in larger clusters. Simulation results suggest that separation of I and (CH3OH)3(-) accompanied by solvent reorganization in the latter can initially stabilize the excited electron, while gradual cluster fragmentation to I, (CH3OH)2(-), and CH3OH ultimately destabilizes it. This work shows, for the first time, that the inability of small CTTS excited I(-)(CH3OH)n to retain a solvated electron may be attributed to the limited hydrogen-bonding capacity of CH3OH, which increases the propensity for fragmentation to smaller clusters with lower excess-electron binding energies, and highlights the critical role of intricate molecular interactions in the electron solvation process.

Quantum chemical calculations and analysis of FTIR, FT-Raman and UV-Vis spectra of temozolomide molecule

NASA Astrophysics Data System (ADS)

Bhat, Sheeraz Ahmad; Ahmad, Shabbir

2015-11-01

A combined experimental and theoretical study of the structure, vibrational and electronic spectra of temozolomide molecule, which is largely used in the treatment of brain tumours, is presented. FTIR (4000-400 cm-1) and FT-Raman spectra (4000‒50 cm-1) have been recorded and analysed using anharmonic frequency calculations using VPT2, VSCF and CC-VSCF levels of theory within B3LYP/6-311++G(d,p) framework. Anharmonic methods give accurate frequencies of fundamental modes, overtones as well as Fermi resonances and account for coupling of different modes. The anharmonic frequencies calculated using VPT2 and CC-VSCF methods show better agreement with the experimental data. Harmonic frequencies including solvent effects are also computed using IEF-PCM model. The magnitudes of coupling between pair of modes have been calculated using coupling integral based on 2MR-QFF approximation. Intermolecular interactions are discussed for three possible dimers of temozolomide. UV-Vis spectrum, examined in ethanol solvent, is compared with the calculated spectrum at TD-DFT/6-311++G(d,p) level of theory. The electronic properties, such as excitation energy, frontier molecular orbital energies and the assignments of the absorption bands are also discussed.

Cyclic Solvent Vapor Annealing for Rapid, Robust Vertical Orientation of Features in BCP Thin Films

NASA Astrophysics Data System (ADS)

Paradiso, Sean; Delaney, Kris; Fredrickson, Glenn

2015-03-01

Methods for reliably controlling block copolymer self assembly have seen much attention over the past decade as new applications for nanostructured thin films emerge in the fields of nanopatterning and lithography. While solvent assisted annealing techniques are established as flexible and simple methods for achieving long range order, solvent annealing alone exhibits a very weak thermodynamic driving force for vertically orienting domains with respect to the free surface. To address the desire for oriented features, we have investigated a cyclic solvent vapor annealing (CSVA) approach that combines the mobility benefits of solvent annealing with selective stress experienced by structures oriented parallel to the free surface as the film is repeatedly swollen with solvent and dried. Using dynamical self-consistent field theory (DSCFT) calculations, we establish the conditions under which the method significantly outperforms both static and cyclic thermal annealing and implicate the orientation selection as a consequence of the swelling/deswelling process. Our results suggest that CSVA may prove to be a potent method for the rapid formation of highly ordered, vertically oriented features in block copolymer thin films.

Effect of solvents on morphology, magnetic and dielectric properties of (α-Fe2O3@SiO2) core-shell nanoparticles.

PubMed

Joshi, Deepika P; Pant, Geeta; Arora, Neha; Nainwal, Seema

2017-02-01

Present work describes the formation of α-Fe 2 O 3 @SiO 2 core shell structure by systematic layer by layer deposition of silica shell on core iron oxide nanoparticles prepared via various solvents. Sol-gel method has been used to synthesize magnetic core and the dielectric shell. The average crystallite size of iron oxide nanoparticles was calculated ∼20 nm by X-ray diffraction pattern. Morphological study by scanning electron microscopy revealed that the core-shell nanoparticles were spherical in shape and the average size of nanoparticles increased by varying solvent from methanol to ethanol to isopropanol due to different chemical structure and nature of the solvents. It was also observed that the particles prepared by solvent ethanol were more regular and homogeneous as compared to other solvents. Magnetic measurements showed the weak ferromagnetic behaviour of both core α-Fe 2 O 3 and silica-coated iron oxide nanoparticles which remained same irrespective of the solvent chosen. However, magnetization showed dependency on the types of solvent chosen due to the variation in shell thickness. At room temperature, dielectric constant and dielectric loss of silica nanoparticles for all the solvents showed decrement with the increment in frequency. Decrement in the value of dielectric constant and increment in dielectric loss was observed for silica coated iron oxide nanoparticles in comparison of pure silica, due to the presence of metallic core. Homogeneous and regular silica layer prepared by using ethanol as a solvent could serve as protecting layer to shield the magnetic behaviour of iron oxide nanoparticles as well as to provide better thermal insulation over pure α-Fe 2 O 3 nanoparticles.

Solubility and thermodynamics of apremilast in different mono solvents: Determination, correlation and molecular interactions.

PubMed

Shakeel, Faiyaz; Haq, Nazrul; Alanazi, Fars K; Alsarra, Ibrahim A

2017-05-15

The solubility data of recently launched poorly soluble antipsoriatic drug apremilast (APM) in any mono solvent or cosolvent mixtures with respect to temperature are not available in literature. Hence, in this research work, the solubility of APM in twelve different mono solvents namely "water, methanol, ethanol, isopropanol (IPA), ethylene glycol (EG), propylene glycol (PG), 1-butanol, 2-butanol, ethyl acetate (EA), dimethyl sulfoxide (DMSO), polyethylene glycol-400 (PEG-400) and Transcutol ® " was determined at temperatures "T=298.2K to 318.2K" and pressure "p=0.1 MPa". Eexperimental solubilities of APM in mole fraction were determined by a static equilibrium method using high performance liquid chromatography at 254nm. Experimental solubilities of APM in mole fraction were correlated well with "Van't Hoff and Apelblat models". The solubilities of APM in mole fraction were recorded highest in DMSO (9.91×10 -2 ), followed by EA (2.54×10 -2 ), Transcutol (2.51×10 -2 ), PEG-400 (2.16×10 -2 ),PG (4.01×10 -3 ), EG (1.61×10 -3 ), IPA (4.96×10 -4 ), 1-butanol (4.18×10 -4 ), 2-butanol (3.91×10 -4 ), methanol (2.25×10 -4 ), ethanol (2.20×10 -4 ) and water (1.29×10 -6 ) at "T=318.2K" and similar results were also obtained at each temperature evaluated. The molecular interactions between solute and solvent molecules were evaluated by the determination of activity coefficients. Based on activity coefficients, the higher solute-solvents molecular interactions were recorded in APM-DMSO, APM-EA, APM-Transcutol and APM-PEG-400 in comparison with other combination of solute and solvents. "Apparent standard thermodynamic parameters" of APM indicated an "endothermic and entropy-driven dissolution" of APM in all mono solvents evaluated. Based on these results, APM was proposed as freely soluble in DMSO, EA and Transcutol, sparingly soluble in PEG0-400, slightly soluble in methanol, ethanol, IPA, EG, PG, 1-butanol and 2-butanol and practically insoluble in water. Hence, DMSO, EA and Transcutol were selected as the best solvents and water and ethanol were selected as the anti-solvents for APM. Copyright © 2017 Elsevier B.V. All rights reserved.

Experimental observations of the hydrodynamic behavior of solvent systems in high-speed counter-current chromatography. I. Hydrodynamic distribution of two solvent phases in a helical column subjected to two types of synchronous planetary motion.

PubMed

Ito, Y

1984-10-05

Hydrodynamic distribution of two-phase solvent systems in a rotating helical column subjected to centrifugal fields produced by two different types of synchronous planetary motion has been studied by the use of the combined horizontal flow-through coil planet centrifuge. With continuous elution of the mobile phase, the simpler type of motion resulted in low retention of the stationary phase in the column whereas a more complex motion, which produces a quasi-radial centrifugal field varying in both intensity and direction, yielded high stationary phase retention for commonly used solvent systems having a wide range of hydrophobicity. These solvent systems display highly complex modes of hydrodynamic interaction in the coil according to their particular physical properties.

Solvent dependent frequency shift and Raman noncoincidence effect of S=O stretching mode of Dimethyl sulfoxide in liquid binary mixtures.

PubMed

Upadhyay, Ganesh; Devi, Th Gomti; Singh, Ranjan K; Singh, A; Alapati, P R

2013-05-15

The isotropic and anisotropic Raman peak frequencies of S=O stretching mode of Dimethyl sulfoxide (DMSO) have been discussed in different chemical and isotopic solvent molecules using different mechanisms. The shifting of peak frequency in further dilution of DMSO with solvent molecule is observed for all solvents. Transition dipole - transition dipole interaction and hydrogen bonding may play a major role in shifting of peak frequencies. The non-coincidence effect (NCE) of DMSO was determined for all the solvents and compared with four theoretical models such as McHale's model, Mirone's modification of McHale's model, Logan's model and Onsager-Fröhlich dielectric continuum model respectively. Most of the theoretical models are largely consistent with our experimental data. Copyright © 2013. Published by Elsevier B.V.

Solvent effect on the conformation of Benzil

NASA Astrophysics Data System (ADS)

Pawelka, Z.; Koll, A.; Zeegers-Huyskens, Th.

2001-10-01

The conformation of benzil is investigated by PM3 and density functional theory (B3LYP) combined with the 6-31G(d,p) basis set. The variation of the relative energy with the Odbnd C-Cdbnd O torsion angle indicates only one rather flat minimum, reflecting the flexibility of the benzil molecule. The dipole moment is measured in several organic solvents of various polarity and the IR and Raman spectra investigated in the Cdbnd O stretching region in the same solvents. The torsional Odbnd C-Cdbnd O angle is evaluated from the dipolar and vibrational data. The results indicate that, in all the solvents, benzil is in a skewed conformation, the cisoid conformation being slightly favoured when the polarity of the solvent increases. The contribution of electrostatic and specific interactions to the reduction of the torsional angle is discussed.

Microfluidic Extraction of Biomarkers using Water as Solvent

NASA Technical Reports Server (NTRS)

Amashukeli, Xenia; Manohara, Harish; Chattopadhyay, Goutam; Mehdi, Imran

2009-01-01

A proposed device, denoted a miniature microfluidic biomarker extractor (mu-EX), would extract trace amounts of chemicals of interest from samples, such as soils and rocks. Traditionally, such extractions are performed on a large scale with hazardous organic solvents; each solvent capable of dissolving only those molecules lying within narrow ranges of specific chemical and physical characteristics that notably include volatility, electric charge, and polarity. In contrast, in the mu-EX, extractions could be performed by use of small amounts (typically between 0.1 and 100 L) of water as a universal solvent. As a rule of thumb, in order to enable solvation and extraction of molecules, it is necessary to use solvents that have polarity sufficiently close to the polarity of the target molecules. The mu-EX would make selection of specific organic solvents unnecessary, because mu-EX would exploit a unique property of liquid water: the possibility of tuning its polarity to match the polarity of organic solvents appropriate for extraction of molecules of interest. The change of the permittivity of water would be achieved by exploiting interactions between the translational states of water molecules and an imposed electromagnetic field in the frequency range of 300 to 600 GHz. On a molecular level, these interactions would result in disruption of the three-dimensional hydrogen-bonding network among liquid-water molecules and subsequent solvation and hydrolysis of target molecules. The mu-EX is expected to be an efficient means of hydrolyzing chemical bonds in complex macromolecules as well and, thus, enabling analysis of the building blocks of these complex chemical systems. The mu-EX device would include a microfluidic channel, part of which would lie within a waveguide coupled to an electronically tuned source of broad-band electromagnetic radiation in the frequency range from 300 to 600 GHz (see figure). The part of the microfluidic channel lying in the waveguide would constitute an interaction volume. The dimensions of the interaction volume would be chosen in accordance with the anticipated amount of solid sample material needed to ensure extraction of sufficient amount of target molecules for detection and analysis. By means that were not specified at the time of reporting the information for this article, the solid sample material would be placed in the interaction volume. Then the electromagnetic field would be imposed within the waveguide and water would be pumped through the interaction volume to effect the extraction.

40 CFR 63.3961 - How do I demonstrate initial compliance?

Code of Federal Regulations, 2012 CFR

2012-07-01

... balances, calculate the organic HAP emission reduction by applying the volatile organic matter collection... device that indicates the cumulative amount of volatile organic matter recovered by the solvent recovery....0 percent of the mass of volatile organic matter recovered. (2) For each solvent recovery system...

40 CFR 63.3961 - How do I demonstrate initial compliance?

Code of Federal Regulations, 2014 CFR

2014-07-01

... balances, calculate the organic HAP emission reduction by applying the volatile organic matter collection... device that indicates the cumulative amount of volatile organic matter recovered by the solvent recovery....0 percent of the mass of volatile organic matter recovered. (2) For each solvent recovery system...

Thermodynamics of cellulose solvation in water and the ionic liquid 1-butyl-3-methylimidazolim chloride.

PubMed

Gross, Adam S; Bell, Alexis T; Chu, Jhih-Wei

2011-11-24

Cellulose is present in biomass as crystalline microfibrils held together by a complex network of intermolecular interactions making it difficult to initiate its hydrolysis and conversion to fuels. While cellulose is insoluble in water and most organic solvents, complete dissolution of cellulose can be achieved in certain classes of ionic liquids (ILs). The present study was undertaken to analyze the thermodynamic driving forces of this process and to understand how the anions and cations comprising an IL interact with the different moieties of glucose residues to cause dissolution. All-atom molecular dynamics (MD) simulations were performed at two extreme states of cellulose dissolution: a crystalline microfibril and a dissociated state in which all the glucan chains of the microfibril are fully separated from each other by at least four solvation shells. MD simulations of the two states were carried out in water and in the IL 1-butyl-3-methylimidazolium chloride (BmimCl) to provide a comprehensive analysis of solvent effects on cellulose dissolution. The results reveal two important molecular aspects of the mechanism of cellulose dissolution. The first is that the perturbation of solvent structures by the dissolved glucan chains can be a crucial factor in determining solubility, particularly for the insolubility of cellulose in water at 300 K. Second, both the Cl(-) and the Bmim(+) ions of BmimCl interact with the moieties of glucan residues that form intersheet contacts, the most robust component of the interaction network of crystalline cellulose. Cl(-) anions can form hydrogen bonds (HBs) with the hydroxyl groups of glucan chains from either the equatorial or the axial directions. For Bmim(+) cations, the calculated density profiles reveal that the contacts with glucan chains along the axial directions are closer than those along the equatorial directions. On the basis of the results of atomistic MD simulations, we propose that interacting with glucan chains along axial directions and disrupting the intersheet contacts of cellulose is an important ability of cellulose pretreatment solvents. © 2011 American Chemical Society

Development of a methodology to compute solvation free energies on the basis of the theory of energy representation for solutions represented with a polarizable force field.

PubMed

Suzuoka, Daiki; Takahashi, Hideaki; Ishiyama, Tatsuya; Morita, Akihiro

2012-12-07

We have developed a method of molecular simulations utilizing a polarizable force field in combination with the theory of energy representation (ER) for the purpose of establishing an efficient and accurate methodology to compute solvation free energies. The standard version of the ER method is, however, based on the assumption that the solute-solvent interaction is pairwise additive for its construction. A crucial step in the present method is to introduce an intermediate state in the solvation process to treat separately the many-body interaction associated with the polarizable model. The intermediate state is chosen so that the solute-solvent interaction can be formally written in the pairwise form, though the solvent molecules are interacting with each other with polarizable charges dependent on the solvent configuration. It is, then, possible to extract the free energy contribution δμ due to the many-body interaction between solute and solvent from the total solvation free energy Δμ. It is shown that the free energy δμ can be computed by an extension of the recent development implemented in quantum mechanical∕molecular mechanical simulations. To assess the numerical robustness of the approach, we computed the solvation free energies of a water and a methanol molecule in water solvent, where two paths for the solvation processes were examined by introducing different intermediate states. The solvation free energies of a water molecule associated with the two paths were obtained as -5.3 and -5.8 kcal∕mol. Those of a methanol molecule were determined as -3.5 and -3.7 kcal∕mol. These results of the ER simulations were also compared with those computed by a numerically exact approach. It was demonstrated that the present approach produces the solvation free energies in comparable accuracies to simulations of thermodynamic integration (TI) method within a tenth of computational time used for the TI simulations.

Crystal growth, structure and morphology of hydrocortisone methanol solvate

NASA Astrophysics Data System (ADS)

Chen, Jianxin; Wang, Jiangkang; Zhang, Ying; Wu, Hong; Chen, Wei; Guo, Zhichao

2004-04-01

Hydrocortisone (HC), an important grucocorticoid, was crystallized from methanol solvent in the form of its methanol solvate. Its crystal structure belongs to orthorhombic, space group P2 12 12 1, with the unit cell parameters a=7.712(3) Å, b=14.392(5) Å, c=18.408(6) Å, Z=4. The methanol takes part in intermolecular hydrogen bonding, so if we change the solvent, the crystal habit of HC maybe different. The long parallelepiped morphology was also predicted by Cerius 2TM simulation program. The influence of intermolecular interaction was taken into account in the attachment energy model. The morphology calculation performed on the potential energy minimized model using a generic DREIDING 2.21 force field and developed minimization protocol with derived partial charges fits the experimental crystal shape well.

Microsolvation of Cl anion by water clusters: Pertubative Monte Carlo simulations using a hybrid HF/MM potential

NASA Astrophysics Data System (ADS)

Truong, Thanh N.; Stefanovich, Eugene V.

1997-05-01

We present a study of micro-solvation of Cl anion by water clusters of the size up to seven molecules using a perturbative Monte Carlo approach with a hybrid HF/MM potential. In this approach, a perturbation theory was used to avoid performing full SCF calculations at every Monte Carlo step. In this study, the anion is treated quantum mechanically at the HF/6-31G ∗ level of theory while interactions between solvent waters are presented by the TIP3P potential force field. Analysis on the solvent induced dipole moment of the ion indicates that the Cl anion resides most of the time on the surface of the clusters. Accuracy of the perturbative MC approach is also discussed.

Modeling 15N NMR chemical shift changes in protein backbone with pressure

NASA Astrophysics Data System (ADS)

La Penna, Giovanni; Mori, Yoshiharu; Kitahara, Ryo; Akasaka, Kazuyuki; Okamoto, Yuko

2016-08-01

Nitrogen chemical shift is a useful parameter for determining the backbone three-dimensional structure of proteins. Empirical models for fast calculation of N chemical shift are improving their reliability, but there are subtle effects that cannot be easily interpreted. Among these, the effects of slight changes in hydrogen bonds, both intramolecular and with water molecules in the solvent, are particularly difficult to predict. On the other hand, these hydrogen bonds are sensitive to changes in protein environment. In this work, the change of N chemical shift with pressure for backbone segments in the protein ubiquitin is correlated with the change in the population of hydrogen bonds involving the backbone amide group. The different extent of interaction of protein backbone with the water molecules in the solvent is put in evidence.

Thermochemistry of paddle wheel MOFs: Cu-HKUST-1 and Zn-HKUST-1.

PubMed

Bhunia, Manas K; Hughes, James T; Fettinger, James C; Navrotsky, Alexandra

2013-06-25

Metal-organic framework (MOF) porosity relies upon robust metal-organic bonds to retain structural rigidity upon solvent removal. Both the as-synthesized and activated Cu and Zn polymorphs of HKUST-1 were studied by room temperature acid solution calorimetry. Their enthalpies of formation from dense assemblages (metal oxide (ZnO or CuO), trimesic acid (TMA), and N,N-dimethylformamide (DMF)) were calculated from the calorimetric data. The enthalpy of formation (ΔHf) of the as-synthesized Cu-HKUST-H2O ([Cu3TMA2·3H2O]·5DMF) is -52.70 ± 0.34 kJ per mole of Cu. The ΔHf for Zn-HKUST-DMF ([Zn3TMA2·3DMF]·2DMF) is -54.22 ± 0.57 kJ per mole of Zn. The desolvated Cu-HKUST-dg [Cu3TMA2] has a ΔHf of 16.66 ± 0.51 kJ/mol per mole Cu. The ΔHf for Zn-HKUST-amorph [Zn3TMA2·2DMF] is -3.57 ± 0.21 kJ per mole of Zn. Solvent stabilizes the Cu-HKUST-H2O by -69.4 kJ per mole of Cu and Zn-HKUST-DMF by at least -50.7 kJ per mole of Zn. Such strong chemisorption of solvent is similar in magnitude to the strongly exothermic binding at low coverage for chemisorbed H2O on transition metal oxide nanoparticle surfaces. The strongly exothermic solvent-framework interaction suggests that solvent can play a critical role in obtaining a specific secondary building unit (SBU) topology.

A combined experimental (IR, Raman and UV-Vis) and quantum chemical study of canadine

NASA Astrophysics Data System (ADS)

Joshi, Bhawani Datt; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha; Ayala, A. P.

2018-02-01

Plant based natural products cover a major sector of the medicinal field, as such focus on plant research has been increased all over the world. As an attempt to aid that research, we have performed structural and spectroscopic analysis of a natural product, an alkaloid: canadine. Both ab initio Hartree-Fock (HF) and density functional theory (DFT) employing B3LYP using 6-311 ++G(d,p) basis set were used for the calculations. The calculated vibrational frequencies were scaled and compared with the experimental infrared and Raman spectra. The complete vibrational assignments were made using potential energy distribution. The structure-activity relation has also been interpreted by mapping electrostatic potential surface and evaluating the reactivity descriptors, which are valuable information for quality control of medicines and drug-receptor interactions. Natural bond orbital analysis has also been performed to understand the stability and hyperconjugative interactions of the molecule. Furthermore, UV-Vis spectra have been recorded in an ethanol solvent (EtOH) and the electronic property has been analyzed employing TD-DFT for both gaseous and solvent phase. The HOMO and LUMO calculation with their energy gap show that charge transfer occurs within the molecule. Additionally, the nonlinear optical properties of the title compound have been interpreted that predicts it's the best candidate for the NLO materials.

Calculations of the Electric Fields in Liquid Solutions

PubMed Central

Fried, Stephen D.; Wang, Lee-Ping; Boxer, Steven G.; Ren, Pengyu; Pande, Vijay S.

2014-01-01

The electric field created by a condensed phase environment is a powerful and convenient descriptor for intermolecular interactions. Not only does it provide a unifying language to compare many different types of interactions, but it also possesses clear connections to experimental observables, such as vibrational Stark effects. We calculate here the electric fields experienced by a vibrational chromophore (the carbonyl group of acetophenone) in an array of solvents of diverse polarities using molecular dynamics simulations with the AMOEBA polarizable force field. The mean and variance of the calculated electric fields correlate well with solvent-induced frequency shifts and band broadening, suggesting Stark effects as the underlying mechanism of these key solution phase spectral effects. Compared to fixed-charge and continuum models, AMOEBA was the only model examined that could describe non-polar, polar, and hydrogen bonding environments in a consistent fashion. Nevertheless, we found that fixed-charge force fields and continuum models were able to replicate some results of the polarizable simulations accurately, allowing us to clearly identify which properties and situations require explicit polarization and/or atomistic representations to be modeled properly, and for which properties and situations simpler models are sufficient. We also discuss the ramifications of these results for modeling electrostatics in complex environments, such as proteins. PMID:24304155

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghosh, Soumya; Soudackov, Alexander V.; Hammes-Schiffer, Sharon

Electron transfer and proton coupled electron transfer (PCET) reactions at electrochemical interfaces play an essential role in a broad range of energy conversion processes. The reorganization energy, which is a measure of the free energy change associated with solute and solvent rearrangements, is a key quantity for calculating rate constants for these reactions. We present a computational method for including the effects of the double layer and ionic environment of the diffuse layer in calculations of electrochemical solvent reorganization energies. This approach incorporates an accurate electronic charge distribution of the solute within a molecular-shaped cavity in conjunction with a dielectricmore » continuum treatment of the solvent, ions, and electrode using the integral equations formalism polarizable continuum model. The molecule-solvent boundary is treated explicitly, but the effects of the electrode-double layer and double layer-diffuse layer boundaries, as well as the effects of the ionic strength of the solvent, are included through an external Green’s function. The calculated total reorganization energies agree well with experimentally measured values for a series of electrochemical systems, and the effects of including both the double layer and ionic environment are found to be very small. This general approach was also extended to electrochemical PCET and produced total reorganization energies in close agreement with experimental values for two experimentally studied PCET systems. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center, funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences.« less

Local phase separation of co-solvents enhances pretreatment of biomass for bioenergy applications

DOE PAGES

Mostofian, Barmak; Cai, Charles M.; Smith, Micholas Dean; ...

2016-08-02

Pretreatment facilitates more complete deconstruction of plant biomass to enable more economic production of lignocellulosic biofuels and byproducts. Various co-solvent pretreatments have demonstrated advantages relative to aqueous-only methods by enhancing lignin removal to allow unfettered access to cellulose. However, there is a limited mechanistic understanding of the interactions between the co-solvents and cellulose that impedes further improvement of such pretreatment methods. Recently, tetrahydrofuran (THF) has been identified as a highly effective co-solvent for the pretreatment and fractionation of biomass. Here, to elucidate the mechanism of the THF water interactions with cellulose, we pair simulation and experimental data demonstrating that enhancedmore » solubilization of cellulose can be achieved by the THF water co-solvent system at equivolume mixtures and moderate temperatures (≤445 K). The simulations show that THF and water spontaneously phase separate on the local surface of a cellulose fiber, owing to hydrogen bonding of water molecules with the hydrophilic cellulose faces and stacking of THF molecules on the hydrophobic faces. Furthermore, a single fully solvated cellulose chain is shown to be preferentially bound by water molecules in the THF water mixture. In light of these findings, co-solvent reactions were performed on microcrystalline cellulose and maple wood to show that THF significantly enhanced cellulose deconstruction and lignocellulose solubilization at simulation conditions, enabling a highly versatile and efficient biomass pretreatment and fractionation method.« less

Longitudinal nuclear spin relaxation of ortho- and para-hydrogen dissolved in organic solvents.

PubMed

Aroulanda, Christie; Starovoytova, Larisa; Canet, Daniel

2007-10-25

The longitudinal relaxation time of ortho-hydrogen (the spin isomer directly observable by NMR) has been measured in various organic solvents as a function of temperature. Experimental data are perfectly interpreted by postulating two mechanisms, namely intramolecular dipolar interaction and spin-rotation, with activation energies specific to these two mechanisms and to the solvent in which hydrogen is dissolved. This permits a clear separation of the two contributions at any temperature. Contrary to the self-diffusion coefficients at a given temperature, the rotational correlation times extracted from the dipolar relaxation contribution do not exhibit any definite trend with respect to solvent viscosity. Likewise, the spin-rotation correlation time obeys Hubbard's relation only in the case of hydrogen dissolved in acetone-d6, yielding in that case a spin-rotation constant in agreement with literature data. Concerning para-hydrogen, which is NMR-silent, the only feasible approach is to dissolve para-enriched hydrogen in these solvents and to follow the back-conversion of the para-isomer into the ortho-isomer. Experimentally, this conversion has been observed to be exponential, with a time constant assumed to be the relaxation time of the singlet state (the spin state of the para-isomer). A theory, based on intermolecular dipolar interactions, has been worked out for explaining the very large values of these relaxation times which appear to be solvent-dependent.

Quantum Chemical Insight into the Interactions and Thermodynamics Present in Choline Chloride Based Deep Eutectic Solvents.

PubMed

Wagle, Durgesh V; Deakyne, Carol A; Baker, Gary A

2016-07-14

We report quantum chemical calculations performed on three popular deep eutectic solvents (DESs) in order to elucidate the molecular interactions, charge transfer interactions, and thermodynamics associated with these systems. The DESs studied comprise 1:2 choline chloride/urea (reline), 1:2 choline chloride/ethylene glycol (ethaline), and 1:1 choline chloride/malonic acid (maloline). The excellent correlation between calculated and experimental vibrational spectra allowed for identification of dominant interactions in the DES systems. The DESs were found to be stabilized by both conventional hydrogen bonds and C-H···O/C-H···π interactions between the components. The hydrogen-bonding network established in the DES is clearly distinct from that which exists within the neat hydrogen-bond donor dimer. Charge decomposition analysis indicates significant charge transfer from choline and chloride to the hydrogen-bond donor with a higher contribution from the cation, and a density of states analysis confirms the direction of the charge transfer. Consequently, the sum of the bond orders of the choline-Cl(-) interactions in the DESs correlates directly with the melting temperatures of the DESs, a correlation that offers insight into the effect of the tuning of the choline-Cl(-) interactions by the hydrogen-bond donors on the physical properties of the DESs. Finally, the differences in the vibrational entropy changes upon DES formation are consistent with the trend in the overall entropy changes upon DES formation.

Analysis of biomolecular solvation sites by 3D-RISM theory.

PubMed

Sindhikara, Daniel J; Hirata, Fumio

2013-06-06

We derive, implement, and apply equilibrium solvation site analysis for biomolecules. Our method utilizes 3D-RISM calculations to quickly obtain equilibrium solvent distributions without either necessity of simulation or limits of solvent sampling. Our analysis of these distributions extracts highest likelihood poses of solvent as well as localized entropies, enthalpies, and solvation free energies. We demonstrate our method on a structure of HIV-1 protease where excellent structural and thermodynamic data are available for comparison. Our results, obtained within minutes, show systematic agreement with available experimental data. Further, our results are in good agreement with established simulation-based solvent analysis methods. This method can be used not only for visual analysis of active site solvation but also for virtual screening methods and experimental refinement.

The influence of anharmonic and solvent effects on the theoretical vibrational spectra of the guanine-cytosine base pairs in Watson-Crick and Hoogsteen configurations.

PubMed

Bende, Attila; Muntean, Cristina M

2014-03-01

The theoretical IR and Raman spectra of the guanine-cytosine DNA base pairs in Watson-Crick and Hoogsteen configurations were computed using DFT method with M06-2X meta-hybrid GGA exchange-correlation functional, including the anharmonic corrections and solvent effects. The results for harmonic frequencies and their anharmonic corrections were compared with our previously calculated values obtained with the B3PW91 hybrid GGA functional. Significant differences were obtained for the anharmonic corrections calculated with the two different DFT functionals, especially for the stretching modes, while the corresponding harmonic frequencies did not differ considerable. For the Hoogtseen case the H⁺ vibration between the G-C base pair can be characterized as an asymmetric Duffing oscillator and therefore unrealistic anharmonic corrections for normal modes where this proton vibration is involved have been obtained. The spectral modification due to the anharmonic corrections, solvent effects and the influence of sugar-phosphate group for the Watson-Crick and Hoogsteen base pair configurations, respectively, were also discussed. For the Watson-Crick case also the influence of the stacking interaction on the theoretical IR and Raman spectra was analyzed. Including the anharmonic correction in our normal mode analysis is essential if one wants to obtain correct assignments of the theoretical frequency values as compared with the experimental spectra.

Solvolysis of para-substituted cumyl chlorides. Brown and Okamoto's electrophilic substituent constants revisited using continuum solvent models.

PubMed

DiLabio, Gino A; Ingold, K U

2004-03-05

Brown and Okamoto (J. Am. Chem. Soc. 1958, 80, 4979) derived their electrophilic substitutent constants, sigma(p)+, from the relative rates of solvolysis of ring-substituted cumyl chlorides in an acetone/water solvent mixture. Application of the Hammett equation to the rates for the meta-substituted cumyl chlorides, where there could be no resonance interaction with the developing carbocation, gave a slope, rho(+) = -4.54 ( identical with 6.2 kcal/mol free energy). Rates for the para-substituted chlorides were then used to obtain sigma(p)+ values. We have calculated gas-phase C-Cl heterolytic bond dissociation enthalpy differences, Delta BDE(het) (= BDE(het)(4-YC(6)H(4)CMe(2)Cl) - BDE(het)(C(6)H(5)CMe(2)Cl)), for 16 of the 4-Y substituents employed by Brown and Okamoto. The plot of Delta BDE(het) vs sigma(p)+ gave rho(+) (SD) = 16.3 (2.3) kcal/mol, i.e., a rho(+) value roughly 2.5 times greater than experiment. Inclusion of solvation (water) energies, calculated using three continuum solvent models, reduced rho(+) and SD. The computationally least expensive model used, SM5.42R (Li et al. Theor. Chem. Acc. 1999, 103, 9) gave the best agreement with experiment. This model yielded rho(+) (SD) = 7.7 (0.9) kcal/mol, i.e., a rho(+) value that is only 24% larger than experiment.

Theoretical modeling of the absorption spectrum of aqueous riboflavin

NASA Astrophysics Data System (ADS)

Zanetti-Polzi, Laura; Aschi, Massimiliano; Daidone, Isabella; Amadei, Andrea

2017-02-01

In this study we report the modeling of the absorption spectrum of riboflavin in water using a hybrid quantum/classical mechanical approach, the MD-PMM methodology. By means of MD-PMM calculations, with which the effect of riboflavin internal motions and of solvent interactions on the spectroscopic properties can be explicitly taken into account, we obtain an absorption spectrum in very good agreement with the experimental spectrum. In particular, the calculated peak maxima show a consistent improvement with respect to previous computational approaches. Moreover, the calculations show that the interaction with the environment may cause a relevant recombination of the gas-phase electronic states.

Theoretical study on substituent and solvent effects for nanocubes formed with gear-shaped amphiphile molecules.

PubMed

Mashiko, T; Hiraoka, S; Nagashima, U; Tachikawa, M

2017-01-04

Gear-shaped amphiphile molecules (1) recently synthesized by Hiraoka et al. self-assemble into a hexameric structure, nanocubes (1 6 ), in 25% aqueous methanol due to a solvophobic effect. Here we have carried out molecular dynamic simulations to elucidate the stability of these hexameric capsules (1 6 and 2 6 ) in water, 25% aqueous methanol, and methanol. In all solvents, the 1 6 nanocubes are maintained for all trajectories. On the other hand, 2 6 was found to collapse for one trajectory in water and seven trajectories in 25% aqueous methanol. In a pure methanol solvent, 2 6 was found to collapse for all trajectories. The number of collapsed trajectories of 2 6 increased with the amount of methanol in the solvent. We therefore focused on the structure of the π-π stacking between pyridyl groups and the CH-π interactions between the methyl and pyridyl groups within the nanocube. Our study clearly shows the role played by the methanol solvent molecules in the assembly of the nanocube in terms of the substituent and solvent effects at the molecular level, and that these substituent and solvent effects are important for the self-assembly of the nanocubes.

Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects.

PubMed

Lomize, Andrei L; Pogozheva, Irina D; Mosberg, Henry I

2011-04-25

A new implicit solvation model was developed for calculating free energies of transfer of molecules from water to any solvent with defined bulk properties. The transfer energy was calculated as a sum of the first solvation shell energy and the long-range electrostatic contribution. The first term was proportional to solvent accessible surface area and solvation parameters (σ(i)) for different atom types. The electrostatic term was computed as a product of group dipole moments and dipolar solvation parameter (η) for neutral molecules or using a modified Born equation for ions. The regression coefficients in linear dependencies of solvation parameters σ(i) and η on dielectric constant, solvatochromic polarizability parameter π*, and hydrogen-bonding donor and acceptor capacities of solvents were optimized using 1269 experimental transfer energies from 19 organic solvents to water. The root-mean-square errors for neutral compounds and ions were 0.82 and 1.61 kcal/mol, respectively. Quantification of energy components demonstrates the dominant roles of hydrophobic effect for nonpolar atoms and of hydrogen-bonding for polar atoms. The estimated first solvation shell energy outweighs the long-range electrostatics for most compounds including ions. The simplicity and computational efficiency of the model allows its application for modeling of macromolecules in anisotropic environments, such as biological membranes.

Joint density-functional theory for energetics and spectroscopy in complex aqueous and nonaqueous solvents

NASA Astrophysics Data System (ADS)

Gunceler, Deniz

Solvents are of great importance in many technological applications, but are difficult to study using standard, off-the-shelf ab initio electronic structure methods. This is because a single configuration of molecular positions in the solvent (a "snapshot" of the fluid) is not necessarily representative of the thermodynamic average. To obtain any thermodynamic averages (e.g. free energies), the phase space of the solvent must be sampled, typically using molecular dynamics. This greatly increases the computational cost involved in studying solvated systems. Joint density-functional theory has made its mark by being a computationally efficient yet rigorous theory by which to study solvation. It replaces the need for thermodynamic sampling with an effective continuum description of the solvent environment that is in-principle exact, computationally efficient and intuitive (easier to interpret). It has been very successful in aqueous systems, with potential applications in (among others) energy materials discovery, catalysis and surface science. In this dissertation, we develop accurate and fast joint density functional theories for complex, non-aqueous solvent enviroments, including organic solvents and room temperature ionic liquids, as well as new methods for calculating electron excitation spectra in such systems. These theories are then applied to a range of physical problems, from dendrite formation in lithium-metal batteries to the optical spectra of solvated ions.

Evaluation of the performance and response of the bacharach TLV sniffer and H-Nu photoionization gas analyzer to common hydrocarbon solvents.

PubMed

Chelton, C F; Zakraysek, N; Lautner, G M; Confer, R G

1983-10-01

Two direct reading instruments, the H-Nu PI 101 photoionization analyzer and the J.W. Bacharach TLV Sniffer, were evaluated under laboratory conditions to determine their performance characteristics when challenged by vapors of common hydrocarbon solvent mixtures. Each instrument was evaluated against the manufacturer's recommended test solvent for rise time, fall time, noise, span drift, zero drift, position sensitivity, battery life, and recharge time. The precision, accuracy, and operating linear range were also determined for the test solvents and some petroleum solvent mixtures which are common refinery products. For these latter mixtures, correction factors are presented which allow for an improved estimate of ambient concentrations when monitoring with each of these instruments. All tests except operating humidity range were performed by challenging each instrument with a known concentration of hydrocarbon generated by evaporating calculated liquid volumes into a static chamber. Humidity tests were performed using a dynamic dilution apparatus generating a fixed concentration of hydrocarbon while relative humidity was varied. Concentrations in both systems were verified by gas injection into gas chromatograph. Each instrument performed well when challenged by manufacturers' recommended test solvents. Humidity was shown to influence each instrument's readings. Also, the instruments were shown to have application as monitors of airborne concentrations of common hydrocarbon solvent mixtures.

A turn-on type stimuli-responsive fluorescent dye with specific solvent effect: Implication for a new prototype of paper using water as the ink

NASA Astrophysics Data System (ADS)

Hu, Xiaochen; Liu, Yang; Duan, Yuai; Han, Jingqi; Li, Zhongfeng; Han, Tianyu

2017-09-01

In this study, we reported the photoluminescence (PL) behaviour of a new intramolecular charge transfer (ICT) compound, ((E)-2-(((2-hydroxynaphthalen-1-yl)methylene)amino)benzoic acid, (HABA), which shows ICT solvent effect in aprotic solvents as confirmed by absorption and emission spectra. While in protic solvents including water and ethanol, the charge transfer (CT) band significantly reduces. Remarkable fluorescence enhancement in the blue region was also observed for HABA in polar protic solvents. We described such phenomena as ;specific solvent effect;. It can be ascribed to the hydrogen bonding formation between HABA and protic solvents, which not only causes significant reduction in the rate of internal conversion but also elevates the energy gap. Density functional theory (DFT) calculations as well as the dynamics analysis were performed to further verify the existence of hydrogen bonding complexes. Stronger emission turn-on effect was observed on HABA solid film when it is treated with water and base solution. The stimuli-responsive fluorescence of HABA enables a new green printing technique that uses water/base as the ink, affording fluorescent handwritings highly distinct from the background. Thermoanalysis of the dye suggests the nice thermostability, which is highly desired for real-world printing in a wide temperature range.

Soft wheat and flour products methods review: solvent retention capacity equation correction

USDA-ARS?s Scientific Manuscript database

This article discusses the results of a significant change to calculations made within AACCI Approved methods 56-10 and 56-11, the Alkaline Water Retention Capacity (AWRC) test and the Solvent Retention Capacity (SRC) test. The AACCI Soft Wheat and Flour Products Technical Committee reviewed propos...

Investigation of Ion-Solvent Interactions in Nonaqueous Electrolytes Using in Situ Liquid SIMS.

PubMed

Zhang, Yanyan; Su, Mao; Yu, Xiaofei; Zhou, Yufan; Wang, Jungang; Cao, Ruiguo; Xu, Wu; Wang, Chongmin; Baer, Donald R; Borodin, Oleg; Xu, Kang; Wang, Yanting; Wang, Xue-Lin; Xu, Zhijie; Wang, Fuyi; Zhu, Zihua

2018-03-06

Ion-solvent interactions in nonaqueous electrolytes are of fundamental interest and practical importance, yet debates regarding ion preferential solvation and coordination numbers persist. In this work, in situ liquid SIMS was used to examine ion-solvent interactions in three representative electrolytes, i.e., lithium hexafluorophosphate (LiPF 6 ) at 1.0 M in ethylene carbonate (EC)-dimethyl carbonate (DMC) and lithium bis(fluorosulfonyl)imide (LiFSI) at both low (1.0 M) and high (4.0 M) concentrations in 1,2-dimethoxyethane (DME). In the positive ion mode, solid molecular evidence strongly supports the preferential solvation of Li + by EC. Besides, from the negative spectra, we also found that PF 6 - forms association with EC, which has been neglected by previous studies due to the relatively weak interaction. In both LiFSI in DME electrolytes, however, no evidence shows that FSI - is associated with DME. Furthermore, strong salt ion cluster signals were observed in the 1.0 M LiPF 6 in EC-DMC electrolyte, suggesting that a significant amount of Li + ions stay in the vicinity of anions. In sharp comparison, weak ion cluster signals were detected in dilute LiFSI in DME electrolyte, suggesting most ions are well separated, in agreement with our molecular dynamics simulation results. These findings indicate that with virtues of little bias on detecting positive and negative ions and the capability of directly analyzing concentrated electrolytes, in situ liquid SIMS is a powerful tool that can provide key evidence for improved understanding on the ion-solvent interactions in nonaqueous electrolytes. Therefore, we anticipate wide applications of in situ liquid SIMS on investigations of various ion-solvent interactions in the near future.

Investigation of Ion-Solvent Interactions in Nonaqueous Electrolytes Using in Situ Liquid SIMS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yanyan; Su, Mao; Yu, Xiaofei

2018-02-06

Ion-solvent interactions in non-aqueous electrolytes are of fundamental interest and practical importance, yet debates regarding ion preferential solvation and coordination numbers persist. In this work, in situ liquid SIMS was used to examine ion-solvent interactions in three representative electrolytes, i.e., lithium hexafluorophosphate (LiPF6) at 1.0 M in ethylene carbonate (EC)-dimethyl carbonate (DMC), and lithium bis(fluorosulfonyl)imide (LiFSI) at both low (1.0 M) and high (4.0 M) concentrations in 1,2-dimethoxyethane (DME). In the positive ion mode, solid molecular evidence strongly supports the preferential solvation of Li+ by EC. Besides, from the negative spectra, we also found that PF6- forms association with EC,more » which has been neglected by previous studies due to the relatively weak interaction. While in both LiFSI in DME electrolytes, no evidence shows that FSI- is associated with DME. Furthermore, strong salt ion cluster signals were observed in the 1.0 M LiPF6 in EC-DMC electrolyte, suggesting that a significant amount of Li+ ions stay in vicinity of anions. In sharp comparison, weak ion cluster signals were detected in dilute LiFSI in DME electrolyte, suggesting most ions are well separated, in agreement with our molecular dynamics (MD) simulation results. These findings indicate that with virtues of little bias on detecting positive and negative ions and the capability of directly analyzing concentrated electrolytes, in situ liquid SIMS is a powerful tool that can provide key evidence for improved understanding on the ion-solvent interactions in non-aqueous electrolytes. Therefore, we anticipate wide applications of in situ liquid SIMS on investigations of various ion-solvent interactions in the near future.« less

Investigation of Ion–Solvent Interactions in Nonaqueous Electrolytes Using in Situ Liquid SIMS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yanyan; Su, Mao; Yu, Xiaofei

Ion-solvent interactions in non-aqueous electrolytes are of fundamental interest and practical importance, yet debates regarding ion preferential solvation and coordination numbers persist. In this work, in situ liquid SIMS was used to examine ion-solvent interactions in three representative electrolytes, i.e., lithium hexafluorophosphate (LiPF6) at 1.0 M in ethylene carbonate (EC)-dimethyl carbonate (DMC), and lithium bis(fluorosulfonyl)imide (LiFSI) at both low (1.0 M) and high (4.0 M) concentrations in 1,2-dimethoxyethane (DME). In the positive ion mode, solid molecular evidence strongly supports the preferential solvation of Li+ by EC. Besides, from the negative spectra, we also found that PF6- forms association with EC,more » which has been neglected by previous studies due to the relatively weak interaction. While in both LiFSI in DME electrolytes, no evidence shows that FSI- is associated with DME. Furthermore, strong salt ion cluster signals were observed in the 1.0 M LiPF6 in EC-DMC electrolyte, suggesting that a significant amount of Li+ ions stay in vicinity of anions. In sharp comparison, weak ion cluster signals were detected in dilute LiFSI in DME electrolyte, suggesting most ions are well separated, in agreement with our molecular dynamics (MD) simulation results. These findings indicate that with virtues of little bias on detecting positive and negative ions and the capability of directly analyzing concentrated electrolytes, in situ liquid SIMS is a powerful tool that can provide key evidence for improved understanding on the ion-solvent interactions in non-aqueous electrolytes. Therefore, we anticipate wide applications of in situ liquid SIMS on investigations of various ion-solvent interactions in the near future.« less

Structure of a tethered polymer under flow using molecular dynamics and hybrid molecular-continuum simulations

NASA Astrophysics Data System (ADS)

Delgado-Buscalioni, Rafael; Coveney, Peter V.

2006-03-01

We analyse the structure of a single polymer tethered to a solid surface undergoing a Couette flow. We study the problem using molecular dynamics (MD) and hybrid MD-continuum simulations, wherein the polymer and the surrounding solvent are treated via standard MD, and the solvent flow farther away from the polymer is solved by continuum fluid dynamics (CFD). The polymer represents a freely jointed chain (FJC) and is modelled by Lennard-Jones (LJ) beads interacting through the FENE potential. The solvent (modelled as a LJ fluid) and a weakly attractive wall are treated at the molecular level. At large shear rates the polymer becomes more elongated than predicted by existing theoretical scaling laws. Also, along the normal-to-wall direction the structure observed for the FJC is, surprisingly, very similar to that predicted for a semiflexible chain. Comparison with previous Brownian dynamics simulations (which exclude both solvent and wall potential) indicates that these effects are due to the polymer-solvent and polymer-wall interactions. The hybrid simulations are in perfect agreement with the MD simulations, showing no trace of finite size effects. Importantly, the extra cost required to couple the MD and CFD domains is negligible.

Controlled Self-Assembly of Low-Dimensional Alq3 Nanostructures from 1D Nanowires to 2D Plates via Intermolecular Interactions

NASA Astrophysics Data System (ADS)

Gu, Jianmin; Yin, Baipeng; Fu, Shaoyan; Jin, Cuihong; Liu, Xin; Bian, Zhenpan; Li, Jianjun; Wang, Lu; Li, Xiaoyu

2018-03-01

Due to the intense influence of the shape and size of the photon building blocks on the limitation and guidance of optical waves, an important strategy is the fabrication of different structures. Herein, organic semiconductor tris-(8-hydroxyquinoline)aluminium (Alq3) nanostructures with controllable morphology, ranging from one-dimensional nanowires to two-dimensional plates, have been prepared through altering intermolecular interactions with employing the anti-solvent diffusion cooperate with solvent-volatilization induced self-assembly method. The morphologies of the formed nanostructures, which are closely related to the stacking modes of the molecules, can be exactly controlled by altering the polarity of anti-solvents that can influence various intermolecular interactions. The synthesis strategy reported here can potentially be extended to other functional organic nanomaterials.

Kamlet-Taft solvent parameters, NMR spectroscopic analysis and thermoelectrochemistry of lithium-glyme solvate ionic liquids and their dilute solutions.

PubMed

Black, Jeffrey J; Dolan, Andrew; Harper, Jason B; Aldous, Leigh

2018-06-06

Solvate ionic liquids are a relatively new class of liquids produced by combining a coordinating solvent with a salt. They have a variety of uses and their suitability for such depends upon the ratio of salt to coordinating solvent. This work investigates the Kamlet-Taft solvent parameters of, NMR chemical shifts of nuclei in, and thermoelectrochemistry of a selected set of solvate ionic liquids produced from glymes (methyl terminated oligomers of ethylene glycol) and lithium bis(trifluoromethylsulfonyl)imide at two different compositions. The aim is to improve the understanding of the interactions occurring in these ionic liquids to help select suitable solvate ionic liquids for future applications.