Maximum likelihood density modification by pattern recognition of structural motifs

DOEpatents

Terwilliger, Thomas C.

2004-04-13

An electron density for a crystallographic structure having protein regions and solvent regions is improved by maximizing the log likelihood of a set of structures factors {F.sub.h } using a local log-likelihood function: (x)+p(.rho.(x).vertline.SOLV)p.sub.SOLV (x)+p(.rho.(x).vertline.H)p.sub.H (x)], where p.sub.PROT (x) is the probability that x is in the protein region, p(.rho.(x).vertline.PROT) is the conditional probability for .rho.(x) given that x is in the protein region, and p.sub.SOLV (x) and p(.rho.(x).vertline.SOLV) are the corresponding quantities for the solvent region, p.sub.H (x) refers to the probability that there is a structural motif at a known location, with a known orientation, in the vicinity of the point x; and p(.rho.(x).vertline.H) is the probability distribution for electron density at this point given that the structural motif actually is present. One appropriate structural motif is a helical structure within the crystallographic structure.

Counterintuitive electron localisation from density-functional theory with polarisable solvent models

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

Dale, Stephen G., E-mail: sdale@ucmerced.edu; Johnson, Erin R., E-mail: erin.johnson@dal.ca

2015-11-14

Exploration of the solvated electron phenomena using density-functional theory (DFT) generally results in prediction of a localised electron within an induced solvent cavity. However, it is well known that DFT favours highly delocalised charges, rendering the localisation of a solvated electron unexpected. We explore the origins of this counterintuitive behaviour using a model Kevan-structure system. When a polarisable-continuum solvent model is included, it forces electron localisation by introducing a strong energetic bias that favours integer charges. This results in the formation of a large energetic barrier for charge-hopping and can cause the self-consistent field to become trapped in local minimamore » thus converging to stable solutions that are higher in energy than the ground electronic state. Finally, since the bias towards integer charges is caused by the polarisable continuum, these findings will also apply to other classical polarisation corrections, as in combined quantum mechanics and molecular mechanics (QM/MM) methods. The implications for systems beyond the solvated electron, including cationic DNA bases, 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.

On the theory of electric double layer with explicit account of a polarizable co-solvent.

PubMed

Budkov, Yu A; Kolesnikov, A L; Kiselev, M G

2016-05-14

We present a continuation of our theoretical research into the influence of co-solvent polarizability on a differential capacitance of the electric double layer. We formulate a modified Poisson-Boltzmann theory, using the formalism of density functional approach on the level of local density approximation taking into account the electrostatic interactions of ions and co-solvent molecules as well as their excluded volume. We derive the modified Poisson-Boltzmann equation, considering the three-component symmetric lattice gas model as a reference system and minimizing the grand thermodynamic potential with respect to the electrostatic potential. We apply present modified Poisson-Boltzmann equation to the electric double layer theory, showing that accounting for the excluded volume of co-solvent molecules and ions slightly changes the main result of our previous simplified theory. Namely, in the case of small co-solvent polarizability with its increase under the enough small surface potentials of electrode, the differential capacitance undergoes the significant growth. Oppositely, when the surface potential exceeds some threshold value (which is slightly smaller than the saturation potential), the increase in the co-solvent polarizability results in a differential capacitance decrease. However, when the co-solvent polarizability exceeds some threshold value, its increase generates a considerable enhancement of the differential capacitance in a wide range of surface potentials. We demonstrate that two qualitatively different behaviors of the differential capacitance are related to the depletion and adsorption of co-solvent molecules at the charged electrode. We show that an additive of the strongly polarizable co-solvent to an electrolyte solution can shift significantly the saturation potential in two qualitatively different manners. Namely, a small additive of strongly polarizable co-solvent results in a shift of saturation potential to higher surface potentials. On the contrary, a sufficiently large additive of co-solvent shifts the saturation potential to lower surface potentials. We obtain that an increase in the co-solvent polarizability makes the electrostatic potential profile longer-ranged. However, increase in the co-solvent concentration in the bulk leads to non-monotonic behavior of the electrostatic potential profile. An increase in the co-solvent concentration in the bulk at its sufficiently small values makes the electrostatic potential profile longer-ranged. Oppositely, when the co-solvent concentration in the bulk exceeds some threshold value, its further increase leads to decrease in electrostatic potential at all distances from the electrode.

Dendritic brushes under theta and poor solvent conditions

NASA Astrophysics Data System (ADS)

Gergidis, Leonidas N.; Kalogirou, Andreas; Charalambopoulos, Antonios; Vlahos, Costas

2013-07-01

The effects of solvent quality on the internal stratification of polymer brushes formed by dendron polymers up to third generation were studied by means of molecular dynamics simulations with Langevin thermostat. The distributions of polymer units, of the free ends, the radii of gyration, and the back folding probabilities of the dendritic spacers were studied at the macroscopic states of theta and poor solvent. For high grafting densities we observed a small decrease in the height of the brush as the solvent quality decreases. The internal stratification in theta solvent was similar to the one we found in good solvent, with two and in some cases three kinds of populations containing short dendrons with weakly extended spacers, intermediate-height dendrons, and tall dendrons with highly stretched spacers. The differences increase as the grafting density decreases and single dendron populations were evident in theta and poor solvent. In poor solvent at low grafting densities, solvent micelles, polymeric pinned lamellae, spherical and single chain collapsed micelles were observed. The scaling dependence of the height of the dendritic brush at high density brushes for both solvents was found to be in agreement with existing analytical results.

Organic-inorganic hybrid perovskite quantum dots with high PLQY and enhanced carrier mobility through crystallinity control by solvent engineering and solid-state ligand exchange.

PubMed

Woo Choi, Jin; Woo, Hee Chul; Huang, Xiaoguang; Jung, Wan-Gil; Kim, Bong-Joong; Jeon, Sie-Wook; Yim, Sang-Youp; Lee, Jae-Suk; Lee, Chang-Lyoul

2018-05-22

The photoluminescence quantum yield (PLQY) and charge carrier mobility of organic-inorganic perovskite QDs were enhanced by the optimization of crystallinity and surface passivation as well as solid-state ligand exchange. The crystallinity of perovskite QDs was determined by the Effective solvent field (Esol) of various solvents for precipitation. The solvent with high Esol could more quickly countervail the localized field generated by the polar solvent, and it causes fast crystallization of the dissolved precursor, which results in poor crystallinity. The post-ligand adding process (PLAP) and post-ligand exchange process (PLEP) increase the PLQY of perovskite QDs by reducing non-radiative recombination and the density of surface defect states through surface passivation. Particularly, the post ligand exchange process (PLEP) in the solid-state improved the charge carrier mobility of perovskite QDs in addition to the PLQY enhancement. The ligand exchange with short alkyl chain length ligands could improve the packing density of perovskite QDs in films by reducing the inter-particle distance between perovskite QDs. The maximum hole mobility of 6.2 × 10-3 cm2 V-1 s-1, one order higher than that of pristine QDs without the PLEP, is obtained at perovskite QDs with hexyl ligands. By using PLEP treatment, compared to the pristine device, a 2.5 times higher current efficiency in perovskite QD-LEDs was achieved due to the improved charge carrier mobility and PLQY.

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.

Electric Double Layer Composed of an Antagonistic Salt in an Aqueous Mixture: Local Charge Separation and Surface Phase Transition

NASA Astrophysics Data System (ADS)

Yabunaka, Shunsuke; Onuki, Akira

2017-09-01

We examine an electric double layer containing an antagonistic salt in an aqueous mixture, where the cations are small and hydrophilic but the anions are large and hydrophobic. In this situation, a strong coupling arises between the charge density and the solvent composition. As a result, the anions are trapped in an oil-rich adsorption layer on a hydrophobic wall. We then vary the surface charge density σ on the wall. For σ >0 the anions remain accumulated, but for σ <0 the cations are attracted to the wall with increasing |σ |. Furthermore, the electric potential drop Ψ (σ ) is nonmonotonic when the solvent interaction parameter χ (T ) exceeds a critical value χc determined by the composition and the ion density in the bulk. This leads to a first-order phase transition between two kinds of electric double layers with different σ and common Ψ . In equilibrium such two-layer regions can coexist. The steric effect due to finite ion sizes is crucial in these phenomena.

First-Principles and Thermodynamic Simulation of Elastic Stress Effect on Energy of Hydrogen Dissolution in Alpha Iron

NASA Astrophysics Data System (ADS)

Rakitin, M. S.; Mirzoev, A. A.; Mirzaev, D. A.

2018-04-01

Mobile hydrogen, when dissolving in metals, redistributes due to the density gradients and elastic stresses, and enables destruction processes or phase transformations in local volumes of a solvent metal. It is rather important in solid state physics to investigate these interactions. The first-principle calculations performed in terms of the density functional theory, are used for thermodynamic simulation of the elastic stress effect on the energy of hydrogen dissolution in α-Fe crystal lattice. The paper presents investigations of the total energy of Fe-H system depending on the lattice parameter. As a result, the relation is obtained between the hydrogen dissolution energy and stress. A good agreement is shown between the existing data and simulation results. The extended equation is suggested for the chemical potential of hydrogen atom in iron within the local stress field. Two parameters affecting the hydrogen distribution are compared, namely local stress and phase transformations.

Counting ions and other nucleophiles at surfaces by chemical trapping.

PubMed

Cuccovia, Iolanda Midea; da Silva Lima, Filipe; Chaimovich, Hernan

2017-10-01

The interfaces of membranes and other aggregates are determined by the polarity, electrical charge, molecular volume, degrees of motional freedom and packing density of the head groups of the amphiphiles. These properties also determine the type of bound ion (ion selectivity) and its local density, i.e. concentration defined by choosing an appropriate volume element at the aggregate interface. Bulk and local ion concentrations can differ by orders of magnitude. The relationships between ion (or other compound) concentrations in the bulk solvent and in the interface are complex but, in some cases, well established. As the local ion concentration, rather than that in the bulk, controls a variety of properties of membranes, micelles, vesicles and other objects of theoretical and applied interests, measurement of local (interfacial, bound) ion concentrations is of relevance for understanding and characterizing such aggregates. Many experimental methods for estimating ion distributions between the bulk solution and the interface provide indirect estimates because they are based on concentration-dependent properties, rather than concentration measurements. Dediazoniation, i.e. the loss of N 2 , of a substituted diazophenyl derivative provides a tool for determining the number of nucleophiles (including neutral or negatively charged ions) surrounding the diazophenyl derivative prior to the dediazoniation event. This reaction, defined as chemical trapping, and the appropriate reference points obtained in bulk solution allow direct measurements of local concentrations of a variety of nucleophiles at the surface of membranes and other aggregates. Here we review our contributions of our research group to the use, and understanding, of this method and applications of chemical trapping to the description of local concentrations of ions and other nucleophiles in micelles, reverse micelles, vesicles and solvent mixtures. Among other results, we have shown that interfacial water determines micellar shape, zwitterionic vesicle-forming amphiphiles display ion selectivity and urea does not accumulate at micellar interfaces. We have also shown that reaction products can be predicted from the composition of the initial state, even in non-ideal solvent mixtures, supporting the usefulness of chemical trapping as a method to determine local concentrations. In addition, we have analysed the mechanism of dediazoniation, both on theoretical and experimental basis, and concluded that the formation of a free phenyl cation is not a necessary part of the reaction pathway.

Solvent selection in ultrasonic-assisted emulsification microextraction: Comparison between high- and low-density solvents by means of novel type of extraction vessel.

PubMed

Nojavan, Saeed; Gorji, Tayebeh; Davarani, Saied Saeed Hosseiny; Morteza-Najarian, Amin

2014-08-01

There are numerous published reports about dispersive liquid phase microextraction of the wide range of substances, however, till now no broadly accepted systematic and purpose oriented selection of extraction solvent has been proposed. Most works deal with the optimization of available solvents without adequate pre-consideration of properness. In this study, it is tried to compare the performances of low- and high-density solvents at the same conditions by means of novel type of extraction vessel with head and bottom conical shape. Extraction efficiencies of seven basic pharmaceutical compounds using eighteen common organic solvents were studied in this work. It was much easier to work with high-density solvents and they mostly showed better performances. This work shows that although exact predicting the performance of the solvents is multifaceted case but the pre-consideration of initial selection of solvents with attention to the physiochemical properties of the desired analytes is feasible and promising. Finally, the practicality of the method for extraction from urine and plasma samples was investigated. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Fluid transition layer between rigid solute and liquid solvent: is there depletion or enrichment?

PubMed

Djikaev, Yuri S; Ruckenstein, Eli

2016-03-21

The fluid layer between solute and liquid solvent is studied by combining the density functional theory with the probabilistic hydrogen bond model. This combination allows one to obtain the equilibrium distribution of fluid molecules, taking into account the hydrogen bond contribution to the external potential whereto they are subjected near the solute. One can find the effective width of the fluid solvent-solute transition layer and fluid average density in that layer, and determine their dependence on temperature, solvent-solute affinity, vicinal hydrogen bond (hb) energy alteration ratio, and solute radius. Numerical calculations are performed for the solvation of a plate and spherical solutes of four different radii in two model solvents (associated liquid and non-associated one) in the temperature range from 293 K to 333 K for various solvent-solute affinities and hydrogen bond energy alteration ratios. The predictions of our model for the effective width and average density of the transition layer are consistent with experiments and simulations. The small-to-large crossover lengthscale for hydrophobic hydration is expected to be about 3-5 nm. Remarkably, characterizing the transition layer with the average density, one can observe that for small hydrophobes, the transition layer becomes enriched with rather than depleted of fluid when the solvent-solute affinity and hb-energy alteration ratio become large enough. The boundary values of solvent-solute affinity and hb-energy alteration ratio, needed for the "depletion-to-enrichment" crossover (in the smoothed density sense), are predicted to decrease with increasing temperature.

Effects of concentration, temperature and solvent composition on density and apparent molar volume of the binary mixtures of cationic-anionic surfactants in methanol-water mixed solvent media.

PubMed

Bhattarai, Ajaya; Chatterjee, Sujeet Kumar; Niraula, Tulasi Prasad

2013-01-01

The accurate measurements on density of the binary mixtures of cetyltrimethylammonium bromide and sodium dodecyl sulphate in pure water and in methanol(1) + water (2) mixed solvent media containing (0.10, 0.20, and 0.30) volume fractions of methanol at 308.15, 318.15, and 323.15 K are reported. The concentrations are varied from (0.03 to 0.12) mol.l(-1) of sodium dodecyl sulphate in presence of ~ 5.0×10(-4) mol.l(-1) cetyltrimethylammonium bromide. The results showed almost increase in the densities with increasing surfactant mixture concentration, also the densities are found to decrease with increasing temperature over the entire concentration range, investigated in a given mixed solvent medium and these values are found to decrease with increasing methanol content in the solvent composition. The concentration dependence of the apparent molar volumes appear to be negligible over the entire concentration range, investigated in a given mixed solvent medium and the apparent molar volumes increase with increasing temperature and are found to decrease with increasing methanol content in the solvent composition.

Solvent effects on the excited-state double proton transfer mechanism in the 7-azaindole dimer: a TDDFT study with the polarizable continuum model.

PubMed

Yu, Xue-Fang; Yamazaki, Shohei; Taketsugu, Tetsuya

2017-08-30

Solvent effects on the excited-state double proton transfer (ESDPT) mechanism in the 7-azaindole (7AI) dimer were investigated using the time-dependent density functional theory (TDDFT) method. Excited-state potential energy profiles along the reaction paths in a locally excited (LE) state and a charge transfer (CT) state were calculated using the polarizable continuum model (PCM) to include the solvent effect. A series of non-polar and polar solvents with different dielectric constants were used to examine the polarity effect on the ESDPT mechanism. The present results suggest that in a non-polar solvent and a polar solvent with a small dielectric constant, ESDPT follows a concerted mechanism, similar to the case in the gas phase. In a polar solvent with a relatively large dielectric constant, however, ESDPT is likely to follow a stepwise mechanism via a stable zwitterionic intermediate in the LE state on the adiabatic potential energy surface, although inclusion of zero-point vibrational energy (ZPE) corrections again suggests the concerted mechanism. In the meantime, the stepwise reaction path involving the CT state with neutral intermediates is also examined, and is found to be less competitive than the concerted or stepwise path in the LE state in both non-polar and polar solvents. The present study provides a new insight into the experimental controversy of the ESDPT mechanism of the 7AI dimer in a solution.

Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins.

PubMed

Nguyen, Bao Linh; Pettitt, B Montgomery

2015-04-14

The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations.

Continuum description of ionic and dielectric shielding for molecular-dynamics simulations of proteins in solution

NASA Astrophysics Data System (ADS)

Egwolf, Bernhard; Tavan, Paul

2004-01-01

We extend our continuum description of solvent dielectrics in molecular-dynamics (MD) simulations [B. Egwolf and P. Tavan, J. Chem. Phys. 118, 2039 (2003)], which has provided an efficient and accurate solution of the Poisson equation, to ionic solvents as described by the linearized Poisson-Boltzmann (LPB) equation. We start with the formulation of a general theory for the electrostatics of an arbitrarily shaped molecular system, which consists of partially charged atoms and is embedded in a LPB continuum. This theory represents the reaction field induced by the continuum in terms of charge and dipole densities localized within the molecular system. Because these densities cannot be calculated analytically for systems of arbitrary shape, we introduce an atom-based discretization and a set of carefully designed approximations. This allows us to represent the densities by charges and dipoles located at the atoms. Coupled systems of linear equations determine these multipoles and can be rapidly solved by iteration during a MD simulation. The multipoles yield the reaction field forces and energies. Finally, we scrutinize the quality of our approach by comparisons with an analytical solution restricted to perfectly spherical systems and with results of a finite difference method.

Qualitative assessment of ultra-fast non-Grotthuss proton dynamics in S1 excited state of liquid H2O from ab initio time-dependent density functional theory★

NASA Astrophysics Data System (ADS)

Ziaei, Vafa; Bredow, Thomas

2017-11-01

We study qualitatively ultra-fast proton transfer (PT) in the first singlet (S1) state of liquid water (absorption onset) through excited-state dynamics by means of time-dependent density functional theory and ab initio Born-Oppenheimer molecular dynamics. We find that after the initial excitation, a PT occurs in S1 in form of a rapid jump to a neighboring water molecule, on which the proton either may rest for a relatively long period of time (as a consequence of possible defect in the hydrogen bond network) followed by back and forth hops to its neighboring water molecule or from which it further moves to the next water molecule accompanied by back and forth movements. In this way, the proton may become delocalized over a long water wire branch, followed again by back and forth jumps or short localization on a water molecule for some femtoseconds. As a result, the mechanism of PT in S1 is in most cases highly non-Grotthuss-like, delayed and discrete. Furthermore, upon PT an excess charge is ejected to the solvent trap, the so-called solvated electron. The spatial extent of the ejected solvated electron is mainly localized within one solvent shell with overlappings on the nearest neighbor water molecules and delocalizing (diffuse) tails extending beyond the first solvent sphere. During the entire ultra-short excited-state dynamics the remaining OH radical from the initially excited water molecule exhibits an extremely low mobility and is non-reactive. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjb/e2017-80329-7.

Design of spray dried insulin microparticles to bypass deposition in the extrathoracic region and maximize total lung dose.

PubMed

Ung, Keith T; Rao, Nagaraja; Weers, Jeffry G; Huang, Daniel; Chan, Hak-Kim

2016-09-25

Inhaled drugs all too often deliver only a fraction of the emitted dose to the target lung site due to deposition in the extrathoracic region (i.e., mouth and throat), which can lead to increased variation in lung exposure, and in some instances increases in local and systemic side effects. For aerosol medications, improved targeting to the lungs may be achieved by tailoring the micromeritic properties of the particles (e.g., size, density, rugosity) to minimize deposition in the mouth-throat and maximize the total lung dose. This study evaluated a co-solvent spray drying approach to modulate particle morphology and dose delivery characteristics of engineered powder formulations of insulin microparticles. The binary co-solvent system studied included water as the primary solvent mixed with an organic co-solvent, e.g., ethanol. Factors such as the relative rate of evaporation of each component of a binary co-solvent mixture, and insulin solubility in each component were considered in selecting feedstock compositions. A water-ethanol co-solvent mixture with a composition range considered suitable for modulating particle shell formation during drying was selected for experimental investigation. An Alberta Idealized Throat model was used to evaluate the in vitro total lung dose of a series of spray dried insulin formulations engineered with different bulk powder properties and delivered with two prototype inhalers that fluidize and disperse powder using different principles. The in vitro total lung dose of insulin microparticles was improved and favored for powders with low bulk density and small primary particle size, with reduction of deposition in the extrathoracic region. The results demonstrated that a total lung dose >95% of the delivered dose can be achieved with engineered particles, indicating a high degree of lung targeting, almost completely bypassing deposition in the mouth-throat. Copyright © 2016 Elsevier B.V. All rights reserved.

Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins

PubMed Central

Nguyen, Bao Linh; Pettitt, B. Montgomery

2015-01-01

The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations. PMID:26388706

Tuned range separated hybrid functionals for solvated low bandgap oligomers

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

Queiroz, Thiago B. de, E-mail: thiago.branquinho-de-queiroz@uni-bayreuth.de; Kümmel, Stephan

2015-07-21

The description of charge transfer excitations has long been a challenge to time dependent density functional theory. The recently developed concept of “optimally tuned range separated hybrid (OT-RSH) functionals” has proven to describe charge transfer excitations accurately in many cases. However, describing solvated or embedded systems is yet a challenge. This challenge is not only computational but also conceptual, because the tuning requires identifying a specific orbital, typically the highest occupied one of the molecule under study. For solvated molecules, this orbital may be delocalized over the solvent. We here demonstrate that one way of overcoming this problem is tomore » use a locally projected self-consistent field diagonalization on an absolutely localized molecular orbital expansion. We employ this approach to determine ionization energies and the optical gap of solvated oligothiophenes, i.e., paradigm low gap systems that are of relevance in organic electronics. Dioxane solvent molecules are explicitly represented in our calculations, and the ambiguities of straightforward parameter tuning in solution are elucidated. We show that a consistent estimate of the optimal range separated parameter (ω) at the limit of bulk solvation can be obtained by gradually extending the solvated system. In particular, ω is influenced by the solvent beyond the first coordination sphere. For determining ionization energies, a considerable number of solvent molecules on the first solvation shell must be taken into account. We demonstrate that accurately calculating optical gaps of solvated systems using OT-RSH can be done in three steps: (i) including the chemical environment when determining the range-separation parameter, (ii) taking into account the screening due to the solvent, and (iii) using realistic molecular geometries.« less

Theoretical study of solvent effects on the coil-globule transition

NASA Astrophysics Data System (ADS)

Polson, James M.; Opps, Sheldon B.; Abou Risk, Nicholas

2009-06-01

The coil-globule transition of a polymer in a solvent has been studied using Monte Carlo simulations of a single chain subject to intramolecular interactions as well as a solvent-mediated effective potential. This solvation potential was calculated using several different theoretical approaches for two simple polymer/solvent models, each employing hard-sphere chains and hard-sphere solvent particles as well as attractive square-well potentials between some interaction sites. For each model, collapse is driven by variation in a parameter which changes the energy mismatch between monomers and solvent particles. The solvation potentials were calculated using two fundamentally different methodologies, each designed to predict the conformational behavior of polymers in solution: (1) the polymer reference interaction site model (PRISM) theory and (2) a many-body solvation potential (MBSP) based on scaled particle theory introduced by Grayce [J. Chem. Phys. 106, 5171 (1997)]. For the PRISM calculations, two well-studied solvation monomer-monomer pair potentials were employed, each distinguished by the closure relation used in its derivation: (i) a hypernetted-chain (HNC)-type potential and (ii) a Percus-Yevick (PY)-type potential. The theoretical predictions were each compared to results obtained from explicit-solvent discontinuous molecular dynamics simulations on the same polymer/solvent model systems [J. Chem. Phys. 125, 194904 (2006)]. In each case, the variation in the coil-globule transition properties with solvent density is mostly qualitatively correct, though the quantitative agreement between the theory and prediction is typically poor. The HNC-type potential yields results that are more qualitatively consistent with simulation. The conformational behavior of the polymer upon collapse predicted by the MBSP approach is quantitatively correct for low and moderate solvent densities but is increasingly less accurate for higher densities. At high solvent densities, the PRISM-HNC and MBSP approaches tend to overestimate, while the PRISM-PY approach underestimates the tendency of the solvent to drive polymer collapse.

Multidimensional equilibria and their stability in copolymer-solvent mixtures

NASA Astrophysics Data System (ADS)

Glasner, Karl; Orizaga, Saulo

2018-06-01

This paper discusses localized equilibria which arise in copolymer-solvent mixtures. A free boundary problem associated with the sharp-interface limit of a density functional model is used to identify both lamellar and concentric domain patterns composed of a finite number of layers. Stability of these morphologies is studied through explicit linearization of the free boundary evolution. For the multilayered lamellar configuration, transverse instability is observed for sufficiently small dimensionless interfacial energies. Additionally, a crossover between small and large wavelength instabilities is observed depending on whether solvent-polymer or monomer-monomer interfacial energy is dominant. Concentric domain patterns resembling multilayered micelles and vesicles exhibit bifurcations wherein they only exist for sufficiently small dimensionless interfacial energies. The bifurcation of large radii vesicle solutions is studied analytically, and a crossover from a supercritical case with only one solution branch to a subcritical case with two is observed. Linearized stability of these configurations shows that azimuthal perturbation may lead to instabilities as interfacial energy is decreased.

Method of filtering a target compound from a first solvent that is above its critical density

DOEpatents

Phelps, Max R [Richland, WA; Yonker, Clement R [Kennewick, WA; Fulton, John L [Richland, WA; Bowman, Lawrence E [Richland, WA

2001-07-24

The present invention is a method of separating a first compound having a macromolecular structure from a mixture. The first solvent is a fluid that is a gas at standard temperature and pressure and is at a density greater than a critical density of the fluid. A macromolecular structure containing a first compound is dissolved therein as a mixture. The mixture is contacted onto a selective barrier and the first solvent passed through the selective barrier thereby retaining the first compound, followed by recovering the first compound. By using a fluid that is a gas at standard temperature and pressure at a density greater than its critical density, separation without depressurization is fast and efficient.

40 CFR 60.433 - Performance test and compliance provisions.

Code of Federal Regulations, 2010 CFR

2010-07-01

.... (6) The density variations with temperature of the raw inks, related coatings, VOC solvents used, and... related coatings measured as used by volume with different amounts of VOC content or different densities... amounts of VOC content or different VOC solvent densities. (2) The total mass of VOC used is determined by...

Metal-doped organic foam

DOEpatents

Rinde, James A.

1982-01-01

Organic foams having a low density and very small cell size and method for producing same in either a metal-loaded or unloaded (nonmetal loaded) form are described. Metal-doped foams are produced by soaking a polymer gel in an aqueous solution of desired metal salt, soaking the gel successively in a solvent series of decreasing polarity to remove water from the gel and replace it with a solvent of lower polarity with each successive solvent in the series being miscible with the solvents on each side and being saturated with the desired metal salt, and removing the last of the solvents from the gel to produce the desired metal-doped foam having desired density cell size, and metal loading. The unloaded or metal-doped foams can be utilized in a variety of applications requiring low density, small cell size foam. For example, rubidium-doped foam made in accordance with the invention has utility in special applications, such as in x-ray lasers.

Method for producing metal oxide aerogels

DOEpatents

Tillotson, Thomas M.; Poco, John F.; Hrubesh, Lawrence W.; Thomas, Ian M.

1995-01-01

A two-step hydrolysis-condensation method was developed to form metal oxide aerogels of any density, including densities of less than 0.003g/cm.sup.3 and greater than 0.27g/cm.sup.3. High purity metal alkoxide is reacted with water, alcohol solvent, and an additive to form a partially condensed metal intermediate. All solvent and reaction-generated alcohol is removed, and the intermediate is diluted with a nonalcoholic solvent. The intermediate can be stored for future use to make aerogels of any density. The aerogels are formed by reacting the intermediate with water, nonalcoholic solvent, and a catalyst, and extracting the nonalcoholic solvent directly. The resulting monolithic aerogels are hydrophobic and stable under atmospheric conditions, and exhibit good optical transparency, high clarity, and homogeneity. The aerogels have high thermal insulation capacity, high porosity, mechanical strength and stability, and require shorter gelation times than aerogels formed by conventional methods.

Method for producing metal oxide aerogels

DOEpatents

Tillotson, T.M.; Poco, J.F.; Hrubesh, L.W.; Thomas, I.M.

1995-04-25

A two-step hydrolysis-condensation method was developed to form metal oxide aerogels of any density, including densities of less than 0.003g/cm{sup 3} and greater than 0.27g/cm{sup 3}. High purity metal alkoxide is reacted with water, alcohol solvent, and an additive to form a partially condensed metal intermediate. All solvent and reaction-generated alcohol is removed, and the intermediate is diluted with a nonalcoholic solvent. The intermediate can be stored for future use to make aerogels of any density. The aerogels are formed by reacting the intermediate with water, nonalcoholic solvent, and a catalyst, and extracting the nonalcoholic solvent directly. The resulting monolithic aerogels are hydrophobic and stable under atmospheric conditions, and exhibit good optical transparency, high clarity, and homogeneity. The aerogels have high thermal insulation capacity, high porosity, mechanical strength and stability, and require shorter gelation times than aerogels formed by conventional methods. 8 figs.

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).

On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase

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

Brokaw, Jason B.; Chu, Jhih-wei

2010-11-17

We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier worksmore » of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro177 on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro177 hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition.« less

Specific material recognition by small peptides mediated by the interfacial solvent structure.

PubMed

Schneider, Julian; Ciacchi, Lucio Colombi

2012-02-01

We present evidence that specific material recognition by small peptides is governed by local solvent density variations at solid/liquid interfaces, sensed by the side-chain residues with atomic-scale precision. In particular, we unveil the origin of the selectivity of the binding motif RKLPDA for Ti over Si using a combination of metadynamics and steered molecular dynamics simulations, obtaining adsorption free energies and adhesion forces in quantitative agreement with corresponding experiments. For an accurate description, we employ realistic models of the natively oxidized surfaces which go beyond the commonly used perfect crystal surfaces. These results have profound implications for nanotechnology and materials science applications, offering a previously missing structure-function relationship for the rational design of materials-selective peptide sequences. © 2011 American Chemical Society

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

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.

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.

Simple liquid models with corrected dielectric constants

PubMed Central

Fennell, Christopher J.; Li, Libo; Dill, Ken A.

2012-01-01

Molecular simulations often use explicit-solvent models. Sometimes explicit-solvent models can give inaccurate values for basic liquid properties, such as the density, heat capacity, and permittivity, as well as inaccurate values for molecular transfer free energies. Such errors have motivated the development of more complex solvents, such as polarizable models. We describe an alternative here. We give new fixed-charge models of solvents for molecular simulations – water, carbon tetrachloride, chloroform and dichloromethane. Normally, such solvent models are parameterized to agree with experimental values of the neat liquid density and enthalpy of vaporization. Here, in addition to those properties, our parameters are chosen to give the correct dielectric constant. We find that these new parameterizations also happen to give better values for other properties, such as the self-diffusion coefficient. We believe that parameterizing fixed-charge solvent models to fit experimental dielectric constants may provide better and more efficient ways to treat solvents in computer simulations. PMID:22397577

Intramolecular vibrational energy redistribution and intermolecular energy transfer of benzene in supercritical CO 2: measurements from the gas phase up to liquid densities

NASA Astrophysics Data System (ADS)

von Benten, R.; Charvat, A.; Link, O.; Abel, B.; Schwarzer, D.

2004-03-01

Femtosecond pump probe spectroscopy was employed to measure intramolecular vibrational energy redistribution (IVR) and intermolecular vibrational energy transfer (VET) of benzene in the gas phase and in supercritical (sc) CO 2. We observe two IVR time scales the faster of which proceeds within τ IVR(1)<0.5 ps. The slower IVR component has a time constant of τ IVR(2)=(48±5) ps in the gas phase and in scCO 2 is accelerated by interactions with the solvent. At the highest CO 2 density it is reduced to τ IVR(2)=(6±1) ps. The corresponding IVR rate constants show a similar density dependence as the VET rate constants. Model calculations suggest that both quantities correlate with the local CO 2 density in the immediate surrounding of the benzene molecule.

The solvent component of macromolecular crystals

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

Weichenberger, Christian X.; Afonine, Pavel V.; Kantardjieff, Katherine

2015-04-30

On average, the mother liquor or solvent and its constituents occupy about 50% of a macromolecular crystal. Ordered as well as disordered solvent components need to be accurately accounted for in modelling and refinement, often with considerable complexity. The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initialmore » phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.« less

Metal-doped organic foam and method of making same. [Patent application

DOEpatents

Rinde, J.A.

Organic foams having a low density and very small cell size and method for producing same in either a metal-loaded or unloaded (nonmetal loaded) form are described. Metal-doped foams are produced by soaking a polymer gel in an aqueous solution of desired metal salt, soaking the gel successively in a solvent series of decreasing polarity to remove water from the gel and replace it with a solvent of lower polarity with each successive solvent in the series being miscible with the solvents on each side and being saturated with the desired metal salt, and removing the last of the solvents from the gel to produce the desired metal-doped foam having desired density cell size, and metal loading. The unloaded or metal-doped foams can be utilized in a variety of applications requiring low density, small cell size foam. For example, rubidium-doped foam made in accordance with the invention has utility in special applications, such as in x-ray lasers.

Method of making metal-doped organic foam products

DOEpatents

Rinde, James A.

1981-01-01

Organic foams having a low density and very small cell size and method for roducing same in either a metal-loaded or unloaded (nonmetal loaded) form are described. Metal-doped foams are produced by soaking a polymer gel in an aqueous solution of desired metal salt, soaking the gel successively in a solvent series of decreasing polarity to remove water from the gel and replace it with a solvent of lower polarity with each successive solvent in the series being miscible with the solvents on each side and being saturated with the desired metal salt, and removing the last of the solvents from the gel to produce the desired metal-doped foam having desired density cell size, and metal loading. The unloaded or metal-doped foams can be utilized in a variety of applications requiring low density, small cell size foam. For example, rubidium-doped foam made in accordance with the invention has utility in special applications, such as in x-ray lasers.

Comparison of polymer induced and solvent induced trypsin denaturation: the role of hydrophobicity.

PubMed

Jasti, Lakshmi S; Fadnavis, Nitin W; Addepally, Uma; Daniels, Siona; Deokar, Sarika; Ponrathnam, Surendra

2014-04-01

Trypsin adsorption from aqueous buffer by various copolymers of allyl glycidyl ether-ethylene glycol dimethacrylate (AGE-EGDM) copolymer with varying crosslink density increases with increasing crosslink density and the effect slowly wears off after reaching a plateau at 50% crosslink density. The copolymer with 25% crosslink density was reacted with different amines with alkyl/aryl side chains to obtain a series of copolymers with 1,2-amino alcohol functional groups and varying hydrophobicity. Trypsin binding capacity again increases with hydrophobicity of the reacting amine and a good correlation between logPoctanol of the amine and protein binding is observed. The bound trypsin is denatured to the extent of 90% in spite of the presence of hydrophilic hydroxyl and amino groups. The behavior was comparable to that in mixtures of aqueous buffer and water-miscible organic co-solvents where the solvent concentration required to deactivate 50% of the enzyme (C50) is dependent on logPoctanol of the co-solvent. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Low density microcellular carbon foams and method of preparation

DOEpatents

Arnold, C. Jr.; Aubert, J.H.; Clough, R.L.; Rand, P.B.; Sylwester, A.P.

1988-06-20

A low density, open-celled microcellular carbon foam is disclosed which is prepared by dissolving a carbonizable polymer or copolymer in a solvent, pouring the solution into a mold, cooling the solution, removing the solvent, and then carbonizing the polymer or copolymer in a high temperature oven to produce the foam. If desired, an additive can be introduced in order to produce a doped carbon foam, and the foams can be made isotropic by selection of a suitable solvent. The low density, microcellular foams produced by this process are particularly useful in the fabrication of inertial confinement fusion targets, but can also be used as catalysts, absorbents, and electrodes.

Low density microcellular carbon foams and method of preparation

DOEpatents

Arnold, Jr., Charles; Aubert, James H.; Clough, Roger L.; Rand, Peter B.; Sylwester, Alan P.

1989-01-01

A low density, open-celled microcellular carbon foam is disclosed which is prepared by dissolving a carbonizable polymer or copolymer in a solvent, pouring the solution into a mold, cooling the solution, removing the solvent, and then carbonizing the polymer or copolymer in a high temperature oven to produce the foam. If desired, an additive can be introduced in order to produce a doped carbon foam, and the foams can be made isotropic by selection of a suitable solvent. The low density, microcellular foams produced by this process are particularly useful in the fabrication of inertial confinement fusion targets, but can also be used as catalysts, absorbents, and electrodes.

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

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.

Chemical reactivity indices for the complete series of chlorinated benzenes: solvent effect.

PubMed

Padmanabhan, J; Parthasarathi, R; Subramanian, V; Chattaraj, P K

2006-03-02

We present a comprehensive analysis to probe the effect of solvation on the reactivity of the complete series of chlorobenzenes through the conceptual density functional theory (DFT)-based global and local descriptors. We propose a multiphilic descriptor in this study to explore the nature of attack at a particular site in a molecule. It is defined as the difference between nucleophilic and electrophilic condensed philicity functions. This descriptor is capable of explaining both the nucleophilicity and electrophilicity of the given atomic sites in the molecule simultaneously. The predictive ability of this descriptor is tested on the complete series of chlorobenzenes in gas and solvent media. A structure-toxicity analysis of these entire sets of chlorobenzenes toward aquatic organisms demonstrates the importance of the electrophilicity index in the prediction of the reactivity/toxicity.

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.

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.

Solvent-Induced Crystallization in Poly(Ethylene Terephthalate) during Mass Transport

NASA Astrophysics Data System (ADS)

Ouyang, Hao

2001-03-01

The solvent transport in poly(ethylene terephthalate) (PET) and related phase transformation were investigated. The data of mass sorption were analyzed according to Harmon¡¦s model for Case I (Fickian), Case II (swelling) and anomalous transport. This transport process in PET is accompanied by the induced crystallization of the original amorphous state. The transformation was studied by wide angle x-ray scattering (WAXS), small angle x-ray scattering (SAXS), Differential Scanning Calorimeter (DSC), density gradient column, and Fourier Transform Infra-Red (FTIR). During this process, the matrix is under a compressive strain that causes different kinetic path of crystallization as compared to that by thermal annealing. This state of strain will assist the development of the solvent-induced crystallization. It also can be explained in terms of the principle of Le Chatelier if the local equilibrium is assumed. The model regarding the crystallization was proposed in terms of the study of long period L, the crystal thickness lc and the thickness of amorphous layer la, obtained from the linear correlation function and interface distribution function.

Microscopic solvent structure of subcritical and supercritical methanol from ultraviolet/visible absorption and fluorescence spectroscopies

NASA Astrophysics Data System (ADS)

Bulgarevich, Dmitry S.; Sako, Takeshi; Sugeta, Tsutomu; Otake, Katsuto; Takebayashi, Yoshihiro; Kamizawa, Chiyoshi; Uesugi, Masayuki; Kato, Masahiro

1999-09-01

Ultraviolet/visible absorption and fluorescence spectroscopies at different temperatures and pressures were applied to investigate the microscopic solvent structures of subcritical and supercritical methanol using 4-nitroanisole, ethyl-(4-dimethylamino)benzoate, Reichardt's dye, and anthracene as the probe molecules. It was found that at temperatures higher than 150 °C the long winding chains of sequentially hydrogen-bonded methanol molecules were probably broken, but the small hydrogen-bonded aggregates possibly existed in methanol even at higher temperature. It was also found that the solvation process of the anthracene molecule in the S0-ground state obeyed the Langmuir adsorption model. However, in the case of fluorescence measurements in supercritical methanol, we detected deviations from the simple Langmuir adsorption model. These deviations were explained in terms of preferential solvation of the solvent molecules around photoexcited anthracene. Judging from the experimental results, it was concluded that the local density augmentation of the supercritical methanol around the nonpolar solute was a short-ranged effect, which did not correspond directly to the large isothermal compressibility of fluid near the critical point.

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.

A salient effect of density on the dynamics of nonaqueous electrolytes.

PubMed

Han, Sungho

2017-04-24

The mobility and solvation of lithium ions in electrolytes are crucial for the performance and safety of lithium ion batteries. It has been known that a single type of solvent cannot satisfy the requirements of both mobility and solvation simultaneously for electrolytes. Therefore, complex solvent mixtures have been used to optimize both properties. Here we present the effects of density on the dynamics and solvation of organic liquid electrolytes via extensive molecular dynamics simulations. Our study finds that a small variation in density can induce a significant effect on the mobility of electrolytes but does not influence the solvation structure of a lithium ion. It turns out that an adjustment of the density of electrolytes could provide a more effective way to enhance mobility than a control of the solvent mixture ratio of electrolytes. Our study reveals that the density change of electrolytes mainly affects the residence time of solvents in the first solvation shell of a lithium ion rather than the structural change of the solvation sheath. Finally, our results suggest an intriguing point for understanding and designing electrolytes of lithium ion batteries for better performance and safety.

A salient effect of density on the dynamics of nonaqueous electrolytes

NASA Astrophysics Data System (ADS)

Han, Sungho

2017-04-01

The mobility and solvation of lithium ions in electrolytes are crucial for the performance and safety of lithium ion batteries. It has been known that a single type of solvent cannot satisfy the requirements of both mobility and solvation simultaneously for electrolytes. Therefore, complex solvent mixtures have been used to optimize both properties. Here we present the effects of density on the dynamics and solvation of organic liquid electrolytes via extensive molecular dynamics simulations. Our study finds that a small variation in density can induce a significant effect on the mobility of electrolytes but does not influence the solvation structure of a lithium ion. It turns out that an adjustment of the density of electrolytes could provide a more effective way to enhance mobility than a control of the solvent mixture ratio of electrolytes. Our study reveals that the density change of electrolytes mainly affects the residence time of solvents in the first solvation shell of a lithium ion rather than the structural change of the solvation sheath. Finally, our results suggest an intriguing point for understanding and designing electrolytes of lithium ion batteries for better performance and safety.

Unravelling the mechanisms of vibrational relaxation in solution.

PubMed

Grubb, Michael P; Coulter, Philip M; Marroux, Hugo J B; Orr-Ewing, Andrew J; Ashfold, Michael N R

2017-04-01

We present a systematic study of the mode-specific vibrational relaxation of NO 2 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 NO 2 fragments produced from the 340 nm photolysis of N 2 O 4 → NO 2 (X) + NO 2 (A) and their separate paths to thermal equilibrium. Distinct relaxation pathways are observed for the NO 2 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. NO 2 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, NO 2 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 NO 2 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.

Theory of complicated liquids. Investigation of liquids, solvents and solvent effects with modern theoretical methods

NASA Astrophysics Data System (ADS)

Kirchner, Barbara

2007-03-01

It is the aim of this work to elucidate the usefulness and feasibility of the first-principles approach and to extend it to the regime of liquid molecular substances of complex structure. Physical and thermodynamic properties of complicated liquids are investigated by means of Car-Parrinello molecular dynamics (CPMD) and also with static quantum chemical methods. The connection between the dynamic and static approach is given by the quantum cluster equilibrium (QCE) theory. Since the QCE theory is not yet well established, a new implementation in the MD post-processing program P EACEMAKER is presented. It can be shown that it is by far more important to include cooperative effects rather than to concentrate the effort on the inclusion of weak dispersion forces not present in current density functionals. Traditionally, investigations of complicated liquids were also undertaken with the tools of simple liquids, because for some problems the size of the system does not allow for a more accurate description. Although linear-scaling techniques are simplifications from the point of view of quantum chemistry, they might be severe improvements when compared to traditional molecular dynamics simulations. For the interpretation of the liquid state the introduction of local properties is inevitable. New methods are presented for the calculation of local dipole moments and for the estimation of hydrogen bond energies in quantum mechanically nondecomposable systems. The latter also allows for the detection of hydrogen bonds in simulations through a wavefunction-based criterion instead of one which is solely grounded on the geometric structure of the atomic nuclei involved. The article then discusses prominent liquids which show properties that are not yet understood. Another part of the work analyzes the effect of solvent molecules on solutes and their reactions in the solvent. Finaly, neoteric solvents, such as ionic liquids are discussed.

Initial solubility & density evaluation of Non-Aqueous system of amino acid salts for CO2 capture: potassium prolinate blended with ethanol and ethylene glycol

NASA Astrophysics Data System (ADS)

Murshid, Ghulam; Garg, Sahil

2018-05-01

Amine scrubbing is the state of the art technology for CO2 capture, and solvent selection can significantly reduce the capital and energy cost of the process. Higher energy requirement for aqueous amine based CO2 removal process is still a most important downside preventive its industrial deployment. Therefore, in this study, novel non-aqueous based amino acid salt system consisting of potassium prolinate, ethanol and ethylene glycol has been studied. This work presents initial CO2 solubility study and important physical properties i.e. density of the studied solvent system. Previous work showed that non-aqueous system of potassium prolinate and ethanol has good absorption rates and requires lower energy for solvent regeneration. However, during regeneration, solvent loss issues were found due to lower boiling point of the ethanol. Therefore, ethylene glycol was added into current studied system for enhancing the overall boiling point of the system. The good initial CO2 solubility and low density of studied solvent system offers several advantages as compared to conventional amine solutions.

The role of the attractive and the repulsive interactions in the nonpolar solvation dynamics in simple fluids from the gas-like to the liquid-like densities

NASA Astrophysics Data System (ADS)

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

1999-09-01

We have performed molecular dynamics (MD) simulations of the nonpolar solvation dynamics in simple fluids composed of particles interacting through the Lennard-Jones (LJ) 12-6 potential or its repulsive part. The attractive or the repulsive part of the solute-solvent interaction is assumed to change on the excitation of a solute. We have followed the transition energy fluctuation of the solute by the equilibrium simulation. The division of the LJ potential followed the method of WCA [J. W. Weeks, D. Chandler, and H. C. Andersen, J. Chem. Phys. 54, 5237 (1971)]. We have surveyed over a wide solvent density region from gas-like to liquid-like densities at the constant temperature. When the attractive part changes, the relaxation becomes faster with an increase of the solvent density. This result contradicts with previous theories that treat the nonpolar solvation dynamics in terms of the diffusion of solvent particles. The time scale of the initial part of the relaxation is well correlated with the static fluctuation divided by the static average, which suggests the importance of the curvature of the free energy surface in the initial part of the solvation. When the repulsive part changes, the initial part of the relaxation is almost density independent, determined by the binary motion between solute and solvent. It is consistent with the result that the static fluctuation is almost proportional to the static average, which indicates the absence of the static correlation between solvent particles. On the other hand, the solvation correlation function shows rather complicated density dependence at the longer time scale. In the case of the binary mixture solvent, the relaxation time is inversely proportional to the diffusion coefficient. On the basis of the nonpolar solvation dynamics, the validity of the isolated binary collision model for the vibrational energy relaxation is also discussed, and the recent hydrodynamic theory on the vibrational energy relaxation [B. J. Cherayil and M. D. Feyer, J. Chem. Phys. 107, 7642 (1997)] is critically examined.

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.

Effects of solvent density on retention in gas-liquid chromatography. I. Alkanes solutes in polyethylene glycol stationary phases.

PubMed

González, F R; Pérez-Parajón, J; García-Domínguez, J A

2002-04-12

Gas-liquid chromatographic columns were prepared coating silica capillaries with poly(oxyethylene) polymers of different molecular mass distributions, in the range of low number-average molar masses, where the density still varies significantly. A novel, high-temperature, rapid evaporation method was developed and applied to the static coating of the low-molecular-mass stationary phases. The analysis of alkanes retention data from these columns reveals that the dependence of the partition coefficient with the solvent macroscopic density is mainly due to a variation of entropy. Enthalpies of solute transfer contribute poorly to the observed variations of retention. Since the alkanes solubility diminishes with the increasing solvent density, and this variation is weakly dependent with temperature, it is concluded that the decrease of free-volume in the liquid is responsible for this behavior.

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...

Solvent Exchange Leading to Nanobubble Nucleation: A Molecular Dynamics Study

PubMed Central

2017-01-01

The solvent exchange procedure has become the most-used protocol to produce surface nanobubbles, while the molecular mechanisms behind the solvent exchange are far from being fully understood. In this paper, we build a simple model and use molecular dynamics simulations to investigate the dynamic characteristics of solvent exchange for producing nanobubbles. We find that at the first stage of solvent exchange, there exists an interface between interchanging solvents of different gas solubility. This interface moves toward the substrate gradually as the exchange process proceeds. Our simulations reveal directed diffusion of gas molecules against the gas concentration gradient, driven by the solubility gradient of the liquid composition across the moving solvent–solvent interface. It is this directed diffusion that causes gas retention and produces a local gas oversaturation much higher near the substrate than far from it. At the second stage of solvent exchange, the high local gas oversaturation leads to bubble nucleation either on the solid surface or in the bulk solution, which is found to depend on the substrate hydrophobicity and the degree of local gas oversaturation. Our findings suggest that solvent exchange could be developed into a standard procedure to produce oversaturation and used to a variety of nucleation applications other than generating nanobubbles. PMID:28742364

Method of altering the effective bulk density of solid material and the resulting product

DOEpatents

Kool, Lawrence B.; Nolen, Robert L.; Solomon, David E.

1983-01-01

A method of adjustably tailoring the effective bulk density of a solid material in which a mixture comprising the solid material, a film-forming polymer and a volatile solvent are sprayed into a drying chamber such that the solvent evaporates and the polymer dries into hollow shells having the solid material captured within the shell walls. Shell density may be varied as a function of solid/polymer concentration, droplet size and drying temperature.

Intramolecular and intermolecular vibrational energy relaxation of CH 2I 2 dissolved in supercritical fluid

NASA Astrophysics Data System (ADS)

Sekiguchi, K.; Shimojima, A.; Kajimoto, O.

2002-04-01

A pump-probe experiment was performed to examine vibrational population relaxation of diiodomethane (CH 2I 2) molecule dissolved in supercritical CO 2. Using an apparatus with femtosecond time resolution, we observed the contributions of intramolecular vibrational energy redistribution (IVR) and intermolecular vibrational energy transfer (VET) separately. IVR and VET rates were measured with varying solvent densities at a constant temperature. It is shown that the IVR rate is not density dependent while the VET rate increases with increasing density from 0.4 to 0.8 g cm-3. This observation suggests that the rate of the VET process is determined by solute-solvent collisions whereas the IVR rate is not much affected by solute-solvent interaction.

Continuum description of solvent dielectrics in molecular-dynamics simulations of proteins

NASA Astrophysics Data System (ADS)

Egwolf, Bernhard; Tavan, Paul

2003-02-01

We present a continuum approach for efficient and accurate calculation of reaction field forces and energies in classical molecular-dynamics (MD) simulations of proteins in water. The derivation proceeds in two steps. First, we reformulate the electrostatics of an arbitrarily shaped molecular system, which contains partially charged atoms and is embedded in a dielectric continuum representing the water. A so-called fuzzy partition is used to exactly decompose the system into partial atomic volumes. The reaction field is expressed by means of dipole densities localized at the atoms. Since these densities cannot be calculated analytically for general systems, we introduce and carefully analyze a set of approximations in a second step. These approximations allow us to represent the dipole densities by simple dipoles localized at the atoms. We derive a system of linear equations for these dipoles, which can be solved numerically by iteration. After determining the two free parameters of our approximate method we check its quality by comparisons (i) with an analytical solution, which is available for a perfectly spherical system, (ii) with forces obtained from a MD simulation of a soluble protein in water, and (iii) with reaction field energies of small molecules calculated by a finite difference method.

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

Solvent evaporation induced graphene powder with high volumetric capacitance and outstanding rate capability for supercapacitors

NASA Astrophysics Data System (ADS)

Zhang, Xiaozhe; Raj, Devaraj Vasanth; Zhou, Xufeng; Liu, Zhaoping

2018-04-01

Graphene-based electrode materials for supercapacitors usually suffer from poor volumetric performance due to the low density. The enhancement of volumetric capacitance by densification of graphene materials, however, is usually accompanied by deterioration of rate capability, as the huge contraction of pore size hinders rapid diffusion of electrolytes. Thus, it is important to develop suitable pore size in graphene materials, which can sustain fast ion diffusion and avoid excessive voids to acquire high density simultaneously for supercapacitor applications. Accordingly, we propose a simple solvent evaporation method to control the pore size of graphene powders by adjusting the surface tension of solvents. Ethanol is used instead of water to reduce the shrinkage degree of graphene powder during solvent evaporation process, due to its lower surface tension comparing with water. Followed by the assistance of mechanical compression, graphene powder having high compaction density of 1.30 g cm-3 and a large proportion of mesopores in the pore size range of 2-30 nm is obtained, which delivers high volumetric capacitance of 162 F cm-3 and exhibits outstanding rate performance of 76% capacity retention at a high current density of 100 A g-1 simultaneously.

Advanced separators based on aromatic polymer for high energy density lithium batteries

DOEpatents

Zhang, Zhengcheng; Woo, Jung-Je; Amine, Khalil

2017-03-21

A process includes casting a solution including poly(phenylene oxide), inorganic nanoparticles, a solvent, and a non-solvent on a substrate; and removing the solvent to form a porous film; wherein: the porous film is configured for use as a porous separator for a lithium ion battery.

Dielectric properties of organic solvents from non-polarizable molecular dynamics simulation with electronic continuum model and density functional theory.

PubMed

Lee, Sanghun; Park, Sung Soo

2011-11-03

Dielectric constants of electrolytic organic solvents are calculated employing nonpolarizable Molecular Dynamics simulation with Electronic Continuum (MDEC) model and Density Functional Theory. The molecular polarizabilities are obtained by the B3LYP/6-311++G(d,p) level of theory to estimate high-frequency refractive indices while the densities and dipole moment fluctuations are computed using nonpolarizable MD simulations. The dielectric constants reproduced from these procedures are evaluated to provide a reliable approach for estimating the experimental data. An additional feature, two representative solvents which have similar molecular weights but are different dielectric properties, i.e., ethyl methyl carbonate and propylene carbonate, are compared using MD simulations and the distinctly different dielectric behaviors are observed at short times as well as at long times.

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.

An ellipsoid-chain model for conjugated polymer solutions

NASA Astrophysics Data System (ADS)

Lee, Cheng K.; Hua, Chi C.; Chen, Show A.

2012-02-01

We propose an ellipsoid-chain model which may be routinely parameterized to capture large-scale properties of semiflexible, amphiphilic conjugated polymers in various solvent media. The model naturally utilizes the defect locations as pivotal centers connecting adjacent ellipsoids (each currently representing ten monomer units), and a variant umbrella-sampling scheme is employed to construct the potentials of mean force (PMF) for specific solvent media using atomistic dynamics data and simplex optimization. The performances, both efficacy and efficiency, of the model are thoroughly evaluated by comparing the simulation results on long, single-chain (i.e., 300-mer) structures with those from two existing, finer-grained models for a standard conjugated polymer (i.e., poly(2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene) or MEH-PPV) in two distinct solvents (i.e., chloroform or toluene) as well as a hybrid, binary-solvent medium (i.e., chloroform/toluene = 1:1 in number density). The coarse-grained Monte Carlo (CGMC) simulation of the ellipsoid-chain model is shown to be the most efficient—about 300 times faster than the coarse-grained molecular dynamics (CGMD) simulation of the finest CG model that employs explicit solvents—in capturing elementary single-chain structures for both single-solvent media, and is a few times faster than the coarse-grained Langevin dynamics (CGLD) simulation of another implicit-solvent polymer model with a slightly greater coarse-graining level than in the CGMD simulation. For the binary-solvent system considered, however, both of the two implicit-solvent schemes (i.e., CGMC and CGLD) fail to capture the effects of conspicuous concentration fluctuations near the polymer-solvent interface, arising from a pronounced coupling between the solvent molecules and different parts of the polymer. Essential physical implications are elaborated on the success as well as the failure of the two implicit-solvent CG schemes under varying solvent conditions. Within the ellipsoid-chain model, the impact of synthesized defects on local segmental ordering as well as bulk chain conformation is also scrutinized, and essential consequences in practical applications discussed. In future perspectives, we remark on strategy that takes advantage of the coordination among various CG models and simulation schemes to warrant computational efficiency and accuracy, with the anticipated capability of simulating larger-scale, many-chain aggregate systems.

Development of multicomponent hybrid density functional theory with polarizable continuum model for the analysis of nuclear quantum effect and solvent effect on NMR chemical shift.

PubMed

Kanematsu, Yusuke; Tachikawa, Masanori

2014-04-28

We have developed the multicomponent hybrid density functional theory [MC_(HF+DFT)] method with polarizable continuum model (PCM) for the analysis of molecular properties including both nuclear quantum effect and solvent effect. The chemical shifts and H/D isotope shifts of the picolinic acid N-oxide (PANO) molecule in chloroform and acetonitrile solvents are applied by B3LYP electron exchange-correlation functional for our MC_(HF+DFT) method with PCM (MC_B3LYP/PCM). Our MC_B3LYP/PCM results for PANO are in reasonable agreement with the corresponding experimental chemical shifts and isotope shifts. We further investigated the applicability of our method for acetylacetone in several solvents.

Polymer brushes in explicit poor solvents studied using a new variant of the bond fluctuation model

NASA Astrophysics Data System (ADS)

Jentzsch, Christoph; Sommer, Jens-Uwe

2014-09-01

Using a variant of the Bond Fluctuation Model which improves its parallel efficiency in particular running on graphic cards we perform large scale simulations of polymer brushes in poor explicit solvent. Grafting density, solvent quality, and chain length are varied. Different morphological structures in particular octopus micelles are observed for low grafting densities. We reconsider the theoretical model for octopus micelles proposed by Williams using scaling arguments with the relevant scaling variable being σ/σc, and with the characteristic grafting density given by σc ˜ N-4/3. We find that octopus micelles only grow laterally, but not in height and we propose an extension of the model by assuming a cylindrical shape instead of a spherical geometry for the micelle-core. We show that the scaling variable σ/σc can be applied to master plots for the averaged height of the brush, the size of the micelles, and the number of chains per micelle. The exponents in the corresponding power law relations for the grafting density and chain length are in agreement with the model for flat cylindrical micelles. We also investigate the surface roughness and find that polymer brushes in explicit poor solvent at grafting densities higher than the stretching transition are flat and surface rippling can only be observed close to the stretching transition.

Ultrasonic studies of intermolecular interactions in binary mixtures of 4-methoxy benzoin with various solvents: Excess molar functions of ultrasonic parameters at different concentrations and in different solvents.

PubMed

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

2012-11-01

Density (ρ), ultrasonic velocity (U), for the binary mixtures of 4-methoxy benzoin (4MB) with ethanol, chloroform, acetonitrile, benzene, and di-oxane were measured at 298K. The solute-solvent interactions and the effect of the polarity of the solvent on the type of intermolecular interactions are discussed here. From the above data, adiabatic compressibility (β), intermolecular free length (L(f)), acoustic impedance (Z), apparent molar volume (Ø), relative association (RA) have been calculated. Other useful parameters such as excess density, excess velocity and excess adiabatic compressibility have also been calculated. These parameters were used to study the nature and extent of intermolecular interactions between component molecules in the binary mixtures. Copyright © 2012 Elsevier B.V. All rights reserved.

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.

End-anchored polymers in good solvents from the single chain limit to high anchoring densities.

PubMed

Whitmore, Mark D; Grest, Gary S; Douglas, Jack F; Kent, Michael S; Suo, Tongchuan

2016-11-07

An increasing number of applications utilize grafted polymer layers to alter the interfacial properties of solid substrates, motivating refinement in our theoretical understanding of such layers. To assess existing theoretical models of them, we have investigated end-anchored polymer layers over a wide range of grafting densities, σ, ranging from a single chain to high anchoring density limits, chain lengths ranging over two orders of magnitude, for very good and marginally good solvent conditions. We compare Monte Carlo and molecular dynamics simulations, numerical self-consistent field calculations, and experimental measurements of the average layer thickness, h, with renormalization group theory, the Alexander-de Gennes mushroom theory, and the classical brush theory. Our simulations clearly indicate that appreciable inter-chain interactions exist at all simulated areal anchoring densities so that there is no mushroom regime in which the layer thickness is independent of σ. Moreover, we find that there is no high coverage regime in which h follows the predicted scaling, h ∼ Nσ 1/3 , for classical polymer brushes either. Given that no completely adequate analytic theory seems to exist that spans wide ranges of N and σ, we applied scaling arguments for h as a function of a suitably defined reduced anchoring density, defined in terms of the solution radius of gyration of the polymer chains and N. We find that such a scaling approach enables a smooth, unified description of h in very good solvents over the full range of anchoring density and chain lengths, although this type of data reduction does not apply to marginal solvent quality conditions.

[Supercritical and near-critical fluid solvents assisted reaction and separation processes].

PubMed

Song, R; Zeng, J; Zhong, B

2001-11-01

The tunability of supercritical and near-critical fluid (S/NCF) solvents offers environmental improvements and economic advantages from improved performances and flexibility for separation and reaction processes through density changes or cosolvents. The paper reviews the sustainable reaction and separation processes in S/NCF solvents such as supercritical carbon dioxide and near-critical water.

Solvent Effects on the Conductance of 1,4-benzenediamine

NASA Astrophysics Data System (ADS)

Fatemi, Valla; Kamenetska, Maria; Neaton, Jeffrey; Venkataraman, Latha

2010-03-01

We measured the conductance of 1,4-benzenediamine (BDA) by mechanically forming and breaking Au point contacts with a modified STM in a solution of molecules in ambient conditions, using a variety of solvents. Here, we present reliable experimental results which show that the conductance of BDA can be increased by over 50% when dissolved in aromatic organic solvents solely by varying halogen groups on the solvent molecule. The trends in conductance do not correlate with the solvent dielectric constant, dipole moment, or direct solvent-BDA interactions. First-principles density functional theory calculations of solvent molecule binding to gold surfaces are used to discuss mechanisms behind the conductance shift of the BDA molecule.

Solvent effects on polysulfide redox kinetics and ionic conductivity in lithium-sulfur batteries

DOE PAGES

Fan, Frank Y.; Pan, Menghsuan Sam; Lau, Kah Chun; ...

2016-11-25

Lithium-sulfur (Li-S) batteries have high theoretical energy density and low raw materials cost compared to present lithium-ion batteries and are thus promising for use in electric transportation and other applications. A major obstacle for Li-S batteries is low rate capability, especially at the low electrolyte/sulfur (E/S) ratios required for high energy density. Herein, we investigate several potentially rate-limiting factors for Li-S batteries. We study the ionic conductivity of lithium polysulfide solutions of varying concentration and in different ether-based solvents and their exchange current density on glassy carbon working electrodes. We believe this is the first such investigation of exchange currentmore » density for lithium polysulfide in solution. Exchange current densities are measured using both electrochemical impedance spectroscopy and steady-state galvanostatic polarization. In the range of interest (1-8 M [S]), the ionic conductivity monotonically decreases with increasing sulfur concentration while exchange current density shows a more complicated relationship to sulfur concentration. The electrolyte solvent dramatically affects ionic conductivity and exchange current density. Finally, the measured ionic conductivities and exchange current densities are also used to interpret the overpotential and rate capability of polysulfide-nanocarbon suspensions; this analysis demonstrates that ionic conductivity is the rate-limiting property in the solution regime (i.e. between Li 2S 8 and Li 2S 4).« less

Relationship between Solvation Thermodynamics from IST and DFT Perspectives.

PubMed

Levy, Ronald M; Cui, Di; Zhang, Bin W; Matubayasi, Nobuyuki

2017-04-20

Inhomogeneous solvation theory (IST) and classical density functional theory (DFT) each provide a framework for relating distribution functions of solutions to their thermodynamic properties. As reviewed in this work, both IST and DFT can be formulated in a way that use two "end point" simulations, one of the pure solvent and the other of the solution, to determine the solute chemical potential and other thermodynamic properties of the solution and of subvolumes in regions local to the solute containing hydrating waters. In contrast to IST, where expressions for the excess energy and entropy of solution are the object of analysis, in the DFT end point formulation of the problem, the solute-solvent potential of mean force (PMF) plays a central role. The indirect part of the PMF corresponds to the lowest order (1-body) truncation of the IST expression. Because the PMF is a free energy function, powerful numerical methods can be used to estimate it. We show that the DFT expressions for the solute excess chemical potential can be written in a form which is local, involving integrals only over regions proximate to the solute. The DFT end point route to estimating solvation free energies provides an alternative path to that of IST for analyzing solvation effects on molecular recognition and conformational changes in solution, which can lead to new insights. In order to illustrate the kind of information that is contained in the solute-solvent PMF, we have carried out simulations of β-cyclodextrin in water. This solute is a well studied "host" molecule to which "guest" molecules bind; host-guest systems serve as models for molecular recognition. We illustrate the range of values the direct and indirect parts of the solute-solvent PMF can have as a water molecule is brought to the interface of β-cyclodextrin from the bulk; we discuss the "competition" between these two terms, and the role it plays in molecular recognition.

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.

Calculation of 125Te NMR Chemical Shifts at the Full Four-Component Relativistic Level with Taking into Account Solvent and Vibrational Corrections: A Gateway to Better Agreement with Experiment.

PubMed

Rusakova, Irina L; Rusakov, Yuriy Yu; Krivdin, Leonid B

2017-06-29

Four-component relativistic calculations of 125 Te NMR chemical shifts were performed in the series of 13 organotellurium compounds, potential precursors of the biologically active species, at the density functional theory level under the nonrelativistic and four-component fully relativistic conditions using locally dense basis set scheme derived from relativistic Dyall's basis sets. The relativistic effects in tellurium chemical shifts were found to be of as much as 20-25% of the total calculated values. The vibrational and solvent corrections to 125 Te NMR chemical shifts are about, accordingly, 6 and 8% of their total values. The PBE0 exchange-correlation functional turned out to give the best agreement of calculated tellurium shifts with their experimental values giving the mean absolute percentage error of 4% in the range of ∼1000 ppm, provided all corrections are taken into account.

Holographic Methods for the Investigation of Photophysical Properties.

DTIC Science & Technology

1983-04-22

terphenyl doped with 10- 3 mol/mol of pentacene . Obtaining k from decay curves as in * A -Fig. 14a and plotting k as a function of 02 (see Fig. 14b...translation diffusion of molecules in liquid solvents can be used to probe solute conformations, solvent-solute interactions and local solvent structure...eiion of 1.7omoAr WauW by TrArWAOn GFarinP So far, local heating by the absorption of the two interfering light pulses has not been taken into

Properties of electronically excited states of four squaraine dyes and their complexes with fullerene C70: A theoretical investigation

NASA Astrophysics Data System (ADS)

Zhang, Jian; Li, Tingyu

2017-09-01

Solar cells sensitized by polypyridyl Ru(II) complexes exhibit relatively high efficiency, however those photo-sensitizers did not absorb the photons in the far-red and near-infrared region. At present, squaraine dyes have received considerable attention as their attractively intrinsic red light absorption and unusual high molar extinction coefficient. Here we applied density functional theory and time dependent density functional theory to investigate the properties of electronically excited states of four squaraine dyes and their complexes with fullerene C70. The influences of different functionals, basis sets and solvent effects are evaluated. To understand the photophysical properties, the investigations are basing on a classification method which splits the squaraine dyes and their complexes with fullerene C70 into two units to characterize the intramolecular density distribution. We present the signatures of their electronically excited states which are characterized as local excitation or charge-transfer excitation. The relationship between open-circuit voltage and the number of intramolecular hydrogen bonds in squaraine dyes are discussed.

Intramolecular vibrational redistribution of CH 2I 2 dissolved in supercritical Xe

NASA Astrophysics Data System (ADS)

Sekiguchi, K.; Shimojima, A.; Kajimoto, O.

2003-03-01

Intramolecular vibrational energy redistribution (IVR) of CH 2I 2 in supercritical Xe has been studied. The first overtone of the C-H stretching mode was excited with a near infrared laser pulse and the transient UV absorption near 390 nm was monitored. Signals showed a rise and decay profile, which gave the IVR and VET (intermolecular vibrational energy transfer) rates, respectively. Solvent density dependence of each rate was obtained by tuning the pressure at a constant temperature. The IVR rate in supercritical Xe increased with increasing solvent density and asymptotically reached a limiting value. This result suggests that the IVR process of CH 2I 2 in condensed phase is a solvent-assisted process.

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.

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.

Intramolecular charge transfer and trans-cis isomerization of the DCM styrene dye in polar solvents. A CS INDO MRCI study

NASA Astrophysics Data System (ADS)

Marguet, S.; Mialocq, J. C.; Millie, P.; Berthier, G.; Momicchioli, F.

1992-03-01

The solvent-induced changes of trans-cis isomerization efficiency and electronic structure of the excited state of the DCM dye have been considered by means of CS INDO MRCI calculations. The potential energy curves, dipole moments and atomic charge densities as a function of two internal coordinates, namely the rotation angle about the central "double" bond and the twisting of the dimethylamino group, have been obtained for the ground state and the lowest excited states. The structural requirements for the existence of ICT (intramolecular charge transfer) excited states have been investigated by considering internal rotations about three single bonds. The reliability of the potential surfaces and of the solvation models has been discussed with reference to test-calculations on the DMABN molecule. In the first excited singlet state of DCM, the low-energy barrier for the trans-cis isomerization has been found unaffected by the solvent polarity. The only singlet excited state presenting a large ICT character has been found to be the S 2 state for a perpendicularly twisted conformation of the dimethylamino group (TICT state). The assumption of a deactivation of the trans-isomer in the locally excited state through the TICT funnel has been largely discussed with reference to the simplifications of the present theoretical approach.

The Nature of the Intramolecular Charge Transfer State in Peridinin

PubMed Central

Wagner, Nicole L.; Greco, Jordan A.; Enriquez, Miriam M.; Frank, Harry A.; Birge, Robert R.

2013-01-01

Experimental and theoretical evidence is presented that supports the theory that the intramolecular charge transfer (ICT) state of peridinin is an evolved state formed via excited-state bond-order reversal and solvent reorganization in polar media. The ICT state evolves in <100 fs and is characterized by a large dipole moment (∼35 D). The charge transfer character involves a shift of electron density within the polyene chain, and it does not involve participation of molecular orbitals localized in either of the β-rings. Charge is moved from the allenic side of the polyene into the furanic ring region and is accompanied by bond-order reversal in the central portion of the polyene chain. The electronic properties of the ICT state are generated via mixing of the “11Bu+” ionic state and the lowest-lying “21Ag–” covalent state. The resulting ICT state is primarily 1Bu+-like in character and exhibits not only a large oscillator strength but an unusually large doubly excited character. In most solvents, two populations exist in equilibrium, one with a lowest-lying ICT ionic state and a second with a lowest-lying “21Ag–” covalent state. The two populations are separated by a small barrier associated with solvent relaxation and cavity formation. PMID:23528091

Computer simulation of the linear and nonlinear optical susceptibilities of p-nitroaniline in cyclohexane, 1,4-dioxane, and tetrahydrofuran in quadrupolar approximation. II. Local field effects and optical susceptibilitities.

PubMed

Reis, H; Papadopoulos, M G; Grzybowski, A

2006-09-21

This is the second part of a study to elucidate the local field effects on the nonlinear optical properties of p-nitroaniline (pNA) in three solvents of different multipolar character, that is, cyclohexane (CH), 1,4-dioxane (DI), and tetrahydrofuran (THF), employing a discrete description of the solutions. By the use of liquid structure information from molecular dynamics simulations and molecular properties computed by high-level ab initio methods, the local field and local field gradients on p-nitroaniline and the solvent molecules are computed in quadrupolar approximation. To validate the simulations and the induction model, static and dynamic (non)linear properties of the pure solvents are also computed. With the exception of the static dielectric constant of pure THF, a good agreement between computed and experimental refractive indices, dielectric constants, and third harmonic generation signals is obtained for the solvents. For the solutions, it is found that multipole moments up to two orders higher than quadrupole have a negligible influence on the local fields on pNA, if a simple distribution model is employed for the electric properties of pNA. Quadrupole effects are found to be nonnegligible in all three solvents but are especially pronounced in the 1,4-dioxane solvent, in which the local fields are similar to those in THF, although the dielectric constant of DI is 2.2 and that of the simulated THF is 5.4. The electric-field-induced second harmonic generation (EFISH) signal and the hyper-Rayleigh scattering signal of pNA in the solutions computed with the local field are in good to fair agreement with available experimental results. This confirms the effect of the "dioxane anomaly" also on nonlinear optical properties. Predictions based on an ellipsoidal Onsager model as applied by experimentalists are in very good agreement with the discrete model predictions. This is in contrast to a recent discrete reaction field calculation of pNA in 1,4-dioxane, which found that the predicted first hyperpolarizability of pNA deviated strongly from the predictions obtained using Onsager-Lorentz local field factors.

Ordering nanoparticles with polymer brushes

NASA Astrophysics Data System (ADS)

Cheng, Shengfeng; Stevens, Mark J.; Grest, Gary S.

2017-12-01

Ordering nanoparticles into a desired super-structure is often crucial for their technological applications. We use molecular dynamics simulations to study the assembly of nanoparticles in a polymer brush randomly grafted to a planar surface as the solvent evaporates. Initially, the nanoparticles are dispersed in a solvent that wets the polymer brush. After the solvent evaporates, the nanoparticles are either inside the brush or adsorbed at the surface of the brush, depending on the strength of the nanoparticle-polymer interaction. For strong nanoparticle-polymer interactions, a 2-dimensional ordered array is only formed when the brush density is finely tuned to accommodate a single layer of nanoparticles. When the brush density is higher or lower than this optimal value, the distribution of nanoparticles shows large fluctuations in space and the packing order diminishes. For weak nanoparticle-polymer interactions, the nanoparticles order into a hexagonal array on top of the polymer brush as long as the grafting density is high enough to yield a dense brush. An interesting healing effect is observed for a low-grafting-density polymer brush that can become more uniform in the presence of weakly adsorbed nanoparticles.

Nitropyrroles, Diels-Alder reactions assisted by microwave irradiation and solvent effect. An experimental and theoretical study

NASA Astrophysics Data System (ADS)

Mancini, Pedro M. E.; Kneeteman, María N.; Cainelli, Mauro; Ormachea, Carla M.; Domingo, Luis R.

2017-11-01

The behaviors of N-tosylnitropyrroles acting as electrophilic dienophiles in polar Diels-Alder reactions joint to different dienes of increeased nucleophilicity are analyzed. The reactions were developed under microwave irradiation using toluene or protic ionic liquids (PILs) as solvents and in free solvent conditions. In all the cases explored we observed good yields in short reaction times. For these reactions, the free solvent condition and the use of protic ionic liquids as solvents offer similar results. However, the free solvent conditions favor environmental sustainability. The role of PILs in these polar Diels-Alder reactions has been theoretically studied within the Molecular Electron Density Theory.

Thermoplastic composite matrices with improved solvent resistance

NASA Technical Reports Server (NTRS)

Hergenrother, P. M.; Jensen, B. J.; Havens, S. J.

1984-01-01

In order to improve solvent resistance of aromatic thermoplastic polymers, ethynyl-terminated aromatic sulfone polymers (ETS), sulfone/ester polymers (SEPE) containing pendent ethynyl groups, and phenoxy resin containing pendent ethynyl groups are synthesized. Cured polysulfones and phenoxy resins containing ethynyl groups on the ends or pendent on the molecules exhibited systematic behavior in solvent resistance, film flexibility, and toughness as a function of crosslink density. The film and composite properties of a cured solvent-resistant ETS were better than those of a commercially available solvent sensitive polysulfone. The study was part of a NASA program to better understand the trade-offs between solvent resistance, processability and mechanical properties which may be useful in designing composite structures for aerospace vehicles.

Droplet-Based Production of Liposomes

NASA Technical Reports Server (NTRS)

Ackley, Donald E.; Forster, Anita

2009-01-01

A process for making monodisperse liposomes having lipid bilayer membranes involves fewer, simpler process steps than do related prior methods. First, a microfluidic, cross junction droplet generator is used to produce vesicles comprising aqueous solution droplets contained in single layer lipid membranes. The vesicles are collected in a lipid-solvent mix that is at most partially soluble in water and is less dense than is water. A layer of water is dispensed on top of the solvent. By virtue of the difference in densities, the water sinks to the bottom and the solvent floats to the top. The vesicles, which have almost the same density as that of water, become exchanged into the water instead of floating to the top. As there are excess lipids in the solvent solution, in order for the vesicles to remain in the water, the addition of a second lipid layer to each vesicle is energetically favored. The resulting lipid bilayers present the hydrophilic ends of the lipid molecules to both the inner and outer membrane surfaces. If lipids of a second kind are dissolved in the solvent in sufficient excess before use, then asymmetric liposomes may be formed.

Extraction of basil leaves (ocimum canum) oleoresin with ethyl acetate solvent by using soxhletation method

NASA Astrophysics Data System (ADS)

Tambun, R.; Purba, R. R. H.; Ginting, H. K.

2017-09-01

The goal of this research is to produce oleoresin from basil leaves (Ocimum canum) by using soxhletation method and ethyl acetate as solvent. Basil commonly used in culinary as fresh vegetables. Basil contains essential oils and oleoresin that are used as flavouring agent in food, in cosmetic and ingredient in traditional medicine. The extraction method commonly used to obtain oleoresin is maceration. The problem of this method is many solvents necessary and need time to extract the raw material. To resolve the problem and to produce more oleoresin, we use soxhletation method with a combination of extraction time and ratio from the material with a solvent. The analysis consists of yield, density, refractive index, and essential oil content. The best treatment of basil leaves oleoresin extraction is at ratio of material and solvent 1:6 (w / v) for 6 hours extraction time. In this condition, the yield of basil oleoresin is 20.152%, 0.9688 g/cm3 of density, 1.502 of refractive index, 15.77% of essential oil content, and the colour of oleoresin product is dark-green.

Compressed air-assisted solvent extraction (CASX) for metal removal.

PubMed

Li, Chi-Wang; Chen, Yi-Ming; Hsiao, Shin-Tien

2008-03-01

A novel process, compressed air-assisted solvent extraction (CASX), was developed to generate micro-sized solvent-coated air bubbles (MSAB) for metal extraction. Through pressurization of solvent with compressed air followed by releasing air-oversaturated solvent into metal-containing wastewater, MSAB were generated instantaneously. The enormous surface area of MSAB makes extraction process extremely fast and achieves very high aqueous/solvent weight ratio (A/S ratio). CASX process completely removed Cr(VI) from acidic electroplating wastewater under A/S ratio of 115 and extraction time of less than 10s. When synthetic wastewater containing Cd(II) of 50mgl(-1) was treated, A/S ratios of higher than 714 and 1190 could be achieved using solvent with extractant/diluent weight ratio of 1:1 and 5:1, respectively. Also, MSAB have very different physical properties, such as size and density, compared to the emulsified solvent droplets, making separation and recovery of solvent from treated effluent very easy.

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.

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.

Low-density microcellular foam and method of making same

DOEpatents

Rinde, James A.

1977-01-01

Low-density microcellular foam having a cell size of not greater than 2 .mu.m and method of making by dissolving cellulose acetate in an acetone-based solvent, gelling the solution in a water bath maintained at 0.degree.-10.degree. C for a selected period of time to allow impurities to diffuse out, freezing the gel, and then freeze-drying wherein water and solvents sublime and the gel structure solidifies into low-density microcellular foam. The foam has a density of 0.065 to 0.6.times.10.sup.3 kg/m.sup.3 and cell size of about 0.3 to 2 .mu.m. The small cell size foam is particularly applicable for encapsulation of laser targets.

Method of making a cellulose acetate low density microcellular foam

DOEpatents

Rinde, James A.

1978-01-01

Low-density microcellular foam having a cell size of not greater than 2 .mu.m and method of making by dissolving cellulose acetate in an acetone-based solvent, gelling the solution in a water bath maintained at 0-10.degree. C for a selected period of time to allow impurities to diffuse out, freezing the gel, and then freeze-drying wherein water and solvents sublime and the gel structure solidifies into low-density microcellular foam. The foam has a density of 0.065 to 0.6.times.10.sup.3 kg/m.sup.3 and cell size of about 0.3 to 2 .mu.m. The small cell size foam is particularly adaptable for encapsulation of laser targets.

Joint density-functional theory and its application to systems in solution

NASA Astrophysics Data System (ADS)

Petrosyan, Sahak A.

The physics of solvation, the interaction of water with solutes, plays a central role in chemistry and biochemistry, and it is essential for the very existence of life. Despite the central importance of water and the advent of the quantum theory early in the twentieth century, the link between the fundamental laws of physics and the observable properties of water remain poorly understood to this day. The central goal of this thesis is to develop a new formalism and framework to make the study of systems (solutes or surfaces) in contact with liquid water as practical and accurate as standard electronic structure calculations without the need for explicit averaging over large ensembles of configurations of water molecules. The thesis introduces a new form of density functional theory for the ab initio description of electronic systems in contact with a molecular liquid environment. This theory rigorously joins an electron density-functional for the electrons of a solute with a classical density-functional theory for the liquid into a single variational principle for the free energy of the combined system. Using the new form of density-functional theory for the ab initio description of electronic systems in contact with a molecular liquid environment, the thesis then presents the first detailed study of the impact of a solvent on the surface chemistry of Cr2O3, the passivating layer of stainless steel alloys. In comparison to a vacuum, we predict that the presence of water has little impact on the adsorption of chloride ions to the oxygen-terminated surface but has a dramatic effect on the binding of hydrogen to that surface. A key ingredient of a successful joint density functional theory is a good approximate functional for describing the solvent. We explore how the simplest examples of the best known class of approximate forms for the classical density functional fail when applied directly to water. The thesis then presents a computationally efficient density-functional theory for water which overcomes this difficulty and gives reasonable agreement with molecular dynamics simulation data for the solvation of hard spheres in water and sufficient agreement with experimental data for hydration of inert gas atoms to justify its use in a joint theory with standard approximate density functionals used in electronic structure calculations. The last study in the thesis combines the previous ideas and presenting an approximate model density functional which includes a description of cavitation effects through a classical density-functional theory; a description of dielectric effects through a non-local polarizability, and a description of the coupling of the solvent to the electrons of the solute through a pseudopotential. Without any empirical fitting of parameters to solvation data, this theory predicts solvation energies at least as well as state-of-the-art quantum-chemical cavity approaches, which do employ such fitting. Although this agreement without adjustable parameters is very encouraging and shows the promise of the joint density-functional approach, the functionals which we develop here are models and do not yet include all of the microscopic physics. The thesis concludes with a description of the directions future work should take to address this weakness.

Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review

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

Wei, Guowei; Baker, Nathan A.

2016-11-11

This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, electrostatic potential, ion density, electron density, etc. Recently, differential geometry theory has been used to define the surfaces that separate the microscopic (solute) domains for biomolecules from the macroscopic (solvent) domains. In thesemore » approaches, the microscopic domains are modeled with atomistic or quantum mechanical descriptions, while continuum mechanics models (including fluid mechanics, elastic mechanics, and continuum electrostatics) are applied to the macroscopic domains. This multiphysics description is integrated through an energy functional formalism and the resulting Euler-Lagrange equation is employed to derive a variety of governing partial differential equations for different solvation and transport processes; e.g., the Laplace-Beltrami equation for the solvent-solute interface, Poisson or Poisson-Boltzmann equations for electrostatic potentials, the Nernst-Planck equation for ion densities, and the Kohn-Sham equation for solute electron density. Extensive validation of these models has been carried out over hundreds of molecules, including proteins and ion channels, and the experimental data have been compared in terms of solvation energies, voltage-current curves, and density distributions. We also propose a new quantum model for electrolyte transport.« less

Polder maps: Improving OMIT maps by excluding bulk solvent

DOE PAGES

Liebschner, Dorothee; Afonine, Pavel V.; Moriarty, Nigel W.; ...

2017-02-01

The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factorsmore » and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. As a result, the tools described in this manuscript have been implemented and are available in PHENIX.« less

Critical Casimir effect in a polymer chain in supercritical solvents.

PubMed

Sumi, Tomonari; Imazaki, Nobuyuki; Sekino, Hideo

2009-03-01

Density fluctuation effects on the conformation of a polymer chain in a supercritical solvent were investigated by performing a multiscale simulation based on the density-functional theory. We found (a) a universal swelling of the polymer chain near the critical point, irrespective of whether the polymer chain is solvophilic or solvophobic, and (b) a characteristic collapse of the polymer chain having a strong solvophilicity at a temperature slightly higher than the critical point, where the isothermal compressibility becomes less than the ideal one.

Thermodynamic Characterization of Hydration Sites from Integral Equation-Derived Free Energy Densities: Application to Protein Binding Sites and Ligand Series.

PubMed

Güssregen, Stefan; Matter, Hans; Hessler, Gerhard; Lionta, Evanthia; Heil, Jochen; Kast, Stefan M

2017-07-24

Water molecules play an essential role for mediating interactions between ligands and protein binding sites. Displacement of specific water molecules can favorably modulate the free energy of binding of protein-ligand complexes. Here, the nature of water interactions in protein binding sites is investigated by 3D RISM (three-dimensional reference interaction site model) integral equation theory to understand and exploit local thermodynamic features of water molecules by ranking their possible displacement in structure-based design. Unlike molecular dynamics-based approaches, 3D RISM theory allows for fast and noise-free calculations using the same detailed level of solute-solvent interaction description. Here we correlate molecular water entities instead of mere site density maxima with local contributions to the solvation free energy using novel algorithms. Distinct water molecules and hydration sites are investigated in multiple protein-ligand X-ray structures, namely streptavidin, factor Xa, and factor VIIa, based on 3D RISM-derived free energy density fields. Our approach allows the semiquantitative assessment of whether a given structural water molecule can potentially be targeted for replacement in structure-based design. Finally, PLS-based regression models from free energy density fields used within a 3D-QSAR approach (CARMa - comparative analysis of 3D RISM Maps) are shown to be able to extract relevant information for the interpretation of structure-activity relationship (SAR) trends, as demonstrated for a series of serine protease inhibitors.

On the nature of the solvated electron in ice Ih.

PubMed

de Koning, Maurice; Fazzio, Adalberto; da Silva, Antônio José Roque; Antonelli, Alex

2016-02-14

The water-solvated excess electron (EE) is a key chemical agent whose hallmark signature, its asymmetric optical absorption spectrum, continues to be a topic of debate. While nearly all investigation has focused on the liquid-water solvent, the fact that the crystalline-water solvated EE shows a very similar visible absorption pattern has remained largely unexplored. Here, we present spin-polarized density-functional theory calculations subject to periodic boundary conditions of the interplay between an EE and a number of intrinsic lattice defects in ice Ih. Our results show that the optical absorption signatures in the presence of three unsaturated hydrogen bonds (HB) are very similar to those observed experimentally. Its low-energy side can be attributed to transitions between the EE ground state and a single localized excited level, in a picture that is different from that for the liquid solvent, where this portion has been associated with hydrogen-like s → p excitations. The blue tail, on the other hand, relates to transitions between the EE ground state and delocalized excited states, which is in line with the bound-to-continuum transition interpretations for the EE in liquid water. Finally, we find that, depending on the number of dangling HBs participating in the EE trap, its charge density may spontaneously break the spin degeneracy through exchange interactions with the surrounding electrons, displaying the many-electron quantum nature of the EE problem in ice Ih.

Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins.

PubMed

Lebard, David N; Matyushov, Dmitry V

2008-12-01

Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of electrostatic fluctuations, expressed in terms of the reorganization energy of changing the redox state of the protein, is related to the formation of the hydrophobic protein-water interface, allowing large-amplitude collective fluctuations of the water density in the protein's first solvation shell. On top of the monotonic increase of the reorganization energy with increasing temperature, we have observed a spike at approximately 220 K also accompanied by a significant slowing of the exponential collective Stokes shift dynamics. In contrast to the local density fluctuations of the hydration-shell waters, these spikes might be related to the global property of the water solvent crossing the Widom line or undergoing a weak first-order transition.

Simulation of electric double-layer capacitors: evaluation of constant potential method

NASA Astrophysics Data System (ADS)

Wang, Zhenxing; Laird, Brian; Yang, Yang; Olmsted, David; Asta, Mark

2014-03-01

Atomistic simulations can play an important role in understanding electric double-layer capacitors (EDLCs) at a molecular level. In such simulations, typically the electrode surface is modeled using fixed surface charges, which ignores the charge fluctuation induced by local fluctuations in the electrolyte solution. In this work we evaluate an explicit treatment of charges, namely constant potential method (CPM)[1], in which the electrode charges are dynamically updated to maintain constant electrode potential. We employ a model system with a graphite electrode and a LiClO4/acetonitrile electrolyte, examined as a function of electrode potential differences. Using various molecular and macroscopic properties as metrics, we compare CPM simulations on this system to results using fixed surface charges. Specifically, results for predicted capacity, electric potential gradient and solvent density profile are identical between the two methods; However, ion density profiles and solvation structure yield significantly different results.

Methods for recovering a solvent from a fluid volume and methods of removing at least one compound from a nonpolar solvent

DOEpatents

Ginosar, Daniel M.; Wendt, Daniel S.; Petkovic, Lucia M.

2014-06-10

A method of removing a nonpolar solvent from a fluid volume that includes at least one nonpolar compound, such as a fat, an oil or a triglyceride, is provided. The method comprises contacting a fluid volume with an expanding gas to expand the nonpolar solvent and form a gas-expanded solvent. The gas-expanded solvent may have a substantially reduced density in comparison to the at least one nonpolar compound and/or a substantially reduced capacity to solubilize the nonpolar compound, causing the nonpolar compounds to separate from the gas-expanded nonpolar solvent into a separate liquid phase. The liquid phase including the at least one nonpolar compound may be separated from the gas-expanded solvent using conventional techniques. After separation of the liquid phase, at least one of the temperature and pressure may be reduced to separate the nonpolar solvent from the expanding gas such that the nonpolar solvent may be recovered and reused.

Adsorption of flexible polymer chains on a surface: Effects of different solvent conditions

NASA Astrophysics Data System (ADS)

Martins, P. H. L.; Plascak, J. A.; Bachmann, M.

2018-05-01

Polymer chains undergoing a continuous adsorption-desorption transition are studied through extensive computer simulations. A three-dimensional self-avoiding walk lattice model of a polymer chain grafted onto a surface has been treated for different solvent conditions. We have used an advanced contact-density chain-growth algorithm, in which the density of contacts can be directly obtained. From this quantity, the order parameter and its fourth-order Binder cumulant are computed, as well as the corresponding critical exponents and the adsorption-desorption transition temperature. As the number of configurations with a given number of surface contacts and monomer-monomer contacts is independent of the temperature and solvent conditions, it can be easily applied to get results for different solvent parameter values without the need of any extra simulations. In analogy to continuous magnetic phase transitions, finite-size-scaling methods have been employed. Quite good results for the critical properties and phase diagram of very long single polymer chains have been obtained by properly taking into account the effects of corrections to scaling. The study covers all solvent effects, going from the limit of super-self-avoiding walks, characterized by effective monomer-monomer repulsion, to poor solvent conditions that enable the formation of compact polymer structures.

Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: comparison between hard-sphere solvent and water.

PubMed

Oshima, Hiraku; Kinoshita, Masahiro

2015-04-14

In earlier works, we showed that the entropic effect originating from the translational displacement of water molecules plays the pivotal role in protein folding and denaturation. The two different solvent models, hard-sphere solvent and model water, were employed in theoretical methods wherein the entropic effect was treated as an essential factor. However, there were similarities and differences in the results obtained from the two solvent models. In the present work, to unveil the physical origins of the similarities and differences, we simultaneously consider structural transition, cold denaturation, and pressure denaturation for the same protein by employing the two solvent models and considering three different thermodynamic states for each solvent model. The solvent-entropy change upon protein folding/unfolding is decomposed into the protein-solvent pair (PA) and many-body (MB) correlation components using the integral equation theories. Each component is further decomposed into the excluded-volume (EV) and solvent-accessible surface (SAS) terms by applying the morphometric approach. The four physically insightful constituents, (PA, EV), (PA, SAS), (MB, EV), and (MB, SAS), are thus obtained. Moreover, (MB, SAS) is discussed by dividing it into two factors. This all-inclusive investigation leads to the following results: (1) the protein-water many-body correlation always plays critical roles in a variety of folding/unfolding processes; (2) the hard-sphere solvent model fails when it does not correctly reproduce the protein-water many-body correlation; (3) the hard-sphere solvent model becomes problematic when the dependence of the many-body correlation on the solvent number density and temperature is essential: it is not quite suited to studies on cold and pressure denaturating of a protein; (4) when the temperature and solvent number density are limited to the ambient values, the hard-sphere solvent model is usually successful; and (5) even at the ambient values, however, the many-body correlation plays significant roles in the β-sheet formation and argument of relative stabilities of very similar structures of a protein. These results are argued in detail with respect to the four physically insightful constituents and the two factors mentioned above. The relevance to the absence or presence of hydrogen-bonding properties in the solvent is also discussed in detail.

Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water

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

Oshima, Hiraku; Kinoshita, Masahiro, E-mail: kinoshit@iae.kyoto-u.ac.jp

In earlier works, we showed that the entropic effect originating from the translational displacement of water molecules plays the pivotal role in protein folding and denaturation. The two different solvent models, hard-sphere solvent and model water, were employed in theoretical methods wherein the entropic effect was treated as an essential factor. However, there were similarities and differences in the results obtained from the two solvent models. In the present work, to unveil the physical origins of the similarities and differences, we simultaneously consider structural transition, cold denaturation, and pressure denaturation for the same protein by employing the two solvent modelsmore » and considering three different thermodynamic states for each solvent model. The solvent-entropy change upon protein folding/unfolding is decomposed into the protein-solvent pair (PA) and many-body (MB) correlation components using the integral equation theories. Each component is further decomposed into the excluded-volume (EV) and solvent-accessible surface (SAS) terms by applying the morphometric approach. The four physically insightful constituents, (PA, EV), (PA, SAS), (MB, EV), and (MB, SAS), are thus obtained. Moreover, (MB, SAS) is discussed by dividing it into two factors. This all-inclusive investigation leads to the following results: (1) the protein-water many-body correlation always plays critical roles in a variety of folding/unfolding processes; (2) the hard-sphere solvent model fails when it does not correctly reproduce the protein-water many-body correlation; (3) the hard-sphere solvent model becomes problematic when the dependence of the many-body correlation on the solvent number density and temperature is essential: it is not quite suited to studies on cold and pressure denaturating of a protein; (4) when the temperature and solvent number density are limited to the ambient values, the hard-sphere solvent model is usually successful; and (5) even at the ambient values, however, the many-body correlation plays significant roles in the β-sheet formation and argument of relative stabilities of very similar structures of a protein. These results are argued in detail with respect to the four physically insightful constituents and the two factors mentioned above. The relevance to the absence or presence of hydrogen-bonding properties in the solvent is also discussed in detail.« less

X-ray diffraction measurement of cosolvent accessible volume in rhombohedral insulin crystals

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

Soares, Alexei S.; Caspar, Donald L. D.

We report x-ray crystallographic measurement of the number of solvent electrons in the unit cell of a protein crystal equilibrated with aqueous solutions of different densities provides information about preferential hydration in the crystalline state. Room temperature and cryo-cooled rhombohedral insulin crystals were equilibrated with 1.2 M trehalose to study the effect of lowered water activity. The native and trehalose soaked crystals were isomorphous and had similar structures. Including all the low resolution data, the amplitudes of the structure factors were put on an absolute scale (in units of electrons per asymmetric unit) by constraining the integrated number of electronsmore » inside the envelope of the calculated protein density map to equal the number deduced from the atomic model. This procedure defines the value of F(0 0 0), the amplitude at the origin of the Fourier transform, which is equal to the total number of electrons in the asymmetric unit (i.e. protein plus solvent). Comparison of the F(0 0 0) values for three isomorphous pairs of room temperature insulin crystals, three with trehalose and three without trehalose, indicates that 75 ± 12 electrons per asymmetric unit were added to the crystal solvent when soaked in 1.2 M trehalose. If all the water in the crystal were available as solvent for the trehalose, 304 electrons would have been added. Thus, the co-solvent accessible volume is one quarter of the total water in the crystal. Finally, determination of the total number of electrons in a protein crystal is an essential first step for mapping the average density distribution of the disordered solvent.« less

X-ray diffraction measurement of cosolvent accessible volume in rhombohedral insulin crystals

DOE PAGES

Soares, Alexei S.; Caspar, Donald L. D.

2017-08-31

We report x-ray crystallographic measurement of the number of solvent electrons in the unit cell of a protein crystal equilibrated with aqueous solutions of different densities provides information about preferential hydration in the crystalline state. Room temperature and cryo-cooled rhombohedral insulin crystals were equilibrated with 1.2 M trehalose to study the effect of lowered water activity. The native and trehalose soaked crystals were isomorphous and had similar structures. Including all the low resolution data, the amplitudes of the structure factors were put on an absolute scale (in units of electrons per asymmetric unit) by constraining the integrated number of electronsmore » inside the envelope of the calculated protein density map to equal the number deduced from the atomic model. This procedure defines the value of F(0 0 0), the amplitude at the origin of the Fourier transform, which is equal to the total number of electrons in the asymmetric unit (i.e. protein plus solvent). Comparison of the F(0 0 0) values for three isomorphous pairs of room temperature insulin crystals, three with trehalose and three without trehalose, indicates that 75 ± 12 electrons per asymmetric unit were added to the crystal solvent when soaked in 1.2 M trehalose. If all the water in the crystal were available as solvent for the trehalose, 304 electrons would have been added. Thus, the co-solvent accessible volume is one quarter of the total water in the crystal. Finally, determination of the total number of electrons in a protein crystal is an essential first step for mapping the average density distribution of the disordered solvent.« less

Separating effective high density polyethylene segments from olefin block copolymers using high temperature liquid chromatography with a preloaded discrete adsorption promoting solvent barrier.

PubMed

Chatterjee, Tirtha; Rickard, Mark A; Pearce, Eric; Pangburn, Todd O; Li, Yongfu; Lyons, John W; Cong, Rongjuan; deGroot, A Willem; Meunier, David M

2016-09-23

Recent advances in catalyst technology have enabled the synthesis of olefin block copolymers (OBC). One type is a "hard-soft" OBC with a high density polyethylene (HDPE) block and a relatively low density polyethylene (VLDPE) block targeted as thermoplastic elastomers. Presently, one of the major challenges is to fractionate HDPE segments from the other components in an experimental OBC sample (block copolymers and VLDPE segments). Interactive high temperature liquid chromatography (HTLC) is ineffective for OBC separation as the HDPE segments and block copolymer chains experience nearly identical enthalpic interactions with the stationary phase and co-elute. In this work we have overcome this challenge by using liquid chromatography under the limiting conditions of desorption (LC LCD). A solvent plug (discrete barrier) is introduced in front of the sample which specifically promotes the adsorption of HDPE segments on the stationary phase (porous graphitic carbon). Under selected thermodynamic conditions, VLDPE segments and block copolymer chains crossed the barrier while HDPE segments followed the pore-included barrier solvent and thus enabled separation. The barrier solvent composition was optimized and the chemical composition of fractionated polymer chains was investigated as a function of barrier solvent strength using an online Fourier-transform infrared (FTIR) detector. Our study revealed that both the HDPE segments as well as asymmetric block copolymer chains (HDPE block length≫VLDPE block length) are retained in the separation and the barrier strength can be tailored to retain a particular composition. At the optimum barrier solvent composition, this method can be applied to separate effective HDPE segments from the other components, which has been demonstrated using an experimental OBC sample. Copyright © 2016 Elsevier B.V. All rights reserved.

Low density microcellular foams

DOEpatents

Aubert, James H.; Clough, Roger L.; Curro, John G.; Quintana, Carlos A.; Russick, Edward M.; Shaw, Montgomery T.

1987-01-01

Low density, microporous polymer foams are provided by a process which comprises forming a solution of polymer and a suitable solvent followed by rapid cooling of the solution to form a phase-separated system and freeze the phase-separated system. The phase-separated system comprises a polymer phase and a solvent phase, each of which is substantially continuous within the other. The morphology of the polymer phase prior to and subsequent to freezing determine the morphology of the resultant foam. Both isotropic and anisotropic foams can be produced. If isotropic foams are produced, the polymer and solvent are tailored such that the solution spontaneously phase-separates prior to the point at which any component freezes. The morphology of the resultant polymer phase determines the morphology of the resultant foam and the morphology of the polymer phase is retained by cooling the system at a rate sufficient to freeze one or both components of the system before a change in morphology can occur. Anisotropic foams are produced by forming a solution of polymer and solvent that will not phase separate prior to freezing of one or both components of the solution. In such a process, the solvent typically freezes before phase separation occurs. The morphology of the resultant frozen two-phase system determines the morphology of the resultant foam. The process involves subjecting the solution to essentially one-dimensional cooling. Means for subjecting such a solvent to one-dimensional cooling are also provided. Foams having a density of less than 0.1 g/cc and a uniform cell size of less than 10 .mu.m and a volume such that the foams have a length greater than 1 cm are provided.

Polarity control at interfaces: Quantifying pseudo-solvent effects in nano-confined systems

DOE PAGES

Singappuli-Arachchige, Dilini; Manzano, J. Sebastian; Sherman, Lindy M.; ...

2016-08-02

Surface functionalization controls local environments and induces solvent-like effects at liquid–solid interfaces. We explored structure–property relationships between organic groups bound to pore surfaces of mesoporous silica nanoparticles and Stokes shifts of the adsorbed solvatochromic dye Prodan. Correlating shifts of the dye on the surfaces with its shifts in solvents resulted in a local polarity scale for functionalized pores. The scale was validated by studying the effects of pore polarity on quenching of Nile Red fluorescence and on the vibronic band structure of pyrene. Measurements were done in aqueous suspensions of porous particles, proving that the dielectric properties in the poresmore » are different from the bulk solvent. The precise control of pore polarity was used to enhance the catalytic activity of TEMPO in the aerobic oxidation of furfuryl alcohol in water. Furthermore, an inverse relationship was found between pore polarity and activity of TEMPO in the pores, demonstrating that controlling the local polarity around an active site allows modulating the activity of nanoconfined catalysts.« less

FINAL REPORT: Room Temperature Hydrogen Storage in Nano-Confined Liquids

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

VAJO, JOHN

2014-06-12

DOE continues to seek solid-state hydrogen storage materials with hydrogen densities of ≥6 wt% and ≥50 g/L that can deliver hydrogen and be recharged at room temperature and moderate pressures enabling widespread use in transportation applications. Meanwhile, development including vehicle engineering and delivery infrastructure continues for compressed-gas hydrogen storage systems. Although compressed gas storage avoids the materials-based issues associated with solid-state storage, achieving acceptable volumetric densities has been a persistent challenge. This project examined the possibility of developing storage materials that would be compatible with compressed gas storage technology based on enhanced hydrogen solubility in nano-confined liquid solvents. These materialsmore » would store hydrogen in molecular form eliminating many limitations of current solid-state materials while increasing the volumetric capacity of compressed hydrogen storage vessels. Experimental methods were developed to study hydrogen solubility in nano-confined liquids. These methods included 1) fabrication of composites comprised of volatile liquid solvents for hydrogen confined within the nano-sized pore volume of nanoporous scaffolds and 2) measuring the hydrogen uptake capacity of these composites without altering the composite composition. The hydrogen storage capacities of these nano-confined solvent/scaffold composites were compared with bulk solvents and with empty scaffolds. The solvents and scaffolds were varied to optimize the enhancement in hydrogen solubility that accompanies confinement of the solvent. In addition, computational simulations were performed to study the molecular-scale structure of liquid solvent when confined within an atomically realistic nano-sized pore of a model scaffold. Confined solvent was compared with similar simulations of bulk solvent. The results from the simulations were used to formulate a mechanism for the enhanced solubility and to guide the experiments. Overall, the combined experimental measurements and simulations indicate that hydrogen storage based on enhanced solubility in nano-confined liquids is unlikely to meet the storage densities required for practical use. Only low gravimetric capacities of < 0.5 wt% were achieved. More importantly, solvent filled scaffolds had lower volumetric capacities than corresponding empty scaffolds. Nevertheless, several of the composites measured did show significant (>~ 5x) enhanced hydrogen solubility relative to bulk solvent solubility, when the hydrogen capacity was attributed only to dissolution in the confined solvent. However, when the hydrogen capacity was compared to an empty scaffold that is known to store hydrogen by surface adsorption on the scaffold walls, including the solvent always reduced the hydrogen capacity. For the best composites, this reduction relative to an empty scaffold was ~30%; for the worst it was ~90%. The highest capacities were obtained with the largest solvent molecules and with scaffolds containing 3- dimensionally confined pore geometries. The simulations suggested that the capacity of the composites originated from hydrogen adsorption on the scaffold pore walls at sites not occupied by solvent molecules. Although liquid solvent filled the pores, not all of the adsorption sites on the pore walls were occupied due to restricted motion of the solvent molecules within the confined pore space.« less

Molecular simulation of CO chemisorption on Co(0001) in presence of supercritical fluid solvent: A potential of mean force study

NASA Astrophysics Data System (ADS)

Asiaee, Alireza; Benjamin, Kenneth M.

2016-08-01

For several decades, heterogeneous catalytic processes have been improved through utilizing supercritical fluids (SCFs) as solvents. While numerous experimental studies have been established across a range of chemistries, such as oxidation, pyrolysis, amination, and Fischer-Tropsch synthesis, still there is little fundamental, molecular-level information regarding the role of the SCF on elementary heterogeneous catalytic steps. In this study, the influence of hexane solvent on the adsorption of carbon monoxide on Co(0001), as the first step in the reaction mechanism of many processes involving syngas conversion, is probed. Simulations are performed at various bulk hexane densities, ranging from ideal gas conditions (no SCF hexane) to various near- and super-critical hexane densities. For this purpose, both density functional theory and molecular dynamics simulations are employed to determine the adsorption energy and free energy change during CO chemisorption. Potential of mean force calculations, utilizing umbrella sampling and the weighted histogram analysis method, provide the first commentary on SCF solvent effects on the energetic aspects of the chemisorption process. Simulation results indicate an enhanced stability of CO adsorption on the catalyst surface in the presence of supercritical hexane within the reduced pressure range of 1.0-1.5 at a constant temperature of 523 K. Furthermore, it is shown that the maximum stability of CO in the adsorbed state as a function of supercritical hexane density at 523 K nearly coincides with the maximum isothermal compressibility of bulk hexane at this temperature.

An evaporation-assisted dispersive liquid-liquid microextraction technique as a simple tool for high performance liquid chromatography tandem-mass spectrometry determination of insecticides in wine.

PubMed

Timofeeva, Irina; Kanashina, Daria; Moskvin, Leonid; Bulatov, Andrey

2017-08-25

A sample pre-treatment technique based on evaporation-assisted dispersive liquid-liquid microextraction (EVA-DLLME), followed by HPLC-MS/MS has been developed for the determination of organophosphate insecticides (malathion, diazinon, phosalone) in wine samples. The procedure includes the addition of mixture of organic solvents (with density higher than water), consisting of the extraction (low density) and volatile (high density) solvents, to aqueous sample followed by heating of the mixture obtained, what promotes the volatile solvent evaporation and moving extraction solvent droplets from down to top of the aqueous sample and, as a consequence, microextraction of target analytes. To initiate the evaporation process an initiator is required. It was established that hexanol (extraction solvent) and dichloromethane (volatile solvent) mixture (1:1, v/v) provides effective microextraction of the insecticides from wine samples with recovery from 92 to 103%. The conditions of insecticides' microextraction such as selection of extraction solvent, ratio of hexanol/dichloromethane and hexanol/sample, type and concentration of initiator, and effect of ethanol as one of the main components of wine have been studied. Under optimal experimental conditions the linear detection ranges were found to be 10 -7 -10 -3 gL -1 for malathion, 10 -9 -10 -4 gL -1 for diazinon, and 10 -6 -10 -2 gL -1 for phosalone. The LODs, calculated from a blank test, based on 3σ, found to be 3×10 -8 gL -1 for malathion, 3×10 -10 gL -1 for diazinon and 3×10 -7 gL -1 for phosalone. The advantages of EVA-DLLME are the rapidity, simplicity, high sample throughput and low cost. As an outcome, the analytical results agreed fairly well with the results obtained by a reference GC-MS method. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Solidification of floating organic droplet in dispersive liquid-liquid microextraction as a green analytical tool.

PubMed

Mansour, Fotouh R; Danielson, Neil D

2017-08-01

Dispersive liquid-liquid microextraction (DLLME) is a special type of microextraction in which a mixture of two solvents (an extracting solvent and a disperser) is injected into the sample. The extraction solvent is then dispersed as fine droplets in the cloudy sample through manual or mechanical agitation. Hence, the sample is centrifuged to break the formed emulsion and the extracting solvent is manually separated. The organic solvents commonly used in DLLME are halogenated hydrocarbons that are highly toxic. These solvents are heavier than water, so they sink to the bottom of the centrifugation tube which makes the separation step difficult. By using solvents of low density, the organic extractant floats on the sample surface. If the selected solvent such as undecanol has a freezing point in the range 10-25°C, the floating droplet can be solidified using a simple ice-bath, and then transferred out of the sample matrix; this step is known as solidification of floating organic droplet (SFOD). Coupling DLLME to SFOD combines the advantages of both approaches together. The DLLME-SFOD process is controlled by the same variables of conventional liquid-liquid extraction. The organic solvents used as extractants in DLLME-SFOD must be immiscible with water, of lower density, low volatility, high partition coefficient and low melting and freezing points. The extraction efficiency of DLLME-SFOD is affected by types and volumes of organic extractant and disperser, salt addition, pH, temperature, stirring rate and extraction time. This review discusses the principle, optimization variables, advantages and disadvantages and some selected applications of DLLME-SFOD in water, food and biomedical analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

[Determination of solubility parameters of high density polyethylene by inverse gas chromatography].

PubMed

Wang, Qiang; Chen, Yali; Liu, Ruiting; Shi, Yuge; Zhang, Zhengfang; Tang, Jun

2011-11-01

Inverse gas chromatographic (IGC) technology was used to determine the solubility parameters of high density polyethylene (HDPE) at the absolute temperatures from 303.15 to 343.15 K. Six solvents were applied as test probes including hexane (n-C6), heptane (n-C7), octane (n-C8), nonane (n-C9), chloroform (CHCl3) and ethyl acetate (EtAc). Some thermodynamic parameters were obtained by IGC data analysis such as the specific retention volumes of the solvents (V(0)(g)), the molar enthalpy of sorption (delta H(S)(1)), the partial molar enthalpy of mixing at infinite dilution (delta H(1)(infinity)), the molar enthalpy of vaporization (delta H(v)), the activity coefficients at infinite dilution (omega (1)(infinity)), and Flow-Huggins interaction parameters (X(1,2)(infinity)) between HDPE and probe solvents. The results showed that the above six probes are poor solvents for HDPE. The solubility parameter of HDPE at room temperature (298.15 K) was also derived as 19.00 (J/cm3)(0.5).

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

Block-localized wavefunction (BLW) method at the density functional theory (DFT) level.

PubMed

Mo, Yirong; Song, Lingchun; Lin, Yuchun

2007-08-30

The block-localized wavefunction (BLW) approach is an ab initio valence bond (VB) method incorporating the efficiency of molecular orbital (MO) theory. It can generate the wavefunction for a resonance structure or diabatic state self-consistently by partitioning the overall electrons and primitive orbitals into several subgroups and expanding each block-localized molecular orbital in only one subspace. Although block-localized molecular orbitals in the same subspace are constrained to be orthogonal (a feature of MO theory), orbitals between different subspaces are generally nonorthogonal (a feature of VB theory). The BLW method is particularly useful in the quantification of the electron delocalization (resonance) effect within a molecule and the charge-transfer effect between molecules. In this paper, we extend the BLW method to the density functional theory (DFT) level and implement the BLW-DFT method to the quantum mechanical software GAMESS. Test applications to the pi conjugation in the planar allyl radical and ions with the basis sets of 6-31G(d), 6-31+G(d), 6-311+G(d,p), and cc-pVTZ show that the basis set dependency is insignificant. In addition, the BLW-DFT method can also be used to elucidate the nature of intermolecular interactions. Examples of pi-cation interactions and solute-solvent interactions will be presented and discussed. By expressing each diabatic state with one BLW, the BLW method can be further used to study chemical reactions and electron-transfer processes whose potential energy surfaces are typically described by two or more diabatic states.

Ordering nanoparticles with polymer brushes

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

Cheng, Shengfeng; Stevens, Mark J.; Grest, Gary S.

Ordering nanoparticles into a desired super-structure is often crucial for their technological applications. We use molecular dynamics simulations to study the assembly of nanoparticles in a polymer brush randomly grafted to a planar surface as the solvent evaporates. Initially, the nanoparticles are dispersed in a solvent that wets the polymer brush. After the solvent evaporates, the nanoparticles are either inside the brush or adsorbed at the surface of the brush, depending on the strength of the nanoparticle-polymer interaction. For strong nanoparticle-polymer interactions, a 2-dimensional ordered array is only formed when the brush density is finely tuned to accommodate a singlemore » layer of nanoparticles. When the brush density is higher or lower than this optimal value, the distribution of nanoparticles shows large fluctuations in space and the packing order diminishes. For weak nanoparticle-polymer interactions, the nanoparticles order into a hexagonal array on top of the polymer brush as long as the grafting density is high enough to yield a dense brush. As a result, an interesting healing effect is observed for a low-grafting-density polymer brush that can become more uniform in the presence of weakly adsorbed nanoparticles.« less

Ordering nanoparticles with polymer brushes

DOE PAGES

Cheng, Shengfeng; Stevens, Mark J.; Grest, Gary S.

2017-12-08

Ordering nanoparticles into a desired super-structure is often crucial for their technological applications. We use molecular dynamics simulations to study the assembly of nanoparticles in a polymer brush randomly grafted to a planar surface as the solvent evaporates. Initially, the nanoparticles are dispersed in a solvent that wets the polymer brush. After the solvent evaporates, the nanoparticles are either inside the brush or adsorbed at the surface of the brush, depending on the strength of the nanoparticle-polymer interaction. For strong nanoparticle-polymer interactions, a 2-dimensional ordered array is only formed when the brush density is finely tuned to accommodate a singlemore » layer of nanoparticles. When the brush density is higher or lower than this optimal value, the distribution of nanoparticles shows large fluctuations in space and the packing order diminishes. For weak nanoparticle-polymer interactions, the nanoparticles order into a hexagonal array on top of the polymer brush as long as the grafting density is high enough to yield a dense brush. As a result, an interesting healing effect is observed for a low-grafting-density polymer brush that can become more uniform in the presence of weakly adsorbed nanoparticles.« less

Signatures of Solvation Thermodynamics in Spectra of Intermolecular Vibrations

PubMed Central

2017-01-01

This study explores the thermodynamic and vibrational properties of water in the three-dimensional environment of solvated ions and small molecules using molecular simulations. The spectrum of intermolecular vibrations in liquid solvents provides detailed information on the shape of the local potential energy surface, which in turn determines local thermodynamic properties such as the entropy. Here, we extract this information using a spatially resolved extension of the two-phase thermodynamics method to estimate hydration water entropies based on the local vibrational density of states (3D-2PT). Combined with an analysis of solute–water and water–water interaction energies, this allows us to resolve local contributions to the solvation enthalpy, entropy, and free energy. We use this approach to study effects of ions on their surrounding water hydrogen bond network, its spectrum of intermolecular vibrations, and resulting thermodynamic properties. In the three-dimensional environment of polar and nonpolar functional groups of molecular solutes, we identify distinct hydration water species and classify them by their characteristic vibrational density of states and molecular entropies. In each case, we are able to assign variations in local hydration water entropies to specific changes in the spectrum of intermolecular vibrations. This provides an important link for the thermodynamic interpretation of vibrational spectra that are accessible to far-infrared absorption and Raman spectroscopy experiments. Our analysis provides unique microscopic details regarding the hydration of hydrophobic and hydrophilic functional groups, which enable us to identify interactions and molecular degrees of freedom that determine relevant contributions to the solvation entropy and consequently the free energy. PMID:28783431

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.

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

A poly(vinyl alcohol)/sodium alginate blend monolith with nanoscale porous structure

PubMed Central

2013-01-01

A stimuli-responsive poly(vinyl alcohol) (PVA)/sodium alginate (SA) blend monolith with nanoscale porous (mesoporous) structure is successfully fabricated by thermally impacted non-solvent induced phase separation (TINIPS) method. The PVA/SA blend monolith with different SA contents is conveniently fabricated in an aqueous methanol without any templates. The solvent suitable for the fabrication of the present blend monolith by TINIPS is different with that of the PVA monolith. The nanostructural control of the blend monolith is readily achieved by optimizing the fabrication conditions. Brunauer Emmett Teller measurement shows that the obtained blend monolith has a large surface area. Pore size distribution plot for the blend monolith obtained by the non-local density functional theory method reveals the existence of the nanoscale porous structure. Fourier transform infrared analysis reveals the strong interactions between PVA and SA. The pH-responsive property of the blend monolith is investigated on the basis of swelling ratio in different pH solutions. The present blend monolith of biocompatible and biodegradable PVA and SA with nanoscale porous structure has large potential for applications in biomedical and environmental fields. PMID:24093494

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

Ab Initio Modeling of the Electronic Absorption Spectrum of Previtamin D in Solution

NASA Astrophysics Data System (ADS)

Zhu, Tianyang

To study the solvent effects of water on the previtamin D absorption spectrum, we use the quantum mechanics (QM)/molecular mechanics (MM) method combined with replica-exchange molecular dynamics (REMD). The QM method is applied for the previtamin D molecule and the MM method is used for the water molecules. To enhance conformational sampling of the flexible previtamin D molecule we apply REMD. Based on the REMD structures, we calculate the macroscopic ensemble of the absorption spectrum in solution by time-dependent density functional theory (TDDFT). Comparison between the calculated spectrum in the gas phase and in the solution reveals minor influences of the solvent on the absorption spectrum. In the conventional molecule dynamics simulation, the previtamin D molecule can be trapped by local minimum and cannot overcome energetics barriers when it is calculated at the room temperature. In addition, the higher temperature calculation for the molecule in REMD allows to overcome energetics barriers and to change the structure to other rotational isomers, then switch to the lower temperature and gives a more complete result in the configuration space for the lower temperature.

A poly(vinyl alcohol)/sodium alginate blend monolith with nanoscale porous structure.

PubMed

Sun, Xiaoxia; Uyama, Hiroshi

2013-10-04

A stimuli-responsive poly(vinyl alcohol) (PVA)/sodium alginate (SA) blend monolith with nanoscale porous (mesoporous) structure is successfully fabricated by thermally impacted non-solvent induced phase separation (TINIPS) method. The PVA/SA blend monolith with different SA contents is conveniently fabricated in an aqueous methanol without any templates. The solvent suitable for the fabrication of the present blend monolith by TINIPS is different with that of the PVA monolith. The nanostructural control of the blend monolith is readily achieved by optimizing the fabrication conditions. Brunauer Emmett Teller measurement shows that the obtained blend monolith has a large surface area. Pore size distribution plot for the blend monolith obtained by the non-local density functional theory method reveals the existence of the nanoscale porous structure. Fourier transform infrared analysis reveals the strong interactions between PVA and SA. The pH-responsive property of the blend monolith is investigated on the basis of swelling ratio in different pH solutions. The present blend monolith of biocompatible and biodegradable PVA and SA with nanoscale porous structure has large potential for applications in biomedical and environmental fields.

Linear-scaling time-dependent density-functional theory beyond the Tamm-Dancoff approximation: Obtaining efficiency and accuracy with in situ optimised local orbitals.

PubMed

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

2015-11-28

We present a solution of the full time-dependent density-functional theory (TDDFT) eigenvalue equation in the linear response formalism exhibiting a linear-scaling computational complexity with system size, without relying on the simplifying Tamm-Dancoff approximation (TDA). The implementation relies on representing the occupied and unoccupied subspaces with two different sets of in situ optimised localised functions, yielding a very compact and efficient representation of the transition density matrix of the excitation with the accuracy associated with a systematic basis set. The TDDFT eigenvalue equation is solved using a preconditioned conjugate gradient algorithm that is very memory-efficient. The algorithm is validated on a small test molecule and a good agreement with results obtained from standard quantum chemistry packages is found, with the preconditioner yielding a significant improvement in convergence rates. The method developed in this work is then used to reproduce experimental results of the absorption spectrum of bacteriochlorophyll in an organic solvent, where it is demonstrated that the TDA fails to reproduce the main features of the low energy spectrum, while the full TDDFT equation yields results in good qualitative agreement with experimental data. Furthermore, the need for explicitly including parts of the solvent into the TDDFT calculations is highlighted, making the treatment of large system sizes necessary that are well within reach of the capabilities of the algorithm introduced here. Finally, the linear-scaling properties of the algorithm are demonstrated by computing the lowest excitation energy of bacteriochlorophyll in solution. The largest systems considered in this work are of the same order of magnitude as a variety of widely studied pigment-protein complexes, opening up the possibility of studying their properties without having to resort to any semiclassical approximations to parts of the protein environment.

Single fiber lignin distributions based on the density gradient column method

Treesearch

Brian Boyer; Alan W. Rudie

2007-01-01

The density gradient column method was used to determine the effects of uniform and non-uniform pulping processes on variation in individual fiber lignin concentrations of the resulting pulps. A density gradient column uses solvents of different densities and a mixing process to produce a column of liquid with a smooth transition from higher density at the bottom to...

A Colorful Solubility Exercise for Organic Chemistry

ERIC Educational Resources Information Center

Shugrue, Christopher R.; Mentzen, Hans H., II; Linton, Brian R.

2015-01-01

A discovery chemistry laboratory has been developed for the introductory organic chemistry student to investigate the concepts of polarity, miscibility, solubility, and density. The simple procedure takes advantage of the solubility of two colored dyes in a series of solvents or solvent mixtures, and the diffusion of colors can be easily…

Measurement of dielectric constant of organic solvents by indigenously developed dielectric probe

NASA Astrophysics Data System (ADS)

Keshari, Ajay Kumar; Rao, J. Prabhakar; Rao, C. V. S. Brahmmananda; Ramakrishnan, R.; Ramanarayanan, R. R.

2018-04-01

The extraction, separation and purification of actinides (uranium and plutonium) from various matrices are an important step in nuclear fuel cycle. One of the separation process adopted in an industrial scale is the liquid-liquid extraction or solvent extraction. Liquid-liquid extraction uses a specific ligand/extractant in conjunction with suitable diluent. Solvent extraction or liquid-liquid extraction, involves the partitioning of the solute between two immiscible phases. In most cases, one of the phases is aqueous, and the other one is an organic solvent. The solvent used in solvent extraction should be selective for the metal of interest, it should have optimum distribution ratio, and the loaded metal from the organic phase should be easily stripped under suitable experimental conditions. Some of the important physical properties which are important for the solvent are density, viscosity, phase separation time, interfacial surface tension and the polarity of the extractant.

Density functional theory and conductivity studies of boron-based anion receptors

DOE PAGES

Leung, Kevin; Chaudhari, Mangesh I.; Rempe, Susan B.; ...

2015-07-10

Anion receptors that bind strongly to fluoride anions in organic solvents can help dissolve the lithium fluoride discharge products of primary carbon monofluoride (CFx) batteries, thereby preventing the clogging of cathode surfaces and improving ion conductivity. The receptors are also potentially beneficial to rechargeable lithium ion and lithium air batteries. We apply Density Functional Theory (DFT) to show that an oxalate-based pentafluorophenyl-boron anion receptor binds as strongly, or more strongly, to fluoride anions than many phenyl-boron anion receptors proposed in the literature. Experimental data shows marked improvement in electrolyte conductivity when this oxalate anion receptor is present. The receptor ismore » sufficiently electrophilic that organic solvent molecules compete with F – for boron-site binding, and specific solvent effects must be considered when predicting its F – affinity. To further illustrate the last point, we also perform computational studies on a geometrically constrained boron ester that exhibits much stronger gas-phase affinity for both F – and organic solvent molecules. After accounting for specific solvent effects, however, its net F – affinity is about the same as the simple oxalate-based anion receptor. Lastly, we propose that LiF dissolution in cyclic carbonate organic solvents, in the absence of anion receptors, is due mostly to the formation of ionic aggregates, not isolated F – ions.« less

Biodiesel production from ethanolysis of palm oil using deep eutectic solvent (DES) as co-solvent

NASA Astrophysics Data System (ADS)

Manurung, R.; Winarta, A.; Taslim; Indra, L.

2017-06-01

Biodiesel produced from ethanolysis is more renewable and have better properties (higher oxidation stability, lower cloud and pour point) compared to methanolysis, but it has a disadvantage such as complicated purification. To improve ethanolysis process, deep eutectic solvent (DES) can be prepared from choline chloride and glycerol and used as co-solvent in ethanolysis. The deep eutectic solvent is formed from a quaternary ammonium salt (choline chloride) and a hydrogen bond donor (Glycerol), it is a non-toxic, biodegradable solvent compared to a conventional volatile organic solvent such as hexane. The deep eutectic solvent is prepared by mixing choline chloride and glycerol with molar ratio 1:2 at temperature 80 °C, stirring speed 300 rpm for 1 hour. The DES is characterized by its density and viscosity. The ethanolysis is performed at a reaction temperature of 70 °C, ethanol to oil molar ratio of 9:1, potassium hydroxide as catalyst concentration of 1.2 wt. DES as co-solvent with concentration 0.5 to 3 wt. stirring speed 400 rpm, and a reaction time 1 hour. The obtained biodiesel is then characterized by its density, viscosity, and ester content. The oil - ethanol phase condition is observed in the reaction tube. The oil - ethanol phase with DES tends to form meniscus compared to without DES, showed that oil and ethanol become more slightly miscible, which favors the reaction. Using DES as co-solvent in ethanolysis showed increasing in yield and easier purification. The esters properties meet the international standards ASTM D6751, with the highest yield achieved 83,67 with 99,77 conversion at DES concentration 2 . Increasing DES concentration above 2 in ethanolysis decrease the conversion and yield, because of the excessive glycerol in the systems makes the reaction equilibrium moves to the reactant side.

Low Density Resin Impregnated Ceramic Article Having an Average Density of 0.15 to 0.40 G/CC

NASA Technical Reports Server (NTRS)

Tran, Huy K. (Inventor); Henline, William D. (Inventor); Hsu, Ming-ta S. (Inventor); Rasky, Daniel J. (Inventor); Riccitiello, Salvatore R. (Inventor)

1996-01-01

A low-density resin impregnated ceramic article advantageously employed as a structural ceramic ablator comprising a fired preform of ceramic fibers. The fibers of the ceramic preform are coated with an organic resin film. The organic resin can be a thermoplastic resin or a cured thermosetting resin. In one embodiment, the resin is uniformly distributed within the ceramic article. In a second embodiment, the resin is distributed so as to provide a density gradient along at least one direction of the ceramic article. The resin impregnated ceramic article is prepared by providing a fired preform of ceramic fibers; immersing the preform of ceramic fibers in a solution of a solvent and an organic resin infiltrant; and removing the solvent to form a resin film on the ceramic fibers.

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

Low density microcellular foams

DOEpatents

Aubert, J.H.; Clough, R.L.; Curro, J.G.; Quintana, C.A.; Russick, E.M.; Shaw, M.T.

1985-10-02

Low density, microporous polymer foams are provided by a process which comprises forming a solution of polymer and a suitable solvent followed by rapid cooling of the solution to form a phase-separated system and freeze the phase-separated system. The phase-separated system comprises a polymer phase and a solvent phase, each of which is substantially continuous within the other. The morphology of the polymer phase prior to and subsequent to freezing determine the morphology of the resultant foam. Both isotropic and anisotropic foams can be produced. If isotropic foams are produced, the polymer and solvent are tailored such that the solution spontaneously phase-separates prior to the point at which any component freezes. The morphology of the resultant polymer phase determines the morphology of the reusltant foam and the morphology of the polymer phase is retained by cooling the system at a rate sufficient to freeze one or both components of the system before a change in morphology can occur. Anisotropic foams are produced by forming a solution of polymer and solvent that will not phase separate prior to freezing of one or both components of the solution. In such a process, the solvent typically freezes before phase separation occurs. The morphology of the resultant frozen two-phase system determines the morphology of the resultant foam. The process involves subjecting the solution to essentially one-dimensional cooling. Foams having a density of less than 0.1 g/cc and a uniform cell size of less than 10 ..mu..m and a volume such that the foams have a length greater than 1 cm are provided.

SOLVENT HOLD TANK SAMPLE RESULTS FOR MCU-11-1452, MCU-11-1453, MCU-11-1454, MCU-11-1455, MCU-11-1456 AND MCU-11-1457

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

Peters, T.; Fondeur, F.; Fink, S.

Solvent Hold Tank (SHT) samples are sent to Savannah River National Laboratory (SRNL) to examine solvent composition changes over time. On December 5, 2011, Operations personnel delivered six samples from the SHT (MCU-11-1452 through -1457) for analysis. These samples are intended to verify that the solvent is within the specified composition range. The results from the analyses are presented in this document. Samples were received in p-nut vials containing {approx}10 mL each. Once taken into the Shielded Cells, the samples were combined. Samples were removed for analysis by density, semi-volatile organic analysis (SVOA), high performance liquid chromatography (HPLC), and Fourier-Transformmore » Infra-Red spectroscopy (FTIR). Details for the work are contained in a controlled laboratory notebook. Each of the six p-nut vials contained a single phase, with no apparent solids contamination or cloudiness. Table 1 contains the results of the analyses for the combined samples. A duplicate density measurement of the organic phase gave a result of 0.844 g/mL (1.2% residual standard deviation - RSD). Using the density as a starting point, we know that the Isopar{reg_sign} L should be slightly higher than nominal and the other components should be slightly lower than nominal. The results as a whole are internally consistent. All measurements indicate Isopar{reg_sign} L higher than nominal, and Modifier lower than nominal. The extractant result is higher than expected - given the other results, the extractant concentration should be under nominal values. Using the measured density as well as the Isopar{reg_sign} L and Modifier concentrations from the FTIR results, we calculate an extractant concentration of 6888 mg/L. This value is outside the analytical uncertainty of the reported HPLC value. Given the other results, this most likely indicates that the HPLC extractant result was biased high. When compared to the MCU density target of 0.845 g/mL, there is no need to add an Isopar{reg_sign} L trim. However, it is advisable to add sufficient trioctylamine (TOA) to return the solvent composition to within specifications as that component has declined to about 64% the concentration since the last analysis. The TOA measurement was performed twice, so the result is not an analytical aberration. TOA has not been added to the system since the previous quarterly sample in October 2011. As with the previous solvent sample results, these analyses indicate that the solvent does not require Isopar{reg_sign} L trimming at this time. However, addition of TOA is warranted. These findings indicate that the new protocols for solvent monitoring and control are yielding favorable results. Nevertheless, the deviation in the TOA concentration since the last analysis indicates continued periodic (i.e., quarterly) monitoring is recommended.« less

Molecular simulation of CO chemisorption on Co(0001) in presence of supercritical fluid solvent: A potential of mean force study

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

Asiaee, Alireza; Benjamin, Kenneth M., E-mail: kenneth.benjamin@sdsmt.edu

2016-08-28

For several decades, heterogeneous catalytic processes have been improved through utilizing supercritical fluids (SCFs) as solvents. While numerous experimental studies have been established across a range of chemistries, such as oxidation, pyrolysis, amination, and Fischer-Tropsch synthesis, still there is little fundamental, molecular-level information regarding the role of the SCF on elementary heterogeneous catalytic steps. In this study, the influence of hexane solvent on the adsorption of carbon monoxide on Co(0001), as the first step in the reaction mechanism of many processes involving syngas conversion, is probed. Simulations are performed at various bulk hexane densities, ranging from ideal gas conditions (nomore » SCF hexane) to various near- and super-critical hexane densities. For this purpose, both density functional theory and molecular dynamics simulations are employed to determine the adsorption energy and free energy change during CO chemisorption. Potential of mean force calculations, utilizing umbrella sampling and the weighted histogram analysis method, provide the first commentary on SCF solvent effects on the energetic aspects of the chemisorption process. Simulation results indicate an enhanced stability of CO adsorption on the catalyst surface in the presence of supercritical hexane within the reduced pressure range of 1.0–1.5 at a constant temperature of 523 K. Furthermore, it is shown that the maximum stability of CO in the adsorbed state as a function of supercritical hexane density at 523 K nearly coincides with the maximum isothermal compressibility of bulk hexane at this temperature.« less

On the applicability of density dependent effective interactions in cluster-forming systems

NASA Astrophysics Data System (ADS)

Montes-Saralegui, Marta; Kahl, Gerhard; Nikoubashman, Arash

2017-02-01

We systematically studied the validity and transferability of the force-matching algorithm for computing effective pair potentials in a system of dendritic polymers, i.e., a particular class of ultrasoft colloids. We focused on amphiphilic dendrimers, macromolecules which can aggregate into clusters of overlapping particles to minimize the contact area with the surrounding implicit solvent. Simulations were performed for both the monomeric and coarse-grained models in the liquid phase at densities ranging from infinite dilution up to values close to the freezing point. The effective pair potentials for the coarse-grained simulations were computed from the monomeric simulations both in the zero-density limit (Φeff0) and at each investigated finite density (Φeff). Conducting the coarse-grained simulations with Φeff0 at higher densities is not appropriate as they failed at reproducing the structural properties of the monomeric simulations. In contrast, we found excellent agreement between the spatial dendrimer distributions obtained from the coarse-grained simulations with Φeff and the microscopically detailed simulations at low densities, where the macromolecules were distributed homogeneously in the system. However, the reliability of the coarse-grained simulations deteriorated significantly as the density was increased further and the cluster occupation became more polydisperse. Under these conditions, the effective pair potential of the coarse-grained model can no longer be computed by averaging over the whole system, but the local density needs to be taken into account instead.

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.

Linear response coupled cluster theory with the polarizable continuum model within the singles approximation for the solvent response.

PubMed

Caricato, Marco

2018-04-07

We report the theory and the implementation of the linear response function of the coupled cluster (CC) with the single and double excitations method combined with the polarizable continuum model of solvation, where the correlation solvent response is approximated with the perturbation theory with energy and singles density (PTES) scheme. The singles name is derived from retaining only the contribution of the CC single excitation amplitudes to the correlation density. We compare the PTES working equations with those of the full-density (PTED) method. We then test the PTES scheme on the evaluation of excitation energies and transition dipoles of solvated molecules, as well as of the isotropic polarizability and specific rotation. Our results show a negligible difference between the PTED and PTES schemes, while the latter affords a significantly reduced computational cost. This scheme is general and can be applied to any solvation model that includes mutual solute-solvent polarization, including explicit models. Therefore, the PTES scheme is a competitive approach to compute response properties of solvated systems using CC methods.

Linear response coupled cluster theory with the polarizable continuum model within the singles approximation for the solvent response

NASA Astrophysics Data System (ADS)

Caricato, Marco

2018-04-01

We report the theory and the implementation of the linear response function of the coupled cluster (CC) with the single and double excitations method combined with the polarizable continuum model of solvation, where the correlation solvent response is approximated with the perturbation theory with energy and singles density (PTES) scheme. The singles name is derived from retaining only the contribution of the CC single excitation amplitudes to the correlation density. We compare the PTES working equations with those of the full-density (PTED) method. We then test the PTES scheme on the evaluation of excitation energies and transition dipoles of solvated molecules, as well as of the isotropic polarizability and specific rotation. Our results show a negligible difference between the PTED and PTES schemes, while the latter affords a significantly reduced computational cost. This scheme is general and can be applied to any solvation model that includes mutual solute-solvent polarization, including explicit models. Therefore, the PTES scheme is a competitive approach to compute response properties of solvated systems using CC methods.

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.

Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

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

Biedermannová, Lada, E-mail: lada.biedermannova@ibt.cas.cz; Schneider, Bohdan

2015-10-27

The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. Themore » results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.« less

Solvent/co-solvent effects on the electronic properties and adsorption mechanism of anticancer drug Thioguanine on Graphene oxide surface as a nanocarrier: Density functional theory investigation and a molecular dynamics

NASA Astrophysics Data System (ADS)

Hasanzade, Zohre; Raissi, Heidar

2017-11-01

In this work, the adsorption of Thioguanine (TG) anticancer drug on the surface of Graphene oxide (GO) nanosheet has investigated using density functional theory (DFT) and molecular dynamics simulation (MDs). Quantum mechanics calculations by two methods including M06-2X/6-31G**and ωB97X-D/6-31G** have been employed to calculate the details of energetic, geometric, and electronic properties of the TG molecule interacting with Graphene oxide nanosheet (GONS). DFT calculations confirmed that the strongest adsorption is observed when hydrogen bond interactions between TG molecule and the functional groups of Graphene oxide nanosheet are predominate. In all calculations, solvent effects have been considered in water using the PCM method. It is found that TG molecule can be adsorbed on Graphene oxide with negative solvation energy, indicating the TG adsorption on Graphene oxide surfaces is thermodynamically favored. Moreover, MD simulations are examined to understand the solvent/co-solvent effect (water, ethanol, nicotine) on the Thioguanine drug delivery through Graphene oxide. The results of RDF patterns and the van der Waals energy calculations show that interaction between TG drugs and the Graphene oxide surface is stronger in water solvent compared to the other co-solvent. The obtained MD results illustrate that when nicotine and ethanol exist in the system, the drug takes longer time to bind with GO nanosheet and the system becomes unstable. It can be concluded that Graphene oxide can be a promising candidate in water media for delivery the TG molecule.

40 CFR 63.5746 - How do I demonstrate compliance with the emission limits for aluminum wipedown solvents and...

Code of Federal Regulations, 2011 CFR

2011-07-01

...) to determine the density of each aluminum surface coating and wipedown solvent. (d) Compliance is... Hazardous Air Pollutants for Boat Manufacturing Standards for Aluminum Recreational Boat Surface Coating... of solids per liter of coating, or volume fraction) of each aluminum surface coating, including...

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.

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.

Dispersive liquid-liquid microextraction based on the solidification of floating organic droplet for the determination of polychlorinated biphenyls in aqueous samples.

PubMed

Dai, Liping; Cheng, Jing; Matsadiq, Guzalnur; Liu, Lu; Li, Jun-Kai

2010-08-03

In the proposed method, an extraction solvent with a lower toxicity and density than the solvents typically used in dispersive liquid-liquid microextraction was used to extract seven polychlorinated biphenyls (PCBs) from aqueous samples. Due to the density and melting point of the extraction solvent, the extract which forms a layer on top of aqueous sample can be collected by solidifying it at low temperatures, which form a layer on top of the aqueous sample. Furthermore, the solidified phase can be easily removed from the aqueous phase. Based on preliminary studies, 1-undecanol was selected as the extraction solvent, and a series of parameters that affect the extraction efficiency were systematically investigated. Under the optimized conditions, enrichment factors for PCBs ranged between 494 and 606. Based on a signal-to-noise ratio of 3, the limit of detection for the method ranged between 3.3 and 5.4 ng L(-1). Good linearity, reproducibility and recovery were also obtained. 2010 Elsevier B.V. All rights reserved.

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.

Influence of electrolyte ion-solvent interactions on the performances of supercapacitors porous carbon electrodes

NASA Astrophysics Data System (ADS)

Decaux, C.; Matei Ghimbeu, C.; Dahbi, M.; Anouti, M.; Lemordant, D.; Béguin, F.; Vix-Guterl, C.; Raymundo-Piñero, E.

2014-10-01

The development of advanced and safe electrochemical supercapacitors or hybrid supercapacitors combining a battery electrode material such as graphite and a porous carbon electrode implies the use of new electrolytes containing a tetra-alkylammonium or lithium salt dissolved preferentially in a safe and environmentally friendly solvent such as alkylcarbonates. In those systems, the carbon porosity of the activated carbon electrode controls the electrochemical behavior of the whole device. In this work, it is demonstrated that electrolytes containing highly polarizing ions such as Li+ dissolved in polar solvents such as alkylcarbonates do not completely loss their solvation shell at the opposite of what is observed for poorly solvated cations like TEABF4. As a consequence, the optimal carbon pore size for obtaining the largest energy density, while keeping a high power density, is wider when strongly solvated cations, like Li+ are used than for conventional organic electrolytes using acetonitrile as solvent and TEA+ as salt cations. TEA+ cations are easily desolvated and hence are able to penetrate in small pores matching the dimensions of bare ions. The dissimilarity of behavior of alkylcarbonates and acetonitrile based electrolytes highlights the importance of ion-solvent interactions when searching the optimal porous texture for the electrode material.

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.

Solvent sensitivity of smart 3D-printed nanocomposite liquid sensor

NASA Astrophysics Data System (ADS)

Aliheidari, Nahal; Ameli, Amir; Pötschke, Petra

2018-03-01

Fused deposition modeling (FDM) is one of the 3D printing methods that has attracted significant attention. In this method, small and complex samples with nearly no limitation in geometry can be fabricated layer by layer to form end-use parts. This work investigates the liquid sensing behavior of FDM printed flexible thermoplastic polyurethane, TPU filled with multiwalled carbon nanotubes, MWCNTs. The sensing capability of printed TPU-MWCNT was studied as a function of MWCNT content and infill density in response to different solvents, i.e., ethanol, acetone and toluene. The solvents were selected based on their widespread use and importance in medical and industrial applications. U-shaped liquid sensors with 2, 3 and 4wt.% MWCNT content were printed at three different infill densities of 50, 75 and 100%. Solvent sensitivity was then characterized by immersing the sensors in the solvents and measuring the resistance evolution over 25s. The results indicated a sensitivity order of acetone > toluene > ethanol, which was in agreement with the predictions of FloryHiggins solubility equation. For all the solvents, the sensitivity was enhanced as the infill density of the printed samples was decreased. This was attributed to the increased surface area to volume ratio and shortened diffusion paths. The MWCNT content was also observed to have a profound effect on the sensitivity; in samples with partial infill, the sensitivity was found to be inversely proportional to the MWCNT content, such that the highest resistance change was obtained for nanocomposites with the lowest MWCNT content of 2wt.%. For instance, a resistance increase of more than 10 times was obtained in 25 s once TPU-2wt.%MWCNT with 50% infill was tested against acetone. The results of this work reveals that highly sensitive liquid sensors can be fabricated with the aid of 3D printing without the need for complex processing methods.

HARMONY: a server for the assessment of protein structures

PubMed Central

Pugalenthi, G.; Shameer, K.; Srinivasan, N.; Sowdhamini, R.

2006-01-01

Protein structure validation is an important step in computational modeling and structure determination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran (φ,ψ) angles. Gross structure prediction methods such as inverse folding procedure and structure determination especially at low resolution can sometimes give rise to models that are incorrect due to assignment of misfolds or mistracing of electron density maps. Such errors are not reflected as strain in internal parameters. HARMONY is a procedure that examines the compatibility between the sequence and the structure of a protein by assigning scores to individual residues and their amino acid exchange patterns after considering their local environments. Local environments are described by the backbone conformation, solvent accessibility and hydrogen bonding patterns. We are now providing HARMONY through a web server such that users can submit their protein structure files and, if required, the alignment of homologous sequences. Scores are mapped on the structure for subsequent examination that is useful to also recognize regions of possible local errors in protein structures. HARMONY server is located at PMID:16844999

Opening Furan for Tailoring Properties of Bio-based Poly(Furfuryl Alcohol) Thermoset.

PubMed

Falco, Guillaume; Guigo, Nathanael; Vincent, Luc; Sbirrazzuoli, Nicolas

2018-06-11

This work shows how furan ring-opening reactions were controlled by polymerization conditions to tune the cross-link density in bio-based poly(furfuryl alcohol) (PFA). The influence of water and isopropyl alcohol (IPA) on the polymerization of furfuryl alcohol, and particularly on furan ring-opening, was investigated by means of 13 C NMR and FT-IR spectroscopy. Results indicated that formation of open structures were favored in the presence of solvents, thus leading to modification of the thermo-mechanical properties compared to PFA cross-linked without solvent. Dynamic mechanical analyses showed that when slightly more open structures were present in PFA it resulted in an important decrease of the cross-link density. Despite lower glass-transition temperature and lower elastic modulus for PFA polymerized with solvent, the thermal stability remains very high (>350 °C) even with more open structures in PFA. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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.

Preferential solvation and solvation shell composition of free base and protonated 5, 10, 15, 20-tetrakis(4-sulfonatophenyl)porphyrin in aqueous organic mixed solvents

NASA Astrophysics Data System (ADS)

Farajtabar, Ali; Jaberi, Fatemeh; Gharib, Farrokh

2011-12-01

The solvatochromic properties of the free base and the protonated 5, 10, 15, 20-tetrakis(4-sulfonatophenyl)porphyrin (TPPS) were studied in pure water, methanol, ethanol (protic solvents), dimethylsulfoxide, DMSO, (non-protic solvent), and their corresponding aqueous-organic binary mixed solvents. The correlation of the empirical solvent polarity scale ( ET) values of TPPS with composition of the solvents was analyzed by the solvent exchange model of Bosch and Roses to clarify the preferential solvation of the probe dyes in the binary mixed solvents. The solvation shell composition and the synergistic effects in preferential solvation of the solute dyes were investigated in terms of both solvent-solvent and solute-solvent interactions and also, the local mole fraction of each solvent composition was calculated in cybotactic region of the probe. The effective mole fraction variation may provide significant physico-chemical insights in the microscopic and molecular level of interactions between TPPS species and the solvent components and therefore, can be used to interpret the solvent effect on kinetics and thermodynamics of TPPS. The obtained results from the preferential solvation and solvent-solvent interactions have been successfully applied to explain the variation of equilibrium behavior of protonation of TPPS occurring in aqueous organic mixed solvents of methanol, ethanol and DMSO.

Theory of molecular crowding in Brownian hard-sphere liquids.

PubMed

Zaccone, Alessio; Terentjev, Eugene M

2012-06-01

We derive an analytical pair potential of mean force for Brownian molecules in the liquid state. Our approach accounts for many-particle correlations of crowding particles of the liquid and for diffusive transport across the spatially modulated local density of crowders in the dense environment. Focusing on the limit of equal-size particles, we show that this diffusive transport leads to additional density- and structure-dependent terms in the interaction potential and to a much stronger attraction (by a factor of ≈4 at average volume fraction of crowders φ{0}=0.25) than in the standard depletion interaction where the diffusive effects are neglected. As an illustration of the theory, we use it to study the size of a polymer chain in a solution of inert crowders. Even in the case of an athermal background solvent, when a classical chain should be fully swollen, we find a sharp coil-globule transition of the ideal chain collapsing at a critical value of the crowder volume fraction φ{c}≈0.145.

Testing the Use of Implicit Solvent in the Molecular Dynamics Modelling of DNA Flexibility

NASA Astrophysics Data System (ADS)

Mitchell, J.; Harris, S.

DNA flexibility controls packaging, looping and in some cases sequence specific protein binding. Molecular dynamics simulations carried out with a computationally efficient implicit solvent model are potentially a powerful tool for studying larger DNA molecules than can be currently simulated when water and counterions are represented explicitly. In this work we compare DNA flexibility at the base pair step level modelled using an implicit solvent model to that previously determined from explicit solvent simulations and database analysis. Although much of the sequence dependent behaviour is preserved in implicit solvent, the DNA is considerably more flexible when the approximate model is used. In addition we test the ability of the implicit solvent to model stress induced DNA disruptions by simulating a series of DNA minicircle topoisomers which vary in size and superhelical density. When compared with previously run explicit solvent simulations, we find that while the levels of DNA denaturation are similar using both computational methodologies, the specific structural form of the disruptions is different.

Structural and thermodynamic properties of the Cm III ion solvated by water and methanol

DOE PAGES

Kelley, Morgan P.; Yang, Ping; Clark, Sue B.; ...

2016-04-27

The geometric and electronic structures of the 9-coordinate Cm 3+ ion solvated with both water and methanol are systematically investigated in the gas phase at each possible solvent-shell composition and configuration using density functional theory and second-order Møller–Plesset perturbation theory. Ab initio molecular dynamics simulations are employed to assess the effects of second and third solvent shells on the gas-phase structure. The ion–solvent dissociation energy for methanol is greater than that of water, potentially because of increased charge donation to the ion made possible by the electron-rich methyl group. Further, the ion–solvent dissociation energy and the ion–solvent distance are shownmore » to be dependent on the solvent-shell composition. Furthermore, this has implications for solvent exchange, which is generally the rate-limiting step in complexation reactions utilized in the separation of curium from complex metal mixtures that derive from the advanced nuclear fuel cycle.« less

Low-density resin impregnated ceramic article and method for making the same

NASA Technical Reports Server (NTRS)

Tran, Huy K. (Inventor); Henline, William D. (Inventor); Hsu, Ming-ta S. (Inventor); Rasky, Daniel J. (Inventor); Riccitiello, Salvatore R. (Inventor)

1997-01-01

A low-density resin impregnated ceramic article advantageously employed as a structural ceramic ablator comprising a matrix of ceramic fibers. The fibers of the ceramic matrix are coated with an organic resin film. The organic resin can be a thermoplastic resin or a cured thermosetting resin. In one embodiment, the resin is uniformly distributed within the ceramic article. In a second embodiment, the resin is distributed so as to provide a density gradient along at least one direction of the ceramic article. The resin impregnated ceramic article is prepared by providing a matrix of ceramic fibers; immersing the matrix of ceramic fibers in a solution of a solvent and an organic resin infiltrant; and removing the solvent to form a resin film on the ceramic fibers.

Ionic Asymmetry and Solvent Excluded Volume Effects on Spherical Electric Double Layers: A Density Functional Approach

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

Medasani, Bharat; Ovanesyan, Zaven; Thomas, Dennis G.

In this article we present a classical density functional theory for electrical double layers of spherical macroions that extends the capabilities of conventional approaches by accounting for electrostatic ion correlations, size asymmetry and excluded volume effects. The approach is based on a recent approximation introduced by Hansen-Goos and Roth for the hard sphere excess free energy of inhomogeneous fluids (J. Chem. Phys. 124, 154506). It accounts for the proper and efficient description of the effects of ionic asymmetry and solvent excluded volume, especially at high ion concentrations and size asymmetry ratios including those observed in experimental studies. Additionally, we utilizemore » a leading functional Taylor expansion approximation of the ion density profiles. In addition, we use the Mean Spherical Approximation for multi-component charged hard sphere fluids to account for the electrostatic ion correlation effects. These approximations are implemented in our theoretical formulation into a suitable decomposition of the excess free energy which plays a key role in capturing the complex interplay between charge correlations and excluded volume effects. We perform Monte Carlo simulations in various scenarios to validate the proposed approach, obtaining a good compromise between accuracy and computational cost. We use the proposed computational approach to study the effects of ion size, ion size asymmetry and solvent excluded volume on the ion profiles, integrated charge, mean electrostatic potential, and ionic coordination number around spherical macroions in various electrolyte mixtures. Our results show that both solvent hard sphere diameter and density play a dominant role in the distribution of ions around spherical macroions, mainly for experimental water molarity and size values where the counterion distribution is characterized by a tight binding to the macroion, similar to that predicted by the Stern model.« less

Influence of membrane thickness and ion concentration on the properties of the gramicidin a channel. Autocorrelation, spectral power density, relaxation and single-channel studies.

PubMed

Kolb, H A; Bamberg, E

1977-01-04

The properties of the gramicidin A channel in membranes made from a series of monoglycerides have been studied. In agreement with previous studies, the dissociation rate constant kD of the dimeric channel was found to increase strongly with increasing chain length of the monoglyceride, corresponding to a decrease of the mean life-time of the channel. The value of kD, however, was not strictly correlated with the membrane thickness, as seen from a comparison of membranes with different solvent content. Furthermore, the life-time of the channel increased with the concentration of the permeable ion. This effect was tentatively explained by an electrostatic stabilization of the channel. The single-channel conductance lambda was found to decrease with increasing membrane thickness d, if d was varied by increasing the chain length of the lipid. On the other hand, if d was changed by varying the solvent content of the membranes formed from one and the same lipid, lambda remained constant. These observations were explained by the assumption of local inhomogeneities in the membrane thickness. A striking difference between the lambda values obtained from autocorrelation analysis in the presence of many presence of many channels (lambda a) and those obtained from single-channel experiments (lambda sc) occurred with membranes from longer chain-length monoglycerides. This difference disappeared at low ion concentrations. Electrostatic interactions between channels in local clusters were proposed for an interpretation of these findings.

40 CFR 63.5746 - How do I demonstrate compliance with the emission limits for aluminum wipedown solvents and...

Code of Federal Regulations, 2014 CFR

2014-07-01

...) to determine the density of each aluminum surface coating and wipedown solvent. (d) Compliance is... Surface Coating Operations § 63.5746 How do I demonstrate compliance with the emission limits for aluminum... (liters of solids per liter of coating, or volume fraction) of each aluminum surface coating, including...

40 CFR 63.5746 - How do I demonstrate compliance with the emission limits for aluminum wipedown solvents and...

Code of Federal Regulations, 2013 CFR

2013-07-01

...) to determine the density of each aluminum surface coating and wipedown solvent. (d) Compliance is... Surface Coating Operations § 63.5746 How do I demonstrate compliance with the emission limits for aluminum... (liters of solids per liter of coating, or volume fraction) of each aluminum surface coating, including...

Evaluation of the constant potential method in simulating electric double-layer capacitors

NASA Astrophysics Data System (ADS)

Wang, Zhenxing; Yang, Yang; Olmsted, David L.; Asta, Mark; Laird, Brian B.

2014-11-01

A major challenge in the molecular simulation of electric double layer capacitors (EDLCs) is the choice of an appropriate model for the electrode. Typically, in such simulations the electrode surface is modeled using a uniform fixed charge on each of the electrode atoms, which ignores the electrode response to local charge fluctuations in the electrolyte solution. In this work, we evaluate and compare this Fixed Charge Method (FCM) with the more realistic Constant Potential Method (CPM), [S. K. Reed et al., J. Chem. Phys. 126, 084704 (2007)], in which the electrode charges fluctuate in order to maintain constant electric potential in each electrode. For this comparison, we utilize a simplified LiClO4-acetonitrile/graphite EDLC. At low potential difference (ΔΨ ⩽ 2 V), the two methods yield essentially identical results for ion and solvent density profiles; however, significant differences appear at higher ΔΨ. At ΔΨ ⩾ 4 V, the CPM ion density profiles show significant enhancement (over FCM) of "inner-sphere adsorbed" Li+ ions very close to the electrode surface. The ability of the CPM electrode to respond to local charge fluctuations in the electrolyte is seen to significantly lower the energy (and barrier) for the approach of Li+ ions to the electrode surface.

Enhanced performance of dicationic ionic liquid electrolytes by organic solvents.

PubMed

Li, Song; Zhang, Pengfei; Fulvio Pasquale, F; Hillesheim Patrick, C; Feng, Guang; Dai, Sheng; Cummings Peter, T

2014-07-16

The use of dicationic ionic liquid (DIL) electrolytes in supercapacitors is impeded by the slow dynamics of DILs, whereas the addition of organic solvents into DIL electrolytes improves ion transport and then enhances the power density of supercapacitors. In this work, the influences of organic solvents on the conductivity of DILs and the electrical double layer (EDL) of DIL-based supercapacitors are investigated using classical molecular dynamics simulation. Two types of organic solvents, acetonitrile (ACN) and propylene carbonate (PC), were used to explore the effects of different organic solvents on the EDL structure and capacitance of DIL/organic solvent-based supercapacitors. Firstly, it was found that the conductivity of DIL electrolytes was greatly enhanced in the presence of the organic solvent ACN. Secondly, a stronger adsorption of PC on graphite results in different EDL structures formed by DIL/ACN and DIL/PC electrolytes. The expulsion of co-ions from EDLs was observed in DIL/organic solvent electrolytes rather than neat DILs and this feature is more evident in DIL/PC. Furthermore, the bell-shaped differential capacitance-electric potential curve was not essentially changed by the presence of organic solvents. Comparing DIL/organic solvent electrolytes with neat DILs, the capacitance is slightly increased by organic solvents, which is in agreement with experimental observation.

Biodiesel production from ethanolysis of DPO using deep eutectic solvent (DES) based choline chloride - ethylene glycol as co-solvent

NASA Astrophysics Data System (ADS)

Taslim, Indra, Leonardo; Manurung, Renita; Winarta, Agus; Ramadhani, Debbie Aditia

2017-03-01

Biodiesel is usually produced from transesterification using methanol or ethanol as alcohol. However, biodiesel produced using methanol has several disadvantages because methanol is toxic and not entirely bio-based as it is generally produced from petroleum, natural gas and coal. On the other hand, ethanol also has several disadvantages such as lower reactivity in transesterification process and formation of stable emulsion between ester and glycerol. To improve ethanolysis process, deep eutectic solvent (DES) was prepared from choline chloride and ethylene glycol to be used as co-solvent in ethanolysis. Deep eutectic solvent was prepared by mixing choline chloride and ethylene glycol at molar ratio of 1:2, temperature of 80 °C, and stirring speed of 300 rpm for 1 hour. The DES was characterized by its density and viscosity. The ethanolysis of DPO / Degummed Palm Oil was performed at 70 °C, ethanol to oil molar ratio of 9:1, catalyst (potassium hydroxide) concentration of 0.75 wt.% concentration, co-solvent (DES) concentration of 1, 2, 3, 4, 5 and 6 wt.%, stirring speed of 600 rpm, and reaction time of 1 hour. The obtained biodiesel was then characterized by its density, viscosity and ester content. The oil - ethanol phase condition was observed in reaction tube. The oil - ethanol phase with DES tends to form meniscus compared to that without DES. Which implied that oil and ethanol become more slightly miscible, which favours the reaction. Using DES as co-solvent in ethanolysis resulted in an increase in yield and easier purification. The esters properties met the international standards ASTM D6751, with highest yield achieved at 81.72 % with 99.35 % ethyl ester contents at 4% DES concentration.

Metal reduction at point-of-use filtration

NASA Astrophysics Data System (ADS)

Umeda, Toru; Daikoku, Shusaku; Varanasi, Rao; Tsuzuki, Shuichi

2016-03-01

We explored the metal removal efficiency of Nylon 6,6 and HDPE (High Density Polyethylene) membrane based filters, in solvents of varying degree of polarity such as Cyclohexanone and 70:30 mixture of PGME (Propylene Glycol Monomethyl Ether) and PGMEA (Propylene Glycol Monomethyl Ether), In all the solvents tested, Nylon 6,6 membrane filtration was found to be significantly more effective in removing metals than HDPE membranes, regardless of their respective membrane pore sizes. Hydrophilic interaction chromatography (HILIC) mechanism was invoked to rationalize metal removal efficiency dependence on solvent hydrophobicity.

Rational Design of Emissive NIR-Absorbing Chromophores: Rh(III) Porphyrin-Aza-BODIPY Conjugates with Orthogonal Metal-Carbon Bonds.

PubMed

Zhou, Jinfeng; Gai, Lizhi; Zhou, Zhikuan; Yang, Wu; Mack, John; Xu, Kejing; Zhao, Jianzhang; Zhao, Yue; Qiu, Hailin; Chan, Kin Shing; Shen, Zhen

2016-09-05

The facile synthesis of Group 9 Rh(III) porphyrin-aza-BODIPY conjugates that are linked through an orthogonal Rh-C(aryl) bond is reported. The conjugates combine the advantages of the near-IR (NIR) absorption and intense fluorescence of aza-BODIPY dyes with the long-lived triplet states of transition metal rhodium porphyrins. Only one emission peak centered at about 720 nm is observed, irrespective of the excitation wavelength, demonstrating that the conjugates act as unique molecules rather than as dyads. The generation of a locally excited (LE) state with intramolecular charge-transfer (ICT) character has been demonstrated by solvatochromic effects in the photophysical properties, singlet oxygen quantum yields in polar solvents, and by the results of density functional theory (DFT) calculations. In nonpolar solvents, the Rh(III) conjugates exhibit strong aza-BODIPY-centered fluorescence at around 720 nm (ΦF =17-34 %), and negligible singlet oxygen generation. In polar solvents, enhancements of the singlet-oxygen quantum yield (ΦΔ =19-27 %, λex =690 nm) have been observed. Nanosecond pulsed time-resolved absorption spectroscopy confirms that relatively long-lived triplet excited states are formed. The synthetic methodology outlined herein provides a useful strategy for the assembly of functional materials that are highly desirable for a wide range of applications in material science and biomedical fields. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chlorinated solvents in groundwater of the United States

USGS Publications Warehouse

Moran, M.J.; Zogorski, J.S.; Squillace, P.J.

2007-01-01

Four chlorinated solvents-methylene chloride, perchloroethene (PCE), 1,1,1-trichloroethane, and trichloroethene (TCE)-were analyzed in samples of groundwater taken throughout the conterminous United States by the U.S. Geological Survey. The samples were collected between 1985 and 2002 from more than 5,000 wells. Of 55 volatile organic compounds (VOCs) analyzed in groundwater samples, solvents were among the most frequently detected. Mixtures of solvents in groundwater were common and may be the result of common usage of solvents or degradation of one solvent to another. Relative to other VOCs with Maximum Contaminant Levels (MCLs), PCE and TCE ranked high in terms of the frequencies of concentrations greater than or near MCLs. The probability of occurrence of solvents in groundwater was associated with dissolved oxygen content of groundwater, sources such as urban land use and population density, and hydraulic properties of the aquifer. The results reinforce the importance of understanding the redox conditions of aquifers and the hydraulic properties of the saturated and vadose zones in determining the intrinsic susceptibility of groundwater to contamination by solvents. The results also reinforce the importance of controlling sources of solvents to groundwater. ?? 2007 American Chemical Society.

Synthesis and characterization of ion containing polymers

NASA Astrophysics Data System (ADS)

Dou, Shichen

Two types of ion-containing polymers are included in this dissertation. The first was focused on the rheology, solvation, and correlation length of polyelectrolyte solutions in terms of charge density, solvent dielectric constant, and solvent quality. The second was focused on the PEO-based polyester ionomers as single ion conductors. A series of polyelectrolytes with varied charge density (0.03 < alpha < 0.6) and counterions (Cl- and I-) were investigated in good solvent (EG, NMF, and GC) and poor solvent (DW and F). The concentration dependence of the specific viscosity and relaxation time of polyelectrolytes in solution agrees with Dobrynin's theoretical predictions at c < c**. Effective charge density greatly impacts the viscosity of polyelectrolyte semidilute solutions, while residual salt significantly reduces the viscosity of polyelectrolyte solutions at concentrations c < 2cs/f. For polyelectrolyte solutions with less condensed counterions, the correlation length obtained from SAXS and rheology perfectly matches and agrees with de Gennes prediction. Dobrynin scaling model successfully predicts the rheology of polyelectrolyte solutions in all cases: without salt, with low residual salt, and with high residual salt concentration. PEO-based polyester ionomers were synthesized by melt polycondensation. Mn was determined using the 1H NMR of ionomers. No ion-cluster was observed from the DSC, SAXS, and rheology measurements. Ionic conductivity greatly depends on the Tg, T-T g and ion content of the ionomers. PEG600-PTMO650 (z)-Li copolyester ionomers show microphase separation and much lower ionic conductivity, compared to that of PE600-Li. PTMO650-Li shows nonconductor behavior.

Formalism for calculation of polymer-solvent-mediated potential

NASA Astrophysics Data System (ADS)

Zhou, Shiqi

2006-07-01

A simple theoretical approach is proposed for calculation of a solvent-mediated potential (SMP) between two colloid particles immersed in a polymer solvent bath in which the polymer is modeled as a chain with intramolecular degrees of freedom. The present recipe is only concerned with the estimation of the density profile of a polymer site around a single solute colloid particle instead of two solute colloid particles separated by a varying distance as done in existing calculational methods for polymer-SMP. Therefore the present recipe is far simpler for numerical implementation than the existing methods. The resultant predictions for the polymer-SMP and polymer solvent-mediated mean force (polymer-SMMF) are in very good agreement with available simulation data. With the present recipe, change tendencies of the contact value and second virial coefficiency of the SMP as a function of size ratio between the colloid particle and polymer site, the number of sites per chain, and the polymer concentration are investigated in detail. The metastable critical polymer concentration as a function of size ratio and the number of sites per chain is also reported for the first time. To yield the numerical solution of the present recipe at less than 1min on a personal computer, a rapid and accurate algorithm for the numerical solution of the classical density functional theory is proposed to supply rapid and accurate estimation of the density profile of the polymer site as an input into the present formalism.

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.

Low density microcellular foams

DOEpatents

LeMay, James D.

1992-01-01

Disclosed is a process of producing microcellular from which comprises the steps of: (a) selecting a multifunctional epoxy oligomer resin; (b) mixing said epoxy resin with a non-reactive diluent to form a resin-diluent mixture; (c) forming a diluent containing cross-linked epoxy gel from said resin-diluent mixture; (d) replacing said diluent with a solvent therefore; (e) replacing said solvent with liquid carbon dioxide; and (f) vaporizing off said liquid carbon dioxide under supercritical conditions, whereby a foam having a density in the range of 35-150 mg/cc and cell diameters less than about 1 .mu.m is produced. Also disclosed are the foams produced by the process.

Low density microcellular foams

DOEpatents

LeMay, J.D.

1991-11-19

Disclosed is a process of producing microcellular foam which comprises the steps of: (a) selecting a multifunctional epoxy oligomer resin; (b) mixing said epoxy resin with a non-reactive diluent to form a resin-diluent mixture; (c) forming a diluent containing cross-linked epoxy gel from said resin-diluent mixture; (d) replacing said diluent with a solvent therefore; (e) replacing said solvent with liquid carbon dioxide; and (f) vaporizing off said liquid carbon dioxide under supercritical conditions, whereby a foam having a density in the range of 35-150 mg/cc and cell diameters less than about 1 [mu]m is produced. Also disclosed are the foams produced by the process. 8 figures.

Low density microcellular foams

DOEpatents

LeMay, James D.

1991-01-01

Disclosed is a process of producing microcellular foam which comprises the steps of: (a) selecting a multifunctional epoxy oligomer resin; (b) mixing said epoxy resin with a non-reactive diluent to form a resin-diluent mixture; (c) forming a diluent containing cross-linked epoxy gel from said resin-diluent mixture; (d) replacing said diluent with a solvent therefore; (e) replacing said solvent with liquid carbon dioxide; and (f) vaporizing off said liquid carbon dioxide under supercritical conditions, whereby a foam having a density in the range of 35-150 mg/cc and cell diameters less than about 1 .mu.m is produced. Also disclosed are the foams produced by the process.

On the ability of trehalose to offset the denaturing activity of urea

NASA Astrophysics Data System (ADS)

Graziano, Giuseppe

2013-01-01

Experimental and computational studies indicate that trehalose offsets the denaturing activity of urea. According to a statistical thermodynamic model, the fundamental stabilizing contribution arises from the difference in the work to create a cavity suitable to host the D-state and the N-state, respectively. The magnitude of this solvent-excluded volume effect increases with aqueous solution density. Trehalose and urea addition to water leads to a density increase, that translates in an increase in the magnitude of the solvent-excluded volume effect which is so large to overwhelm the destabilizing contribution arising from the energetic attractions of urea with protein surface groups.

Multiply Reduced Oligofluorenes: Their Nature and Pairing with THF-Solvated Sodium Ions

DOE PAGES

Wu, Qin; Zaikowski, Lori; Kaur, Parmeet; ...

2016-07-01

Conjugated oligofluorenes are chemically reduced up to five charges in tetrahydrofuran solvent and confirmed with clear spectroscopic evidence. Stimulated by these experimental results, we have conducted a comprehensive computational study of the electronic structure and the solvation structure of representative oligofluorene anions with a focus on the pairing between sodium ions and these multianions. In addition, using density functional theory (DFT) methods and a solvation model of both explicit solvent molecules and implicit polarizable continuum, we first elucidate the structure of tightly solvated free sodium ions, and then explore the pairing of sodium ions either in contact with reduced oligofluorenesmore » or as solvent-separated ion pairs. Computed time-dependent-DFT absorption spectra are compared with experiments to assign the dominant ion pairing structure for each multianion. Computed ion pair binding energies further support our assignment. Lastly, the availability of different length and reducing level of oligofluorenes enables us to investigate the effects of total charge and charge density on the binding with sodium ions, and our results suggest both factors play important roles in ion pairing for small molecules. However, as the oligofluorene size grows, its charge density determines the binding strength with the sodium ion.« less

Relativistic Zeroth-Order Regular Approximation Combined with Nonhybrid and Hybrid Density Functional Theory: Performance for NMR Indirect Nuclear Spin-Spin Coupling in Heavy Metal Compounds.

PubMed

Moncho, Salvador; Autschbach, Jochen

2010-01-12

A benchmark study for relativistic density functional calculations of NMR spin-spin coupling constants has been performed. The test set contained 47 complexes with heavy metal atoms (W, Pt, Hg, Tl, Pb) with a total of 88 coupling constants involving one or two heavy metal atoms. One-, two-, three-, and four-bond spin-spin couplings have been computed at different levels of theory (nonhybrid vs hybrid DFT, scalar vs two-component relativistic). The computational model was based on geometries fully optimized at the BP/TZP scalar relativistic zeroth-order regular approximation (ZORA) and the conductor-like screening model (COSMO) to include solvent effects. The NMR computations also employed the continuum solvent model. Computations in the gas phase were performed in order to assess the importance of the solvation model. The relative median deviations between various computational models and experiment were found to range between 13% and 21%, with the highest-level computational model (hybrid density functional computations including scalar plus spin-orbit relativistic effects, the COSMO solvent model, and a Gaussian finite-nucleus model) performing best.

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

Wu, Qin; Zaikowski, Lori; Kaur, Parmeet

Conjugated oligofluorenes are chemically reduced up to five charges in tetrahydrofuran solvent and confirmed with clear spectroscopic evidence. Stimulated by these experimental results, we have conducted a comprehensive computational study of the electronic structure and the solvation structure of representative oligofluorene anions with a focus on the pairing between sodium ions and these multianions. In addition, using density functional theory (DFT) methods and a solvation model of both explicit solvent molecules and implicit polarizable continuum, we first elucidate the structure of tightly solvated free sodium ions, and then explore the pairing of sodium ions either in contact with reduced oligofluorenesmore » or as solvent-separated ion pairs. Computed time-dependent-DFT absorption spectra are compared with experiments to assign the dominant ion pairing structure for each multianion. Computed ion pair binding energies further support our assignment. Lastly, the availability of different length and reducing level of oligofluorenes enables us to investigate the effects of total charge and charge density on the binding with sodium ions, and our results suggest both factors play important roles in ion pairing for small molecules. However, as the oligofluorene size grows, its charge density determines the binding strength with the sodium ion.« less

Protomers of benzocaine: solvent and permittivity dependence.

PubMed

Warnke, Stephan; Seo, Jongcheol; Boschmans, Jasper; Sobott, Frank; Scrivens, James H; Bleiholder, Christian; Bowers, Michael T; Gewinner, Sandy; Schöllkopf, Wieland; Pagel, Kevin; von Helden, Gert

2015-04-01

The immediate environment of a molecule can have a profound influence on its properties. Benzocaine, the ethyl ester of para-aminobenzoic acid that finds an application as a local anesthetic, is found to adopt in its protonated form at least two populations of distinct structures in the gas phase, and their relative intensities strongly depend on the properties of the solvent used in the electrospray ionization process. Here, we combine IR-vibrational spectroscopy with ion mobility-mass spectrometry to yield gas-phase IR spectra of simultaneously m/z and drift-time-resolved species of benzocaine. The results allow for an unambiguous identification of two protomeric species: the N- and O-protonated forms. Density functional theory calculations link these structures to the most stable solution and gas-phase structures, respectively, with the electric properties of the surrounding medium being the main determinant for the preferred protonation site. The fact that the N-protonated form of benzocaine can be found in the gas phase is owed to kinetic trapping of the solution-phase structure during transfer into the experimental setup. These observations confirm earlier studies on similar molecules where N- and O-protonation have been suggested.

Optimization of flavanones extraction by modulating differential solvent densities and centrifuge temperatures.

PubMed

Chebrolu, Kranthi K; Jayaprakasha, G K; Jifon, J; Patil, Bhimanagouda S

2011-07-15

Understanding the factors influencing flavonone extraction is critical for the knowledge in sample preparation. The present study was focused on the extraction parameters such as solvent, heat, centrifugal speed, centrifuge temperature, sample to solvent ratio, extraction cycles, sonication time, microwave time and their interactions on sample preparation. Flavanones were analyzed in a high performance liquid chromatography (HPLC) and later identified by liquid chromatography and mass spectrometry (LC-MS). The five flavanones were eluted by a binary mobile phase with 0.03% phosphoric acid and acetonitrile in 20 min and detected at 280 nm, and later identified by mass spectral analysis. Dimethylsulfoxide (DMSO) and dimethyl formamide (DMF) had optimum extraction levels of narirutin, naringin, neohesperidin, didymin and poncirin compared to methanol (MeOH), ethanol (EtOH) and acetonitrile (ACN). Centrifuge temperature had a significant effect on flavanone distribution in the extracts. The DMSO and DMF extracts had homogeneous distribution of flavanones compared to MeOH, EtOH and ACN after centrifugation. Furthermore, ACN showed clear phase separation due to differential densities in the extracts after centrifugation. The number of extraction cycles significantly increased the flavanone levels during extraction. Modulating the sample to solvent ratio increased naringin quantity in the extracts. Current research provides critical information on the role of centrifuge temperature, extraction solvent and their interactions on flavanone distribution in extracts. Published by Elsevier B.V.

Stretch-collapse transition of polyelectrolyte brushes in a poor solvent

NASA Astrophysics Data System (ADS)

von Goeler, F.; Muthukumar, M.

1996-12-01

This paper describes the behavior of charged, polymer brushes in electrolyte solutions of varying solvent quality. The brush height, d, dependence on the chain length, L (=Nl, where l is the Kuhn length), the grafting density σ, and solvent conditions is determined. We consider a monomer-monomer potential consisting of three components: (1) a long-ranged, screened Coulombic component of strength v¯/l (l is the Kuhn length) and range κ-1; (2) a short-ranged, two-body component of strength w¯l; and (3) a short-ranged, three-body component of strength ūl3. In particular, we examine the transition from a stretched state to a collapsed state in a poor solvent (w¯<0) as the solvent quality is decreased. Using dimensional analysis, Monte Carlo methods, and a variational technique, a first order transition is observed as predicted by the scaling arguments of Ross et al. and Borisov et al. for high charge/grafting densities. Using a variational procedure, we derive an analytical expression for the brush size and determine, quantitatively, the critical conditions for a first order transition in terms of key dimensionless variables, vN5/2, κlN1/2, wN3/2, and uN2 (where v=2πσl2v¯, w=σl2w¯, and u=σ2l4ū).

N-Succinyl-chitosan nanoparticles coupled with low-density lipoprotein for targeted osthole-loaded delivery to low-density lipoprotein receptor-rich tumors

PubMed Central

Zhang, Chun-ge; Zhu, Qiao-ling; Zhou, Yi; Liu, Yang; Chen, Wei-liang; Yuan, Zhi-Qiang; Yang, Shu-di; Zhou, Xiao-feng; Zhu, Ai-jun; Zhang, Xue-nong; Jin, Yong

2014-01-01

N-Succinyl-chitosan (NSC) was synthesized and NSC nanoparticles (NPs) with loaded osthole (Ost) (Ost/NSC-NPs) were prepared by emulsion solvent diffusion. Subsequently, low-density lipoprotein (LDL)-mediated NSC-NPs with loaded Ost (Ost/LDL-NSC-NPs) were obtained by coupling LDL with Ost/NSC-NPs through amide linkage. The average particle size of Ost/NSC-NPs was approximately 145 nm, the entrapment efficiency was 78.28%±2.06%, and the drug-loading amount was 18.09%±0.17%. The release of Ost from Ost/NSC-NPs in vitro showed a more evident sustained effect than the native material. The half maximal inhibitory concentration of Ost/LDL-NSC-NPs was only 16.23% that of the free Ost at 24 hours in HepG2 cells. Ost inhibited HepG2 cell proliferation by arresting cells in the synthesis phase of the cell cycle and by triggering apoptosis. Cellular uptake and subcellular localization in vitro and near-infrared fluorescence real-time imaging in vivo showed that Ost/LDL-NSC-NPs had high targeting efficacy. Therefore, LDL-NSC-NPs are a promising system for targeted Ost delivery to liver tumor. PMID:24966673

Learning about Biomolecular Solvation from Water in Protein Crystals.

PubMed

Altan, Irem; Fusco, Diana; Afonine, Pavel V; Charbonneau, Patrick

2018-03-08

Water occupies typically 50% of a protein crystal and thus significantly contributes to the diffraction signal in crystallography experiments. Separating its contribution from that of the protein is, however, challenging because most water molecules are not localized and are thus difficult to assign to specific density peaks. The intricateness of the protein-water interface compounds this difficulty. This information has, therefore, not often been used to study biomolecular solvation. Here, we develop a methodology to surmount in part this difficulty. More specifically, we compare the solvent structure obtained from diffraction data for which experimental phasing is available to that obtained from constrained molecular dynamics (MD) simulations. The resulting spatial density maps show that commonly used MD water models are only partially successful at reproducing the structural features of biomolecular solvation. The radial distribution of water is captured with only slightly higher accuracy than its angular distribution, and only a fraction of the water molecules assigned with high reliability to the crystal structure is recovered. These differences are likely due to shortcomings of both the water models and the protein force fields. Despite these limitations, we manage to infer protonation states of some of the side chains utilizing MD-derived densities.

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.

Energy decomposition analysis for exciplexes using absolutely localized molecular orbitals

NASA Astrophysics Data System (ADS)

Ge, Qinghui; Mao, Yuezhi; Head-Gordon, Martin

2018-02-01

An energy decomposition analysis (EDA) scheme is developed for understanding the intermolecular interaction involving molecules in their excited states. The EDA utilizes absolutely localized molecular orbitals to define intermediate states and is compatible with excited state methods based on linear response theory such as configuration interaction singles and time-dependent density functional theory. The shift in excitation energy when an excited molecule interacts with the environment is decomposed into frozen, polarization, and charge transfer contributions, and the frozen term can be further separated into Pauli repulsion and electrostatics. These terms can be added to their counterparts obtained from the ground state EDA to form a decomposition of the total interaction energy. The EDA scheme is applied to study a variety of systems, including some model systems to demonstrate the correct behavior of all the proposed energy components as well as more realistic systems such as hydrogen-bonding complexes (e.g., formamide-water, pyridine/pyrimidine-water) and halide (F-, Cl-)-water clusters that involve charge-transfer-to-solvent excitations.

Electronic functions of solid-to-liquid interfaces of organic semiconductor crystals and ionic liquid

NASA Astrophysics Data System (ADS)

Takeya, J.

2008-10-01

The environment of surface electrons at 'solid-to-liquid' interfaces is somewhat extreme, subjected to intense local electric fields or harsh chemical pressures that high-density ionic charge or polarization of mobile molecules create. In this proceedings, we argue functions of electronic carriers generated at the surface of organic semiconductor crystals in response to the local electric fields in the very vicinity of the interface to ionic liquid. The ionic liquids (ILs), or room temperature molten salts, are gaining considerable interest in the recent decade at the prospect of nonvolatile 'green solvents', with the development of chemically stable and nontoxic compounds. Moreover, such materials are also applied to electrolytes for lithium ion batteries and electric double-layer (EDL) capacitors. Our present solid-to-liquid interfaces of rubrene single crystals and ionic liquids work as fast-switching organic field-effect transistors (OFETs) with the highest transconductance, i.e. the most efficient response of the output current to the input voltage, among the OFETs ever built.

Radiation processed polychloroprene-co-ethylene-propene diene terpolymer blends: Effect of radiation vulcanization on solvent transport kinetics

NASA Astrophysics Data System (ADS)

Dubey, K. A.; Bhardwaj, Y. K.; Chaudhari, C. V.; Kumar, Virendra; Goel, N. K.; Sabharwal, S.

2009-03-01

Blends of polychloroprene rubber (PCR) and ethylene propylene diene terpolymer rubber (EPDM) of different compositions were made and exposed to different gamma radiation doses. The radiation sensitivity and radiation vulcanization efficiency of blends was estimated by gel-content analysis, Charlesby-Pinner parameter determination and crosslinking density measurements. Gamma radiation induced crosslinking was most efficient for EPDM ( p0/ q0 ˜ 0.08), whereas it was the lowest for blends containing 40% PCR ( p0/ q0 ˜ 0.34). The vulcanized blends were characterized for solvent diffusion characteristics by following the swelling dynamics. Blends with higher PCR content showed anomalous swelling. The sorption and permeability of the solvent were not strictly in accordance with each other and the extent of variation in two parameters was found to be a function of blend composition. The Δ G values for solvent diffusion were in the range -2.97 to -9.58 kJ/mol and indicated thermodynamically favorable sorption for all blends. These results were corroborated by dynamic swelling, experimental as well as simulated profiles and have been explained on the basis of correlation between crosslinking density, diffusion kinetics, thermodynamic parameters and polymer-polymer interaction parameter.

Effect of binder liquid type on spherical crystallization.

PubMed

Maghsoodi, Maryam; Hajipour, Ali

2014-11-01

Spherical crystallization is a process of formation of agglomerates of crystals held together by binder liquid. This research focused on understanding the effect of type of solvents used as binder liquid on the agglomeration of crystals. Carbamazepine and ethanol/water were used respectively as a model drug and crystallization system. Eight solvents as binder liquid including chloroform, dichloromethane, isopropyl acetate, ethyl acetate, n-hexane, dimethyl aniline, benzene and toluene were examined to better understand the relationship between the physical properties of the binder liquid and its ability to bring about the formation of the agglomerates. Moreover, the agglomerates obtained from effective solvents as binder liquid were evaluated in term of size, apparent particle density and compressive strength. In this study the clear trend was observed experimentally in the agglomerate formation as a function of physical properties of the binder liquid such as miscibility with crystallization system. Furthermore, the properties of obtained agglomerates such as size, apparent particle density and compressive strength were directly related to physical properties of effective binder liquids. RESULTS of this study offer a useful starting point for a conceptual framework to guide the selection of solvent systems for spherical crystallization.

UV-Vis spectroscopy and density functional study of solvent effect on the charge transfer band of the n → σ* complexes of 2-Methylpyridine and 2-Chloropyridine with molecular iodine

NASA Astrophysics Data System (ADS)

Gogoi, Pallavi; Mohan, Uttam; Borpuzari, Manash Protim; Boruah, Abhijit; Baruah, Surjya Kumar

2017-03-01

UV-Vis spectroscopy has established that Pyridine substitutes form n→σ* charge transfer (CT) complexes with molecular Iodine. This study is a combined approach of purely experimental UV-Vis spectroscopy, Multiple linear regression theory and Computational chemistry to analyze the effect of solvent upon the charge transfer band of 2-Methylpyridine-I2 and 2-Chloropyridine-I2 complexes. Regression analysis verifies the dependence of the CT band upon different solvent parameters. Dielectric constant and refractive index are considered among the bulk solvent parameters and Hansen, Kamlet and Catalan parameters are taken into consideration at the molecular level. Density Functional Theory results explain well the blue shift of the CT bands in polar medium as an outcome of stronger donor acceptor interaction. A logarithmic relation between the bond length of the bridging atoms of the donor and the acceptor with the dielectric constant of the medium is established. Tauc plot and TDDFT study indicates a non-vertical electronic transition in the complexes. Buckingham and Lippert Mataga equations are applied to check the Polarizability effect on the CT band.

Solute-Solvent Charge-Transfer Excitations and Optical Absorption of Hydrated Hydroxide from Time-Dependent Density-Functional Theory.

PubMed

Opalka, Daniel; Sprik, Michiel

2014-06-10

The electronic structure of simple hydrated ions represents one of the most challenging problems in electronic-structure theory. Spectroscopic experiments identified the lowest excited state of the solvated hydroxide as a charge-transfer-to-solvent (CTTS) state. In the present work we report computations of the absorption spectrum of the solvated hydroxide ion, treating both solvent and solute strictly at the same level of theory. The average absorption spectrum up to 25 eV has been computed for samples taken from periodic ab initio molecular dynamics simulations. The experimentally observed CTTS state near the onset of the absorption threshold has been analyzed at the generalized-gradient approximation (GGA) and with a hybrid density-functional. Based on results for the lowest excitation energies computed with the HSE hybrid functional and a Davidson diagonalization scheme, the CTTS transition has been found 0.6 eV below the first absorption band of liquid water. The transfer of an electron to the solvent can be assigned to an excitation from the solute 2pπ orbitals, which are subject to a small energetic splitting due to the asymmetric solvent environment, to the significantly delocalized lowest unoccupied orbital of the solvent. The distribution of the centers of the excited state shows that CTTS along the OH(-) axis of the hydroxide ion is avoided. Furthermore, our simulations indicate that the systematic error arising in the calculated spectrum at the GGA originates from a poor description of the valence band energies in the solution.

Water Dynamics at Protein-Protein Interfaces: Molecular Dynamics Study of Virus-Host Receptor Complexes.

PubMed

Dutta, Priyanka; Botlani, Mohsen; Varma, Sameer

2014-12-26

The dynamical properties of water at protein-water interfaces are unlike those in the bulk. Here we utilize molecular dynamics simulations to study water dynamics in interstitial regions between two proteins. We consider two natural protein-protein complexes, one in which the Nipah virus G protein binds to cellular ephrin B2 and the other in which the same G protein binds to ephrin B3. While the two complexes are structurally similar, the two ephrins share only a modest sequence identity of ∼50%. X-ray crystallography also suggests that these interfaces are fairly extensive and contain exceptionally large amounts of waters. We find that while the interstitial waters tend to occupy crystallographic sites, almost all waters exhibit residence times of less than hundred picoseconds in the interstitial region. We also find that while the differences in the sequence of the two ephrins result in quantitative differences in the dynamics of interstitial waters, the trends in the shifts with respect to bulk values are similar. Despite the high wetness of the protein-protein interfaces, the dynamics of interstitial waters are considerably slower compared to the bulk-the interstitial waters diffuse an order of magnitude slower and have 2-3 fold longer hydrogen bond lifetimes and 2-1000 fold slower dipole relaxation rates. To understand the role of interstitial waters, we examine how implicit solvent models compare against explicit solvent models in producing ephrin-induced shifts in the G conformational density. Ephrin-induced shifts in the G conformational density are critical to the allosteric activation of another viral protein that mediates fusion. We find that in comparison with the explicit solvent model, the implicit solvent model predicts a more compact G-B2 interface, presumably because of the absence of discrete waters at the G-B2 interface. Simultaneously, we find that the two models yield strikingly different induced changes in the G conformational density, even for those residues whose conformational densities in the apo state are unaffected by the treatment of the bulk solvent. Together, these results show that the explicit treatment of interstitial water molecules is necessary for a proper description of allosteric transitions.

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.

Photo-dynamics of roseoflavin and riboflavin in aqueous and organic solvents

NASA Astrophysics Data System (ADS)

Zirak, P.; Penzkofer, A.; Mathes, T.; Hegemann, P.

2009-03-01

Roseoflavin (8-dimethylamino-8-demethyl- D-riboflavin) and riboflavin in aqueous and organic solvents are studied by optical absorption spectroscopy, fluorescence spectroscopy, and fluorescence decay kinetics. Solvent polarity dependent absorption shifts are observed. The fluorescence quantum yields are solvent dependent. For roseoflavin the fluorescence decay shows a bi-exponential dependence (ps to sub-ps time constant, and 100 ps to a few ns time constant). The roseoflavin photo-dynamics is explained in terms of fast intra-molecular charge transfer (diabatic electron transfer) from the dimethylamino electron donor group to the pteridin carbonyl electron acceptor followed by intra-molecular charge recombination. The fast fluorescence component is due to direct locally-excited-state emission, and the slow fluorescence component is due to delayed locally-excited-state emission and charge transfer state emission. The fluorescence decay of riboflavin is mono-exponential. The S 1-state potential energy surface is determined by vibronic relaxation and solvation dynamics due to excited-state dipole moment changes (adiabatic optical electron transfer).

Differential Microscopic Mobility of Components within a Deep Eutectic Solvent

DOE PAGES

Wagle, Durgesh V.; Baker, Gary A.; Mamontov, Eugene

2015-07-13

From macroscopic measurements of deep eutectic solvents such as glyceline (1:2 molar ratio of choline chloride to glycerol), the long-range translational diffusion of the larger cation (choline) is known to be slower compared to that of the smaller hydrogen bond donor (glycerol). However, when the diffusion dynamics are analyzed on the subnanometer length scale, we discover that the displacements associated with the localized diffusive motions are actually larger for choline. This counterintuitive diffusive behavior can be understood as follows. The localized diffusive motions confined in the transient cage of neighbor particles, which precede the cage-breaking long-range diffusion jumps, are moremore » spatially constrained for glycerol than for choline because of the stronger hydrogen bonds the former makes with chloride anions. The implications of differential localized mobility of the constituents should be especially important for applications where deep eutectic solvents are confined on the nanometer length scale and their long-range translational diffusion is strongly inhibited (e.g., within microporous media).« less

Solubility behavior of lamivudine crystal forms in recrystallization solvents.

PubMed

Jozwiakowski, M J; Nguyen, N A; Sisco, J M; Spancake, C W

1996-02-01

Lamivudine can be obtained as acicular crystals (form I, 0.2 hydrate) from water or methanol and as bipyramidal crystals (form II, nonsolvated) from many nonaqueous solvents. Form II is thermodynamically favored in the solid state (higher melting point and greater density than form I) at ambient relative humidities. Solubility measurements on both forms versus solvent and temperature was used to determine whether entropy or enthalpy was the driving force for solubility. Solution calorimetry data indicated that form I is favored (less soluble) in all solvents studied on the basis of enthalpy alone. In higher alcohols and other organic solvents, form I has a larger entropy of solution than form II, which compensates for the enthalpic factors and results in physical stability for form II in these systems. The metastable crystal form solubility at 25 degrees C was estimated to be 1.2-2.3 times as high as the equilibrium solubility of the stable form, depending on the temperature, solvent, and crystal form. Binary solvent studies showed that > 18-20% water must be present in ethanol to convert the excess solid to form I at equilibrium.

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.

Effect of solvent volume on the physical properties of aluminium doped nanocrystalline zinc oxide thin films deposited using a simplified spray pyrolysis technique

NASA Astrophysics Data System (ADS)

Jabena Begum, N.; Mohan, R.; Ravichandran, K.

2013-01-01

Aluminium doped zinc oxide (AZO) thin films were deposited by employing a low cost and simplified spray technique using a perfume atomizer from starting solutions having different volumes (10, 20, … , 50 mL) of solvent. The effect of solvent volume on the structural, electrical, optical, photoluminescence (PL) and surface morphological properties was studied. The electrical resistivity of the AZO films is remarkably influenced by the variation in the solvent volume. The X-ray diffraction profiles clearly showed that all the films have preferential orientation along the (0 0 2) plane irrespective of the solvent volume. The crystallite size was found to be in the nano range of 35-46 nm. The optical transmittance in the visible region is desirably high (>85%). The AFM images show columnar morphology with varying grain size. The PL studies revealed that the AZO film deposited from 50 mL of solvent volume has good quality with lesser defect density.

Solvent effects on the Raman spectra of the isolated carbon-hydrogen stretches of cyclohexane-d11: A molecular dynamics simulation study of liquid and supercritical solvation

NASA Astrophysics Data System (ADS)

Frankland, Sarah-Jane Victoria

Molecular dynamics simulations of solvent effects on the Raman spectra of isotopically isolated C-H stretches of cyclohexane-d11 were performed in liquids and supercritical CO2. The red spectral shifts from the gas phase origin were derived three different ways: (1) from the Lennard-Jones force on the normal coordinate of the vibration; (2) from this force with an additional term to account for the polarizabilily change on excitation, and (3) as an empirical difference potential between the v = 0 and v = 1 state of the hydrogen atom involved in the vibration. Model 3 was successfully parametrized to reproduce the experimental spectral shifts and linewidths. The simulated lineshapes from these models were homogeneously broadened from gas to liquid densities primarily by collisions of nearby solvent molecules with the solute. Both the simulations and isolated binary collision theory showed the density dependence of the linewidth to be related to that of the collision rate. Two additional projects were done which use Monte-Carlo algorithms involving two molecules. In the first project 1:1 complexes of solute and solvent were formed at the potential surface minima such that the geometries of conformers, energies of formation, and electronic spectral shifts could be studied. Complexes between 7- azaindole, indole, carbazole, and 1-azacarbazole and hydrogen-bonding solvents were most stable when the solvent was hydrogen-bonded at the solute N-H site. The energies of formation compared well with values obtained from ab initio calculations. Complexes of coumarins 102 and 153 and fluorinated alcohols showed the more stable conformers to have the alcohols bound at the coumarin carbonyl group. In the second project, one solvent molecule was randomly placed around the solute molecule in order to simplify bulk liquid simulation to only two molecules. This approximation was rised to show that the dynamic Stokes shift of coumarin 153 in over 30 solvents correlates with the permanent charge distribution of the solvent.

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.

Structural analysis of benzothienobenzothiophene-based soluble organic semiconducting crystals grown by liquid crystal solvent

NASA Astrophysics Data System (ADS)

Shibata, Yosei; Matsuzaki, Tomoya; Ishinabe, Takahiro; Fujikake, Hideo

2018-06-01

In this study, we analyzed organic semiconducting single crystals composed of benzothienobenzothiophene derivatives (2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene, C8-BTBT) grown by nematic-phase liquid crystal (LC) solvent. As a result, we clarified that the crystal b-axis direction of the C8-BTBT single crystals was consistent with the LC alignment direction. By optical evaluation and simulation based on density functional theory, we found that the C8-BTBT single crystals in LC solvent exhibited a novel molecular conformation having alkyl chains oriented toward the b-axis.

Membrane formation in liquids by adding an antagonistic salt

NASA Astrophysics Data System (ADS)

Sadakane, Koichiro; Seto, Hideki

2018-03-01

Antagonistic salts are composed of hydrophilic and hydrophobic ions. In a binary mixture, such as water and organic solvent, these ion pairs preferentially dissolve to those phases, respectively, and there is a coupling between the charge density and the composition. The heterogeneous distribution of ions forms a large electric double layer at the interface between these solvents. This reduces the interfacial tension between water and organic solvent, and stabilizes an ordered structure, such as a membrane. These phenomena have been extensively studied from both theoretical and experimental point of view. In addition, the numerical simulations can reproduce such ordered structures.

Liquid Quinones for Solvent-Free Redox Flow Batteries.

PubMed

Shimizu, Akihiro; Takenaka, Keisuke; Handa, Naoyuki; Nokami, Toshiki; Itoh, Toshiyuki; Yoshida, Jun-Ichi

2017-11-01

Liquid benzoquinone and naphthoquinone having diethylene glycol monomethyl ether groups are designed and synthesized as redox active materials that dissolve supporting electrolytes. The Li-ion batteries based on the liquid quinones using LiBF 4 /PC show good performance in terms of voltage, capacity, energy efficiency, and cyclability in both static and flow modes. A battery is constructed without using intentionally added organic solvent, and its high energy density (264 W h L -1 ) demonstrates the potential of solvent-free organic redox flow batteries using liquid active materials. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantum dynamics in continuum for proton transport II: Variational solvent-solute interface.

PubMed

Chen, Duan; Chen, Zhan; Wei, Guo-Wei

2012-01-01

Proton transport plays an important role in biological energy transduction and sensory systems. Therefore, it has attracted much attention in biological science and biomedical engineering in the past few decades. The present work proposes a multiscale/multiphysics model for the understanding of the molecular mechanism of proton transport in transmembrane proteins involving continuum, atomic, and quantum descriptions, assisted with the evolution, formation, and visualization of membrane channel surfaces. We describe proton dynamics quantum mechanically via a new density functional theory based on the Boltzmann statistics, while implicitly model numerous solvent molecules as a dielectric continuum to reduce the number of degrees of freedom. The density of all other ions in the solvent is assumed to obey the Boltzmann distribution in a dynamic manner. The impact of protein molecular structure and its charge polarization on the proton transport is considered explicitly at the atomic scale. A variational solute-solvent interface is designed to separate the explicit molecule and implicit solvent regions. We formulate a total free-energy functional to put proton kinetic and potential energies, the free energy of all other ions, and the polar and nonpolar energies of the whole system on an equal footing. The variational principle is employed to derive coupled governing equations for the proton transport system. Generalized Laplace-Beltrami equation, generalized Poisson-Boltzmann equation, and generalized Kohn-Sham equation are obtained from the present variational framework. The variational solvent-solute interface is generated and visualized to facilitate the multiscale discrete/continuum/quantum descriptions. Theoretical formulations for the proton density and conductance are constructed based on fundamental laws of physics. A number of mathematical algorithms, including the Dirichlet-to-Neumann mapping, matched interface and boundary method, Gummel iteration, and Krylov space techniques are utilized to implement the proposed model in a computationally efficient manner. The gramicidin A channel is used to validate the performance of the proposed proton transport model and demonstrate the efficiency of the proposed mathematical algorithms. The proton channel conductances are studied over a number of applied voltages and reference concentrations. A comparison with experimental data verifies the present model predictions and confirms the proposed model. Copyright © 2011 John Wiley & Sons, Ltd.

Debinding and Sintering of an Injection-Moulded Hypereutectic Al⁻Si Alloy.

PubMed

Ni, Jiaqi; Yu, Muhuo; Han, Keqing

2018-05-16

Hypereutectic Al⁻Si (20 wt.%) alloy parts were fabricated by employing a powder injection moulding (PIM) technique with a developed multi-component binder system composed of high-density polyethylene (35 wt.%), carnauba wax (62 wt.%) and stearic acid (3 wt.%). The feedstocks contained 83 wt.% metal powders. The debinding process was carried out by a combination of solvent extraction and thermal decomposition. The effects of solvent debinding variables such as kind of solvents, debinding temperatures and time, and the bulk surface area to volume ratios on the debinding process were investigated. Thermal debinding and the subsequent sintering process were carried out in a heating sequence under a nitrogen atmosphere. The influences of sintering temperature and sintering time on the mechanical properties and structure were considered. Under the optimal sintering condition, sintering at 550 °C for 3 h, the final sintering parts were free of distortion and exhibited good mechanical properties. Relative sintered density, Brinell hardness, and tensile strength were ~95.5%, 58 HBW and ~154, respectively.

Intermolecular interaction studies of glyphosate with water

NASA Astrophysics Data System (ADS)

Manon, Priti; Juglan, K. C.; Kaur, Kirandeep; Sethi, Nidhi; Kaur, J. P.

2017-07-01

The density (ρ), viscosity (η) and ultrasonic velocity (U) of glyphosate with water have been measured on different ultrasonic frequency ranges from 1MHz, 2MHz, 3MHz & 5MHz by varying concentrations (0.05%, 0.10%, 0.15%, 0.20%, 0.25%, 0.30%, 0.35%, & 0.40%) at 30°C. The specific gravity bottle, Ostwald's viscometer and quartz crystal interferometer were used to determine density (ρ), viscosity (η) and ultrasonic velocity (U). These three factors contribute in evaluating the other parameters as acoustic impedance (Z), adiabatic compressibility (β), relaxation time (τ), intermolecular free length (Lf), free volume (Vf), ultrasonic attenuation (α/f2), Rao's constant (R), Wada's constant (W) and relative strength (R). Solute-solvent interaction is confirmed by ultrasonic velocity and viscosity values, which increases with increase in concentration indicates stronger association between solute and solvent molecules. With rise in ultrasonic frequency the interaction between the solute and solvent particles decreases. The linear variations in Rao's constant and Wada's constant suggest the absence of complex formation.

Mechanism insight into the cyanide-catalyzed benzoin condensation: a density functional theory study.

PubMed

He, Yunqing; Xue, Ying

2010-09-02

The reaction mechanism of the cyanide-catalyzed benzoin condensation without protonic solvent assistance has been studied computationally for the first time employing the density functional theory (B3LYP) method in conjunction with 6-31+G(d,p) basis set. Four possible pathways have been investigated. A new proposed pathway on the basis of the Lapworth mechanism is determined to be the dominant pathway in aprotic solvent, in which the formation of the Lapworth's cyanohydrin intermediate is a sequence including three steps assisted by benzaldehyde, clearly manifesting that the reaction can take place in aprotic solvents such as DMSO. In this favorable pathway with six possible transition states located along the potential energy surface, the reaction of the cyanide/benzaldehyde complex with another benzaldehyde to afford an alpha-hydroxy ether is the rate-determining dynamically with the activation free energy barrier of 26.9 kcal/mol, and the step to form cyanohydrin intermediate from alpha-hydroxy ether is partially rate-determining for its relatively significant barrier 20.0 kcal/mol.

Solubility, stability, and electrochemical studies of sulfur-sulfide solutions in organic solvents

NASA Technical Reports Server (NTRS)

Fielder, W. L.; Singer, J.

1978-01-01

A preliminary study of the sulfur electrode in organic solvents suggests that the system warrants further investigation for use in a low temperature (100 deg to 120 C) Na-S secondary battery. A qualitative screening was undertaken at 120 C to determine the solubilities and stabilities of Na2S and Na2S2 in representatives of many classes of organic solvents. From the screening and quantitative studies, two classes of solvents were selected for work; amides and cyclic polyalcohols. Voltammetric and Na-S cell charge discharge studies of sulfide solutions in organic solvents (e.g., N, N-dimethylformamide) at 120 C suggested that the reversibilities of the reactions on Pt or high density graphite were moderately poor. However, the sulfur electrode was indeed reducible (and oxidizable) through the range of elemental sulfur to Na2S. Reactions and mechanisms are proposed for the oxidation reduction processes occurring at the sulfur electrode.

Method for solvent extraction with near-equal density solutions

DOEpatents

Birdwell, Joseph F.; Randolph, John D.; Singh, S. Paul

2001-01-01

Disclosed is a modified centrifugal contactor for separating solutions of near equal density. The modified contactor has a pressure differential establishing means that allows the application of a pressure differential across fluid in the rotor of the contactor. The pressure differential is such that it causes the boundary between solutions of near-equal density to shift, thereby facilitating separation of the phases. Also disclosed is a method of separating solutions of near-equal density.

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

Solvated molecular dynamics of LiCN isomerization: All-atom argon solvent versus a generalized Langevin bath.

PubMed

Junginger, Andrej; Garcia-Muller, Pablo L; Borondo, F; Benito, R M; Hernandez, Rigoberto

2016-01-14

The reaction rate rises and falls with increasing density or friction when a molecule is activated by collisions with the solvent particles. This so-called Kramers turnover has recently been observed in the isomerization reaction of LiCN in an argon bath. In this paper, we demonstrate by direct comparison with those results that a reduced-dimensional (generalized) Langevin description gives rise to similar reaction dynamics as the corresponding (computationally expensive) full molecular dynamics calculations. We show that the density distributions within the Langevin description are in direct agreement with the full molecular dynamics results and that the turnover in the reaction rates is reproduced qualitatively and quantitatively at different temperatures.

Scaling features of the tribology of polymer brushes of increasing grafting density around the mushroom-to-brush transition.

PubMed

Mayoral, E; Klapp, J; Gama Goicochea, A

2017-01-01

Nonequilibrium coarse-grained, dissipative particle dynamics simulations of complex fluids, made up of polymer brushes tethered to planar surfaces immersed in a solvent yield nonmonotonic behavior of the friction coefficient as a function of the polymer grating density on the substrates, Γ, while the viscosity shows a monotonically increasing dependence on Γ. This effect is shown to be independent of the degree of polymerization, N, and the size of the system. It arises from the composition and the structure of the first particle layer adjacent to each surface that results from the confinement of the fluid. Whenever such layers are made up of as close a proportion of polymer beads to solvent particles as there are in the fluid, the friction coefficient shows a minimum, while for disparate proportions the friction coefficient grows. At the mushroom-to-brush transition (MBT) the viscosity scales with an exponent that depends on the characteristic exponent of the MBT (6/5) and the solvent quality exponent (ν=0.5, for θsolvent), but it is independent of the polymerization degree (N). On the other hand, the friction coefficient at the MBT scales as μ∼N^{6/5}, while the grafting density at the MBT scales as Γ∼N^{-6/5} when friction is minimal, in agreement with previous scaling theories. We argue these aspects are the result of cooperative phenomena that have important implications for the understanding of biological brushes and the design of microfluidics devices, among other applications of current academic and industrial interest.

Negative corona discharge-ion mobility spectrometry as a detection system for low density extraction solvent-based dispersive liquid-liquid microextraction.

PubMed

Ebrahimi, Amir; Jafari, Mohammad T

2015-03-01

This paper deals with a method based on negative corona discharge ionization ion mobility spectrometry (NCD-IMS) for the analysis of ethion (as an organophosphorus pesticide). The negative ions such as O2(-) and NO(x)(-) were eliminated from the background spectrum to increase the instrument sensitivity. The method was used to specify the sample extracted via dispersive liquid-liquid microextraction (DLLME) based on low density extraction solvent. The ion mobility spectrum of ethion in the negative mode and the reduced mobility value for its ion peak are firstly reported and compared with those of the positive mode. In order to combine the low density solvent DLLME directly with NCD-IMS, cyclohexane was selected as the extraction solvent, helping us to have a direct injection up to 20 µL solution, without any signal interference. The method was exhaustively validated in terms of sensitivity, enrichment factor, relative recovery, and repeatability. The linear dynamic range of 0.2-100.0 µg L(-1), detection limit of 0.075 µg L(-1), and the relative standard deviation (RSD) of about 5% were obtained for the analysis of ethion through this method. The average recoveries were calculated about 68% and 92% for the grape juice and underground water, respectively. Finally, some real samples were analyzed and the feasibility of the proposed method was successfully verified by the efficient extraction of the analyte using DLLME before the analysis by NCD-IMS. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Entropy Production in Field Theories without Time-Reversal Symmetry: Quantifying the Non-Equilibrium Character of Active Matter

NASA Astrophysics Data System (ADS)

Nardini, Cesare; Fodor, Étienne; Tjhung, Elsen; van Wijland, Frédéric; Tailleur, Julien; Cates, Michael E.

2017-04-01

Active-matter systems operate far from equilibrium because of the continuous energy injection at the scale of constituent particles. At larger scales, described by coarse-grained models, the global entropy production rate S quantifies the probability ratio of forward and reversed dynamics and hence the importance of irreversibility at such scales: It vanishes whenever the coarse-grained dynamics of the active system reduces to that of an effective equilibrium model. We evaluate S for a class of scalar stochastic field theories describing the coarse-grained density of self-propelled particles without alignment interactions, capturing such key phenomena as motility-induced phase separation. We show how the entropy production can be decomposed locally (in real space) or spectrally (in Fourier space), allowing detailed examination of the spatial structure and correlations that underly departures from equilibrium. For phase-separated systems, the local entropy production is concentrated mainly on interfaces, with a bulk contribution that tends to zero in the weak-noise limit. In homogeneous states, we find a generalized Harada-Sasa relation that directly expresses the entropy production in terms of the wave-vector-dependent deviation from the fluctuation-dissipation relation between response functions and correlators. We discuss extensions to the case where the particle density is coupled to a momentum-conserving solvent and to situations where the particle current, rather than the density, should be chosen as the dynamical field. We expect the new conceptual tools developed here to be broadly useful in the context of active matter, allowing one to distinguish when and where activity plays an essential role in the dynamics.

Linear-scaling time-dependent density-functional theory beyond the Tamm-Dancoff approximation: Obtaining efficiency and accuracy with in situ optimised local orbitals

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

Zuehlsdorff, T. J., E-mail: tjz21@cam.ac.uk; Payne, M. C.; Hine, N. D. M.

2015-11-28

We present a solution of the full time-dependent density-functional theory (TDDFT) eigenvalue equation in the linear response formalism exhibiting a linear-scaling computational complexity with system size, without relying on the simplifying Tamm-Dancoff approximation (TDA). The implementation relies on representing the occupied and unoccupied subspaces with two different sets of in situ optimised localised functions, yielding a very compact and efficient representation of the transition density matrix of the excitation with the accuracy associated with a systematic basis set. The TDDFT eigenvalue equation is solved using a preconditioned conjugate gradient algorithm that is very memory-efficient. The algorithm is validated on amore » small test molecule and a good agreement with results obtained from standard quantum chemistry packages is found, with the preconditioner yielding a significant improvement in convergence rates. The method developed in this work is then used to reproduce experimental results of the absorption spectrum of bacteriochlorophyll in an organic solvent, where it is demonstrated that the TDA fails to reproduce the main features of the low energy spectrum, while the full TDDFT equation yields results in good qualitative agreement with experimental data. Furthermore, the need for explicitly including parts of the solvent into the TDDFT calculations is highlighted, making the treatment of large system sizes necessary that are well within reach of the capabilities of the algorithm introduced here. Finally, the linear-scaling properties of the algorithm are demonstrated by computing the lowest excitation energy of bacteriochlorophyll in solution. The largest systems considered in this work are of the same order of magnitude as a variety of widely studied pigment-protein complexes, opening up the possibility of studying their properties without having to resort to any semiclassical approximations to parts of the protein environment.« less

Lithium-Based High Energy Density Flow Batteries

NASA Technical Reports Server (NTRS)

Bugga, Ratnakumar V. (Inventor); West, William C. (Inventor); Kindler, Andrew (Inventor); Smart, Marshall C. (Inventor)

2014-01-01

Systems and methods in accordance with embodiments of the invention implement a lithium-based high energy density flow battery. In one embodiment, a lithium-based high energy density flow battery includes a first anodic conductive solution that includes a lithium polyaromatic hydrocarbon complex dissolved in a solvent, a second cathodic conductive solution that includes a cathodic complex dissolved in a solvent, a solid lithium ion conductor disposed so as to separate the first solution from the second solution, such that the first conductive solution, the second conductive solution, and the solid lithium ionic conductor define a circuit, where when the circuit is closed, lithium from the lithium polyaromatic hydrocarbon complex in the first conductive solution dissociates from the lithium polyaromatic hydrocarbon complex, migrates through the solid lithium ionic conductor, and associates with the cathodic complex of the second conductive solution, and a current is generated.

Influence of solvents on species crossover and capacity decay in non-aqueous vanadium redox flow batteries: Characterization of acetonitrile and 1, 3 dioxolane solvent mixture

NASA Astrophysics Data System (ADS)

Bamgbopa, Musbaudeen O.; Almheiri, Saif

2017-02-01

The importance of the choice of solvent in a non-aqueous redox flow battery (NARFB) cannot be overemphasized. Several studies demonstrated the influence of the solvent on electrolyte performance in terms of reaction rates, energy/power densities, and efficiencies. In this work, we investigate capacity decay as a direct consequence of varying reactant crossover rates through membranes in different solvent environments. Specifically, we demonstrate the superiority of an 84/16 vol% acetonitrile/1,3 dioxolane solvent mixture over pure acetonitrile in terms of energy efficiency (up to 89%) and capacity retention for vanadium NARFBs - while incorporating a Nafion 115 membrane. The permeability of Nafion to the vanadium acetylacetonate active species is an order of magnitude lower when pure acetonitrile is replaced by the solvent mixture. A method to estimate relative membrane permeability is formulated from numerical analysis of self-discharge experimental data. Furthermore, tests on a modified Nafion/SiO2 membrane, which generally offered low species permeability, also show that different solvents alter membrane permeability. Elemental and morphological analyses of cycled Nafion and NafionSi membranes in different solvent environments indicate that different crossover rates induced by the choice of solvent during cycling are due to changes in the membrane microstructure, intrinsic permeability, swelling rates, and chemical stability.

Sensitive determination of methadone in human serum and urine by dispersive liquid-liquid microextraction based on the solidification of a floating organic droplet followed by HPLC-UV.

PubMed

Taheri, Salman; Jalali, Fahimeh; Fattahi, Nazir; Jalili, Ronak; Bahrami, Gholamreza

2015-10-01

Dispersive liquid-liquid microextraction based on solidification of floating organic droplet was developed for the extraction of methadone and determination by high-performance liquid chromatography with UV detection. In this method, no microsyringe or fiber is required to support the organic microdrop due to the usage of an organic solvent with a low density and appropriate melting point. Furthermore, the extractant droplet can be collected easily by solidifying it at low temperature. 1-Undecanol and methanol were chosen as extraction and disperser solvents, respectively. Parameters that influence extraction efficiency, i.e. volumes of extracting and dispersing solvents, pH, and salt effect, were optimized by using response surface methodology. Under optimal conditions, enrichment factor for methadone was 134 and 160 in serum and urine samples, respectively. The limit of detection was 3.34 ng/mmL in serum and 1.67 ng/mL in urine samples. Compared with the traditional dispersive liquid-liquid microextraction, the proposed method obtained lower limit of detection. Moreover, the solidification of floating organic solvent facilitated the phase transfer. And most importantly, it avoided using high-density and toxic solvents of traditional dispersive liquid-liquid microextraction method. The proposed method was successfully applied to the determination of methadone in serum and urine samples of an addicted individual under methadone therapy. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Permeability of starch gel matrices and select films to solvent vapors.

PubMed

Glenn, Gregory M; Klamczynski, Artur P; Ludvik, Charles; Shey, Justin; Imam, Syed H; Chiou, Bor-Sen; McHugh, Tara; DeGrandi-Hoffman, Gloria; Orts, William; Wood, Delilah; Offeman, Rick

2006-05-03

Volatile agrochemicals such as 2-heptanone have potential in safely and effectively controlling important agricultural pests provided that they are properly delivered. The present study reports the permeability of starch gel matrices and various coatings, some of which are agricultural-based, that could be used in controlled release devices. Low-density, microcellular starch foam was made from wheat, Dent corn, and high amylose corn starches. The foam density ranged from 0.14 to 0.34 g/cm3, the pore volume ranged from 74 to 89%, and the loading capacity ranged from 2.3 to 7.2 times the foam weight. The compressive properties of the foam were not markedly affected by saturating the pore volume with silicone oil. The vapor transmission rate (VTR) and vapor permeability (VP) were measured in dry, porous starch foam and silicone-saturated starch gels. VTR values were highest in foam samples containing solvents with high vapor pressures. Silicone oil-saturated gels had lower VTR and VP values as compared to the dry foam. However, the silicone oil gel did not markedly reduce the VP for 2-heptanone and an additional vapor barrier or coating was needed to adequately reduce the evaporation rate. The VP of films of beeswax, paraffin, ethylene vinyl alcohol, a fruit film, and a laminate comprised of beeswax and fruit film was measured. The fruit film had a relatively high VP for polar solvents and a very low VP for nonpolar solvents. The laminate film provided a low VP for polar and nonpolar solvents. Perforating the fruit film portion of the laminate provided a method of attaining the target flux rate of 2-heptanone. The results demonstrate that the vapor flux rate of biologically active solvents can be controlled using agricultural materials.

The solvent dependent shift of the amide I band of a fully solvated peptide in methanol/water mixtures as a local probe for the solvent composition in the peptide/solvent interface

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

Gnanakaran, S

2008-01-01

We determine the shift and line-shape of the amide I band of a model AK-peptide from molecular dynamics (MD) simulations of the peptide dissolved in methanol/water mixtures with varying composition. The IR-spectra are determined from a transition dipole coupling exciton model. A simplified empirical model Hamiltonian is employed, taking both the effect of hydrogen bonding, as well as intramolecular vibrational coupling into account. We consider a single isolated AK-peptide in a mostly helical conformation, while the solvent is represented by 2600 methanol or water molecules, simulated for a pressure of 1 bar and a temperature of 300 K. Over themore » course of the simulations minor reversible conformational changes at the termini are observed, which are found to only slightly affect the calculated spectral properties. Over the entire composition range, varying from pure water to the pure methanol solvent, a monotonous blue-shift of the IR amide I band of about 8 wavenumbers is observed. The shift is found to be caused by two counter-compensating effects: An intramolecular red-shift of about 1.2 wavenumbers, due to stronger intramolecular hydrogen-bonding in a methanol-rich environment. Dominating, however, is the intermolecular solvent-dependent blue-shift of about 10 wavenumbers, being attributed to the less effective hydrogen bond donor capabilities of methanol compared to water. The importance of solvent-contribution to the IR-shift, as well as the significantly different hydrogen formation capabilities of water and methanol make the amide I band sensitive to composition changes in the local environment close the peptide/solvent interface. This allows, in principle, an experimental determination of the composition of the solvent in close proximity to the peptide surface. For the AK-peptide case they observe at low methanol concentrations a significantly enhanced methanol concentration at the peptide/solvent-interface, supposedly promoted by the partially hydrophobic character of the AK-peptide's solvent accessible surface.« less

Improved optics for an ultracentrifuge

NASA Technical Reports Server (NTRS)

Miller, C. G.; Stephens, J. B.

1980-01-01

Ultracentrifuge is important tool in study of polymers, biomolecules, and cell structures. In typical ultracentrifuge rotor supports pair of optically matched vials; one contains sample mixed in solvent, and other is reference that contains only solvent. Doubleslit optical system, transverse to rotor, creates interference pattern on photographic plate each time vials pass through optics. Medium in sample vial displaces interference maximums such that shift gives measurement of density distribution along length of sample.

Biofoam

DOEpatents

Morrison, Robert L.

1995-01-01

Biofoam is a rigid, opaque microcellular organic foam made from organic materials derived from natural products and biological organisms. Typical organic materials are agar, agarose, gelatin, algin, alginates, gellan gum, and microcrystalline cellulose. The organic material is dissolved in a polar solvent, typically water, and the solution can be gelled immediately. The gel is frozen and freeze-dried to form the biofoam. Alternatively, a nonpolar solvent is added to the solution and emulsified. The resulting emulsion is then gelled, frozen, and freeze-dried. A variety of crystalline, fibrous, or metallic additives may be added to produce lightweight composite materials with enhanced strength and insulating properties. The amount of dilution of the organic material in the solvent(s) determines the density of the resulting biofoams, which ranges from about 1.0 mg/cm.sup.3 to about 500 mg/cm.sup.3.

Influence of polar solvents on photovoltaic performance of Monascusred dye-sensitized solar cell

NASA Astrophysics Data System (ADS)

Lee, Jae Wook; Kim, Tae Young; Ko, Hyun Seok; Han, Shin; Lee, Suk-Ho; Park, Kyung Hee

Dye-sensitized solar cells (DSSCs) were assembled using natural dyes extracted from Monascus red pigment as a sensitizer. In this work, we studied the adsorption characteristics for harvesting sunlight and the electrochemical behavior for electron transfer in Monascus red DSSC using different solvents. The effect of polar aprotic and protic solvents including water, ethanol, and dimethylsulfoxide (DMSO) used in the sensitization process was investigated for the improvement in conversion efficiency of a cell. As for the Monascus red dye-sensitized electrode in DMSO solvent, the solar cell yields a short-circuit current density (Jsc) of 1.23 mA/cm2, a photovoltage (Voc) of 0.75 V, and a fill factor of 0.72, corresponding to an energy conversion efficiency (η) of 0.66%.

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.

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.

Temperature effect on pyrene as a polarity probe for supercritical fluid and liquid solutions

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

Chen, H.H.; McGuffin, V.L.

1994-05-01

The effect of temperature on the fluorescence spectrum of pyrene in supercritical and liquid carbon dioxide and liquid organic solvents is systematically studied. The Py parameter (intensity ratio of vibronic bands 1 and 3) is found to increase with the density of supercritical carbon dioxide in the range from 0.54 to 0.75 g/cm{sup 3}. This observation is consistent with the fact that dispersion forces which represent the major interaction between pyrene and carbon dioxide, depend inversely on the sixth power of distance. However, the Py parameter of both supercritical and liquid carbon dioxide is also found to decrease with temperaturemore » at constant density, which is not consistent with expectations for dispersion forces. Carbon dioxide, which is generally regarded as a nonpopular solvent, shows a temperature effect comparable to that for polar liquid solvents. The origin of this temperature effect is examined in this study by computer simulation using both semispherical molecular orbital and molecular mechanic methods. On the basis of these simulations, a strong electrostatic attraction arises between pyrene and carbon dioxide which is similiar in magnitude to that with polar solvents. The temperature dependence of the Py parameter can be qualitatively explained by these simulation results. 45 refs., 15 fig., 5 tab.« less

A Sustainable Redox-Flow Battery with an Aluminum-Based, Deep-Eutectic-Solvent Anolyte.

PubMed

Zhang, Changkun; Ding, Yu; Zhang, Leyuan; Wang, Xuelan; Zhao, Yu; Zhang, Xiaohong; Yu, Guihua

2017-06-19

Nonaqueous redox-flow batteries are an emerging energy storage technology for grid storage systems, but the development of anolytes has lagged far behind that of catholytes due to the major limitations of the redox species, which exhibit relatively low solubility and inadequate redox potentials. Herein, an aluminum-based deep-eutectic-solvent is investigated as an anolyte for redox-flow batteries. The aluminum-based deep-eutectic solvent demonstrated a significantly enhanced concentration of circa 3.2 m in the anolyte and a relatively low redox potential of 2.2 V vs. Li + /Li. The electrochemical measurements highlight that a reversible volumetric capacity of 145 Ah L -1 and an energy density of 189 Wh L -1 or 165 Wh kg -1 have been achieved when coupled with a I 3 - /I - catholyte. The prototype cell has also been extended to the use of a Br 2 -based catholyte, exhibiting a higher cell voltage with a theoretical energy density of over 200 Wh L -1 . The synergy of highly abundant, dendrite-free, multi-electron-reaction aluminum anodes and environmentally benign deep-eutectic-solvent anolytes reveals great potential towards cost-effective, sustainable redox-flow batteries. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transferring pharmaceuticals into the gas phase

NASA Astrophysics Data System (ADS)

Christen, Wolfgang; Krause, Tim; Rademann, Klaus

2008-11-01

The dissolution of molecules of biological interest in supercritical carbon dioxide is investigated using pulsed molecular beam mass spectrometry. Due to the mild processing temperatures of most supercritical fluids, their adiabatic expansion into vacuum permits to transfer even thermally very sensitive substances into the gas phase, which is particularly attractive for pharmaceutical and biomedical applications. In addition, supercritical CO2constitutes a chemically inert solvent that is compatible with hydrocarbon-free ultrahigh vacuum conditions. Here, we report on the dissolution and pulsed supersonic jet expansion of caffeine (C8H10N4O2), the provitamin menadione (C11H8O2), and the amino acid derivative l-phenylalanine tert-butyl ester hydrochloride (C6H5CH2CH(NH2)COOC(CH3)3[dot operator]HCl), into vacuum. An on-axis residual gas analyzer is used to monitor the relative amounts of solute and solvent in the molecular beam as a function of solvent densityE The excellent selectivity and sensitivity provided by mass spectrometry permits to probe even trace amounts of solutes. The strong density variation of CO2 close to the critical point results in a pronounced pressure dependence of the relative ion currents of solute and solvent molecules, reflecting a substantial change in solubility.

Feasibility of Surfactant-Free Supported Emulsion Liquid Membrane Extraction

NASA Technical Reports Server (NTRS)

Hu, Shih-Yao B.; Li, Jin; Wiencek, John M.

2001-01-01

Supported emulsion liquid membrane (SELM) is an effective means to conduct liquid-liquid extraction. SELM extraction is particularly attractive for separation tasks in the microgravity environment where density difference between the solvent and the internal phase of the emulsion is inconsequential and a stable dispersion can be maintained without surfactant. In this research, dispersed two-phase flow in SELM extraction is modeled using the Lagrangian method. The results show that SELM extraction process in the microgravity environment can be simulated on earth by matching the density of the solvent and the stripping phase. Feasibility of surfactant-free SELM (SFSELM) extraction is assessed by studying the coalescence behavior of the internal phase in the absence of the surfactant. Although the contacting area between the solvent and the internal phase in SFSELM extraction is significantly less than the area provided by regular emulsion due to drop coalescence, it is comparable to the area provided by a typical hollow-fiber membrane. Thus, the stripping process is highly unlikely to become the rate-limiting step in SFSELM extraction. SFSELM remains an effective way to achieve simultaneous extraction and stripping and is able to eliminate the equilibrium limitation in the typical solvent extraction processes. The SFSELM design is similar to the supported liquid membrane design in some aspects.

The covalently bound diazo group as an infrared probe for hydrogen bonding environments.

PubMed

You, Min; Liu, Liyuan; Zhang, Wenkai

2017-07-26

Covalently bound diazo groups are frequently found in biomolecular substrates. The C[double bond, length as m-dash]N[double bond, length as m-dash]N asymmetric stretching vibration (ν as ) of the diazo group has a large extinction coefficient and appears in an uncongested spectral region. To evaluate the solvatochromism of the C[double bond, length as m-dash]N[double bond, length as m-dash]N ν as band for studying biomolecules, we recorded the infrared (IR) spectra of a diazo model compound, 2-diazo-3-oxo-butyric acid ethyl ester, in different solvents. The width of the C[double bond, length as m-dash]N[double bond, length as m-dash]N ν as band was linearly dependent on the Kamlet-Taft solvent parameter, which reflects the polarizability and hydrogen bond accepting ability of the solvent. Therefore, the width of the C[double bond, length as m-dash]N[double bond, length as m-dash]N ν as band could be used to probe these properties for a solvent. We found that the position of the C[double bond, length as m-dash]N[double bond, length as m-dash]N ν as band was linearly correlated with the density of hydrogen bond donor groups in the solvent. We studied the relaxation dynamics and spectral diffusion of the C[double bond, length as m-dash]N[double bond, length as m-dash]N ν as band of a natural amino acid, 6-diazo-5-oxo-l-norleucine, in water using nonlinear IR spectroscopy. The relaxation and spectral diffusion time constants of the C[double bond, length as m-dash]N[double bond, length as m-dash]N ν as band were similar to those of the N[double bond, length as m-dash]N[double bond, length as m-dash]N ν as band. We concluded that the position and width of the C[double bond, length as m-dash]N[double bond, length as m-dash]N ν as band of the diazo group could be used to probe the hydrogen bond donating and accepting ability of a solvent, respectively. These results suggest that the diazo group could be used as a site-specific IR probe for the local hydration environments.

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.

Development of high energy density electrical double layer capacitors

NASA Astrophysics Data System (ADS)

Devarajan, Thamarai selvi

Electrochemical Double Layer capacitors (EDLCs) have shown themselves as a viable energy storage alternative. EDLCs have high power density, faster charge/discharge, wide operating temperature and long cycle life compared to batteries since it stores charge by physical separation. Despites all their advantages, their low energy density stand as a bottleneck for capacitors. This research aims to increase the energy density of EDLC without compromising the power density. Energy is proportional to the square of cell voltage. Cell voltage is mainly dependent on electrolyte breakdown. Electrolytes also provide ions for charge separation and conduction. Therefore various electrolytes (Solutes and Solvents) which can give high concentration, solubility and decomposition potential were characterized in the first part of the research. In that study, a novel ionic liquid OPBF4 had higher capacitance and comparable voltage window compared to commercial TEABF4 in Acetonitrile. However, the increased polarity of the fixed ring O-atom and the ion-ion interaction in OPBF4 was responsible for lowering its conductivity. Oxygenated ionic compounds with alkyl groups had lower stability due to beta elimination between two electron withdrawing atoms. Volume based thermodynamics and quantum chemical calculations were used to calculate ion size, HOMO/LUMO energies, and free energy changes and establish relationship with capacitance, redox potential and melting points respectively. In addition free energy of fusion was used to predict the melting point. Ion size had correlation with capacitance due to compact double layer formation. Free energy changes did not explain the differences in melting point and predicted dielectric constant was inconsistent with the polarity. This is presumably due to using Van der Waals volume instead of crystal structure volume and insufficient incorporation of polarization term. The HOMO/LUMO energies gave direct relation between oxidation and reduction potential at 1mA/cm 2. A brief study on non-polar co-solvents for EDLC was studied. Among the solvents studied, fluorinated solvents had low melting point and viscosity due to incorporation of asymmetry. However, because of low dielectric constant, TEABF4 is insoluble and had to be mixed with other solvents. The mixed fluorinated solvents had slightly higher voltage window due to decreased donicity of lone pairs of electrons. The second approach to increasing energy density is to increase capacitance. Capacitance is mainly dependent on surface area and porosity of electrodes. Nanostructured materials which can offer multiple charge storage are currently of interest. Hence, novel NiSi nanotubes were studied as electrodes for supercapacitor applications. Silicon material has high capacity and these inert electrodes can enable higher capacitance by controlling the porosity and functional groups in specific electrolytes. The Silicon wafers were made porous by anodization using hydrofluoric acid. In order to improve the conductivity, the porous silicon was doped, then plated with Ni using electroless plating method and annealed to form nickel mono silicide. Gold was deposited on the back side of the electrode to enhance conductivity. Our porous NiSi electrodes gave capacitance of about 1185muF /cm2 in 0.5 M H 2SO4. Further investigation of oxide formation and modification of functional groups will help achieve higher capacitance.

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

Communication: Stiff and soft nano-environments and the "Octopus Effect" are the crux of ionic liquid structural and dynamical heterogeneity

NASA Astrophysics Data System (ADS)

Daly, Ryan P.; Araque, Juan C.; Margulis, Claudio J.

2017-08-01

In a recent set of articles [J. C. Araque et al., J. Phys. Chem. B 119(23), 7015-7029 (2015) and J. C. Araque et al., J. Chem. Phys. 144, 204504 (2016)], we proposed the idea that for small neutral and charged solutes dissolved in ionic liquids, deviation from simple hydrodynamic predictions in translational and rotational dynamics can be explained in terms of diffusion through nano-environments that are stiff (high electrostriction, charge density, and number density) and others that are soft (charge depleted). The current article takes a purely solvent-centric approach in trying to provide molecular detail and intuitive visual understanding of time-dependent local mobility focusing on the most common case of an ionic liquid with well defined polar and apolar nano-domains. We find that at intermediate time scales, apolar regions are fluid, whereas the charge network is much less mobile. Because apolar domains and cationic heads must diffuse as single species, at long time the difference in mobility also necessarily dissipates.

Theoretical calculation of reorganization energy for electron self-exchange reaction by constrained density functional theory and constrained equilibrium thermodynamics.

PubMed

Ren, Hai-Sheng; Ming, Mei-Jun; Ma, Jian-Yi; Li, Xiang-Yuan

2013-08-22

Within the framework of constrained density functional theory (CDFT), the diabatic or charge localized states of electron transfer (ET) have been constructed. Based on the diabatic states, inner reorganization energy λin has been directly calculated. For solvent reorganization energy λs, a novel and reasonable nonequilibrium solvation model is established by introducing a constrained equilibrium manipulation, and a new expression of λs has been formulated. It is found that λs is actually the cost of maintaining the residual polarization, which equilibrates with the extra electric field. On the basis of diabatic states constructed by CDFT, a numerical algorithm using the new formulations with the dielectric polarizable continuum model (D-PCM) has been implemented. As typical test cases, self-exchange ET reactions between tetracyanoethylene (TCNE) and tetrathiafulvalene (TTF) and their corresponding ionic radicals in acetonitrile are investigated. The calculated reorganization energies λ are 7293 cm(-1) for TCNE/TCNE(-) and 5939 cm(-1) for TTF/TTF(+) reactions, agreeing well with available experimental results of 7250 cm(-1) and 5810 cm(-1), respectively.

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.

Molecular accessibility in solvent swelled coal

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

Kispert, L.D.

1991-08-01

Research continued on the determination of pore size and number distribution changes after swelling the coal samples with various solvents. A paper has just been submitted to the journal Fuel on the Low temperature Swelling of Argonne Premium Coal samples using solvents of varying polarity. The variation in the shape of the pore was followed as a function of temperature and swelling solvent polarity. This change in pore structure was attributed to break-up of the hydrogen bonding network in coal by polar solvents. The modification in pore shape from spherical to cylindrical was attributed to anisotropy in hydrogen bond densities.more » A copy of this paper has been attached to this report. Wojciech Sady has determine the structural changes in the pores that occur when APCS coal is dehydrated prior to swelling with polar solvents. These changes are different from those that occur in the absence of prior dehydration. He has also completed a study on the variation in the hydrogen bonding character of the pore wall as the coals are swelled with various polar solvents. A statistical analysis of the data is currently underway to determine important trends in his data. 9 refs.« less

Fast automated dual-syringe based dispersive liquid-liquid microextraction coupled with gas chromatography-mass spectrometry for the determination of polycyclic aromatic hydrocarbons in environmental water samples.

PubMed

Guo, Liang; Tan, Shufang; Li, Xiao; Lee, Hian Kee

2016-03-18

An automated procedure, combining low density solvent based solvent demulsification dispersive liquid-liquid microextraction (DLLME) with gas chromatography-mass spectrometry analysis, was developed for the determination of polycyclic aromatic hydrocarbons (PAHs) in environmental water samples. Capitalizing on a two-rail commercial autosampler, fast solvent transfer using a large volume syringe dedicated to the DLLME process, and convenient extract collection using a small volume microsyringe for better GC performance were enabled. Extraction parameters including the type and volume of extraction solvent, the type and volume of dispersive solvent and demulsification solvent, extraction and demulsification time, and the speed of solvent injection were investigated and optimized. Under the optimized conditions, the linearity ranged from 0.1 to 50 μg/L, 0.2 to 50 μg/L, and 0.5 to 50 μg/L, depending on the analytes. Limits of detection were determined to be between 0.023 and 0.058 μg/L. The method was applied to determine PAHs in environmental water samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Effects of solvent evaporation conditions on solvent vapor annealed cylinder-forming block polymer thin films

NASA Astrophysics Data System (ADS)

Grant, Meagan; Jakubowski, William; Nelson, Gunnar; Drapes, Chloe; Baruth, A.

Solvent vapor annealing is a less time and energy intensive method compared to thermal annealing, to direct the self-assembly of block polymer thin films. Periodic nanostructures have applications in ultrafiltration, magnetic arrays, or other structures with nanometer dimensions, driving its continued interest. Our goal is to create thin films with hexagonally packed, perpendicular aligned cylinders of poly(lactide) in a poly(styrene) matrix that span the thickness of the film with low anneal times and low defect densities, all with high reproducibility, where the latter is paramount. Through the use of our computer-controlled, pneumatically-actuated, purpose-built solvent vapor annealing chamber, we have the ability to monitor and control vapor pressure, solvent concentration within the film, and solvent evaporation rate with unprecedented precision and reliability. Focusing on evaporation, we report on two previously unexplored areas, chamber pressure during solvent evaporation and the flow rate of purging gas aiding the evaporation. We will report our exhaustive results following atomic force microscopy analysis of films exposed to a wide range of pressures and flow rates. Reliably achieving well-ordered films, while occurring within a large section of this parameter space, was correlated with high-flow evaporation rates and low chamber pressures. These results have significant implications on other methods of solvent annealing, including ``jar'' techniques.

Simulating Ru L 3 -Edge X-ray Absorption Spectroscopy with Time-Dependent Density Functional Theory: Model Complexes and Electron Localization in Mixed-Valence Metal Dimers

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

Van Kuiken, Benjamin E.; Valiev, Marat; Daifuku, Stephanie L.

2013-05-30

Ruthenium L3-edge X-ray absorption (XA) spectroscopy probes unoccupied 4d orbitals of the metal atom and is increasingly being used to investigate the local electronic structure in ground and excited electronic states of Ru complexes. The simultaneous development of computational tools for simulating Ru L3-edge spectra is crucial for interpreting the spectral features at a molecular level. This study demonstrates that time-dependent density functional theory (TDDFT) is a viable and predictive tool for simulating ruthenium L3-edge XA spectroscopy. We systematically investigate the effects of exchange correlation functional and implicit and explicit solvent interactions on a series of RuII and RuIII complexesmore » in their ground and electronic excited states. The TDDFT simulations reproduce all of the experimentally observed features in Ru L3-edge XA spectra within the experimental resolution (0.4 eV). Our simulations identify ligand-specific charge transfer features in complicated Ru L3-edge spectra of [Ru(CN)6]4- and RuII polypyridyl complexes illustrating the advantage of using TDDFT in complex systems. We conclude that the B3LYP functional most accurately predicts the transition energies of charge transfer features in these systems. We use our TDDFT approach to simulate experimental Ru L3-edge XA spectra of transition metal mixed-valence dimers of the form [(NC)5MII-CN-RuIII(NH3)5] (where M = Fe or Ru) dissolved in water. Our study determines the spectral signatures of electron delocalization in Ru L3-edge XA spectra. We find that the inclusion of explicit solvent molecules is necessary for reproducing the spectral features and the experimentally determined valencies in these mixed-valence complexes. This study validates the use of TDDFT for simulating Ru 2p excitations using popular quantum chemistry codes and providing a powerful interpretive tool for equilibrium and ultrafast Ru L3-edge XA spectroscopy.« less

Simulating Ru L3-edge X-ray Absorption Spectroscopy with Time-Dependent Density Functional Theory: Model Complexes and Electron Localization in Mixed-Valence Metal Dimers

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

Van Kuiken, Benjamin E.; Valiev, Marat; Daifuku, Stephanie L.

2013-05-01

Ruthenium L2,3-edge X-ray absorption (XA) spectroscopy probes transitions from core 2p orbitals to the 4d levels of the atom and is a powerful tool for interrogating the local electronic and molecular structure around the metal atom. However, a molecular-level interpretation of the Ru L2,3-edge spectral lineshapes is often complicated by spin–orbit coupling (SOC) and multiplet effects. In this study, we develop spin-free time-dependent density functional theory (TDDFT) as a viable and predictive tool to simulate the Ru L3-edge spectra. We successfully simulate and analyze the ground state Ru L3-edge XA spectra of a series of RuII and RuIII complexes: [Ru(NH3)6]2+/3+,more » [Ru(CN)6]4-/3-, [RuCl6]4-/3-, and the ground (1A1) and photoexcited (3MLCT) transient states of [Ru(bpy)3]2+ and Ru(dcbpy)2(NCS)2 (termed N3). The TDDFT simulations reproduce all the experimentally observed features in Ru L3-edge XA spectra. The advantage of using TDDFT to assign complicated Ru L3-edge spectra is illustrated by its ability to identify ligand specific charge transfer features in complex molecules. We conclude that the B3LYP functional is the most reliable functional for accurately predicting the location of charge transfer features in these spectra. Experimental and simulated Ru L3-edge XA spectra are presented for the transition metal mixed-valence dimers [(NC)5MII-CN-RuIII(NH3)5]- (where M = Fe or Ru) dissolved in water. We explore the spectral signatures of electron delocalization in Ru L3-edge XA spectroscopy and our simulations reveal that the inclusion of explicit solvent molecules is crucial for reproducing the experimentally determined valencies, highlighting the importance of the role of the solvent in transition metal charge transfer chemistry.« less

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.

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.

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.

Investigations on the role of mixed-solvent for improved efficiency in perovskite solar cell

NASA Astrophysics Data System (ADS)

Singh, Ranbir; Suranagi, Sanjaykumar R.; Kumar, Manish; Shukla, Vivek Kumar

2017-12-01

The morphology of the spin-coated photoactive layer is one of the major factors affecting the performance of perovskite solar cells. In this work, we have employed a mixed-solvent strategy to obtain a high quality MAPbI3 (MA = CH3NH3) perovskite film, without pinholes and reduced grain boundaries. Perovskite films formed with single and mixed-solvents are systematically characterized for their optical, structural, and morphological properties using UV-vis absorption, photoluminescence (PL), X-ray diffraction (XRD), atomic force microscopy (AFM), and scanning electron microscopy (SEM) tools. The power conversion efficiency (PCE) of the devices fabricated using the mixed-solvent showed better performance than the devices made using the single solvent. The best-optimized mixed-solvent perovskite film exhibited a PCE of 15.2% with uniform film coverage on the substrate, better charge generation, and a high hole mobility of 1.16 × 10-4cm2/V s. The disparities in photovoltaic properties have been analyzed with the intensity dependent current density-voltage (J-V), transient photovoltage (TPV), and relationship between photocurrent (Jph) and effective voltage (Veff).

Modeling the absorption spectrum of the permanganate ion in vacuum and in aqueous solution

NASA Astrophysics Data System (ADS)

Olsen, Jógvan Magnus Haugaard; Hedegård, Erik Donovan

The absorption spectrum of the MnO$_{4}$$^{-}$ ion has been a test-bed for quantum-chemical methods over the last decades. Its correct description requires highly-correlated multiconfigurational methods, which are incompatible with the inclusion of finite-temperature and solvent effects due to their high computational demands. Therefore, implicit solvent models are usually employed. Here we show that implicit solvent models are not sufficiently accurate to model the solvent shift of MnO$_{4}$$^{-}$, and we analyze the origins of their failure. We obtain the correct solvent shift for MnO$_{4}$$^{-}$ in aqueous solution by employing the polarizable embedding (PE) model combined with a range-separated complete active space short-range density functional theory method (CAS-srDFT). Finite-temperature effects are taken into account by averaging over structures obtained from ab initio molecular dynamics simulations. The explicit treatment of finite-temperature and solvent effects facilitates the interpretation of the bands in the low-energy region of the MnO$_{4}$$^{-}$ absorption spectrum, whose assignment has been elusive.

Simulating Osmotic Equilibria: A New Tool for Calculating Activity Coefficients in Concentrated Aqueous Salt Solutions.

PubMed

Bley, Michael; Duvail, Magali; Guilbaud, Philippe; Dufrêche, Jean-François

2017-10-19

Herein, a new theoretical method is presented for predicting osmotic equilibria and activities, where a bulk liquid and its corresponding vapor phase are simulated by means of molecular dynamics using explicit polarization. Calculated time-averaged number density profiles provide the amount of evaporated molecules present in the vapor phase and consequently the vapor-phase density. The activity of the solvent and the corresponding osmotic coefficient are determined by the vapor density at different solute concentrations with respect to the reference vapor density of the pure solvent. With the extended Debye-Hückel equation for the activity coefficient along with the corresponding Gibbs-Duhem relation, the activity coefficients of the solutes are calculated by fitting the osmotic coefficients. A simple model based on the combination of Poisson processes and Maxwell-Boltzmann velocity distributions is introduced to interpret statistical phenomena observed during the simulations, which are related to evaporation and recondensation. This method is applied to aqueous dysprosium nitrate [Dy(NO 3 ) 3 ] solutions at different concentrations. The obtained densities of the liquid bulk and the osmotic and activity coefficients are in good agreement with the experimental results for concentrated and saturated solutions. Density profiles of the liquid-vapor interface at different concentrations provide detailed insight into the spatial distributions of all compounds.

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

Liu, Xingchen; Salahub, Dennis R.

There is no doubt that a huge gap exists in understanding heterogeneous catalysis between a cluster model of a few atoms and a bulk model of periodic slabs. Nanoparticles, which are crucial in heterogeneous catalysis in industry, lie in the middle of the gap. We present here our work on the computational modelling of molybdenum carbide nanoparticles (MCNPs) as the catalysts for the upgrading of oil sands in the in-situ environment, using benzene hydrogenation as a model reaction. With a cluster model, efforts were first made to understand the mechanism of the reaction with a density functional theory (DFT) studymore » on the adsorption of benzene and its hydrogenation product – cyclohexane, as well as the cyclic hydrogenation reaction intermediates on the Mo{sub 2}C(0001) surface. From the thermodynamic data, along with literature information, it was found that the benzene hydrogenation reaction on molybdenum carbide happens most likely through a Langmuir-Hinshelwood mechanism with the gradual lifting up of the benzene molecule. The electron localization function (ELF) was then used to help understand the nature of the interactions between the MCNPs, identifying strong multi-center interactions between the adsorbates and the MCNPs. To enable the treatment of larger nanoparticles, a fast semi-empirical density functional tight-binding (DFTB) method was parameterized. With this method, the potential energy profiles of benzene hydrogenation reactions on different sizes of MCNPs are calculated. The study was then extended to consider a MCNP embedded in solvent (benzene), using a quantum mechanical (DFTB) / molecular mechanical approach. Calculations on the free energies profiles with the umbrella sampling method show that the entropy of the MCNPs and the solvent are essential in understanding the catalytic activity of the transition metal related nanoparticles for solid/liquid heterogeneous catalysis.« less

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.

Biofoam

DOEpatents

Morrison, R.L.

1995-01-17

Biofoam is a rigid, opaque microcellular organic foam made from organic materials derived from natural products and biological organisms. Typical organic materials are agar, agarose, gelatin, algin, alginates, gellan gum, and microcrystalline cellulose. The organic material is dissolved in a polar solvent, typically water, and the solution can be gelled immediately. The gel is frozen and freeze-dried to form the biofoam. Alternatively, a nonpolar solvent is added to the solution and emulsified. The resulting emulsion is then gelled, frozen, and freeze-dried. A variety of crystalline, fibrous, or metallic additives may be added to produce lightweight composite materials with enhanced strength and insulating properties. The amount of dilution of the organic material in the solvent(s) determines the density of the resulting biofoams, which ranges from about 1.0 mg/cm[sup 3] to about 500 mg/cm[sup 3]. 4 figures.

Influence of polar solvents on photovoltaic performance of Monascusred dye-sensitized solar cell.

PubMed

Lee, Jae Wook; Kim, Tae Young; Ko, Hyun Seok; Han, Shin; Lee, Suk-Ho; Park, Kyung Hee

2014-05-21

Dye-sensitized solar cells (DSSCs) were assembled using natural dyes extracted from Monascus red pigment as a sensitizer. In this work, we studied the adsorption characteristics for harvesting sunlight and the electrochemical behavior for electron transfer in Monascus red DSSC using different solvents. The effect of polar aprotic and protic solvents including water, ethanol, and dimethylsulfoxide (DMSO) used in the sensitization process was investigated for the improvement in conversion efficiency of a cell. As for the Monascus red dye-sensitized electrode in DMSO solvent, the solar cell yields a short-circuit current density (Jsc) of 1.23mA/cm(2), a photovoltage (Voc) of 0.75V, and a fill factor of 0.72, corresponding to an energy conversion efficiency (η) of 0.66%. Copyright © 2014 Elsevier B.V. All rights reserved.

Environment-dependent conformation investigation of 3-amino-1,2,4-triazole (3-AT): Raman Spectroscopy and density functional theory

NASA Astrophysics Data System (ADS)

Meng, Shuang; Zhao, Yanying; Xue, Jiadan; Zheng, Xuming

2018-02-01

In the paper, diverse tautomers of 3-amino-1,2,4-triazole (3AT) in solid and polar solvent have been explored by FT-IR, FT-Raman and 488 nm Raman experiments combing with quantum chemical theoretical calculation using PCM solvent model and normal mode analysis. The vibrational spectra prefer the 3-amino-1,2,4-2H-triazole (2H-3AT) dimer in solid, while in a polar solvent 3AT is apt to the 3-amino-1,2,4-2H-triazole (2H-3AT) monomer. The significant wavenumber difference and Raman intensity patterns in solid and different solvents are induced by hydrogen bond perturbation along > NH ⋯ N ≤ hydrogen bonds on five-membered N-heterocyclic ring. The ground state proton transfer reaction mechanism along the five-membered N-heterocyclic ring is supported by intermolecular hydrogen bonding between 3AT and protonic solvent molecules.

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.

On the magnetic circular dichroism of benzene. A density-functional study

NASA Astrophysics Data System (ADS)

Kaminský, Jakub; Kříž, Jan; Bouř, Petr

2017-04-01

Spectroscopy of magnetic circular dichroism (MCD) provides enhanced information on molecular structure and a more reliable assignment of spectral bands than absorption alone. Theoretical modeling can significantly enhance the information obtained from experimental spectra. In the present study, the time dependent density functional theory is employed to model the lowest-energy benzene transitions, in particular to investigate the role of the Rydberg states and vibrational interference in spectral intensities. The effect of solvent is explored on model benzene-methane clusters. For the lowest-energy excitation, the vibrational sub-structure of absorption and MCD spectra is modeled within the harmonic approximation, providing a very good agreement with the experiment. The simulations demonstrate that the Rydberg states have a much stronger effect on the MCD intensities than on the absorption, and a very diffuse basis set must be used to obtain reliable results. The modeling also indicates that the Rydberg-like states and associated transitions may persist in solutions. Continuum-like solvent models are thus not suitable for their modeling; solvent-solute clusters appear to be more appropriate, providing they are large enough.

Physicochemical properties of betaine monohydrate-carboxylic acid mixtures

NASA Astrophysics Data System (ADS)

Zahrina, I.; Nasikin, M.; Mulia, K.

2018-05-01

Green solvents are widely used to minimize environmental problems associated with the use of volatile organic solvents in many industries. DES are new green solvents in recent. The physicochemical properties of DES can be varied by properly combining of salts with different hydrogen bond donors. The objective of this work is to investigate the effect of varying molar ratios on the physicochemical properties of betaine monohydrate-carboxylic acid (i.e,. propionic or acetic acid) mixtures. Properties of mixtures were measured at 40°C. The viscosity, polarity scale (ENR), density, pH, and water content tend to decrease with the decrease in a molar ratio of betaine monohydrate to acid. Conversely, the ionic conductivity was increased. The physicochemical properties of these mixtures depend on the hydrogen bonding interactions between betaine, water and acid molecules. Betaine monohydratecarboxylic acid mixtures have wide range of polarity, low viscosity, high ionic conductivity, and density higher than 1 g·cm-3 that make them fit for numerous various applications. Additionally, due to these mixtures have acidic pH, it should be properly selected of metal type to minimize corrosion problems in industrial application.

Removal of common organic solvents from aqueous waste streams via supercritical C02 extraction: a potential green approach to sustainable waste management in the pharmaceutical industry.

PubMed

Leazer, Johnnie L; Gant, Sean; Houck, Anthony; Leonard, William; Welch, Christopher J

2009-03-15

Supercritical CO2 extraction of aqueous streams is a convenient and effective method to remove commonly used solvents of varying polarities from aqueous waste streams. The resulting aqueous layers can potentially be sewered; whereas the organic layer can be recovered for potential reuse. Supercritical fluid extraction (SFE) is a technology that is increasingly being used in commercial processes (1). Supercritical fluids are well suited for extraction of a variety of media, including solids, natural products, and liquid products. Many supercritical fluids have low critical temperatures, allowing for extractions to be done at modestly low temperatures, thus avoiding any potential thermal decomposition of the solutes under study (2). Furthermore, the CO2 solvent strength is easily tuned by adjusting the density of the supercritical fluid (The density is proportional to the pressure of the extraction process). Since many supercritical fluids are gases at ambient temperature, the extract can be concentrated by simply venting the reaction mixture to a cyclone collection vessel, using appropriate safety protocols.

In Search of Functional Advantages of Knots in Proteins.

PubMed

Dabrowski-Tumanski, Pawel; Stasiak, Andrzej; Sulkowska, Joanna I

2016-01-01

We analysed the structure of deeply knotted proteins representing three unrelated families of knotted proteins. We looked at the correlation between positions of knotted cores in these proteins and such local structural characteristics as the number of intra-chain contacts, structural stability and solvent accessibility. We observed that the knotted cores and especially their borders showed strong enrichment in the number of contacts. These regions showed also increased thermal stability, whereas their solvent accessibility was decreased. Interestingly, the active sites within these knotted proteins preferentially located in the regions with increased number of contacts that also have increased thermal stability and decreased solvent accessibility. Our results suggest that knotting of polypeptide chains provides a favourable environment for the active sites observed in knotted proteins. Some knotted proteins have homologues without a knot. Interestingly, these unknotted homologues form local entanglements that retain structural characteristics of the knotted cores.

41 CFR 101-26.602-3 - Procurement of gasoline, fuel oil (diesel and burner), kerosene, and solvents.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 41 Public Contracts and Property Management 2 2014-07-01 2012-07-01 true Procurement of gasoline... § 101-26.602-3 Procurement of gasoline, fuel oil (diesel and burner), kerosene, and solvents. (a... capability to procure locally. Item Minimum annual requirement (gallons) Gasoline 10,000 Burner fuel oil 10...

41 CFR 101-26.602-3 - Procurement of gasoline, fuel oil (diesel and burner), kerosene, and solvents.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 41 Public Contracts and Property Management 2 2013-07-01 2012-07-01 true Procurement of gasoline... § 101-26.602-3 Procurement of gasoline, fuel oil (diesel and burner), kerosene, and solvents. (a... capability to procure locally. Item Minimum annual requirement (gallons) Gasoline 10,000 Burner fuel oil 10...

41 CFR 101-26.602-3 - Procurement of gasoline, fuel oil (diesel and burner), kerosene, and solvents.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 41 Public Contracts and Property Management 2 2011-07-01 2007-07-01 true Procurement of gasoline... § 101-26.602-3 Procurement of gasoline, fuel oil (diesel and burner), kerosene, and solvents. (a... capability to procure locally. Item Minimum annual requirement (gallons) Gasoline 10,000 Burner fuel oil 10...

41 CFR 101-26.602-3 - Procurement of gasoline, fuel oil (diesel and burner), kerosene, and solvents.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 41 Public Contracts and Property Management 2 2012-07-01 2012-07-01 false Procurement of gasoline... § 101-26.602-3 Procurement of gasoline, fuel oil (diesel and burner), kerosene, and solvents. (a... capability to procure locally. Item Minimum annual requirement (gallons) Gasoline 10,000 Burner fuel oil 10...

41 CFR 101-26.602-3 - Procurement of gasoline, fuel oil (diesel and burner), kerosene, and solvents.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 41 Public Contracts and Property Management 2 2010-07-01 2010-07-01 true Procurement of gasoline... § 101-26.602-3 Procurement of gasoline, fuel oil (diesel and burner), kerosene, and solvents. (a... capability to procure locally. Item Minimum annual requirement (gallons) Gasoline 10,000 Burner fuel oil 10...

Tolerance engineering in bacteria for the production of advanced biofuels and chemicals.

PubMed

Mukhopadhyay, Aindrila

2015-08-01

During microbial production of solvent-like compounds, such as advanced biofuels and bulk chemicals, accumulation of the final product can negatively impact the cultivation of the host microbe and limit the production levels. Consequently, improving solvent tolerance is becoming an essential aspect of engineering microbial production strains. Mechanisms ranging from chaperones to transcriptional factors have been used to obtain solvent-tolerant strains. However, alleviating growth inhibition does not invariably result in increased production. Transporters specifically have emerged as a powerful category of proteins that bestow tolerance and often improve production but are difficult targets for cellular expression. Here we review strain engineering, primarily as it pertains to bacterial solvent tolerance, and the benefits and challenges associated with the expression of membrane-localized transporters in improving solvent tolerance and production. Copyright © 2015 Elsevier Ltd. All rights reserved.

Direct Push Optical Screening Tool for High-Resolution, Real-Time Mapping of Chlorinated Solvent DNAPL Architecture

DTIC Science & Technology

2016-04-01

due to higher densities, lower viscosities , and increased weathering (mass depletion) of residual chlorinated solvent DNAPL compared to those other...demonstration area can be generally classified as stratified layers of fine sand and silt with few clay layers. A silt layer was penetrated consistently at...toxic and carcinogenic. Another potential issue evaluated was that in plastic soils (stiff clays for example) there is potential for the thickness of

Direct Push Optical Screening Tool for High Resolution, Real-Time Mapping of Chlorinated Solvent DNAPL Architecture

DTIC Science & Technology

2016-07-01

petroleum hydrocarbon fuels due to higher densities, lower viscosities , and increased weathering (mass depletion) of residual chlorinated solvent DNAPL...generally classified as stratified layers of fine sand and silt with few clay layers. A silt layer was penetrated consistently at a depth of about 45...e.g., stiff clays ) there is potential for the thickness of the dye interaction zone to increase to approximately 1-2 mm. Intuition suggests that this

SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules.

PubMed

Bardhan, Jaydeep; Park, Sanghyun; Makowski, Lee

2009-10-01

This paper describes a computational approach to estimating wide-angle X-ray solution scattering (WAXS) from proteins, which has been implemented in a computer program called SoftWAXS. The accuracy and efficiency of SoftWAXS are analyzed for analytically solvable model problems as well as for proteins. Key features of the approach include a numerical procedure for performing the required spherical averaging and explicit representation of the solute-solvent boundary and the surface of the hydration layer. These features allow the Fourier transform of the excluded volume and hydration layer to be computed directly and with high accuracy. This approach will allow future investigation of different treatments of the electron density in the hydration shell. Numerical results illustrate the differences between this approach to modeling the excluded volume and a widely used model that treats the excluded-volume function as a sum of Gaussians representing the individual atomic excluded volumes. Comparison of the results obtained here with those from explicit-solvent molecular dynamics clarifies shortcomings inherent to the representation of solvent as a time-averaged electron-density profile. In addition, an assessment is made of how the calculated scattering patterns depend on input parameters such as the solute-atom radii, the width of the hydration shell and the hydration-layer contrast. These results suggest that obtaining predictive calculations of high-resolution WAXS patterns may require sophisticated treatments of solvent.

Controlling morphology and chain aggregation in semiconducting conjugated polymers: the role of solvent on optical gain in MEH-PPV.

PubMed

Lampert, Zach E; Reynolds, C Lewis; Papanikolas, John M; Aboelfotoh, M Osama

2012-10-25

We report the results of a detailed investigation that addresses the influence of polymer morphology and chain aggregation, as controlled by the chemical nature of the solvent, on the optical gain properties of the conjugated polymer poly[2-methoxy-5-(2'-ethylhexyloxy)-p-phenylene vinylene] (MEH-PPV). Using the variable stripe length technique in the picosecond regime, we have extensively studied the optical gain performance of asymmetric planar waveguides formed with thin MEH-PPV films spin-cast from concentrated chlorobenzene (CB) and tetrahydrofuran (THF) solutions onto thermally oxidized silicon substrates. CB and THF solvents were chosen based on their known ability to promote and effectively limit aggregate formation, respectively. Very large net gain coefficients are demonstrated, reaching values of 330 and 365 cm(-1), respectively, when optically pumping the waveguides with a maximum energy density of 85 μJ/cm(2). Our results clearly demonstrate that polymer morphology, and hence, the chain conformation dependence of the degree of aggregation in the films as controlled by the solvent, has minimal impact on the net gain. Moreover, the waveguides exhibit low loss coefficients of 10-20 cm(-1) at the ASE wavelength. These results question the importance of polymer morphology and aggregate formation in polymer-based optical devices operating at high excitation densities in the stimulated emission regime as would be characteristic of lasers and optical amplifiers.

Rapid pretreatment and determination of bisphenol A in water samples based on vortex-assisted liquid-liquid microextraction followed by high-performance liquid chromatography with fluorescence detection.

PubMed

Yang, Xiao; Diao, Chun-Peng; Sun, Ai-Ling; Liu, Ren-Min

2014-10-01

A method for the rapid pretreatment and determination of bisphenol A in water samples based on vortex-assisted liquid-liquid microextraction followed by high-performance liquid chromatography with fluorescence detection was proposed in this paper. A simple apparatus consisting of a test tube and a cut-glass dropper was designed and applied to collect the floating extraction drop in liquid-liquid microextraction when low-density organic solvent was used as the extraction solvent. Solidification and melting steps that were tedious but necessary once the low-density organic solvent used as extraction solvent could be avoided by using this apparatus. Bisphenol A was selected as model pollutant and vortex-assisted liquid-liquid microextraction was employed to investigate the usefulness of the apparatus. High-performance liquid chromatography with fluorescence detection was selected as the analytical tool for the detection of bisphenol A. The linear dynamic range was from 0.10 to 100 μg/L for bisphenol A, with good squared regression coefficient (r(2) = 0.9990). The relative standard deviation (n = 7) was 4.7% and the limit of detection was 0.02 μg/L. The proposed method had been applied to the determination of bisphenol A in natural water samples and was shown to be economical, fast, and convenient. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Physico-chemical properties of binary mixtures of aliphatic and aromatic solvents at 313 K on acoustical data

NASA Astrophysics Data System (ADS)

Dahire, S. L.; Morey, Y. C.; Agrawal, P. S.

2015-12-01

Density (ρ), viscosity (η), and ultrasonic velocity ( U) of binary mixtures of aliphatic solvents like dimethylformamide (DMF) and dimethylsulfoxide (DMSO) with aromatic solvents viz. chlorobenzene (CB), bromobenzene (BB), and nitrobenzene (NB) have been determined at 313 K. These parameters were used to calculate the adiabatic compressibility (β), intermolecular free length ( L f), molar volume ( V m), and acoustic impedance ( Z). From the experimental data excess molar volume ( V m E ), excess intermolecular free length ( L f E )), excess adiabatic compressibility (βE), and excess acoustic impedance ( Z E) have been computed. The excess values were correlated using Redlich-Kister polynomial equation to obtain their coefficients and standard deviations (σ).

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.

Small angle x-ray scattering study on the conformation of polystyrene in toluene during adding anti-solvent CO2

NASA Astrophysics Data System (ADS)

Liu, Yi; Chen, Dong-Feng; Wang, Hong-Li; Chen, Na; Li, Dan; Han, Bu-Xing; Rong, Li-Xia; Zhao, Hui; Wang, Jun; Dong, Bao-Zhong

2002-10-01

The conformation of polystyrene in the anti-solvent process of supercritical fluids (compressed CO2 + polystyrene + toluene) has been studied by small angle x-ray scattering with synchrotron radiation as an x-ray source. Coil-to-globule transformation of the polystyrene chain was observed with the increase of the anti-solvent CO2 pressure; i.e. polystyrene coiled at a pressure lower than the cloud point pressure (Pc) and turned into a globule with a uniform density at pressures higher than Pc. Fractal behaviour was also found in the chain contraction and the mass fractal dimension increased with increasing CO2 pressure.

Electronic Excitations in Solution: The Interplay between State Specific Approaches and a Time-Dependent Density Functional Theory Description.

PubMed

Guido, Ciro A; Jacquemin, Denis; Adamo, Carlo; Mennucci, Benedetta

2015-12-08

We critically analyze the performances of continuum solvation models when coupled to time-dependent density functional theory (TD-DFT) to predict solvent effects on both absorption and emission energies of chromophores in solution. Different polarization schemes of the polarizable continuum model (PCM), such as linear response (LR) and three different state specific (SS) approaches, are considered and compared. We show the necessity of introducing a SS model in cases where large electron density rearrangements are involved in the excitations, such as charge-transfer transitions in both twisted and quadrupolar compounds, and underline the very delicate interplay between the selected polarization method and the chosen exchange-correlation functional. This interplay originates in the different descriptions of the transition and ground/excited state multipolar moments by the different functionals. As a result, the choice of both the DFT functional and the solvent polarization scheme has to be consistent with the nature of the studied electronic excitation.

Atomistic and molecular effects in electric double layers at high surface charges

DOE PAGES

Templeton, Jeremy Alan; Lee, Jonathan; Mani, Ali

2015-06-16

Here, the Poisson–Boltzmann theory for electrolytes near a charged surface is known to be invalid due to unaccounted physics associated with high ion concentration regimes. In order to investigate this regime, fluids density functional theory (f-DFT) and molecular dynamics (MD) simulations were used to determine electric surface potential as a function of surface charge. Based on these detailed computations, for electrolytes with nonpolar solvent, the surface potential is shown to depend quadratically on the surface charge in the high charge limit. We demonstrate that modified Poisson–Boltzmann theories can model this limit if they are augmented with atomic packing densities providedmore » by MD. However, when the solvent is a highly polar molecule water an intermediate regime is identified in which a constant capacitance is realized. Simulation results demonstrate the mechanism underlying this regime, and for the salt water system studied here, it persists throughout the range of physically realistic surface charge densities so the potential’s quadratic surface charge dependence is not obtained.« less

Ab initio calculation of the deprotonation constants of an atomistically defined nanometer-sized, aluminium hydroxide oligomer

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

Wander, Matthew C. F.; Shuford, Kevin L.; Rustad, James R.

Aluminium possesses significant and diverse chemistry. Numerous compounds have been defined, and the elucidation of their chemistry is of significant geochemical interest. In this paper, a brucite-like, eight-aluminium aqueous cluster is modelled with density functional theory to identify its primary site of deprotonation and the associated pK(a) constant using both explicit (a full first solvent shell) and implicit solvent. Two methods for calculating the pK(a) are compared. We found that a bond density approach is better than a direct energy calculation for ions with large charge and high symmetry. The terminal aluminium atoms have equatorial ligated waters that in solventmore » have one long O-H bond. This site is more reactive than any of the other protons on the particle. Insights into the experimental crystal structure and Bader's Atoms in Molecules density analysis are presented as routes to reduce the computational time required for the identification of protonation sites.« less

Method for foam encapsulating laser targets

DOEpatents

Hendricks, Charles D.

1977-01-01

Foam encapsulated laser fusion targets are made by positioning a fusion fuel-filled sphere within a mold cavity of suitable configuration and dimensions, and then filling the cavity with a material capable of producing a low density, microcellular foam, such as cellulose acetate dissolved in an acetone-based solvent. The mold assembly is dipped into an ice water bath to gel the material and thereafter soaked in the water bath to leach out undesired components, after which the gel is frozen, then freeze-dried wherein water and solvents sublime and the gel structure solidifies into a low-density microcellular foam, thereafter the resulting foam encapsulated target is removed from the mold cavity. The fuel-filled sphere is surrounded by foam having a thickness of about 10 to 100 .mu.m, a cell size of less than 2 .mu.m, and density of 0.065 to 0.6 .times. 10.sup.3 kg/m.sup.3. Various configured foam-encapsulated targets capable of being made by this encapsulation method are illustrated.

Gas-Expanded Liquids: Synergism of Experimental and Computational Determinations of Local Structure

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

Charles A. Eckert; Charles L. Liotta; Rigoberto Hernandez

2007-06-26

This project focuses on the characterization of a new class of solvent systems called gas-expanded liquids (GXLs), targeted for green-chemistry processing. The collaboration has adopted a synergistic approach combining elements of molecular dynamics (MD) simulation and spectroscopic experiments to explore the local solvent behavior that could not be studied by simulation or experiment alone. The major accomplishments from this project are: • Applied MD simulations to explore the non-uniform structure of CO2/methanol and CO2/acetone GXLs and studied their dynamic behavior with self-diffusion coefficients and correlation functions • Studied local solvent structure and solvation behavior with a combination of spectroscopy andmore » MD simulations • Measured transport properties of heterocyclic solutes in GXLs through Taylor-Aris diffusion techniques and compared these findings to those of MD simulations • Probed local polarity and specific solute-solvent interactions with Diels-Alder and SN2 reaction studies The broader scientific impact resulting from the research activities of this contract have been recognized by two recent awards: the Presidential Green Chemistry Award (Eckert & Liotta) and a fellowship in the American Association for the Advancement of Science (Hernandez). In addition to the technical aspects of this contract, the investigators have been engaged in a number of programs extending the broader impacts of this project. The project has directly supported the development of two postdoctoral researcher, four graduate students, and five undergraduate students. Several of the undergraduate students were co-funded by a Georgia Tech program, the Presidential Undergraduate Research Award. The other student, an African-American female graduated from Georgia Tech in December 2005, and was co-funded through an NSF Research and Education for Undergraduates (REU) award.« less

Production of al-si alloy feedstocks using the solvent hot mixing method

NASA Astrophysics Data System (ADS)

Ni, J. Q.; Han, K. Q.; Yu, M. H.

2018-05-01

Powder injection molding is a promising low-cost technique for net shape processing of metal and ceramic components. This study aimed to investigate a new method for preparing aluminium (Al) – silicon (Si) alloy feedstock using the solvent hot mixing process. For this purpose, micron-sized Al-Si (20 wt. %) alloy powder was mixed with a binder consisting of 55 wt. % carnauba wax, 45 wt. % high-density polyethylene, and 3 wt. % stearic acid in a hot xylene bath. The scanning electron microscopy technique, thermogravimetric analysis, density measurement and torque measurements were used to verify the homogeneity of the feedstock. Moreover, the feedstock was chosen to perform the molding, debinding cycle and sintering. An Al-Si (20 wt. %) alloy part was successfully produced using this new method.

Kinetics of (3-aminopropyl)triethoxylsilane (APTES) silanization of superparamagnetic iron oxide nanoparticles.

PubMed

Liu, Yue; Li, Yueming; Li, Xue-Mei; He, Tao

2013-12-10

Silanization of magnetic ironoxide nanoparticles with (3-aminopropyl)triethoxylsilane (APTES) is reported. The kinetics of silanization toward saturation was investigated using different solvents including water, water/ethanol (1/1), and toluene/methanol (1/1) at different reaction temperature with different APTES loading. The nanoparticles were characterized by Fourier transform infrared spectroscopy, vibrating sample magnetometry, transmission electron microscopy, and thermal gravimetric analysis (TGA). Grafting density data based on TGA were used for the kinetic modeling. It is shown that initial silanization takes place very fast but the progress toward saturation is very slow, and the mechanism may involve adsorption, chemical sorption, and chemical diffusion processes. The highest equilibrium grafting density of 301 mg/g was yielded when using toluene/methanol mixture as the solvent at a reaction temperature of 70 °C.

Method of producing optical quality glass having a selected refractive index

DOEpatents

Poco, John F.; Hrubesh, Lawrence W.

2000-01-01

Optical quality glass having a selected refractive index is produced by a two stage drying process. A gel is produced using sol-gel chemistry techniques and first dried by controlled evaporation until the gel volume reaches a pre-selected value. This pre-selected volume determines the density and refractive index of the finally dried gel. The gel is refilled with solvent in a saturated vapor environment, and then dried again by supercritical extraction of the solvent to form a glass. The glass has a refractive index less than the full density of glass, and the range of achievable refractive indices depends on the composition of the glass. Glasses having different refractive indices chosen from an uninterrupted range of values can be produced from a single precursor solution.

Molecular receptors in metal oxide sol-gel materials prepared via molecular imprinting

DOEpatents

Sasaki, Darryl Y.; Brinker, C. Jeffrey; Ashley, Carol S.; Daitch, Charles E.; Shea, Kenneth J.; Rush, Daniel J.

2000-01-01

A method is provided for molecularly imprinting the surface of a sol-gel material, by forming a solution comprised of a sol-gel material, a solvent, an imprinting molecule, and a functionalizing siloxane monomer of the form Si(OR).sub.3-n X.sub.n, wherein n is an integer between zero and three and X is a functional group capable of reacting with the imprinting molecule, evaporating the solvent, and removing the imprinting molecule to form the molecularly imprinted metal oxide sol-gel material. The use of metal oxide sol-gels allows the material porosity, pore size, density, surface area, hardness, electrostatic charge, polarity, optical density, and surface hydrophobicity to be tailored and be employed as sensors and in catalytic and separations operations.

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.

The importance of excluded solvent volume effects in computing hydration free energies.

PubMed

Yang, Pei-Kun; Lim, Carmay

2008-11-27

Continuum dielectric methods such as the Born equation have been widely used to compute the electrostatic component of the solvation free energy, DeltaG(solv)(elec), because they do not need to include solvent molecules explicitly and are thus far less costly compared to molecular simulations. All of these methods can be derived from Gauss Law of Maxwell's equations, which yields an analytical solution for the solvation free energy, DeltaG(Born), when the solute is spherical. However, in Maxwell's equations, the solvent is assumed to be a structureless continuum, whereas in reality, the near-solute solvent molecules are highly structured unlike far-solute bulk solvent. Since we have recently reformulated Gauss Law of Maxwell's equations to incorporate the near-solute solvent structure by considering excluded solvent volume effects, we have used it in this work to derive an analytical solution for the hydration free energy of an ion. In contrast to continuum solvent models, which assume that the normalized induced solvent electric dipole density P(n) is constant, P(n) mimics that observed from simulations. The analytical formula for the ionic hydration free energy shows that the Born radius, which has been used as an adjustable parameter to fit experimental hydration free energies, is no longer ill defined but is related to the radius and polarizability of the water molecule, the hydration number, and the first peak position of the solute-solvent radial distribution function. The resulting DeltaG(solv)(elec) values are shown to be close to the respective experimental numbers.

Hydrogen Bond Lifetimes and Energetics for Solute-Solvent Complexes Studied with 2D-IR Vibrational Echo Spectroscopy

PubMed Central

Zheng, Junrong; Fayer, Michael D.

2008-01-01

Weak π hydrogen bonded solute-solvent complexes are studied with ultrafast two dimensional infrared (2D-IR) vibrational echo chemical exchange spectroscopy, temperature dependent IR absorption spectroscopy, and density functional theory calculations. Eight solute-solvent complexes composed of a number of phenol derivatives and various benzene derivatives are investigated. The complexes are formed between the phenol derivative (solute) in a mixed solvent of the benzene derivative and CCl4. The time dependence of the 2D-IR vibrational echo spectra of the phenol hydroxyl stretch is used to directly determine the dissociation and formation rates of the hydrogen bonded complexes. The dissociation rates of the weak hydrogen bonds are found to be strongly correlated with their formation enthalpies. The correlation can be described with an equation similar to the Arrhenius equation. The results are discussed in terms of transition state theory. PMID:17373792

Solvent screening for a hard-to-dissolve molecular crystal.

PubMed

Maiti, A; Pagoria, P F; Gash, A E; Han, T Y; Orme, C A; Gee, R H; Fried, L E

2008-09-01

Materials with a high-degree of inter- and intra-molecular hydrogen bonding generally have limited solubility in conventional organic solvents. This presents a problem for the dissolution, manipulation and purification of these materials. Using a state-of-the-art density-functional-theory based quantum chemical solvation model we systematically evaluated solvents for a known hydrogen-bonded molecular crystal. This, coupled with direct solubility measurements, uncovered a class of ionic liquids involving fluoride anions that possess more than two orders of magnitude higher solvation power as compared with the best conventional solvents. The crystal structure of one such ionic liquid, determined by X-ray diffraction spectroscopy, indicates that F- ions are stabilized through H-bonded chains with water. The presence of coordinating water in such ionic liquids seems to facilitate the dissolution process by keeping the chemical activity of the F- ions in check.

EFFECT OF DEUTERIUM OXIDE ON LOCAL ANESTHETIC ACTIVITY OF PROCAINE

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

Susina, S.V.; Hiter, F.D.; Siegel, F.P.

1962-12-01

Since it appears that D/sub 2/O is toxic in animals only when the concentration in the body fluids reaches high levels (> 20%), and since D/sub 2/O resembles the common solvent protium oxide more closely than any other, possible pharmaceutical applications of this solvent were explored. In studies in mice, D/ sub 2/O was used as a solvent for procaine and the effect on the stability and local anesthetic activity was noted. The ED/sub 50/ was determined by the method using corneal sensitivity, and comparison was made with procaine solutions in H/ sub 2/O. In H/sub 2/O the ED/sub 50/more » was 1.8% while in D/sub 2/O it was 1.0%. The LD/sub 50/was determined by intraperitoneal injection in mice. There appeared to be no significant difference in the toxicity of procaine in either solvent. Stability studies indicate that procaine is more stable in D/sub 2/O than H/sub 2/O at apparent pH values of 8.0, 8.5, and 9.0. Hence, the increased local anesthetic activity of procaine in D/sub 2/O may be accounted for by the fact that procaine free base is more stable in D/sub 2/O solutions, or that at the same apparent pH a D/sub 2/O solution of procaine will contain more free base than in the corresponding aqueous solution. (H.H.D.)« less

Theory and simulation of explicit solvent effects on protein folding in vitro and in vivo

NASA Astrophysics Data System (ADS)

England, Jeremy L.

The aim of this work is to develop theoretical tools for understanding what happens to water that is confined in amphipathic cavities, and for testing the consequences of this understanding for protein folding in vitro and in vivo. We begin in the first chapter with a brief review of the theoretical and simulation literature on the hydrophobic effect and the aqueous solvation of charged species that also puts forward a simple theoretical framework within which various solvation phenomena reported in past studies may be unified. Subsequently, in the second chapter we also review past computational and theoretical work on the specific question of how chaperonin complexes assist the folding of their substrates. With the context set, we turn in Chapter 3 to the case of an open system with water trapped between hydrophobic plates that experiences a uniform electric field normal to and between the plates. Classic bulk theory of electrostriction in polarizable fluids tells us that the electric field should cause an increase in local water density as it rises, yet some simulations have suggested the opposite. We present a mean-field Potts model we have developed to explain this discrepancy, and show how such a simple, coarse-grained lattice description can capture the fundamental consequences of the fact that external electric fields can frustrate the hydrogen bond network in confined water. Chapter 4 continues to pursue the issue of solvent evacuation between hydrophobic plates, but focuses on the impact of chemical denaturants on hydrophobic effects using molecular dynamics simulations of hydrophobic dewetting. We find that while urea and guanidinium have similar qualitative effects at the bulk level, they seem to differ in the microscopic mechanism by which they denature proteins, although both inhibit the onset of dewetting. Lastly, Chapters 5 and 6 examine the potential importance of solvent-mediated forces to protein folding in vivo. Chapter 5 develops a Landau-Ginzburg-type model for solvent free energy and lays out a theoretical argument for a mechanism by which chaperonins may promote the folding of their substrates through a local enhancement of the hydrophobic effect. With this argument in hand, we show results in Chapter 6 from molecular dynamics simulations we performed of different mutants of the bacterial chaperonin GroEL, which demonstrate that the hydrophilicity of the chaperonin cavity correlates with the experimentally measured ability of the cavity to facilitate folding.

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.

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.

Temperature-dependent micellar structures in poly(styrene-b-isoprene) diblock copolymer solutions near the critical micelle temperature

NASA Astrophysics Data System (ADS)

Bang, Joona; Viswanathan, Karthik; Lodge, Timothy P.; Park, Moon Jeong; Char, Kookheon

2004-12-01

The temperature dependence of the micelle structures formed by poly(styrene-b-isoprene) (SI) diblock copolymers in the selective solvents diethyl phthalate (DEP) and tetradecane (C14), which are selective for the PS and PI blocks, respectively, have been investigated by small angle neutron scattering (SANS). Two nearly symmetric SI diblock copolymers, one with a perdeuterated PS block and the other with a perdeuterated PI block, were examined in both DEP and C14. The SANS scattering length density of the solvent was matched closely to either the core or the corona block. The resulting core and corona contrast data were fitted with a detailed model developed by Pedersen and co-workers. The fits provide quantitative information on micellar characteristics such as aggregation number, core size, overall size, solvent fraction in the core, and corona thickness. As temperature increases, the solvent selectivity decreases, leading to substantial solvent swelling of the core and a decrease in the aggregation number and core size. Both core and corona chains are able to relax their conformations near the critical micelle temperature due to a decrease in the interfacial tension, even though the corona chains are always under good solvent conditions.

Solvent Dependent Dynamics of Salicylidene Aniline in Binary Mixtures of Supercritical CO2 with 1-Propanol or Cyclohexane.

PubMed

Kieda, Ryan D; Dunkelberger, Adam D; Case, Amanda S; Crim, F Fleming

2017-02-02

The role of different solvent environments in determining the behavior of molecules in solution is a fundamental aspect of chemical reactivity. We present an approach for exploring the influence of solvent properties on condensed-phase dynamics using ultrafast transient absorption spectroscopy in supercritical CO 2 . Using supercritical CO 2 permits adjustment of the density, by varying the temperature and pressure, whereas varying the concentration or identity of a second solvent, the cosolvent, in a binary mixture allows for adjustments of the degree of interaction between the solute and the solvent. Salicylidene aniline, a prototypical excited-state intramolecular proton-transfer system, is the subject of this study. In this system, the decay rate of the transient absorption signal decreases as the fraction of the cosolvent (for both 1-propanol and cyclohexane) increases. The decay rate also decreases with an increase in the viscosity of the mixture, but the effect is much larger for the 1-propanol cosolvent than for cyclohexane. These observations illustrate that the decay rate of the photoexcited salicylidene aniline depends on more than just the solvent viscosity, suggesting that properties such as polarity also play a role in the dynamics.

Nonuniform continuum model for solvatochromism based on frozen-density embedding theory.

PubMed

Shedge, Sapana Vitthal; Wesolowski, Tomasz A

2014-10-20

Frozen-density embedding theory (FDET) provides the formal framework for multilevel numerical simulations, such that a selected subsystem is described at the quantum mechanical level, whereas its environment is described by means of the electron density (frozen density; ${\\rho _{\\rm{B}} (\\vec r)}$). The frozen density ${\\rho _{\\rm{B}} (\\vec r)}$ is usually obtained from some lower-level quantum mechanical methods applied to the environment, but FDET is not limited to such choices for ${\\rho _{\\rm{B}} (\\vec r)}$. The present work concerns the application of FDET, in which ${\\rho _{\\rm{B}} (\\vec r)}$ is the statistically averaged electron density of the solvent ${\\left\\langle {\\rho _{\\rm{B}} (\\vec r)} \\right\\rangle }$. The specific solute-solvent interactions are represented in a statistical manner in ${\\left\\langle {\\rho _{\\rm{B}} (\\vec r)} \\right\\rangle }$. A full self-consistent treatment of solvated chromophore, thus involves a single geometry of the chromophore in a given state and the corresponding ${\\left\\langle {\\rho _{\\rm{B}} (\\vec r)} \\right\\rangle }$. We show that the coupling between the two descriptors might be made in an approximate manner that is applicable for both absorption and emission. The proposed protocol leads to accurate (error in the range of 0.05 eV) descriptions of the solvatochromic shifts in both absorption and emission. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular Origins of Internal Friction Effects on Protein Folding Rates

PubMed Central

Sirur, Anshul

2014-01-01

Recent experiments on protein folding dynamics have revealed strong evidence for internal friction effects. That is, observed relaxation times are not simply proportional to the solvent viscosity as might be expected if the solvent were the only source of friction. However, a molecular interpretation of this remarkable phenomenon is currently lacking. Here, we use all-atom simulations of peptide and protein folding in explicit solvent, to probe the origin of the unusual viscosity dependence. We find that an important contribution to this effect, explaining the viscosity dependence of helix formation and the folding of a helix-containing protein, is the insensitivity of torsion angle isomerization to solvent friction. The influence of this landscape roughness can, in turn, be quantitatively explained by a rate theory including memory friction. This insensitivity of local barrier crossing to solvent friction is expected to contribute to the viscosity dependence of folding rates in larger proteins. PMID:24986114

Molecular origins of internal friction effects on protein-folding rates.

PubMed

de Sancho, David; Sirur, Anshul; Best, Robert B

2014-07-02

Recent experiments on protein-folding dynamics have revealed strong evidence for internal friction effects. That is, observed relaxation times are not simply proportional to the solvent viscosity as might be expected if the solvent were the only source of friction. However, a molecular interpretation of this remarkable phenomenon is currently lacking. Here, we use all-atom simulations of peptide and protein folding in explicit solvent, to probe the origin of the unusual viscosity dependence. We find that an important contribution to this effect, explaining the viscosity dependence of helix formation and the folding of a helix-containing protein, is the insensitivity of torsion angle isomerization to solvent friction. The influence of this landscape roughness can, in turn, be quantitatively explained by a rate theory including memory friction. This insensitivity of local barrier crossing to solvent friction is expected to contribute to the viscosity dependence of folding rates in larger proteins.

A generalized method for alignment of block copolymer films: solvent vapor annealing with soft shear.

PubMed

Qiang, Zhe; Zhang, Yuanzhong; Groff, Jesse A; Cavicchi, Kevin A; Vogt, Bryan D

2014-08-28

One of the key issues associated with the utilization of block copolymer (BCP) thin films in nanoscience and nanotechnology is control of their alignment and orientation over macroscopic dimensions. We have recently reported a method, solvent vapor annealing with soft shear (SVA-SS), for fabricating unidirectional alignment of cylindrical nanostructures. This method is a simple extension of the common SVA process by adhering a flat, crosslinked poly(dimethylsiloxane) (PDMS) pad to the BCP thin film. The impact of processing parameters, including annealing time, solvent removal rate and the physical properties of the PDMS pad, on the quality of alignment quantified by the Herman's orientational factor (S) is systematically examined for a model system of polystyrene-block-polyisoprene-block-polystyrene (SIS). As annealing time increases, the SIS morphology transitions from isotropic rods to highly aligned cylinders. Decreasing the rate of solvent removal, which impacts the shear rate imposed by the contraction of the PDMS, improves the orientation factor of the cylindrical domains; this suggests the nanostructure alignment is primarily induced by contraction of PDMS during solvent removal. Moreover, the physical properties of the PDMS controlled by the crosslink density impact the orientation factor by tuning its swelling extent during SVA-SS and elastic modulus. Decreasing the PDMS crosslink density increases S; this effect appears to be primarily driven by the changes in the solubility of the SVA-SS solvent in the PDMS. With this understanding of the critical processing parameters, SVA-SS has been successfully applied to align a wide variety of BCPs including polystyrene-block-polybutadiene-block-polystyrene (SBS), polystyrene-block-poly(N,N-dimethyl-n-octadecylammonium p-styrenesulfonate) (PS-b-PSS-DMODA), polystyrene-block-polydimethylsiloxane (PS-b-PDMS) and polystyrene-block-poly(2-vinlypyridine) (PS-b-P2VP). These results suggest that SVA-SS is a generalizable method for the alignment of BCP thin films.

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.

Method for making monolithic metal oxide aerogels

DOEpatents

Coronado, Paul R.

1999-01-01

Transparent, monolithic metal oxide aerogels of varying densities are produced using a method in which a metal alkoxide solution and a catalyst solution are prepared separately and reacted. The resulting hydrolyzed-condensed colloidal solution is gelled, and the wet gel is contained within a sealed, but gas permeable, containment vessel during supercritical extraction of the solvent. The containment vessel is enclosed within an aqueous atmosphere that is above the supercritical temperature and pressure of the solvent of the metal alkoxide solution.

Application of dispersive liquid-liquid microextraction coupled with vortex-assisted hydrophobic magnetic nanoparticles based solid-phase extraction for determination of aflatoxin M1 in milk samples by sensitive micelle enhanced spectrofluorimetry.

PubMed

Amoli-Diva, Mitra; Taherimaslak, Zohreh; Allahyari, Mehdi; Pourghazi, Kamyar; Manafi, Mohammad Hanif

2015-03-01

An efficient, simple and fast low-density solvent based dispersive liquid-liquid microextraction (LDS-DLLME) followed by vortex-assisted dispersive solid phase extraction (VA-D-SPE) has been developed as a new approach for extraction and preconcentration of aflatoxin M1 in milk samples prior to its micelle enhanced spectrofluorimetic determination. In this LDS-DLLME coupled VA-D-SPE method, milk samples were first treated with methanol/water (80:20, v/v) after removing the fat layer. This solvent was directly used as the dispersing solvent in DLLME along with using 1-heptanol (as a low-density solvent with respect to water) as the extracting solvent. In VA-D-SPE approach, hydrophobic oleic acid modified Fe3O4 nanoparticles were used to retrieve the analyte from the DLLME step. It is considerably that the target of VA-D-SPE was 1-heptanol rather than the aflatoxin M1 directly. The main parameters affecting the efficiency of LDS-DLLME and VA-D-SPE procedures and signal enhancement of aflatoxin M1 were investigated and optimized. Under the optimum conditions, the method was linear in the range from 0.02 to 200 µg L(-1) with the correlation coefficient (R(2)) of 0.9989 and detection limit of 13 ng L(-1). The intra-day precision was 2.9 and 4.3% and the inter-day precision was 2.1 and 3.3% for concentration of 2 and 50 µg L(-1) respectively. The developed method was applied for extraction and preconcentration of AFM1 in three commercially available milk samples and the results were compared with the official AOAC method. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Comparison of Molecular Dynamics with Classical Density Functional and Poisson–Boltzmann Theories of the Electric Double Layer in Nanochannels

PubMed Central

2012-01-01

Comparisons are made among Molecular Dynamics (MD), Classical Density Functional Theory (c-DFT), and Poisson–Boltzmann (PB) modeling of the electric double layer (EDL) for the nonprimitive three component model (3CM) in which the two ion species and solvent molecules are all of finite size. Unlike previous comparisons between c-DFT and Monte Carlo (MC), the present 3CM incorporates Lennard-Jones interactions rather than hard-sphere and hard-wall repulsions. c-DFT and MD results are compared over normalized surface charges ranging from 0.2 to 1.75 and bulk ion concentrations from 10 mM to 1 M. Agreement between the two, assessed by electric surface potential and ion density profiles, is found to be quite good. Wall potentials predicted by PB begin to depart significantly from c-DFT and MD for charge densities exceeding 0.3. Successive layers are observed to charge in a sequential manner such that the solvent becomes fully excluded from each layer before the onset of the next layer. Ultimately, this layer filling phenomenon results in fluid structures, Debye lengths, and electric surface potentials vastly different from the classical PB predictions. PMID:23316120

Precise colloids with tunable interactions for confocal microscopy

PubMed Central

Kodger, Thomas E.; Guerra, Rodrigo E.; Sprakel, Joris

2015-01-01

Model colloidal systems studied with confocal microscopy have led to numerous insights into the physics of condensed matter. Though confocal microscopy is an extremely powerful tool, it requires a careful choice and preparation of the colloid. Uncontrolled or unknown variations in the size, density, and composition of the individual particles and interactions between particles, often influenced by the synthetic route taken to form them, lead to difficulties in interpreting the behavior of the dispersion. Here we describe the straightforward synthesis of copolymer particles which can be refractive index- and density-matched simultaneously to a non-plasticizing mixture of high dielectric solvents. The interactions between particles are accurately tuned by surface grafting of polymer brushes using Atom Transfer Radical Polymerization (ATRP), from hard-sphere-like to long-ranged electrostatic repulsion or mixed charge attraction. We also modify the buoyant density of the particles by altering the copolymer ratio while maintaining their refractive index match to the suspending solution resulting in well controlled sedimentation. The tunability of the inter-particle interactions, the low volatility of the solvents, and the capacity to simultaneously match both the refractive index and density of the particles to the fluid opens up new possibilities for exploring the physics of colloidal systems. PMID:26420044

Tuning surface grafting density of CeO2 nanocrystals with near- and supercritical solvent characteristics.

PubMed

Giroire, B; Slostowski, C; Marre, S; Aymonier, C; Aida, T; Hojo, D; Aoki, N; Takami, S; Adschiri, T

2016-01-21

In this work, the solvent effect on the synthesis of CeO2 nanocrystals synthesized in near- and supercritical alcohols is discussed. The materials prepared displayed a unique morphology of small nanocrystals (<10 nm) aggregated into larger nanospheres (∼100-200 nm). In such syntheses, alcohol molecules directly interact with the nanocrystal surface through alkoxide and carboxylate bondings. The grafting density was quantified from the weight loss measured using thermogravimetric analysis. A direct correlation between the grafting density and the alcohol chain length can be established. It was demonstrated that the shorter the alcohol chain length (i.e. methanol), the higher the surface coverage is. This trend is independent of the synthesis mode (batch or continuous). Additionally, an influence of the grafting density on the resulting nanocrystal size was established. It is suggested that the surface coverage has a high influence on the early stages of the nucleation and growth. Indeed, when high surface coverages are reached, all surface active sites are blocked, limiting the growth step and therefore leading to smaller particles. This effect was noticed with the materials prepared in the continuous mode where shorter reaction time was performed.

Solvent dynamical control of ultrafast ground state electron transfer: implications for Class II-III mixed valency.

PubMed

Lear, Benjamin J; Glover, Starla D; Salsman, J Catherine; Londergan, Casey H; Kubiak, Clifford P

2007-10-24

We relate the solvent and temperature dependence of the rates of intramolecular electron transfer (ET) of mixed valence complexes of the type {[Ru3O(OAc)6(CO)(L)]2-BL}-1, where L = pyridyl ligand and BL = pyrazine. Complexes were reduced chemically or electrochemically to obtain the mixed valence anions in seven solvents: acetonitrile, methylene chloride, dimethylformamide, tetrahydrofuran, dimethylsulfoxide, chloroform, and hexamethylphosphoramide. Rate constants for intramolecular ET were estimated by simulating the observed degree of nu(CO) IR band shape coalescence in the mixed valence state. Correlations between rate constants for ET and solvent properties including static dielectric constant, optical dielectric constant, the quantity 1/epsilonop - 1/epsilonS, microscopic solvent polarity, viscosity, cardinal rotational moments of inertia, and solvent relaxation times were examined. In the temperature study, the complexes displayed a sharp increase in the ket as the freezing points of the solvents methylene chloride and acetonitrile were approached. The solvent phase transition causes a localized-to-delocalized transition in the mixed valence ions and an acceleration in the rate of ET. This is explained in terms of decoupling the slower solvent motions involved in the frequency factor nuN which increases the value of nuN. The observed solvent and temperature dependence of the ket for these complexes is used in order to formulate a new definition for Robin-Day class II-III mixed valence compounds. Specifically, it is proposed that class II-III compounds are those for which thermodynamic properties of the solvent exert no control over ket, but the dynamic properties of the solvent still influence ket.

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.

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.

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

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.

Lithium-Air and ionic Liquids

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

Kellar, Michael

2015-09-01

The final portion of this project was accomplished at Sandia National Labs, Livermore, with the overall goal being to optimize lithium-air cells with an ionic liquid electrolyte. Both of these are potential future routes for lithium-ion technology. Lithiumair presents the advantage of higher gravimetric energy density, and ionic liquids present the advantage of greater hydrophobicity and much lower volatility, along with a larger window of electrochemical stability. Ionic liquids however have several drawbacks for the battery industry. Currently they are not as cost effective as many organic solvents. Additionally, because of the added viscosity of ionic interactions compared to themore » typical dipole interactions of a solvent, the ionic conductivity is lower than for common organic solvents.« less

GenLocDip: A Generalized Program to Calculate and Visualize Local Electric Dipole Moments.

PubMed

Groß, Lynn; Herrmann, Carmen

2016-09-30

Local dipole moments (i.e., dipole moments of atomic or molecular subsystems) are essential for understanding various phenomena in nanoscience, such as solvent effects on the conductance of single molecules in break junctions or the interaction between the tip and the adsorbate in atomic force microscopy. We introduce GenLocDip, a program for calculating and visualizing local dipole moments of molecular subsystems. GenLocDip currently uses the Atoms-In-Molecules (AIM) partitioning scheme and is interfaced to various AIM programs. This enables postprocessing of a variety of electronic structure output formats including cube and wavefunction files, and, in general, output from any other code capable of writing the electron density on a three-dimensional grid. It uses a modified version of Bader's and Laidig's approach for achieving origin-independence of local dipoles by referring to internal reference points which can (but do not need to be) bond critical points (BCPs). Furthermore, the code allows the export of critical points and local dipole moments into a POVray readable input format. It is particularly designed for fragments of large systems, for which no BCPs have been calculated for computational efficiency reasons, because large interfragment distances prevent their identification, or because a local partitioning scheme different from AIM was used. The program requires only minimal user input and is written in the Fortran90 programming language. To demonstrate the capabilities of the program, examples are given for covalently and non-covalently bound systems, in particular molecular adsorbates. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Calculation of nuclear spin-spin coupling constants using frozen density embedding

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

Götz, Andreas W., E-mail: agoetz@sdsc.edu; Autschbach, Jochen; Visscher, Lucas, E-mail: visscher@chem.vu.nl

2014-03-14

We present a method for a subsystem-based calculation of indirect nuclear spin-spin coupling tensors within the framework of current-spin-density-functional theory. Our approach is based on the frozen-density embedding scheme within density-functional theory and extends a previously reported subsystem-based approach for the calculation of nuclear magnetic resonance shielding tensors to magnetic fields which couple not only to orbital but also spin degrees of freedom. This leads to a formulation in which the electron density, the induced paramagnetic current, and the induced spin-magnetization density are calculated separately for the individual subsystems. This is particularly useful for the inclusion of environmental effects inmore » the calculation of nuclear spin-spin coupling constants. Neglecting the induced paramagnetic current and spin-magnetization density in the environment due to the magnetic moments of the coupled nuclei leads to a very efficient method in which the computationally expensive response calculation has to be performed only for the subsystem of interest. We show that this approach leads to very good results for the calculation of solvent-induced shifts of nuclear spin-spin coupling constants in hydrogen-bonded systems. Also for systems with stronger interactions, frozen-density embedding performs remarkably well, given the approximate nature of currently available functionals for the non-additive kinetic energy. As an example we show results for methylmercury halides which exhibit an exceptionally large shift of the one-bond coupling constants between {sup 199}Hg and {sup 13}C upon coordination of dimethylsulfoxide solvent molecules.« less

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.

Dynamics and reactivity of trapped electrons on supported ice crystallites.

PubMed

Stähler, Julia; Gahl, Cornelius; Wolf, Martin

2012-01-17

The solvation dynamics and reactivity of localized excess electrons in aqueous environments have attracted great attention in many areas of physics, chemistry, and biology. This manifold attraction results from the importance of water as a solvent in nature as well as from the key role of low-energy electrons in many chemical reactions. One prominent example is the electron-induced dissociation of chlorofluorocarbons (CFCs). Low-energy electrons are also critical in the radiation chemistry that occurs in nuclear reactors. Excess electrons in an aqueous environment are localized and stabilized by the local rearrangement of the surrounding water dipoles. Such solvated or hydrated electrons are known to play an important role in systems such as biochemical reactions and atmospheric chemistry. Despite numerous studies over many years, little is known about the microscopic details of these electron-induced chemical processes, and interest in the fundamental processes involved in the reactivity of trapped electrons continues. In this Account, we present a surface science study of the dynamics and reactivity of such localized low-energy electrons at D(2)O crystallites that are supported by a Ru(001) single crystal metal surface. This approach enables us to investigate the generation and relaxation dynamics as well as dissociative electron attachment (DEA) reaction of excess electrons under well-defined conditions. They are generated by photoexcitation in the metal template and transferred to trapping sites at the vacuum interface of crystalline D(2)O islands. In these traps, the electrons are effectively decoupled from the electronic states of the metal template, leading to extraordinarily long excited state lifetimes on the order of minutes. Using these long-lived, low-energy electrons, we study the DEA to CFCl(3) that is coadsorbed at very low concentrations (∼10(12) cm(-2)). Using rate equations and direct measurement of the change of surface dipole moment, we estimated the electron surface density for DEA, yielding cross sections that are orders of magnitude higher than the electron density measured in the gas phase.

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.

Charge transfer optical absorption and fluorescence emission of 4-(9-acridyl)julolidine from long-range-corrected time dependent density functional theory in polarizable continuum approach.

PubMed

Kityk, A V

2014-07-15

A long-range-corrected time-dependent density functional theory (LC-TDDFT) in combination with polarizable continuum model (PCM) have been applied to study charge transfer (CT) optical absorption and fluorescence emission energies basing on parameterized LC-BLYP xc-potential. The molecule of 4-(9-acridyl)julolidine selected for this study represents typical CT donor-acceptor dye with strongly solvent dependent optical absorption and fluorescence emission spectra. The result of calculations are compared with experimental spectra reported in the literature to derive an optimal value of the model screening parameter ω. The first absorption band appears to be quite well predictable within DFT/TDDFT/PCM with the screening parameter ω to be solvent independent (ω ≈ 0.245 Bohr(-1)) whereas the fluorescence emission exhibits a strong dependence on the range separation with ω-value varying on a rising solvent polarity from about 0.225 to 0.151 Bohr(-1). Dipolar properties of the initial state participating in the electronic transition have crucial impact on the effective screening. Copyright © 2014 Elsevier B.V. All rights reserved.

Synthesis, characterization and calculated non-linear optical properties of two new chalcones

NASA Astrophysics Data System (ADS)

Singh, Ashok Kumar; Saxena, Gunjan; Prasad, Rajendra; Kumar, Abhinav

2012-06-01

Two new chalcones viz 3-(4-(benzyloxy)phenyl)-1-(2-hydroxyphenyl)prop-2-en-1-one (1) and 3-(4-chlorophenyl)-1-(2-hydroxyphenyl)prop-2-en-1-one (2) have been prepared and characterized by micro analyses, 1H NMR, IR, UV-Vis spectroscopy and single crystal X-ray. The first static hyperpolarizability (β) for both the compounds has been investigated by density functional theory (DFT). Also, the solvent-induced effects on the non-linear optical properties (NLO) were studied by using self-consistent reaction field (SCRF) method. As the solvent polarity increases, the β value increases monotonically. The electronic absorption bands of both 1 and 2 have been assigned by time dependent density functional theory (TD-DFT). Both the compounds displayed better non-linear optical (NLO) responses than the standard p-nitroaniline (pNA).

Improving Protocols for Protein Mapping through Proper Comparison to Crystallography Data

PubMed Central

Lexa, Katrina W.; Carlson, Heather A.

2013-01-01

Computational approaches to fragment-based drug design (FBDD) can complement experiments and facilitate the identification of potential hot spots along the protein surface. However, the evaluation of computational methods for mapping binding sites frequently focuses upon the ability to reproduce crystallographic coordinates to within a low RMSD threshold. This dependency on the deposited coordinate data overlooks the original electron density from the experiment, thus techniques may be developed based upon subjective - or even erroneous - atomic coordinates. This can become a significant drawback in applications to systems where the location of hot spots is unknown. Based on comparison to crystallographic density, we previously showed that mixed-solvent molecular dynamics (MixMD) accurately identifies the active site for HEWL, with acetonitrile as an organic solvent. Here, we concentrated on the influence of protic solvent on simulation and refined the optimal MixMD approach for extrapolation of the method to systems without established sites. Our results establish an accurate approach for comparing simulations to experiment. We have outlined the most efficient strategy for MixMD, based on simulation length and number of runs. The development outlined here makes MixMD a robust method which should prove useful across a broad range of target structures. Lastly, our results with MixMD match experimental data so well that consistency between simulations and density may be a useful way to aid the identification of probes vs waters during the refinement of future MSCS crystallographic structures. PMID:23327200

Superinsulating Polyisocyanate Based Aerogels: A Targeted Search for the Optimum Solvent System.

PubMed

Zhu, Zhiyuan; Snellings, Geert M B F; Koebel, Matthias M; Malfait, Wim J

2017-05-31

Polyisocyanate based aerogels combine ultralow thermal conductivities with better mechanical properties than silica aerogel, but these properties critically depend on the nature of the gelation solvent, perhaps more so than on any other parameter. Here, we present a systematic study of the relationship between the polyurethane-polyisocyanurate (PUR-PIR) aerogel microstructure, surface area, thermal conductivity, and density and the gelation solvent's Hansen solubility parameters for an industrially relevant PUR-PIR rigid foam formulation. We first investigated aerogels prepared in acetone-dimethyl sulfoxide (DMSO) blends and observed a minimum in thermal conductivity (λ) and maximum in specific surface area for an acetone:DMSO ratio of 85:15 v/v. We then prepared PUR-PIR aerogels in 32 different solvent blends, divided into three series with δ Dispersion , δ Polarity , and δ H-bonding fixed at 15.94, 11.30, and 7.48 MPa 1/2 , respectively, corresponding to the optimum parameters for the acetone:DMSO series. The aerogel properties display distinct dependencies on the various solubility parameters: aerogels with low thermal conductivity can be synthesized in solvents with a high δ H-bonding parameter (above 7.2) and δ Dispersion around 16.3 MPa 1/2 . In contrast, the δ Polarity parameter is of lesser importance. Our study highlights the importance of the gelation solvent, clarifies the influence of the different solvent properties, and provides a methodology for a targeted search across the solvent chemical space based on the Hansen solubility parameters.

Solvatochromism and preferential solvation of 1,4-dihydroxy-2,3-dimethyl-9,10-anthraquinone by UV-vis absorption and laser-induced fluorescence measurements

NASA Astrophysics Data System (ADS)

Sasirekha, V.; Vanelle, P.; Terme, T.; Ramakrishnan, V.

2008-12-01

Solvation characteristics of 1,4-dihydroxy-2,3-dimethyl-9,10-anthraquinone ( 1) in pure and binary solvent mixtures have been studied by UV-vis absorption spectroscopy and laser-induced fluorescence techniques. The binary solvent mixtures used as CCl 4 (tetrachloromethane)-DMF ( N, N-dimethylformamide), AN (acetonitrile)-DMSO (dimethylsulfoxide), CHCl 3 (chloroform)-DMSO, CHCl 3-MeOH (methanol), and MeOH-DMSO. The longest wavelength band of 1 has been studied in pure solvents as well as in binary solvent mixtures as a function of the bulk mole fraction. The Vis absorption band maxima show an unusual blue shift with increasing solvent polarity. The emission maxima of 1 show changes with varying the pure solvents and the composition in the case of binary solvent mixtures. Non-ideal solvation characteristics are observed in all binary solvent mixtures. It has been observed that the quantity [ ν-(Xν+Xν)] serves as a measure of the extent of preferential solvation, where ν˜ and X are the position of band maximum in wavenumbers (cm -1) and the bulk mole fraction values, respectively. The preferential solvation parameters local mole fraction ( X2L), solvation index ( δs2), and exchange constant ( k12) are evaluated.

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.

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.

The study on the extraction and recovery of Au from scrap of the used computer using chloride solvent

NASA Astrophysics Data System (ADS)

Oh, Su-ji; Choi, Eunju; Choi, Nagchoul; Park, Cheonyoung

2013-04-01

Recently, due to the realization of environmental problems of cyanide, it is a worldwide quest to find viable alternatives. One of the alternatives is a chloride solvent(chlorine-hypochlorite acid) with an appropriate oxidizing agent. The rate of dissolution of Au by chloride solvent is much faster than that by cyanide. Also, due to presence of chloride ions, there is no passivation of gold surfaces during chlorination. The objective of this work was to investigate the effect of Au extraction efficiency under various experimental conditions(pulp density, chlorine-hypochlorite ratio and concentration of NaCl) from scrap of the used computer by chloride solvent. In addition, the recovery experiment was conducted to examine of the precipitation efficiency of Au under various metabisulfite concentration from extracted solution. In an EDS analysis, valuable metals such as Cu, Sn, Sb, Al, Ni, Pb and Au were observed in scrap of the used computer. The result of extraction experiment showed that the highest extraction rate was obtained under 1% of pulp density with a chlorine-hypochlorite ratio of 2:1, and a concentration of NaCl at 2M. The highest Au recovery(precipitation) rate was observed the addition of sodium metabisulfite at 2M concentration. Under these conditions, chlorine-hypochlorite could effectively Au extraction from scrap of the used computer sections and the additive reagent using sodium metabisulfite could easily precipitate the Au from the chlorine-hypochlorite solution.

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.

Probing the solvation structure and dynamics in ionic liquids by time-resolved infrared spectroscopy of 4-(dimethylamino)benzonitrile.

PubMed

Ando, Rômulo A; Brown-Xu, Samantha E; Nguyen, Lisa N Q; Gustafson, Terry L

2017-09-20

In this work we demonstrate the use of the push-pull model system 4-(dimethylamino)benzonitrile (DMABN) as a convenient molecular probe to investigate the local solvation structure and dynamics by means of time-resolved infrared spectroscopy (TRIR). The photochemical features associated with this system provide several advantages due to the high charge separation between the ground and charge transfer states involving the characteristic nitrile bond, and an excited state lifetime that is long enough to observe the slow solvation dynamics in organic solvents and ionic liquids. The conversion from a locally excited state to an intramolecular charge transfer state (LE-ICT) in ionic liquids shows similar kinetic lifetimes in comparison to organic solvents. This similarity confirms that such conversion depends solely on the intramolecular reorganization of DMABN in the excited state, and not by the dynamics of solvation. In contrast, the relative shift of the ν(CN) vibration during the relaxation of the ICT state reveals two distinct lifetimes that are sensitive to the solvent environment. This study reveals a fast time component which is attributed to the dipolar relaxation of the solvent and a slower time component related to the rotation of the dimethylamino group of DMABN.

Photophysics and photochemistry of dyes bound to human serum albumin are determined by the dye localization.

PubMed

Alarcón, Emilio; Edwards, Ana Maria; Aspee, Alexis; Moran, Faustino E; Borsarelli, Claudio D; Lissi, Eduardo A; Gonzalez-Nilo, Danilo; Poblete, Horacio; Scaiano, J C

2010-01-01

The photophysics and photochemistry of rose bengal (RB) and methylene blue (MB) bound to human serum albumin (HSA) have been investigated under a variety of experimental conditions. Distribution of the dyes between the external solvent and the protein has been estimated by physical separation and fluorescence measurements. The main localization of protein-bound dye molecules was estimated by the intrinsic fluorescence quenching, displacement of fluorescent probes bound to specific protein sites, and by docking modelling. All the data indicate that, at low occupation numbers, RB binds strongly to the HSA site I, while MB localizes predominantly in the protein binding site II. This different localization explains the observed differences in the dyes' photochemical behaviour. In particular, the environment provided by site I is less polar and considerably less accessible to oxygen. The localization of RB in site I also leads to an efficient quenching of the intrinsic protein fluorescence (ascribed to the nearby Trp residue) and the generation of intra-protein singlet oxygen, whose behaviour is different to that observed in the external solvent or when it is generated by bound MB.

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.

Ultrasonic speed, densities and viscosities of xylitol in water and in aqueous tyrosine and phenylalanine solutions at different temperatures

NASA Astrophysics Data System (ADS)

Ali, A.; Bidhuri, P.; Uzair, S.

2014-07-01

Ultrasonic speed u, densities ρ and viscosities η of xylitol in water and in 0.001 m aqueous l-tyrosine (Tyr) and l-phenylalanine (Phe) have been measured at different temperatures. From the density and ultrasonic speed measurements apparent molar isentropic compression κ_{φ}, apparent molar isentropic compressions at infinite dilution κ_{{S,φ}}0 , experimental slope S K , hydration number n H , transfer partial molar isentropic compressibility Δ_{tr} κ_{{S,φ}}0 of xylitol from water to aqueous Tyr and Phe have been obtained. From the viscosity data, B-coefficient and B-coefficient of transfer Δ tr B of xylitol from water to aqueous Phe and Tyr at different temperatures have also been estimated. Gibbs free energies of activation of viscous flow per mole of solvent Δ μ 1 0# and per mole of solute Δ μ 2 0# have been calculated by using Feakins transition state theory for the studied systems. The calculated parameters have been interpreted in terms of solute-solute and solute-solvent interactions and hydration behavior of xylitol.

Retention mechanism of hypercrosslinked polystyrene silica hybrid phase in normal phase chromatography.

PubMed

Wu, Di; Nedev, Georgi K; Lucy, Charles A

2014-11-28

Hypercrosslinked polystyrene phases have been described as quasi-normal phase because they lack discrete polar sites. Retention on the HC-Tol column is investigated using the Snyder-Soczewinski model. Solvent strength of different hexane-solvent binary mobile phase compositions can be predicted with solvent strength of pure dichloromethane (DCM, 0.159), tetrahydrofuran (THF, 0.22), and benzene (0.127). The HC-Tol column is shown to be a localizing adsorptive phase. Also, site-competition delocalization on HC-Tol demonstrates that whatever its adsorption groups are, they are able to participate in lateral interactions. Copyright © 2014 Elsevier B.V. All rights reserved.

Effect of solute nature on the polyamorphic transition in glassy polyol aqueous solutions.

PubMed

Suzuki, Yoshiharu

2017-08-14

I examined the polyamorphic behavior of glassy dilute aqueous solutions of polyols (ethylene glycol, glycerol, meso-erythritol, xylitol, and D-sorbitol) under pressure at low temperatures. Although the volume change of the glassy aqueous solution varied continuously against pressure, the rate of the volume change appeared to vary discontinuously at the onset pressure of the gradual polyamorphic transition. It is thought that low-density liquid-like solvent water and high-density liquid-like solvent water coexist during the transition. Moreover, the existence of a solute induces the shift of polyamorphic transition to the lower-pressure side. The effect of a solute on the polyamorphic transition becomes larger in the order ethylene glycol, glycerol, meso-erythritol, xylitol, and D-sorbitol. Therefore, the solute can become a variable controlling the polyamorphic state of liquid water. This experimental result suggests that the metastable-equilibrium phase boundary between the low-density and the high-density amorphs for pure water is likely to be located at 0.22-0.23 GPa at about 150 K, which is slightly larger than the previously estimated pressure. Moreover, the solute-nature dependence on the polyamorphic transition seems to connect to that on the homogeneous nucleation temperature of polyol aqueous solution at ambient pressure. The region in which a low-density liquid appears coincides with the region in which the nucleus of ice Ih appears, suggesting that the formation of a low-density liquid is a precursory phenomenon of the nucleation of ice Ih.

Ground-State Charge-Density Distribution in a Crystal of the Luminescent ortho-Phenylenediboronic Acid Complex with 8-Hydroxyquinoline.

PubMed

Jarzembska, Katarzyna N; Kamiński, Radosław; Durka, Krzysztof; Woźniak, Krzysztof

2018-05-10

This contribution is devoted to the first electron density studies of a luminescent oxyquinolinato boron complex in the solid state. ortho-Phenylenediboronic acid mixed with 8-hydroxyquinoline in dioxane forms high-quality single crystals via slow solvent evaporation, which allows successful high resolution data collection (sin θ/λ = 1.2 Å -1 ) and charge density distribution modeling. Particular attention has been paid to the boron-oxygen fragment connecting the two parts of the complex, and to the solvent species exhibiting anharmonic thermal motion. The experiment and theory compared rather well in terms of atomic charges and volumes, except for the boron centers. Boron atoms, as expected, constitute the most electron-deficient species in the complex molecule, whereas the neighboring oxygen and carbon atoms are the most significantly negatively charged ones. This part of the molecule appears to be very much involved in the charge transfer occurring between the acid fragment and oxyquinoline moiety leading to the observed fluorescence, as supported by the time-dependent density functional theory (TDDFT) results and the generated transition density maps. TDDFT calculations indicated that p-type atomic orbitals contributing to the HOMO-1, HOMO, and LUMO play the major role in the lowest energy transitions, and enabled further comparison with the charge density features, which is discussed in details. Furthermore, the results confirmed the known fact the Q ligand character is most important for the spectroscopic properties of this class of complexes.

Effect of solute nature on the polyamorphic transition in glassy polyol aqueous solutions

NASA Astrophysics Data System (ADS)

Suzuki, Yoshiharu

2017-08-01

I examined the polyamorphic behavior of glassy dilute aqueous solutions of polyols (ethylene glycol, glycerol, meso-erythritol, xylitol, and D-sorbitol) under pressure at low temperatures. Although the volume change of the glassy aqueous solution varied continuously against pressure, the rate of the volume change appeared to vary discontinuously at the onset pressure of the gradual polyamorphic transition. It is thought that low-density liquid-like solvent water and high-density liquid-like solvent water coexist during the transition. Moreover, the existence of a solute induces the shift of polyamorphic transition to the lower-pressure side. The effect of a solute on the polyamorphic transition becomes larger in the order ethylene glycol, glycerol, meso-erythritol, xylitol, and D-sorbitol. Therefore, the solute can become a variable controlling the polyamorphic state of liquid water. This experimental result suggests that the metastable-equilibrium phase boundary between the low-density and the high-density amorphs for pure water is likely to be located at 0.22-0.23 GPa at about 150 K, which is slightly larger than the previously estimated pressure. Moreover, the solute-nature dependence on the polyamorphic transition seems to connect to that on the homogeneous nucleation temperature of polyol aqueous solution at ambient pressure. The region in which a low-density liquid appears coincides with the region in which the nucleus of ice Ih appears, suggesting that the formation of a low-density liquid is a precursory phenomenon of the nucleation of ice Ih.

X-ray Reflectivity Study of Ionic Liquids at Electrified Surfaces

NASA Astrophysics Data System (ADS)

Chu, Miaoqi

X-ray reflectivity (XRR) versatile technique that characterize the surface structures. However, due to the lack of phase information of X-ray data, the reconstruction of electron density profile (EDP) from XRR data is an ill-posed inverse problem that requires extra attention. In Chapter 1, several key concepts in XRR data analysis are reviewed. The typical XRR data acquisition procedure and methods of modeling electron density are introduced. The widely used logarithm form of merit function is justified with mathematical deduction and numerical experiment. A scheme that generates artificial reflectivity data with theoretical statistical error but not systematical error is proposed. With the methods and schemes described in Chapter 1, simulated reflectivity data of a simple one-slab model is generated and fitted to test the efficient of EDP reconstruction. By isolating the parameters, the effects of slab width, electron density contrast and maximal wave transfer are studied individually. It?s demonstrated that best-fit/global minima, result reported by most XRR studies, don?t necessary reflect the real EDP. By contrast, mapping the merit function in the parametric space can capture much more details. Additionally, the widely accepted concept about the XRR theoretical spatial resolution (pi/q_{max}) as well the using Patterson function are brought to test. In the perspective of XRR data analysis, this chapter puts forward general rules to design and optimize XRR experiments. It also demonstrates how susceptible the fitting result will be if it?s not done carefully. In Chapter 3, the interface between hydrophobic OTS film and several solvents is studied with XRR in a transmission-cell setup. The solvents, from water, acetone, to alcohol (methanol, ethanol, 1-propanol), to alkane (pentane, hexane and heptane), vary significantly in terms of polarity and hydrogen bonding. However, the XRR data from different solvents are subtle. The methods and principles elicited in previous chapters are employed to extract information about the solid-liquid interface. Electron density depletion due to methyl terminal of solvent molecules (methyl gap) and due to the reduced surface density compared to the bulk density (density gap) are analyzed. In the next Chapter, XRR technique is employed to study the structures and dynamics of room temperature ionic liquids (RTILs) at an electrified surface. RTILs are molten salts at room temperature, consisted purely by anions and cations, with potential applications in energy storage, electro-synthesis, electrodeposition etc. The solvent-free and high charge concentrated novel liquids process many unique properties that not seen in normal dilute salt solution. It is predicted that when a surface isn't highly charged, RTILs form alternating layers of anion/cation to screen the surface charge; when it's highly charged, a crowding layer with ions with like charge forms. The alternating structure has been observed experimentally but not the crowding layer. Following the rules of optimization XRR experiment in Chapter 2, conductive silicon which has small electron density is used which maximize the EDP contrast. This makes it possible to directly observe the formation of crowding layer. The thickness of this crowding layer, charge distributions and compositions as a function of applied voltage. The dynamics of anion/cation reorganization in RTILs determine the power density for RTILs? energy application. In Chapter 5, the time-dependence of the formation and dissipation of the crowding layer is studied with XRR. An ultra-slow dynamic, much longer than the typical RC time constant, is revealed. Comparisons with theoretical predications and experiments studies are made in order to understand the origin of this process. The thesis is summarized in Chapter 6, along with several proposals for future work.

Minimizing graphene defects enhances titania nanocomposite-based photocatalytic reduction of CO2 for improved solar fuel production.

PubMed

Liang, Yu Teng; Vijayan, Baiju K; Gray, Kimberly A; Hersam, Mark C

2011-07-13

With its unique electronic and optical properties, graphene is proposed to functionalize and tailor titania photocatalysts for improved reactivity. The two major solution-based pathways for producing graphene, oxidation-reduction and solvent exfoliation, result in nanoplatelets with different defect densities. Herein, we show that nanocomposites based on the less defective solvent-exfoliated graphene exhibit a significantly larger enhancement in CO(2) photoreduction, especially under visible light. This counterintuitive result is attributed to their superior electrical mobility, which facilitates the diffusion of photoexcited electrons to reactive sites.

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.

Solvents effect on photoluminescence of nitrogen incorporated graphene oxide using light emitting diode as an excitation source

NASA Astrophysics Data System (ADS)

Kumara, K.; Shetty, T. C. S.; Patil, P. S.; Dharmaprakash, S. M.

2018-05-01

The present study investigates linear and third order nonlinear optical (TNLO) properties of nitrogen incorporated graphene oxide (NGO). A simple pyrolysis method is followed to obtain NGO powder which is soluble in polar aprotic and protic solvents. The normalized emission intensity of NGO for aprotic solvents shows better than polar protic solvents. The surface morphology and element analysis of NGO displayed a leaf like morphology and the elemental compositions of carbon, nitrogen and oxygen in NGO respectively. TNLO property of NGO is investigated by employing z-scan technique in which a continuous wave of wavelength 632.8 nm from He-Ne source was used. This investigation reveals the reverse saturation behaviour and negative nonlinear refractive (NLR) index in NGO. Negative NLR index sign arises mainly from local heating of solvents during continuous interactions of NGO with laser beam. The photoluminescence and TNLO data recorded for NGO revealed its potentiality for bio-sensing, bio-imaging and optoelectronic applications.

Phase Behavior of a Single Structured Ionomer Chain in Solution

DOE PAGES

Aryal, Dipak; Etampawala, Thusitha; Perahia, Dvora; ...

2014-08-14

Structured polymers offer a means to tailor transport pathways within mechanically stable manifolds. Here we examine the building block of such a membrane, namely a single large pentablock co-polymer that consist of a center block of a randomly sulfonated polystyrene, designed for transport, tethered to poly-ethylene-r-propylene and end-capped by poly-t-butyl styrene, for mechanical stability,using molecular dynamics simulations. The polymer structure in a cyclohexane-heptane mixture, a technologically viable solvent, and in water, a poor solvent for all segments and a ubiquitous substance is extracted. In all solvents the pentablock collapsed into nearly spherical aggregates where the ionic block is segregated. Inmore » hydrophobic solvents, the ionic block resides in the center, surrounded by swollen intermix of flexible and end blocks. In water all blocks are collapsed with the sulfonated block residing on the surface. Our results demonstrate that solvents drive different local nano-segregation, providing a gateway to assemble membranes with controlled topology.« less

Free energy landscape of a minimalist salt bridge model.

PubMed

Li, Xubin; Lv, Chao; Corbett, Karen M; Zheng, Lianqing; Wu, Dongsheng; Yang, Wei

2016-01-01

Salt bridges are essential to protein stability and dynamics. Despite the importance, there has been scarce of detailed discussion on how salt bridge partners interact with each other in distinct solvent exposed environments. In this study, employing a recent generalized orthogonal space tempering (gOST) method, we enabled efficient molecular dynamics simulation of repetitive breaking and reforming of salt bridge structures within a minimalist salt-bridge model, the Asp-Arg dipeptide and thereby were able to map its detailed free energy landscape in aqueous solution. Free energy surface analysis shows that although individually-solvated states are more favorable, salt-bridge states still occupy a noticeable portion of the overall population. Notably, the competing forces, e.g. intercharge attractions that drive the formation of salt bridges and solvation forces that pull the charged groups away from each other, are energetically comparable. As the result, the salt bridge stability is highly tunable by local environments; for instance when local water molecules are perturbed to interact more strongly with each other, the population of the salt-bridge states is likely to increase. Our results reveal the critical role of local solvent structures in modulating salt-bridge partner interactions and imply the importance of water fluctuations on conformational dynamics that involves solvent accessible salt bridge formations. © 2015 The Protein Society.

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

PubMed

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

2013-12-28

The partial molar volumes, 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. V(i) is determined with the direct method, while the composition of 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 V(i) deviate only 3.4 cm(3) mol(-1) (7.1%) from experimental literature values. Experimental 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 V(i) variations. In all solutions, larger 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 V(i). Additionally, attractive electrostatic interactions of CO2 and the solvents, which do not depend on internal solvent interactions only, partially reversed the 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 V(i). Overall, the applied methodology reproduces V(i) and its variations reliably and the used V(i) decompositions identify the underlying reasons behind observed V(i) variations.

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.

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.

Poly(ethylene glycol)-based ionic liquids: properties and uses as alternative solvents in organic synthesis and catalysis.

PubMed

Cecchini, Martina Maya; Charnay, Clarence; De Angelis, Francesco; Lamaty, Frédéric; Martinez, Jean; Colacino, Evelina

2014-01-01

PEG-based ionic liquids are a new appealing group of solvents making the link between two distinct but very similar fluids: ionic liquids and poly(ethylene glycol)s. They find applications across a range of innumerable disciplines in science, technology, and engineering. In the last years, the possibility to use these as alternative solvents for organic synthesis and catalysis has been increasingly explored. This Review highlights strategies for their synthesis, their physical properties (critical point, glass transition temperature, density, rheological properties), and their application in reactions catalyzed by metals (such as Pd, Cu, W, or Rh) or as organic solvent (for example for multicomponent reactions, organocatalysis, CO2 transformation) with special emphasis on their toxicity, environmental impact, and biodegradability. These aspects, very often neglected, need to be considered in addition to the green criteria usually considered to establish ecofriendly processes. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High pressure Raman spectroscopy of single-walled carbon nanotubes: Effect of chemical environment on individual nanotubes and the nanotube bundle

NASA Astrophysics Data System (ADS)

Proctor, John E.; Halsall, Matthew P.; Ghandour, Ahmad; Dunstan, David J.

2006-12-01

The pressure-induced tangential mode Raman peak shifts for single-walled carbon nanotubes (SWNTs) have been studied using a variety of different solvents as hydrostatic pressure-transmitting media. The variation in the nanotube response to hydrostatic pressure with different pressure transmitting media is evidence that the common solvents used are able to penetrate the interstitial spaces in the nanotube bundle. With hexane, we find the surprising result that the individual nanotubes appear unaffected by hydrostatic pressures (i.e. a flat Raman response) up to 0.7 GPa. Qualitatively similar results have been obtained with butanol. Following the approach of Amer et al. [J. Chem. Phys. 121 (2004) 2752], we speculate that this is due to the inability of SWNTs to adsorb some solvents onto their surface at lower pressures. We also find that the role of cohesive energy density in the solvent nanotube interaction is more complex than previously thought.

Ultra-lightweight and highly porous carbon aerogels from bamboo pulp fibers as an effective sorbent for water treatment

NASA Astrophysics Data System (ADS)

Yuan, Wei; Zhang, Xiaofang; Zhao, Jiangqi; Li, Qingye; Ao, Chenghong; Xia, Tian; Zhang, Wei; Lu, Canhui

Sorbents derived from biomass provide a novel approach to settle issues of organic solvent and/or oil leakage. In this work, a novel carbon aerogel (CA) was prepared as sorbents using the cheap and abundant bamboo pulp fibers as precursors through the pyrolysis method. The CA displayed an ultra-low density (5.65 mg cm-3), high hydrophobicity (water contact angle of 135.9°) and a large specific surface area (379.39 m2 g-1) as well as great mechanical properties. The absorption capacities of CA for organic solvents/oils were extraordinary (50-150 g/g). Particularly, its absorption on organic solvents was superior to many other bio-based CAs. The reusability of CA was also found impressive. For over five absorption-desorption cycles, the CA still showed excellent absorption behaviors on organic solvents and oils. Importantly, the fabrication process of CA is quite simple and environmentally friendly, demonstrating high potentials for future water treatment applications.

Equilibrium swelling of elastomeric materials in solvent environments

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

Green, P.F.

1990-03-01

The equilibrium swelling of silicones, fluorosilicones, VITON and ethylene-propylene-diene (EPDM) elastomers in an environment of the jet fuel JP4 was investigated. The volume of silicone and DPDM elastomers increased by approximately 100% when they were placed in a saturated environment of JP4. Conversely, the volume of the fluorosilicone elastomer increased by approximately 15% and that of VITON less than 1%. In acetone, a commonly used solvent, the equilibrium swelling of VITON and the fluorosilicone elastomer was excessive, on the order of 100%, wheras the silicone and EPDM elastomers exhibited small changes in dimensions. Reasons for these observations are discussed inmore » detail. We also present a simple scheme by which one may, qualitatively, determine the dimensional stability of these elastomers in different solvents if the cohesive energy density of the solvent, which is readily available in a number of handbooks, is known. We also evaluated the vulnerability of some commonly used engineering thermoplastics to JP4. The results are tabulated. 13 refs., 6 figs., 3 tab.« less

Protein hydration in solution: Experimental observation by x-ray and neutron scattering

PubMed Central

Svergun, D. I.; Richard, S.; Koch, M. H. J.; Sayers, Z.; Kuprin, S.; Zaccai, G.

1998-01-01

The structure of the protein–solvent interface is the subject of controversy in theoretical studies and requires direct experimental characterization. Three proteins with known atomic resolution crystal structure (lysozyme, Escherichia coli thioredoxin reductase, and protein R1 of E. coli ribonucleotide reductase) were investigated in parallel by x-ray and neutron scattering in H2O and D2O solutions. The analysis of the protein–solvent interface is based on the significantly different contrasts for the protein and for the hydration shell. The results point to the existence of a first hydration shell with an average density ≈10% larger than that of the bulk solvent in the conditions studied. Comparisons with the results of other studies suggest that this may be a general property of aqueous interfaces. PMID:9482874

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

Wang, Jianping, E-mail: jwang@iccas.ac.cn; Yang, Fan; Zhao, Juan

In this work, the structural dynamics of N-ethylpropionamide (NEPA), a model molecule of β-peptides, in four typical solvents (DMSO, CH{sub 3}CN, CHCl{sub 3}, and CCl{sub 4}), were examined using the N—H stretching vibration (or the amide-A mode) as a structural probe. Steady-state and transient infrared spectroscopic methods in combination with quantum chemical computations and molecular dynamics simulations were used. It was found that in these solvents, NEPA exists in different aggregation forms, including monomer, dimer, and oligomers. Hydrogen-bonding interaction and local-solvent environment both affect the amide-A absorption profile and its vibrational relaxation dynamics and also affect the structural dynamics ofmore » NEPA. In particular, a correlation between the red-shifted frequency for the NEPA monomer from nonpolar to polar solvent and the vibrational excitation relaxation rate of the N—H stretching mode was observed.« less

Experimental and theoretical study on DPPH radical scavenging mechanism of some chalcone quinoline derivatives

NASA Astrophysics Data System (ADS)

Hamlaoui, Ikram; Bencheraiet, Reguia; Bensegueni, Rafik; Bencharif, Mustapha

2018-03-01

In this study, the antioxidant capacity of three chalcone derivatives was evaluated by DPPH free radical scavenging. Experimental data showed low antioxidant activity (IC50±SD) of these molecules in comparison with BHT. The mechanism of DPPH radical scavenging elucidated by means of density functional theory (DFT) calculations. The tested compounds and their corresponding radicals and anions were optimized using B3LYP functional with 6-31G (d,p) basis set in the gas phase. The C-PCM model was used to perform solvent medium calculations. On the basis of theoretical calculations, it was shown that HAT mechanism was predominant in the gas phase, whereas SET-PT and SPLET mechanisms were favored in the presence of the solvent. Moreover, the HOMO orbitals and spin density distribution was evaluated to predict the probable sites for free radical attack.

Modifying Poisson equation for near-solute dielectric polarization and solvation free energy

NASA Astrophysics Data System (ADS)

Yang, Pei-Kun

2016-06-01

The dielectric polarization P is important for calculating the stability of protein conformation and the binding affinity of protein-protein/ligand interactions and for exploring the nonthermal effect of an external electric field on biomolecules. P was decomposed into the product of the electric dipole moment per molecule p; bulk solvent density Nbulk; and relative solvent molecular density g. For a molecular solute, 4πr2p(r) oscillates with the distance r to the solute, and g(r) has a large peak in the near-solute region, as observed in molecular dynamics (MD) simulations. Herein, the Poisson equation was modified for computing p based on the modified Gauss's law of Maxwell's equations, and the potential of the mean force was used for computing g. For one or two charged atoms in a water cluster, the solvation free energies of the solutes obtained by these equations were similar to those obtained from MD simulations.

Fast Computation of Solvation Free Energies with Molecular Density Functional Theory: Thermodynamic-Ensemble Partial Molar Volume Corrections.

PubMed

Sergiievskyi, Volodymyr P; Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel

2014-06-05

Molecular density functional theory (MDFT) offers an efficient implicit-solvent method to estimate molecule solvation free-energies, whereas conserving a fully molecular representation of the solvent. Even within a second-order approximation for the free-energy functional, the so-called homogeneous reference fluid approximation, we show that the hydration free-energies computed for a data set of 500 organic compounds are of similar quality as those obtained from molecular dynamics free-energy perturbation simulations, with a computer cost reduced by 2-3 orders of magnitude. This requires to introduce the proper partial volume correction to transform the results from the grand canonical to the isobaric-isotherm ensemble that is pertinent to experiments. We show that this correction can be extended to 3D-RISM calculations, giving a sound theoretical justification to empirical partial molar volume corrections that have been proposed recently.

Lithium sulfur batteries and electrolytes and sulfur cathodes thereof

DOEpatents

Visco, Steven J.; Goncharenko, Nikolay; Nimon, Vitaliy; Petrov, Alexei; Nimon, Yevgeniy S.; De Jonghe, Lutgard C.; Katz, Bruce D.; Loginova, Valentina

2017-05-23

Lithium sulfur battery cells that use water as an electrolyte solvent provide significant cost reductions. Electrolytes for the battery cells may include water solvent for maintaining electroactive sulfur species in solution during cell discharge and a sufficient amount of a cycle life-enhancing compound that facilitates charging at the cathode. The combination of these two components enhances one or more of the following cell attributes: energy density, power density and cycle life. For instance, in applications where cost per Watt-Hour (Wh) is paramount, such as grid storage and traction applications, the use of an aqueous electrolyte in combination with inexpensive sulfur as the cathode active material can be a key enabler for the utility and automotive industries, for example, providing a cost effective and compact solution for load leveling, electric vehicles and renewable energy storage. Sulfur cathodes, and methods of fabricating lithium sulfur cells, in particular for loading lithium sulfide into the cathode structures, provide further advantages.

Solvatochromism and prototropic reactions of 2-quinoxalinone

NASA Astrophysics Data System (ADS)

Santra, Swadeshmukul; Dogra, Sneh K.

1996-06-01

Spectral characteristics of 2-quinoxalinone (QNH) in twelve different solvents and those of N-methyl-2-quinoxalinone (QNM) and 2-methoxyquinoxaline (QOM) in five solvents have been studied. Spectral data, along with prototropic reactions have confirmed that QNH possesses a cyclic amide structure. Charge density and electrostatic potential energy mapping calculations carried out using semi-empirical quantum mechanical methods predict that the monocations of QNH and QNM are formed by protonating carbonyl O-11, whereas that of QOM, by protonating, N-1. Dications of all the molecules are formed by protonating N-4. Deprotonation of QNH takes place after QNH reorganizing to enol form, whereas CNDO/S-CI calculations predict that monoanion formed by deprotonation has a structure where charge density is delocalized over C-2, N-1 and O-11. p Ka and pK a∗ values for the various prototropic reactions have been measured and discussed.

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.

Synthesis, theoretical studies and molecular docking of a novel chlorinated tetracyclic: (Z/E)-3-(1,8-dichloro-9,10-dihydro-9,10-ethanoanthracen-11-yl)acrylaldehyde

NASA Astrophysics Data System (ADS)

Sultan, Mujeeb A.; Almansour, Abdulrahman I.; Pillai, Renjith Raveendran; Kumar, Raju Suresh; Arumugam, Natarajan; Armaković, Stevan; Armaković, Sanja J.; Soliman, Saied M.

2017-12-01

(Z/E)-3-(1,8-Dichloro-9,10-dihydro-9,10-ethanoanthracen-11-yl)acrylaldehyde 2 has been investigated experimentally and theoretically. The Wittig reaction of 1,8-dichloro-9,10-dihydro-9,10-ethanoanthracene-11-carbaldehyde 1 and (triphenylphosphoranylidene) acetaldehyde in toluene under reflux conditions resulted in compound 2. Spectroscopic characterization of compound 2 was performed by the Fourier-transform infrared spectroscopy, nuclear magnetic resonance, and high-resolution mass spectroscopy techniques. Density functional theory (DFT) calculations were conducted to study various global and local reactive properties. The spectra were also obtained by DFT calculations and corresponding comparisons were performed to validate the level of theory. Using DFT calculations, reactivity has been studied based on frontier molecular orbitals, charge distribution, average local ionization energies, Fukui functions, and bond dissociation energies for hydrogen abstraction. Molecular dynamics simulations have been used to investigate the influence of water as a solvent for compound 2. Finally, compound 2 was docked into the central and allosteric binding sites of the serotonin transporter enzyme and was found to be a good candidate as an antidepressant-like compound.

Structural Properties and UV-Visible Absorption Spectroscopy of Retinal-pyridyl-CN Re(I) Carbonyl Bipyridine Complex: A Theoretical Study.

PubMed

Eng, Julien; Daniel, Chantal

2015-10-29

The structural, electronic, and optical properties of the all-trans and five cis conformers of [Re(CO)3(bpy)(ret-pyr-CN)](+) (bpy = 2,2'-bipyridine; ret-pyr-CN = pyridyl-CN-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-2-n)-none-(2,4,6,8-tetraen) were studied in solvent by means of density functional theory (DFT) and time-dependent DFT. The isolated retinal-like chromophore ret-pyr-CN was investigated as well for comparison. By coordination to the complex the two lowest intraligand (IL) states localized on the retinal group are slightly red-shifted from 627 to 690 nm and from 415 to 450 nm, respectively. Several isomerization pathways are open upon irradiation of the Re(I) complex by visible light (400-450 nm), especially to two cis conformers corresponding to the isomerization of the two double bonds of the retinal-like ligand close to the pyridyl group linked to the Re(I) fragment. The metal-to-ligand charge transfer states localized either on the retinal group or on the bpy ligand should play a minor role in the isomerization process itself but could improve its efficiency via ultra-fast intersystem crossing.

Hard-sphere fluid adsorbed in an annular wedge: The depletion force of hard-body colloidal physics

NASA Astrophysics Data System (ADS)

Herring, A. R.; Henderson, J. R.

2007-01-01

Many important issues of colloidal physics can be expressed in the context of inhomogeneous fluid phenomena. When two large colloids approach one another in solvent, they interact at least partly by the response of the solvent to finding itself adsorbed in the annular wedge formed between the two colloids. At shortest range, this fluid mediated interaction is known as the depletion force/interaction because solvent is squeezed out of the wedge when the colloids approach closer than the diameter of a solvent molecule. An equivalent situation arises when a single colloid approaches a substrate/wall. Accurate treatment of this interaction is essential for any theory developed to model the phase diagrams of homogeneous and inhomogeneous colloidal systems. The aim of our paper is a test of whether or not we possess sufficient knowledge of statistical mechanics that can be trusted when applied to systems of large size asymmetry and the depletion force in particular. When the colloid particles are much larger than a solvent diameter, the depletion force is dominated by the effective two-body interaction experienced by a pair of solvated colloids. This low concentration limit of the depletion force has therefore received considerable attention. One route, which can be rigorously based on statistical mechanical sum rules, leads to an analytic result for the depletion force when evaluated by a key theoretical tool of colloidal science known as the Derjaguin approximation. A rival approach has been based on the assumption that modern density functional theories (DFT) can be trusted for systems of large size asymmetry. Unfortunately, these two theoretical predictions differ qualitatively for hard sphere models, as soon as the solvent density is higher than about 2/3 that at freezing. Recent theoretical attempts to understand this dramatic disagreement have led to the proposal that the Derjaguin and DFT routes represent opposite limiting behavior, for very large size asymmetry and molecular sized mixtures, respectively. This proposal implies that nanocolloidal systems lie in between the two limits, so that the depletion force no longer scales linearly with the colloid radius. That is, by decreasing the size ratio from mesoscopic to molecular sized solutes, one moves smoothly between the Derjaguin and the DFT predictions for the depletion force scaled by the colloid radius. We describe the results of a simulation study designed specifically as a test of compatibility with this complex scenario. Grand canonical simulation procedures applied to hard-sphere fluid adsorbed in a series of annular wedges, representing the depletion regime of hard-body colloidal physics, confirm that neither the Derjaguin approximation, nor advanced formulations of DFT, apply at moderate to high solvent density when the geometry is appropriate to nanosized colloids. Our simulations also allow us to report structural characteristics of hard-body solvent adsorbed in hard annular wedges. Both these aspects are key ingredients in the proposal that unifies the disparate predictions, via the introduction of new physics. Our data are consistent with this proposed physics, although as yet limited to a single colloidal size asymmetry.

Assessing the Impact of Chlorinated-Solvent Sites on Metropolitan Groundwater Resources

PubMed Central

Brusseau, Mark L.; Narter, Matthew

2014-01-01

Chlorinated-solvent compounds are among the most common groundwater contaminants in the U.S.A. The majority of the many sites contaminated by chlorinated-solvent compounds are located in metropolitan areas, and most such areas have one or more chlorinated-solvent contaminated sites. Thus, contamination of groundwater by chlorinated-solvent compounds may pose a potential risk to the sustainability of potable water supplies for many metropolitan areas. The impact of chlorinated-solvent sites on metropolitan water resources was assessed for Tucson, AZ, by comparing the aggregate volume of extracted groundwater for all pump-and-treat systems associated with contaminated sites in the region to the total regional groundwater withdrawal. The analysis revealed that the aggregate volume of groundwater withdrawn for the pump-and-treat systems operating in Tucson, all of which are located at chlorinated-solvent contaminated sites, was 20% of the total groundwater withdrawal in the city for the study period. The treated groundwater was used primarily for direct delivery to local water supply systems or for reinjection as part of the pump-and-treat system. The volume of the treated groundwater used for potable water represented approximately 13% of the total potable water supply sourced from groundwater, and approximately 6% of the total potable water supply. This case study illustrates the significant impact chlorinated-solvent contaminated sites can have on groundwater resources and regional potable-water supplies. PMID:24116872

An ab initio time-dependent Hartree Fock study of solvent effects on the polarizability and second hyperpolarizability of polyacetylene chains within the polarizable continuum model

NASA Astrophysics Data System (ADS)

Champagne, Benoı̂t; Mennucci, Benedetta; Cossi, Maurizio; Cammi, Roberto; Tomasi, Jacopo

1998-11-01

The solvent effects upon the longitudinal polarizability ( αL) and second hyperpolarizability ( γL) of small all-trans polyacetylene (PA) chains ranging from C 2H 4 to C 10H 12 have been evaluated at the time-dependent Hartree-Fock (TDHF) level within the framework of the polarizable continuum model. The solvent effects, which correspond to the solvent-induced modifications of the solute properties, result in large increases of the linear and nonlinear responses even for solvents with low dielectric constants. When the dielectric constant is increased, the αL values tend to saturate at values 30%-40% larger than in vacuo, whereas for γL it ranges from 100% to 400% depending upon the nonlinear optical process and the length of the PA chain. These solvent-induced αL and γL enhancements can partially be accounted for by the corresponding decrease of the energy of the lowest optically-allowed electronic excitation. The geometrical parameters of the ground state of the PA chains are almost unaffected by the solvent. This shows that the solvent effects are mainly of electronic nature. In addition, the local field factors, which relate the macroscopic or Maxwell field to the field experienced by the solute, tend towards unity with increasing chain length for the longitudinal PA axis.

Electrophoretic and Electrolytic Deposition of Ceramic Particles on Porous Substrates

DTIC Science & Technology

1990-08-30

hydrodynamic drag force exerted on the particle due to the electroosmotic flow of the solvent inside the pore, the electrophoretic force exerted on the...8217 - electrophoretic velocity UN - electroosmotic velocity b - pore mean radius D - diffusion coefficient k - local deposition rate Large Peclet numbers and small...experimentally as the charge is acquired spontaneously on mixing the particles with the solvent and it may be reversed upon addition ot ionic compounds. The

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.

Preparation of large porous deslorelin-PLGA microparticles with reduced residual solvent and cellular uptake using a supercritical carbon dioxide process.

PubMed

Koushik, Kavitha; Kompella, Uday B

2004-03-01

The purpose of this study was to prepare large-porous peptide-encapsulating polymeric particles with low residual solvent that retain deslorelin integrity, sustain drug release, and exhibit reduced epithelial and macrophage uptake. We hypothesized that supercritical carbon dioxide (SC CO2) pressure-quench treatment of microparticles prepared using conventional approach expands these particles and extracts the residual organic solvent. Initial studies with crystalline L-lactide (L-PLA) and amorphous copolymers of lactide-co-glycolide (PLGA) 50:50, 65:35, and 75:25 indicated that PLGA 50:50 was the most amenable to morphological changes upon SC CO2 treatment. Therefore, we prepared deslorelin-PLGA (50:50) microparticles using the conventional emulsion-solvent evaporation method, and in a second step equilibrated with SC CO2 at various temperatures (33-37 degrees C) and pressures (1200-2000 psi) for discrete intervals followed by rapid isothermal depressurization. The particles were then characterized for morphology, polymer thermal properties, particle size, porosity, bulk density, and residual solvent content. Also, deslorelin integrity, conformation, release, and cellular uptake before and after SC CO2 treatment was determined. Upon SC CO2 treatment (1200 psi, 33 degrees C for 30 min), the mean particle size of the deslorelin PLGA microparticles increased from 2.2 to 13.8 microm, the mean porosity increased from 39 to 92.38% the mean pore diameter increased from 90 to 190 nm, the mean bulk density reduced from 0.7 to 0.082 g/cc, mass spectrometry indicated structural integrity of released deslorelin, the circular dichroism spectrum indicated stabilization of beta-turn conformation, and the scanning electron microscopy confirmed increased particle size and pore formation. The deslorelin release was sustained during the 7-day study period. Also, the peak Tg of PLGA decreased from 51 to 45 degrees C, and the residual solvent content was reduced from 4500 ppm to below detection limit (< 25 ppm). The accumulation of drug from SC CO2 treated particles in cell layers of Calu-3, A549, and rat alveolar macrophages was reduced by 87, 91 and 50%, respectively, compared to untreated particles. An SCF-derived process could be successfully applied to prepare large porous deslorelin-PLGA particles with reduced residual solvent content, which retained deslorelin integrity, sustained deslorelin release, and reduced cellular uptake.

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.

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)

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.

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.

Characterization of Microwave-Induced Electric Discharge Phenomena in Metal–Solvent Mixtures

PubMed Central

Chen, Wen; Gutmann, Bernhard; Kappe, C Oliver

2012-01-01

Electric discharge phenomena in metal–solvent mixtures are investigated utilizing a high field density, sealed-vessel, single-mode 2.45 GHz microwave reactor with a built-in camera. Particular emphasis is placed on studying the discharges exhibited by different metals (Mg, Zn, Cu, Fe, Ni) of varying particle sizes and morphologies in organic solvents (e.g., benzene) at different electric field strengths. Discharge phenomena for diamagnetic and paramagnetic metals (Mg, Zn, Cu) depend strongly on the size of the used particles. With small particles, short-lived corona discharges are observed that do not lead to a complete breakdown. Under high microwave power conditions or with large particles, however, bright sparks and arcs are experienced, often accompanied by solvent decomposition and formation of considerable amounts of graphitized material. Small ferromagnetic Fe and Ni powders (<40 μm) are heated very rapidly in benzene suspensions and start to glow in the microwave field, whereas larger particles exhibit extremely strong discharges. Electric discharges were also observed when Cu metal or other conductive materials such as silicon carbide were exposed to the microwave field in the absence of a solvent in an argon or nitrogen atmosphere. PMID:24551491

Characterization of microwave-induced electric discharge phenomena in metal-solvent mixtures.

PubMed

Chen, Wen; Gutmann, Bernhard; Kappe, C Oliver

2012-02-01

Electric discharge phenomena in metal-solvent mixtures are investigated utilizing a high field density, sealed-vessel, single-mode 2.45 GHz microwave reactor with a built-in camera. Particular emphasis is placed on studying the discharges exhibited by different metals (Mg, Zn, Cu, Fe, Ni) of varying particle sizes and morphologies in organic solvents (e.g., benzene) at different electric field strengths. Discharge phenomena for diamagnetic and paramagnetic metals (Mg, Zn, Cu) depend strongly on the size of the used particles. With small particles, short-lived corona discharges are observed that do not lead to a complete breakdown. Under high microwave power conditions or with large particles, however, bright sparks and arcs are experienced, often accompanied by solvent decomposition and formation of considerable amounts of graphitized material. Small ferromagnetic Fe and Ni powders (<40 μm) are heated very rapidly in benzene suspensions and start to glow in the microwave field, whereas larger particles exhibit extremely strong discharges. Electric discharges were also observed when Cu metal or other conductive materials such as silicon carbide were exposed to the microwave field in the absence of a solvent in an argon or nitrogen atmosphere.

Supercritical fluid reverse micelle separation

DOEpatents

Fulton, John L.; Smith, Richard D.

1993-01-01

A method of separating solute material from a polar fluid in a first polar fluid phase is provided. The method comprises combining a polar fluid, a second fluid that is a gas at standard temperature and pressure and has a critical density, and a surfactant. The solute material is dissolved in the polar fluid to define the first polar fluid phase. The combined polar and second fluids, surfactant, and solute material dissolved in the polar fluid is maintained under near critical or supercritical temperature and pressure conditions such that the density of the second fluid exceeds the critical density thereof. In this way, a reverse micelle system defining a reverse micelle solvent is formed which comprises a continuous phase in the second fluid and a plurality of reverse micelles dispersed in the continuous phase. The solute material is dissolved in the polar fluid and is in chemical equilibrium with the reverse micelles. The first polar fluid phase and the continuous phase are immiscible. The reverse micelles each comprise a dynamic aggregate of surfactant molecules surrounding a core of the polar fluid. The reverse micelle solvent has a polar fluid-to-surfactant molar ratio W, which can vary over a range having a maximum ratio W.sub.o that determines the maximum size of the reverse micelles. The maximum ratio W.sub.o of the reverse micelle solvent is then varied, and the solute material from the first polar fluid phase is transported into the reverse micelles in the continuous phase at an extraction efficiency determined by the critical or supercritical conditions.

Fluctuation-driven anisotropy in effective pair interactions between nanoparticles: Thiolated gold nanoparticles in ethane

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

Jabes, B. Shadrack; Yadav, Hari O. S.; Chakravarty, Charusita, E-mail: charus@chemistry.iitd.ac.in

2014-10-21

Fluctuations within the ligand shell of a nanoparticle give rise to a significant degree of anisotropy in effective pair interactions for low grafting densities [B. Bozorgui, D. Meng, S. K. Kumar, C. Chakravarty, and A. Cacciuto, Nano Lett. 13, 2732 (2013)]. Here, we examine the corresponding fluctuation-driven anisotropy for gold nanocrystals densely passivated with short ligands. In particular, we consider gold nanocrystals capped by alkylthiols, both in vacuum and in ethane solvent at high density. As in the preceding study, we show that the anisotropy in the nanoparticle pair potential can be quantified by an angle-dependent correction term to themore » isotropic potential of mean force (PMF). We find that the anisotropy of the ligand shells is distance dependent, and strongly influenced by ligand interdigitation effects as well as expulsion of ligand chains from the interparticle region at short distances. Such fluctuation-driven anisotropy can be significant for alkylthiol-coated gold nanoparticles, specially for longer chain lengths, under good solvent conditions. The consequences of such anisotropy for self-assembly, specially as a function of grafting density, solvent quality and at interfaces, should provide some interesting insights in future work. Our results clearly show that an isotropic two-body PMF cannot adequately describe the thermodynamics and assembly behavior of nanoparticles in this dense grafting regime and inclusion of anisotropic effects, as well as possibly many-body interactions, is necessary. Extensions of this approach to other passivated nanoparticle systems and implications for self-assembly are considered.« less

Supercritical fluid reverse micelle separation

DOEpatents

Fulton, J.L.; Smith, R.D.

1993-11-30

A method of separating solute material from a polar fluid in a first polar fluid phase is provided. The method comprises combining a polar fluid, a second fluid that is a gas at standard temperature and pressure and has a critical density, and a surfactant. The solute material is dissolved in the polar fluid to define the first polar fluid phase. The combined polar and second fluids, surfactant, and solute material dissolved in the polar fluid is maintained under near critical or supercritical temperature and pressure conditions such that the density of the second fluid exceeds the critical density thereof. In this way, a reverse micelle system defining a reverse micelle solvent is formed which comprises a continuous phase in the second fluid and a plurality of reverse micelles dispersed in the continuous phase. The solute material is dissolved in the polar fluid and is in chemical equilibrium with the reverse micelles. The first polar fluid phase and the continuous phase are immiscible. The reverse micelles each comprise a dynamic aggregate of surfactant molecules surrounding a core of the polar fluid. The reverse micelle solvent has a polar fluid-to-surfactant molar ratio W, which can vary over a range having a maximum ratio W[sub o] that determines the maximum size of the reverse micelles. The maximum ratio W[sub o] of the reverse micelle solvent is then varied, and the solute material from the first polar fluid phase is transported into the reverse micelles in the continuous phase at an extraction efficiency determined by the critical or supercritical conditions. 27 figures.

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.

Influence of a Confined Methanol Solvent on the Reactivity of Active Sites in UiO-66.

PubMed

Caratelli, Chiara; Hajek, Julianna; Rogge, Sven M J; Vandenbrande, Steven; Meijer, Evert Jan; Waroquier, Michel; Van Speybroeck, Veronique

2018-02-19

UiO-66, composed of Zr-oxide bricks and terephthalate linkers, is currently one of the most studied metal-organic frameworks due to its exceptional stability. Defects can be introduced in the structure, creating undercoordinated Zr atoms which are Lewis acid sites. Here, additional Brønsted sites can be generated by coordinated protic species from the solvent. In this Article, a multilevel modeling approach was applied to unravel the effect of a confined methanol solvent on the active sites in UiO-66. First, active sites were explored with static periodic density functional theory calculations to investigate adsorption of water and methanol. Solvent was then introduced in the pores with grand canonical Monte Carlo simulations, followed by a series of molecular dynamics simulations at operating conditions. A hydrogen-bonded network of methanol molecules is formed, allowing the protons to shuttle between solvent methanol, adsorbed water, and the inorganic brick. Upon deprotonation of an active site, the methanol solvent aids the transfer of protons and stabilizes charged configurations via hydrogen bonding, which could be crucial in stabilizing reactive intermediates. The multilevel modeling approach adopted here sheds light on the important role of a confined solvent on the active sites in the UiO-66 material, introducing dynamic acidity in the system at finite temperatures by which protons may be easily shuttled from various positions at the active sites. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Structure and thermodynamics of a mixture of patchy and spherical colloids: A multi-body association theory with complete reference fluid information

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

Bansal, Artee; Asthagiri, D.; Cox, Kenneth R.

A mixture of solvent particles with short-range, directional interactions and solute particles with short-range, isotropic interactions that can bond multiple times is of fundamental interest in understanding liquids and colloidal mixtures. Because of multi-body correlations, predicting the structure and thermodynamics of such systems remains a challenge. Earlier Marshall and Chapman [J. Chem. Phys. 139, 104904 (2013)] developed a theory wherein association effects due to interactions multiply the partition function for clustering of particles in a reference hard-sphere system. The multi-body effects are incorporated in the clustering process, which in their work was obtained in the absence of the bulk medium.more » The bulk solvent effects were then modeled approximately within a second order perturbation approach. However, their approach is inadequate at high densities and for large association strengths. Based on the idea that the clustering of solvent in a defined coordination volume around the solute is related to occupancy statistics in that defined coordination volume, we develop an approach to incorporate the complete information about hard-sphere clustering in a bulk solvent at the density of interest. The occupancy probabilities are obtained from enhanced sampling simulations but we also develop a concise parametric form to model these probabilities using the quasichemical theory of solutions. We show that incorporating the complete reference information results in an approach that can predict the bonding state and thermodynamics of the colloidal solute for a wide range of system conditions.« less

A novel dispersive liquid-liquid microextraction based on solidification of floating organic droplet method for determination of polycyclic aromatic hydrocarbons in aqueous samples.

PubMed

Xu, Hui; Ding, Zongqing; Lv, Lili; Song, Dandan; Feng, Yu-Qi

2009-03-16

A new dispersive liquid-liquid microextraction based on solidification of floating organic droplet method (DLLME-SFO) was developed for the determination of five kinds of polycyclic aromatic hydrocarbons (PAHs) in environmental water samples. In this method, no specific holder, such as the needle tip of microsyringe and the hollow fiber, is required for supporting the organic microdrop due to the using of organic solvent with low density and proper melting point. Furthermore, the extractant droplet can be collected easily by solidifying it in the lower temperature. 1-Dodecanol was chosen as extraction solvent in this work. A series of parameters that influence extraction were investigated systematically. Under optimal conditions, enrichment factors (EFs) for PAHs were in the range of 88-118. The limit of detections (LODs) for naphthalene, diphenyl, acenaphthene, anthracene and fluoranthene were 0.045, 0.86, 0.071, 1.1 and 0.66ngmL(-1), respectively. Good reproducibility and recovery of the method were also obtained. Compared with the traditional liquid-phase microextraction (LPME) and dispersive liquid-liquid microextraction (DLLME) methods, the proposed method obtained about 2 times higher enrichment factor than those in LPME. Moreover, the solidification of floating organic solvent facilitated the phase transfer. And most importantly, it avoided using high-density and toxic solvent in the traditional DLLME method. The proposed method was successfully applied to determinate PAHs in the environmental water samples. The simple and low-cost method provides an alternative method for the analysis of non-polar compounds in complex environmental water.

Molecular Dynamics Study of the Solution Structure, Clustering, and Diffusion of Four Aqueous Alkanolamines.

PubMed

Melnikov, Sergey M; Stein, Matthias

2018-03-15

CO 2 sequestration from anthropogenic resources is a challenge to the design of environmental processes at a large scale. Reversible chemical absorption by amine-based solvents is one of the most efficient methods of CO 2 removal. Molecular simulation techniques are very useful tools to investigate CO 2 binding by aqueous alkanolamine molecules for further technological application. In the present work, we have performed detailed atomistic molecular dynamics simulations of aqueous solutions of three prototype amines: monoethanolamine (MEA) as a standard, 3-aminopropanol (MPA), 2-methylaminoethanol (MMEA), and 4-diethylamino-2-butanol (DEAB) as potential novel CO 2 absorptive solvents. Solvent densities, radial distribution functions, cluster size distributions, hydrogen-bonding statistics, and diffusion coefficients for a full range of mixture compositions have been obtained. The solvent densities and diffusion coefficients from simulations are in good agreement with those in the experiment. In aqueous solution, MEA, MPA, and MMEA molecules prefer to be fully solvated by water molecules, whereas DEAB molecules tend to self-aggregate. In a range from 30/70-50/50 (w/w) alkanolamine/water mixtures, they form a bicontinuous phase (both alkanolamine and water are organized in two mutually percolating clusters). Among the studied aqueous alkanolamine solutions, the diffusion coefficients decrease in the following order MEA > MPA = MMEA > DEAB. With an increase of water content, the diffusion coefficients increase for all studied alkanolamines. The presented results are a first step for process-scale simulation and provide important qualitative and quantitative information for the design and engineering of efficient new CO 2 removal processes.

Unconstrained Structure Formation in Coarse-Grained Protein Simulations

NASA Astrophysics Data System (ADS)

Bereau, Tristan

The ability of proteins to fold into well-defined structures forms the basis of a wide variety of biochemical functions in and out of the cell membrane. Many of these processes, however, operate at time- and length-scales that are currently unattainable by all-atom computer simulations. To cope with this difficulty, increasingly more accurate and sophisticated coarse-grained models are currently being developed. In the present thesis, we introduce a solvent-free coarse-grained model for proteins. Proteins are modeled by four beads per amino acid, providing enough backbone resolution to allow for accurate sampling of local conformations. It relies on simple interactions that emphasize structure, such as hydrogen bonds and hydrophobicity. Realistic alpha/beta content is achieved by including an effective nearest-neighbor dipolar interaction. Parameters are tuned to reproduce both local conformations and tertiary structures. By studying both helical and extended conformations we make sure the force field is not biased towards any particular secondary structure. Without any further adjustments or bias a realistic oligopeptide aggregation scenario is observed. The model is subsequently applied to various biophysical problems: (i) kinetics of folding of two model peptides, (ii) large-scale amyloid-beta oligomerization, and (iii) protein folding cooperativity. The last topic---defined by the nature of the finite-size thermodynamic transition exhibited upon folding---was investigated from a microcanonical perspective: the accurate evaluation of the density of states can unambiguously characterize the nature of the transition, unlike its corresponding canonical analysis. Extending the results of lattice simulations and theoretical models, we find that it is the interplay between secondary structure and the loss of non-native tertiary contacts which determines the nature of the transition. Finally, we combine the peptide model with a high-resolution, solvent-free, lipid model. The lipid force field was systematically tuned to reproduce the structural and mechanical properties of phosphatidylcholine bilayers. The two models were cross-parametrized against atomistic potential of mean force curves for the insertion of single amino acid side chains into a bilayer. Coarse-grained transmembrane protein simulations were then compared with experiments and atomistic simulations to validate the force field. The transferability of the two models across amino acid sequences and lipid species permits the investigation of a wide variety of scenarios, while the absence of explicit solvent allows for studies of large-scale phenomena.

Effect of the ordered interfacial water layer in protein complex formation: a non-local electrostatic approach

NASA Astrophysics Data System (ADS)

Rubinstein, Alexander; Sabirianov, Renat

2011-03-01

Using a non-local electrostatic approach that incorporates the short-range structure of the contacting media, we evaluated the electrostatic contribution to the energy of the complex formation of two model proteins. In this study, we have demonstrated that the existence of an low-dielectric interfacial water layer at the protein-solvent interface reduces the charging energy of the proteins in the aqueous solvent, and consequently increases the electrostatic contribution to the protein binding (change in free energy upon the complex formation of two proteins). This is in contrast with the finding of the continuum electrostatic model, which suggests that electrostatic interactions are not strong enough to compensate for the unfavorable desolvation effects.

[On the influence of local molecular environment on the redox potential of electron transfer cofactors in bacterial photosynthetic reaction centers].

PubMed

Krasil'nikov, P M; Noks, P P; Rubin, A B

2011-01-01

The addition of cryosolvents (glycerol, dimethylsulfoxide) to a water solution containing bacterial photosynthetic reaction centers changes the redox potential of the bacteriochlorophyll dimer, but does not affect the redox potential of the quinone primary acceptor. It has been shown that the change in redox potential can be produced by changes of the electrostatic interactions between cofactors and the local molecular environment modified by additives entered into the solution. The degree of influence of a solvent on the redox potential of various cofactors is determined by degree of availability of these cofactors for molecules of solvent, which depends on the arrangement of cofactors in the structure of reaction centers.

Task 3 - Pyrolysis of Plastic Waste. Semiannual report, November 1, 1996--March 31, 1997

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

Ness, Robert O.; Aulich, Ted R.

1997-12-31

Over the last 50 years, the U.S. Department of Energy (DOE) has produced a wide variety of radioactive wastes from activities associated with nuclear defense and nuclear power generation. These wastes include low-level radioactive solid wastes, mixed wastes, and transuranic (TRU) wastes. A portion of these wastes consists of high- organic-content materials, such as resins, plastics, and other polymers; synthetic and natural rubbers; cellulosic-based materials; and oils, organic solvents, and chlorinated organic solvents. Many of these wastes contain hazardous and/or pyrophoric materials in addition to radioactive species. Physical forms of the waste include ion-exchange resins used to remove radioactive elementsmore » from nuclear reactor cooling water, lab equipment and tools (e.g., measurement and containment vessels, hoses, wrappings, equipment coverings and components, and countertops), oil products (e.g., vacuum pump and lubrication oils), bags and other storage containers (for liquids, solids, and gases), solvents, gloves, lab coats and anti-contamination clothing, and other items. Major polymer and chemical groups found in high-organic-content radioactive wastes include polyvinyl chloride (PVC), low-density polyethylene (LDPE), polypropylene (PP), Teflon(TM), polystyrene (PS), nylon, latex, polyethylene terephthalate (PET), vinyl, high-density polyethylene (HDPE), polycarbonate, nitriles, Tygon(R), butyl, and Tyvec(R).« less

Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods

NASA Astrophysics Data System (ADS)

Gilbert, Kathleen M.; Skawinski, William J.; Misra, Milind; Paris, Kristina A.; Naik, Neelam H.; Buono, Ronald A.; Deutsch, Howard M.; Venanzi, Carol A.

2004-11-01

Methylphenidate (MP) binds to the cocaine binding site on the dopamine transporter and inhibits reuptake of dopamine, but does not appear to have the same abuse potential as cocaine. This study, part of a comprehensive effort to identify a drug treatment for cocaine abuse, investigates the effect of choice of calculation technique and of solvent model on the conformational potential energy surface (PES) of MP and a rigid methylphenidate (RMP) analogue which exhibits the same dopamine transporter binding affinity as MP. Conformational analysis was carried out by the AM1 and AM1/SM5.4 semiempirical molecular orbital methods, a molecular mechanics method (Tripos force field with the dielectric set equal to that of vacuum or water) and the HF/6-31G* molecular orbital method in vacuum phase. Although all three methods differ somewhat in the local details of the PES, the general trends are the same for neutral and protonated MP. In vacuum phase, protonation has a distinctive effect in decreasing the regions of space available to the local conformational minima. Solvent has little effect on the PES of the neutral molecule and tends to stabilize the protonated species. The random search (RS) conformational analysis technique using the Tripos force field was found to be capable of locating the minima found by the molecular orbital methods using systematic grid search. This suggests that the RS/Tripos force field/vacuum phase protocol is a reasonable choice for locating the local minima of MP. However, the Tripos force field gave significantly larger phenyl ring rotational barriers than the molecular orbital methods for MP and RMP. For both the neutral and protonated cases, all three methods found the phenyl ring rotational barriers for the RMP conformers/invertamers (denoted as cte, tte, and cta) to be: cte, tte> MP > cta. Solvation has negligible effect on the phenyl ring rotational barrier of RMP. The B3LYP/6-31G* density functional method was used to calculate the phenyl ring rotational barrier for neutral MP and gave results very similar to those of the HF/6-31G* method.

Non-aqueous cleaning solvent substitution

NASA Technical Reports Server (NTRS)

Meier, Gerald J.

1994-01-01

A variety of environmental, safety, and health concerns exist over use of chlorinated and fluorinated cleaning solvents. Sandia National Laboratories, Lawrence Livermore National Laboratories, and the Kansas City Division of AlliedSignal have combined efforts to focus on finding alternative cleaning solvents and processes which are effective, environmentally safe, and compliant with local, state, and federal regulations. An alternative solvent has been identified, qualified, and implemented into production of complex electronic assemblies, where aqueous and semi-aqueous cleaning processes are not allowed. Extensive compatibility studies were performed with components, piece-parts, and materials. Electrical testing and accelerated aging were used to screen for detrimental, long-term effects. A terpene, d-limonene, was selected as the solvent of choice, and it was found to be compatible with the components and materials tested. A brief history of the overall project will be presented, along with representative cleaning efficiency results, compatibility results, and residual solvent data. The electronics industry is constantly searching for proven methods and environmentally-safe materials to use in manufacturing processes. The information in this presentation will provide another option to consider on future projects for applications requiring high levels of quality, reliability, and cleanliness from non-aqueous cleaning processes.

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

Mukherji, Debashish; Stuehn, Torsten; Kremer, Kurt

Smart polymers are a modern class of polymeric materials that often exhibit unpredictable behavior in mixtures of solvents. One such phenomenon is co-non-solvency. Co-non-solvency occurs when two (perfectly) miscible and competing good solvents, for a given polymer, are mixed together. As a result, the same polymer collapses into a compact globule within intermediate mixing ratios. More interestingly, polymer collapses when the solvent quality remains good and even gets increasingly better by the addition of the better cosolvent. This is a puzzling phenomenon that is driven by strong local concentration fluctuations. Because of the discrete particle based nature of the interactions,more » Flory-Huggins type mean field arguments become unsuitable. In this work, we extend the analysis of the co-non-solvency effect presented earlier [D. Mukherji et al., Nat. Commun. 5, 4882 (2014)]. We explain why co-non-solvency is a generic phenomenon, which can only be understood by the thermodynamic treatment of the competitive displacement of (co)solvent components. This competition can result in a polymer collapse upon improvement of the solvent quality. Specific chemical details are not required to understand these complex conformational transitions. Therefore, a broad range of polymers are expected to exhibit similar reentrant coil-globule-coil transitions in competing good solvents.« less

Understanding reactivity of two newly synthetized imidazole derivatives by spectroscopic characterization and computational study

NASA Astrophysics Data System (ADS)

Hossain, Mossaraf; Thomas, Renjith; Mary, Y. Sheena; Resmi, K. S.; Armaković, Stevan; Armaković, Sanja J.; Nanda, Ashis Kumar; Vijayakumar, G.; Van Alsenoy, C.

2018-04-01

Two newly synthetized imidazole derivatives (1-(4-methoxyphenyl)-4,5-dimethyl-1H-imidazole-2-yl acetate (MPDIA) and 1-(4-bromophenyl)-4,5-dimethyl-1H-imidazole-2-yl acetate (BPDIA)) have been prepared by solvent-free synthesis pathway and their specific spectroscopic and reactive properties have been discussed based on combined experimental and computational approaches. Aside of synthesis, experimental part of this work included measurements of IR, FT-Raman and NMR spectra. All of the aforementioned spectra were also obtained computationally, within the framework of density functional theory (DFT) approach. Additionally, DFT calculations have been used in order to investigate local reactivity properties based on molecular orbital theory, molecular electrostatic potential (MEP), average local ionization energy (ALIE), Fukui functions and bond dissociation energy (BDE). Molecular dynamics (MD) simulations have been used in order to obtain radial distribution functions (RDF), which were used for identification of the atoms with pronounced interactions with water molecules. MEP showed negative regions are mainly localized over N28, O29, O35 atoms, it is represent with red colour in rainbow color scheme for MPDIA and BPDIA (which are most reactive sites for electrophilic attack). The first order hyperpolarizabilities of MPDIA and BPDIA are 20.15 and 6.10 times that of the standard NLO material urea. Potential interaction with antihypertensive protein hydrolase.

Molecular Dynamics Simulations of the Initial-State Predict Product Distributions of Dediazoniation of Aryldiazonium in Binary Solvents.

PubMed

Cruz, Gustavo N; Lima, Filipe S; Dias, Luís G; El Seoud, Omar A; Horinek, Dominik; Chaimovich, Hernan; Cuccovia, Iolanda M

2015-09-04

The dediazoniation of aryldiazonium salts in mixed solvents proceeds by a borderline SN1 and SN2 pathway, and product distribution should be proportional to the composition of the solvation shell of the carbon attached to the -N2 group (ipso carbon). The rates of dediazoniation of 2,4,6-trimethylbenzenediazonium in water, methanol, ethanol, propanol, and acetonitrile were similar, but measured product distributions were noticeably dependent on the nature of the water/cosolvent mixture. Here we demonstrated that solvent distribution in the first solvation shell of the ipso carbon, calculated from classical molecular dynamics simulations, is equal to the measured product distribution. Furthermore, we showed that regardless of the charge distribution of the initial state, i.e., whether the positive charge is smeared over the molecule or localized on phenyl moiety, the solvent distribution around the reaction center is nearly the same.

Enhancement of room temperature ferromagnetism in tin oxide nanocrystal using organic solvents

NASA Astrophysics Data System (ADS)

Sakthiraj, K.; Hema, M.; Balachandra Kumar, K.

2017-10-01

The effect of organic solvents (ethanol & ethylene glycol) on the room temperature ferromagnetism in nanocrystalline tin oxide has been studied. The samples were synthesized using sol-gel method with the mixture of water & organic liquid as solvent. It is found that pristine SnO2 nanocrystal contain two different types of paramagnetic centres over their surface:(i) surface chemisorbed oxygen species and (ii) Sn interstitial & oxygen vacancy defect pair. The magnetic moment induced in the as-prepared samples is mainly contributed by the alignment of local spin moments resulting from these defects. These surface defect states are highly activated by the usage of ethylene glycol solvent rather than ethylene in tin oxide nanostructure synthesis. Powder X-ray diffraction, transmission electron microscope imaging, energy dispersive spectrometry, Fourier transformed infrared spectroscopy, UV-vis absorption spectroscopy, photoluminescence spectroscopy, vibrating sample magnetometer measurement and electron spin resonance spectroscopy were employed to characterize the nanostructured tin oxide materials.

Method of preparation of removable syntactic foam

DOEpatents

Arnold, C. Jr.; Derzon, D.K.; Nelson, J.S.; Rand, P.B.

1995-07-11

Easily removable, environmentally safe, low-density, syntactic foams are disclosed which are prepared by mixing insoluble microballoons with a solution of water and/or alcohol-soluble polymer to produce a pourable slurry, optionally vacuum filtering the slurry in varying degrees to remove unwanted solvent and solute polymer, and drying to remove residual solvent. The properties of the foams can be controlled by the concentration and physical properties of the polymer, and by the size and properties of the microballoons. The suggested solute polymers are non-toxic and soluble in environmentally safe solvents such as water or low-molecular weight alcohols. The syntactic foams produced by this process are particularly useful in those applications where ease of removability is beneficial, and could find use in packaging recoverable electronic components, in drilling and mining applications, in building trades, in art works, in the entertainment industry for special effects, in manufacturing as temporary fixtures, in agriculture as temporary supports and containers and for delivery of fertilizer, in medicine as casts and splints, as temporary thermal barriers, as temporary protective covers for fragile objects, as filters for particulate matter, which matter may be easily recovered upon exposure to a solvent, as in-situ valves (for one-time use) which go from maximum to minimum impedance when solvent flows through, and for the automatic opening or closing of spring-loaded, mechanical switches upon exposure to a solvent, among other applications. 1 fig.

Method of preparation of removable syntactic foam

DOEpatents

Arnold, Jr., Charles; Derzon, Dora K.; Nelson, Jill S.; Rand, Peter B.

1995-01-01

Easily removable, environmentally safe, low-density, syntactic foams are disclosed which are prepared by mixing insoluble microballoons with a solution of water and/or alcohol-soluble polymer to produce a pourable slurry, optionally vacuum filtering the slurry in varying degrees to remove unwanted solvent and solute polymer, and drying to remove residual solvent. The properties of the foams can be controlled by the concentration and physical properties of the polymer, and by the size and properties of the microballoons. The suggested solute polymers are non-toxic and soluble in environmentally safe solvents such as water or low-molecular weight alcohols. The syntactic foams produced by this process are particularly useful in those applications where ease of removability is beneficial, and could find use in packaging recoverable electronic components, in drilling and mining applications, in building trades, in art works, in the entertainment industry for special effects, in manufacturing as temporary fixtures, in agriculture as temporary supports and containers and for delivery of fertilizer, in medicine as casts and splints, as temporary thermal barriers, as temporary protective covers for fragile objects, as filters for particulate matter, which matter may be easily recovered upon exposure to a solvent, as in-situ valves (for one-time use) which go from maximum to minimum impedance when solvent flows through, and for the automatic opening or closing of spring-loaded, mechanical switches upon exposure to a solvent, among other applications.

The Role of Interfacial Water in Protein-Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force.

PubMed

Cui, Di; Zhang, Bin W; Matubayasi, Nobuyuki; Levy, Ronald M

2018-02-13

Classical density functional theory (DFT) can be used to relate the thermodynamic properties of solutions to the indirect solvent mediated part of the solute-solvent potential of mean force (PMF). Standard, but powerful numerical methods can be used to estimate the solute-solvent PMF from which the indirect part can be extracted. In this work we show how knowledge of the direct and indirect parts of the solute-solvent PMF for water at the interface of a protein receptor can be used to gain insights about how to design tighter binding ligands. As we show, the indirect part of the solute-solvent PMF is equal to the sum of the 1-body (energy + entropy) terms in the inhomogeneous solvation theory (IST) expansion of the solvation free energy. To illustrate the effect of displacing interfacial water molecules with particular direct/indirect PMF signatures on the binding of ligands, we carry out simulations of protein binding with several pairs of congeneric ligands. We show that interfacial water locations that contribute favorably or unfavorably at the 1-body level (energy + entropy) to the solvation free energy of the solute can be targeted as part of the ligand design process. Water locations where the indirect PMF is larger in magnitude provide better targets for displacement when adding a functional group to a ligand core.

Reaction Mechanism of Organocatalytic Michael Addition of Nitromethane to Cinnamaldehyde: A Case Study on Catalyst Regeneration and Solvent Effects.

PubMed

Świderek, Katarzyna; Nödling, Alexander R; Tsai, Yu-Hsuan; Luk, Louis Y P; Moliner, Vicent

2018-01-11

The Michael addition of nitromethane to cinnamaldehyde has been computationally studied in the absence of a catalyst and the presence of a biotinylated secondary amine by a combined computational and experimental approach. The calculations were performed at the density functional theory (DFT) level with the M06-2X hybrid functional, and a polarizable continuum model has been employed to mimic the effect of two different solvents: dichloromethane (DCM) and water. Contrary to common assumption, the product-derived iminium intermediate was absent in both of the solvents tested. Instead, hydrating the C1-C2 double bond in the enamine intermediate directly yields the tetrahedral intermediate, which is key for forming the product and regenerating the catalyst. Enamine hydration is concerted and found to be rate-limiting in DCM but segregated into two non-rate-limiting steps when the solvent is replaced with water. However, further analysis revealed that the use of water as solvent also raises the energy barriers for other chemical steps, particularly the critical step of C-C bond formation between the iminium intermediate and nucleophile; this consequently lowers both the reaction yield and enantioselectivity of this LUMO-lowering reaction, as experimentally detected. These findings provide a logical explanation to why water often enhances organocatalysis when used as an additive but hampers the reaction progress when employed as a solvent.

Reaction Mechanism of Organocatalytic Michael Addition of Nitromethane to Cinnamaldehyde: A Case Study on Catalyst Regeneration and Solvent Effects

PubMed Central

2017-01-01

The Michael addition of nitromethane to cinnamaldehyde has been computationally studied in the absence of a catalyst and the presence of a biotinylated secondary amine by a combined computational and experimental approach. The calculations were performed at the density functional theory (DFT) level with the M06-2X hybrid functional, and a polarizable continuum model has been employed to mimic the effect of two different solvents: dichloromethane (DCM) and water. Contrary to common assumption, the product-derived iminium intermediate was absent in both of the solvents tested. Instead, hydrating the C1–C2 double bond in the enamine intermediate directly yields the tetrahedral intermediate, which is key for forming the product and regenerating the catalyst. Enamine hydration is concerted and found to be rate-limiting in DCM but segregated into two non-rate-limiting steps when the solvent is replaced with water. However, further analysis revealed that the use of water as solvent also raises the energy barriers for other chemical steps, particularly the critical step of C–C bond formation between the iminium intermediate and nucleophile; this consequently lowers both the reaction yield and enantioselectivity of this LUMO-lowering reaction, as experimentally detected. These findings provide a logical explanation to why water often enhances organocatalysis when used as an additive but hampers the reaction progress when employed as a solvent. PMID:29256614

Nucleophilic Substitution in Solution: Activation Strain Analysis of Weak and Strong Solvent Effects

PubMed Central

Hamlin, Trevor A.; van Beek, Bas; Wolters, Lando P.

2018-01-01

Abstract We have quantum chemically studied the effect of various polar and apolar solvents on the shape of the potential energy surface (PES) of a diverse collection of archetypal nucleophilic substitution reactions at carbon, silicon, phosphorus, and arsenic by using density functional theory at the OLYP/TZ2P level. In the gas phase, all our model SN2 reactions have single‐well PESs, except for the nucleophilic substitution reaction at carbon (SN2@C), which has a double‐well energy profile. The presence of the solvent can have a significant effect on the shape of the PES and, thus, on the nature of the SN2 process. Solvation energies, charges on the nucleophile or leaving group, and structural features are compared for the various SN2 reactions in a spectrum of solvents. We demonstrate how solvation can change the shape of the PES, depending not only on the polarity of the solvent, but also on how the charge is distributed over the interacting molecular moieties during different stages of the reaction. In the case of a nucleophilic substitution at three‐coordinate phosphorus, the reaction can be made to proceed through a single‐well [no transition state (TS)], bimodal barrier (two TSs), and then through a unimodal transition state (one TS) simply by increasing the polarity of the solvent. PMID:29457865

Solvent effects on the vibronic one-photon absorption profiles of dioxaborine heterocycles

NASA Astrophysics Data System (ADS)

Wang, Yan-Hua; Halik, Marcus; Wang, Chuan-Kui; Marder, Seth R.; Luo, Yi

2005-11-01

The vibronic profiles of one-photon absorption spectra of dioxaborine heterocycles in gas phase and solution have been calculated at the Hartree-Fock and density-functional-theory levels. The polarizable continuum model has been applied to simulate the solvent effect, while the linear coupling model is used to compute the Franck-Condon and Herzberg-Teller contributions. It is found that a good agreement between theory and experiment can be achieved when the solvent effect and electron correlation are taken into account simultaneously. For the first excited charge-transfer state, the maximum of its Herzberg-Teller profile is blueshifted from that of the Franck-Condon profile. The shifted energy is found to be around 0.2eV, which agrees well with the measured energy difference between two- and one-photon absorptions of the first excited state.

Semiflexible polymers confined in a slit pore with attractive walls: two-dimensional liquid crystalline order versus capillary nematization.

PubMed

Milchev, Andrey; Egorov, Sergei A; Binder, Kurt

2017-03-01

Semiflexible polymers under good solvent conditions interacting with attractive planar surfaces are investigated by Molecular Dynamics (MD) simulations and classical Density Functional Theory (DFT). A bead-spring type potential complemented by a bending potential is used, allowing variation of chain stiffness from completely flexible coils to rod-like polymers whose persistence length by far exceeds their contour length. Solvent is only implicitly included, monomer-monomer interactions being purely repulsive, while two types of attractive wall-monomer interactions are considered: (i) a strongly attractive Mie-type potential, appropriate for a strictly structureless wall, and (ii) a corrugated wall formed by Lennard-Jones particles arranged on a square lattice. It is found that in dilute solutions the former case leads to the formation of a strongly adsorbed surface layer, and the profile of density and orientational order in the z-direction perpendicular to the wall is predicted by DFT in nice agreement with MD. While for very low bulk densities a Kosterlitz-Thouless type transition from the isotropic phase to a phase with power-law decay of nematic correlations is suggested to occur in the strongly adsorbed layer, for larger densities a smectic-C phase in the surface layer is detected. No "capillary nematization" effect at higher bulk densities is found in this system, unlike systems with repulsive walls. This finding is attributed to the reduction of the bulk density (in the center of the slit pore) due to polymer adsorption on the attractive wall, for a system studied in the canonical ensemble. Consequently in a system with two attractive walls nematic order in the slit pore can occur only at a higher density than for a bulk system.

Structure factor of blends of solvent-free nanoparticle-organic hybrid materials: density-functional theory and small angle X-ray scattering.

PubMed

Yu, Hsiu-Yu; Srivastava, Samanvaya; Archer, Lynden A; Koch, Donald L

2014-12-07

We investigate the static structure factor S(q) of solvent-free nanoparticle-organic hybrid materials consisting of silica nanocores and space-filling polyethylene glycol coronas using a density-functional theory and small angle X-ray scattering measurements. The theory considers a bidisperse suspension of hard spheres with different radii and tethered bead-spring oligomers with different grafting densities to approximate the polydispersity effects in experiments. The experimental systems studied include pure samples with different silica core volume fractions and the associated mean corona grafting densities, and blends with different mixing ratios of the pure samples, in order to introduce varying polydispersity of corona grafting density. Our scattering experiments and theory show that, compared to the hard-sphere suspension with the same core volume fraction, S(q) for pure samples exhibit both substantially smaller values at small q and stronger particle correlations corresponding to a larger effective hard core at large q, indicating that the tethered incompressible oligomers enforce a more uniform particle distribution, and the densely grafted brush gives rise to an additional exclusionary effect between the nanoparticles. According to the theory, polydispersity in the oligomer grafting density controls the deviation of S(q) from the monodisperse system at smaller q, and the interplay of the enhanced effective core size and the entropic attraction among the particles is responsible for complex variations in the particle correlations at larger q. The successful comparison between the predictions and the measurements for the blends further suggests that S(q) can be used to assess the uniformity of grafting density in polymer-grafted nanoparticle materials.

Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges.

PubMed

Lara, A; Riquelme, M; Vöhringer-Martinez, E

2018-05-11

Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases, the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account, and when the energy needed to polarize the electron density of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogs. Comparison of the two partitioning methods, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS), revealed some deficiencies in the Hirshfeld-I method related to the unstable isolated anionic nitrogen pro-atom used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

A new ether-based electrolyte for dendrite-free lithium-metal based rechargeable batteries

PubMed Central

Miao, Rongrong; Yang, Jun; Xu, Zhixin; Wang, Jiulin; Nuli, Yanna; Sun, Limin

2016-01-01

A new ether-based electrolyte to match lithium metal electrode is prepared by introducing 1, 4-dioxane as co-solvent into lithium bis(fluorosulfonyl)imide/1,2-dimethoxyethane solution. Under the synergetic effect of solvents and salt, this simple liquid electrolyte presents stable Li cycling with dendrite-free Li deposition even at relatively high current rate, high coulombic efficiency of ca. 98%, and good anodic stability up to ~4.87 V vs Li RE. Its excellent performance will open up a new possibility for high energy-density rechargeable Li metal battery system. PMID:26878890

Density functional theory of gas-liquid phase separation in dilute binary mixtures

NASA Astrophysics Data System (ADS)

Okamoto, Ryuichi; Onuki, Akira

2016-06-01

We examine statics and dynamics of phase-separated states of dilute binary mixtures using density functional theory. In our systems, the difference of the solvation chemical potential between liquid and gas Δ {μ\\text{s}} (the Gibbs energy of transfer) is considerably larger than the thermal energy {{k}\\text{B}}T for each solute particle and the attractive interaction among the solute particles is weaker than that among the solvent particles. In these conditions, the saturated vapor pressure increases by {{k}\\text{B}}Tn2\\ell\\exp ≤ft(Δ {μ\\text{s}}/{{k}\\text{B}}T\\right) , where n2\\ell is the solute density added in liquid. For \\exp ≤ft(Δ {μ\\text{s}}/{{k}\\text{B}}T\\right)\\gg 1 , phase separation is induced at low solute densities in liquid and the new phase remains in gaseous states, even when the liquid pressure is outside the coexistence curve of the solvent. This explains the widely observed formation of stable nanobubbles in ambient water with a dissolved gas. We calculate the density and stress profiles across planar and spherical interfaces, where the surface tension decreases with increasing interfacial solute adsorption. We realize stable solute-rich bubbles with radius about 30 nm, which minimize the free energy functional. We then study dynamics around such a bubble after a decompression of the surrounding liquid, where the bubble undergoes a damped oscillation. In addition, we present some exact and approximate expressions for the surface tension and the interfacial stress tensor.

The roles of the solute and solvent cavities in charge-transfer-to-solvent dynamics: Ultrafast studies of potasside and sodide in diethyl ether

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

Cavanagh, Molly C.; Young, Ryan M.; Schwartz, Benjamin J.

2008-10-07

Although electron transfer reactions are among the most fundamental in chemistry, it is still not clear how to isolate the roles of the solute and solvent in moving charge between reactants in solution. In this paper, we address this question by comparing the ultrafast charge-transfer-to-solvent (CTTS) dynamics of potasside (K{sup -}) in diethyl ether (DEE) to those of sodide (Na{sup -}) in both DEE and tetrahydrofuran (THF). We find that for sodide in both DEE and THF, CTTS excitation leads to delayed ejection of a solvated electron that appears with its equilibrium absorption spectrum. This indicates that the ejected electronsmore » are localized in pre-existing solvent traps, suggesting that the structure of liquid DEE is characterized by cavities that are favorably polarized to localize an excess electron, as has been previously shown is the case for liquid THF. We also find that the geminate recombination dynamics following CTTS excitation of sodide in THF and DEE are similar, suggesting that the nature of the CTTS excited states and their coupling to the electronic states supported by the naturally occurring solvent cavities are similar in the two solvents. In contrast, the geminate recombination dynamics of potasside and sodide in DEE are different, with red-edge excitation of the K{sup -} CTTS band producing a greater number of long-lived electrons than is seen following the corresponding red-edge excitation of the Na{sup -} CTTS band. This indicates that the CTTS excited states of K{sup -} are better able to couple to the electronic states supported by the naturally occurring solvent cavities, allowing us to compare the energetic positions of the potasside and sodide ground and CTTS excited states on a common absolute scale. Finally, we also observe a strong transient absorption following the CTTS excitation of potasside in DEE that correlates well with the 766 nm position of the gas-phase potassium D-line. The data indicate that CTTS excitation of alkali metal anions essentially instantaneously produces a gas-phase-like neutral alkali metal atom, which then spontaneously undergoes partial ejection of the remaining valence electron to form a neutral alkali metal cation:solvated electron tight-contact pair.« less

Heterogeneity in a room-temperature ionic liquid: persistent local environments and the red-edge effect.

PubMed

Hu, Zhonghan; Margulis, Claudio J

2006-01-24

In this work, we investigate the slow dynamics of 1-butyl-3-methylimidazolium hexafluorophosphate, a very popular room-temperature ionic solvent. Our study predicts the existence of heterogeneity in the liquid and shows that this heterogeneity is the underlying microscopic cause for the recently reported "red-edge effect" (REE) observed in the study of fluorescence of the organic probe 2-amino-7-nitrofluorene. This theoretical work explains in microscopic terms the relation between REE and dynamic heterogeneity in a room-temperature ionic liquid (IL). The REE is typical of micellar or colloidal systems, which are characterized by microscopic environments that are structurally very different. In contrast, in the case of this room-temperature IL, the REE occurs because of the long period during which molecules are trapped in quasistatic local solvent cages. This trapping time, which is longer than the lifetime of the excited-state probe, together with the inability of the surroundings to adiabatically relax, induces a set of site-specific spectroscopic responses. Subensembles of fluorescent molecules associated with particular local environments absorb and emit at different frequencies. We describe in detail the absorption wavelength-dependent emission spectra of 2-amino-7-nitrofluorene and show that this dependence on lambda(ex) is characteristic of the IL and, as is to be expected, is absent in the case of a normal solvent such as methanol.

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

PubMed

Hrnjez, Bruce J; Sultan, Samuel T; Natanov, Georgiy R; Kastner, David B; Rosman, Michael R

2005-11-17

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

A novel carbon electrode material for highly improved EDLC performance.

PubMed

Fang, Baizeng; Binder, Leo

2006-04-20

Porous materials, developed by grafting functional groups through chemical surface modification with a surfactant, represent an innovative concept in energy storage. This work reports, in detail, the first practical realization of a novel carbon electrode based on grafting of vinyltrimethoxysilane (vtmos) functional group for energy storage in electric double layer capacitor (EDLC). Surface modification with surfactant vtmos enhances the hydrophobisation of activated carbon and the affinity toward propylene carbonate (PC) solvent, which improves the wettability of activated carbon in the electrolyte solution based on PC solvent, resulting in not only a lower resistance to the transport of electrolyte ions within micropores of activated carbon but also more usable surface area for the formation of electric double layer, and accordingly, higher specific capacitance, energy density, and power capability available from the capacitor based on modified carbon. Especially, the effects from surface modification become superior at higher discharge rate, at which much better EDLC performance (i.e., much higher energy density and power capability) has been achieved by the modified carbon, suggesting that the modified carbon is a novel and very promising electrode material of EDLC for large current applications where both high energy density and power capability are required.

Salting out of methane by sodium chloride: A scaled particle theory study.

PubMed

Graziano, Giuseppe

2008-08-28

The salting out of methane by adding NaCl to water at 25 degrees C and 1 atm is investigated by calculating the work of cavity creation by means of scaled particle theory and the methane-solvent energy of attraction. The latter quantity changes to little extent on passing from pure water to an aqueous 4M NaCl solution, whereas the magnitude of the work of cavity creation increases significantly, accounting for the salting out effect. There is quantitative agreement between the experimental values of the hydration Gibbs energy and the calculated ones. The behavior of the work of cavity creation is due to the increase in the volume packing density of NaCl solutions, since the average effective molecular diameter does not change, being always 2.80 A. The same approach allows the rationalization of the difference in methane salting out along the alkali chloride series. These results indicate that, fixed the aqueous solution density, the solubility of nonpolar species is mainly determined by the effective diameter of solvent molecules and the corresponding volume packing density. There is no need to take into account the H-bond rearrangement because it is characterized by an almost complete enthalpy-entropy compensation.

Development of a poly(dimethylacrylamide) based matrix material for solid phase high density peptide array synthesis employing a laser based material transfer

NASA Astrophysics Data System (ADS)

Ridder, Barbara; Foertsch, Tobias C.; Welle, Alexander; Mattes, Daniela S.; von Bojnicic-Kninski, Clemens M.; Loeffler, Felix F.; Nesterov-Mueller, Alexander; Meier, Michael A. R.; Breitling, Frank

2016-12-01

Poly(dimethylacrylamide) (PDMA) based matrix materials were developed for laser-based in situ solid phase peptide synthesis to produce high density arrays. In this specific array synthesis approach, amino acid derivatives are embedded into a matrix material, serving as a ;solid; solvent material at room temperature. Then, a laser pulse transfers this mixture to the target position on a synthesis slide, where the peptide array is synthesized. Upon heating above the glass transition temperature of the matrix material, it softens, allowing diffusion of the amino acid derivatives to the synthesis surface and serving as a solvent for peptide bond formation. Here, we synthesized PDMA six-arm star polymers, offering the desired matrix material properties, using atom transfer radical polymerization. With the synthesized polymers as matrix material, we structured and synthesized arrays with combinatorial laser transfer. With densities of up to 20,000 peptide spots per cm2, the resolution could be increased compared to the commercially available standard matrix material. Time-of-Flight Secondary Ion Mass Spectrometry experiments revealed the penetration behavior of an amino acid derivative into the prepared acceptor synthesis surface and the effectiveness of the washing protocols.

Mesoscale Simulation and Machine Learning of Asphaltene Aggregation Phase Behavior and Molecular Assembly Landscapes.

PubMed

Wang, Jiang; Gayatri, Mohit A; Ferguson, Andrew L

2017-05-11

Asphaltenes constitute the heaviest fraction of the aromatic group in crude oil. Aggregation and precipitation of asphaltenes during petroleum processing costs the petroleum industry billions of dollars each year due to downtime and production inefficiencies. Asphaltene aggregation proceeds via a hierarchical self-assembly process that is well-described by the Yen-Mullins model. Nevertheless, the microscopic details of the emergent cluster morphologies and their relative stability under different processing conditions remain poorly understood. We perform coarse-grained molecular dynamics simulations of a prototypical asphaltene molecule to establish a phase diagram mapping the self-assembled morphologies as a function of temperature, pressure, and n-heptane:toluene solvent ratio informing how to control asphaltene aggregation by regulating external processing conditions. We then combine our simulations with graph matching and nonlinear manifold learning to determine low-dimensional free energy surfaces governing asphaltene self-assembly. In doing so, we introduce a variant of diffusion maps designed to handle data sets with large local density variations, and report the first application of many-body diffusion maps to molecular self-assembly to recover a pseudo-1D free energy landscape. Increasing pressure only weakly affects the landscape, serving only to destabilize the largest aggregates. Increasing temperature and toluene solvent fraction stabilizes small cluster sizes and loose bonding arrangements. Although the underlying molecular mechanisms differ, the strikingly similar effect of these variables on the free energy landscape suggests that toluene acts upon asphaltene self-assembly as an effective temperature.

Pseudolatex preparation using a novel emulsion-diffusion process involving direct displacement of partially water-miscible solvents by distillation.

PubMed

Quintanar-Guerrero, D; Allémann, E; Fessi, H; Doelker, E

1999-10-25

Pseudolatexes were obtained by a new process based on an emulsification-diffusion technique involving partially water-miscible solvents. The preparation method consisted of emulsifying an organic solution of polymer (saturated with water) in an aqueous solution of a stabilizing agent (saturated with solvent) using conventional stirrers, followed by direct solvent distillation. The technique relies on the rapid displacement of the solvent from the internal into the external phase which thereby provokes polymer aggregation. Nanoparticle formation is believed to occur because rapid solvent diffusion produces regions of local supersaturation near the interface, and nanoparticles are formed due to the ensuing interfacial phase transformations and polymer aggregation that occur in these interfacial domains. Using this method, it was possible to prepare pseudolatexes of biodegradable and non-biodegradable polymers such as poly(D,L-lactic acid) and poly(epsilon-caprolactone), Eudragit E, cellulose acetate phthalate, cellulose acetate trimellitate using ethyl acetate or 2-butanone as partially water-miscible solvents and poly(vinyl alcohol) or poloxamer 407 as stabilizing agent. A transition from nano- to microparticles was observed at high polymer concentrations. At concentrations above 30% w/v of Eudragit E in ethyl acetate or cellulose acetate phthalate in 2-butanone only microparticles were obtained. This behaviour was attributed to decreased transport of polymer molecules into the aqueous phase.

Influence of a strong sample solvent on analyte dispersion in chromatographic columns.

PubMed

Mishra, Manoranjan; Rana, Chinar; De Wit, A; Martin, Michel

2013-07-05

In chromatographic columns, when the eluting strength of the sample solvent is larger than that of the carrier liquid, a deformation of the analyte zone occurs because its frontal part moves at a relatively high velocity due to a low retention factor in the sample solvent while the rear part of the analyte zone is more retained in the carrier liquid and hence moves at a lower velocity. The influence of this solvent strength effect on the separation of analytes is studied here theoretically using a mass balance model describing the spatio-temporal evolution of the eluent, the sample solvent and the analyte. The viscosity of the sample solvent and carrier fluid is supposed to be the same (i.e. no viscous fingering effects are taken into account). A linear isotherm adsorption with a retention factor depending upon the local concentration of the liquid phase is considered. The governing equations are numerically solved by using a Fourier spectral method and parametric studies are performed to analyze the effect of various governing parameters on the dispersion and skewness of the analyte zone. The distortion of this zone is found to depend strongly on the difference in eluting strength between the mobile phase and the sample solvent as well as on the sample volume. Copyright © 2013 Elsevier B.V. All rights reserved.

Mechanisms of solvent resistance mediated by interplay of cellular factors in Pseudomonas putida.

PubMed

Ramos, Juan-Luis; Sol Cuenca, Maria; Molina-Santiago, Carlos; Segura, Ana; Duque, Estrella; Gómez-García, María R; Udaondo, Zulema; Roca, Amalia

2015-07-01

A number of microorganisms have the ability to thrive in the presence of a range of toxic solvents. Tolerance to these chemicals is a multifactorial process, meaning that bacterial cells use a set of physiological and gene expression changes to overcome the damage imparted by these chemicals. This review focuses mainly on issues related to tolerance to aromatic hydrocarbons and butanol in Pseudomonas, although other microorganisms are also discussed. Pseudomonas putida strains contain a circular chromosome of approximately 6 Mbp which encodes about 5300 genes. A combination of physiological and biochemical assays, a genome-wide collection of mutants and several omics approaches have provided useful information to help identify functions involved in solvent tolerance in P. putida. The solvent response involves fine-tuning of lipid fluidity to adjust membrane functions including impermeabilization, activation of a general stress-response system, increased energy generation and induction of specific efflux pumps that extrude solvents to the medium. These responses are modulated at the transcriptional level by local and global regulators as well as by a number of sRNAs whose levels fluctuate with the presence of solvents in the environment. Taken as a whole these regulatory inputs orchestrate the complex network of metabolic responses observed after solvent addition. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Additive effect on reductive decomposition and binding of carbonate-based solvent toward solid electrolyte interphase formation in lithium-ion battery.

PubMed

Ushirogata, Keisuke; Sodeyama, Keitaro; Okuno, Yukihiro; Tateyama, Yoshitaka

2013-08-14

The solid-electrolyte interphase (SEI) formed through the reductive decomposition of solvent molecules plays a crucial role in the stability and capability of a lithium-ion battery (LIB). Here we investigated the effects of adding vinylene carbonate (VC) to ethylene carbonate (EC) solvent, a typical electrolyte in LIBs, on the reductive decomposition. We focused on both thermodynamics and kinetics of the possible processes and used density functional theory-based molecular dynamics with explicit solvent and Blue-moon ensemble technique for the free energy change. We considered Li(+) in only EC solvent (EC system) and in EC solvent with a VC additive (EC/VC system) to elucidate the additive effects. In addition to clarifying the equilibrium properties, we evaluated the free energy changes along several EC or VC decomposition pathways under one-electron (1e) reduction condition. Two-electron (2e) reduction and attacks of anion radicals to intact molecules were also examined. The present results completely reproduce the gaseous products observed in the experiments. We also found a new mechanism involving the VC additive: the VC additive preferentially reacts with the EC anion radical to suppress the 2e reduction of EC and enhance the initial SEI formation, contrary to the conventional scenario in which VC additive is sacrificially reduced and its radical oligomerization becomes the source of SEI. Because our mechanism needs only 1e reduction, the irreversible capacity at the SEI formation will decrease, which is also consistent with the experimental observations. These results reveal the primary role of VC additive in the EC solvent.

Derivatization and diffusive motion of molecular fullerenes: Ab initio and atomistic simulations

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

Berdiyorov, G., E-mail: gberdiyorov@qf.org.qa; Tabet, N.; Harrabi, K.

2015-07-14

Using first principles density functional theory in combination with the nonequilibrium Green's function formalism, we study the effect of derivatization on the electronic and transport properties of C{sub 60} fullerene. As a typical example, we consider [6,6]-phenyl-C{sub 61}-butyric acid methyl ester (PCBM), which forms one of the most efficient organic photovoltaic materials in combination with electron donating polymers. Extra peaks are observed in the density of states (DOS) due to the formation of new electronic states localized at/near the attached molecule. Despite such peculiar behavior in the DOS of an isolated molecule, derivatization does not have a pronounced effect onmore » the electronic transport properties of the fullerene molecular junctions. Both C{sub 60} and PCBM show the same response to finite voltage biasing with new features in the transmission spectrum due to voltage induced delocalization of some electronic states. We also study the diffusive motion of molecular fullerenes in ethanol solvent and inside poly(3-hexylthiophene) lamella using reactive molecular dynamics simulations. We found that the mobility of the fullerene reduces considerably due to derivatization; the diffusion coefficient of C{sub 60} is an order of magnitude larger than the one for PCBM.« less

Electron Transfer Mechanism in Gold Surface Modified with Self-Assembly Monolayers from First Principles

NASA Astrophysics Data System (ADS)

Lima, Filipe C. D. A.; Iost, Rodrigo M.; Crespilho, Frank N.; Caldas, Marília J.; Calzolari, Arrigo; Petrilli, Helena M.

2013-03-01

We report the investigation of electron tunneling mechanism of peptide ferrocenyl-glycylcystamine self-assembled monolayers (SAMs) onto Au (111) electrode surfaces. Recent experimental investigations showed that electron transfer in peptides can occur across long distances by separating the donor from the acceptor. This mechanism can be further fostered by the presence of electron donor terminations of Fc terminal units on SAMs but the charge transfer mechanism is still not clear. We study the interaction of the peptide ferrocenyl-glycylcystamine on the Au (111) from first principles calculations to evaluate the electron transfer mechanism. For this purpose, we used the Kohn Sham (KS) scheme for the Density Functional Theory (DFT) as implemented in the Quantum-ESPRESSO suit of codes, using Vandebilt ultrasoft pseudopotentials and GGA-PBE exchange correlation functional to evaluate the ground-state atomic and electronic structure of the system. The analysis of KS orbital at the Fermi Energy showed high electronic density localized in Fc molecules and the observation of a minor contribution from the solvent and counter ion. Based on the results, we infer evidences of electron tunneling mechanism from the molecule to the Au(111). We acknowledge FAPESP for grant support. Also, LCCA/USP, RICE and CENAPAD for computational resources.

Wang-Landau density of states based study of the folding-unfolding transition in the mini-protein Trp-cage (TC5b)

NASA Astrophysics Data System (ADS)

Singh, Priya; Sarkar, Subir K.; Bandyopadhyay, Pradipta

2014-07-01

We present the results of a high-statistics equilibrium study of the folding/unfolding transition for the 20-residue mini-protein Trp-cage (TC5b) in water. The ECEPP/3 force field is used and the interaction with water is treated by a solvent-accessible surface area method. A Wang-Landau type simulation is used to calculate the density of states and the conditional probabilities for the various values of the radius of gyration and the number of native contacts at fixed values of energy—along with a systematic check on their convergence. All thermodynamic quantities of interest are calculated from this information. The folding-unfolding transition corresponds to a peak in the temperature dependence of the computed specific heat. This is corroborated further by the structural signatures of folding in the distributions for radius of gyration and the number of native contacts as a function of temperature. The potentials of mean force are also calculated for these variables, both separately and jointly. A local free energy minimum, in addition to the global minimum, is found in a temperature range substantially below the folding temperature. The free energy at this second minimum is approximately 5 kBT higher than the value at the global minimum.

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.

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.

Apparatus and methods for regeneration of precipitating solvent

DOEpatents

Liu, Guohai; Vimalchand, Pannalal; Peng, Wan Wang; Bonsu, Alexander

2015-08-25

A regenerator that can handle rich loaded chemical solvent containing precipitated absorption reaction products is disclosed. The invention is particularly suitable for separating CO.sub.2 from large gas streams that are typical of power plant processes. The internally circulating liquid stream in the regenerator (ICLS regenerator) rapidly heats-up the in-coming rich solvent stream in a downcomer standpipe as well as decreases the overall concentration of CO.sub.2 in the mixed stream. Both these actions lead to dissolution of precipitates. Any remaining precipitate further dissolves as heat is transferred to the mixed solution with an inverted bayonet tube heat exchanger in the riser portion of the regenerator. The evolving CO.sub.2 bubbles in the riser portion of the regenerator lead to substantial gas hold-up and the large density difference between the solutions in the downcomer standpipe and riser portions promotes internal circulation of the liquid stream in the regenerator. As minor amounts of solvent components present in the exit gas stream are condensed and returned back to the regenerator, pure CO.sub.2 gas stream exits the disclosed regenerator and condenser system.

UV-Vis spectrophotometric studies of self-oxidation/dissociation of quaternary ammonium permanganates (QAP) - impact of solvent polarity

NASA Astrophysics Data System (ADS)

Bank, Suraj Prakash; Guru, Partha Sarathi; Dash, Sukalyan

2015-05-01

Self-oxidation/dissociation of some quaternary ammonium permanganates (QAPs), such as cetyltrimethylammonium permanganate (CTAP) and tetrabutylammonium permanganate (TBAP), have been studied spectrophotometrically in six different organic solvent media of different polarities wherein the compounds show good solubility and stability. The optical densities of the substrates at zero time (ODo) and first-order rate constants of dissociation (k1) have been determined from their successive scanning for 40 min. At comparable experimental conditions, absorption capabilities of the substrates are compared from the ODo values in various organic media; the stability of the solutions is compared from the successive scan spectra in those media. The ODo values and the k1 values have been plotted against some solvent parameters to understand their effects on the absorbance and reactivity of the QAPs. These data are also subjected to multiple regression analysis to explain the influence of various solvent parameters on the ion-pairing properties of the substrates, thus elucidating their effects on the process of self-oxidation/dissociation of the substrates.

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.

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.

Annotation of the Clostridium Acetobutylicum Genome

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

Daly, M. J.

The genome sequence of the solvent producing bacterium Clostridium acetobutylicum ATCC824, has been determined by the shotgun approach. The genome consists of a 3.94 Mb chromosome and a 192 kb megaplasmid that contains the majority of genes responsible for solvent production. Comparison of C. acetobutylicum to Bacillus subtilis reveals significant local conservation of gene order, which has not been seen in comparisons of other genomes with similar, or, in some cases, closer, phylogenetic proximity. This conservation allows the prediction of many previously undetected operons in both bacteria.

Automated Solvent Seaming of Large Polyimide Membranes

NASA Technical Reports Server (NTRS)

Rood, Robert; Moore, James D.; Talley, Chris; Gierow, Paul A.

2006-01-01

A solvent-based welding process enables the joining of precise, cast polyimide membranes at their edges to form larger precise membranes. The process creates a homogeneous, optical-quality seam between abutting membranes, with no overlap and with only a very localized area of figure disturbance. The seam retains 90 percent of the strength of the parent material. The process was developed for original use in the fabrication of wide-aperture membrane optics, with areal densities of less than 1 kg/m2, for lightweight telescopes, solar concentrators, antennas, and the like to be deployed in outer space. The process is just as well applicable to the fabrication of large precise polyimide membranes for flat or inflatable solar concentrators and antenna reflectors for terrestrial applications. The process is applicable to cast membranes made of CP1 (or equivalent) polyimide. The process begins with the precise fitting together and fixturing of two membrane segments. The seam is formed by applying a metered amount of a doped solution of the same polyimide along the abutting edges of the membrane segments. After the solution has been applied, the fixtured films are allowed to dry and are then cured by convective heating. The weld material is the same as the parent material, so that what is formed is a homogeneous, strong joint that is almost indistinguishable from the parent material. The success of the process is highly dependent on formulation of the seaming solution from the correct proportion of the polyimide in a suitable solvent. In addition, the formation of reliable seams depends on the deposition of a precise amount of the seaming solution along the seam line. To ensure the required precision, deposition is performed by use of an automated apparatus comprising a modified commercially available, large-format, ink-jet print head on an automated positioning table. The printing head jets the seaming solution into the seam area at a rate controlled in coordination with the movement of the positioning table.

A path integral molecular dynamics study of the hyperfine coupling constants of the muoniated and hydrogenated acetone radicals

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

Oba, Yuki; Kawatsu, Tsutomu; Tachikawa, Masanori, E-mail: tachi@yokohama-cu.ac.jp

2016-08-14

The on-the-fly ab initio density functional path integral molecular dynamics (PIMD) simulations, which can account for both the nuclear quantum effect and thermal effect, were carried out to evaluate the structures and “reduced” isotropic hyperfine coupling constants (HFCCs) for muoniated and hydrogenated acetone radicals (2-muoxy-2-propyl and 2-hydoxy-2-propyl) in vacuo. The reduced HFCC value from a simple geometry optimization calculation without both the nuclear quantum effect and thermal effect is −8.18 MHz, and that by standard ab initio molecular dynamics simulation with only the thermal effect and without the nuclear quantum effect is 0.33 MHz at 300 K, where these twomore » methods cannot distinguish the difference between muoniated and hydrogenated acetone radicals. In contrast, the reduced HFCC value of the muoniated acetone radical by our PIMD simulation is 32.1 MHz, which is about 8 times larger than that for the hydrogenated radical of 3.97 MHz with the same level of calculation. We have found that the HFCC values are highly correlated with the local molecular structures; especially, the Mu—O bond length in the muoniated acetone radical is elongated due to the large nuclear quantum effect of the muon, which makes the expectation value of the HFCC larger. Although our PIMD result calculated in vacuo is about 4 times larger than the measured experimental value in aqueous solvent, the ratio of these HFCC values between muoniated and hydrogenated acetone radicals in vacuo is in reasonable agreement with the ratio of the experimental values in aqueous solvent (8.56 MHz and 0.9 MHz); the explicit presence of solvent molecules has a major effect on decreasing the reduced muon HFCC of in vacuo calculations for the quantitative reproduction.« less

Nontrivial behavior of water in the vicinity and inside lipid bilayers as probed by molecular dynamics simulations.

PubMed

Krylov, Nikolay A; Pentkovsky, Vladimir M; Efremov, Roman G

2013-10-22

The atomic-scale diffusion of water in the presence of several lipid bilayers mimicking biomembranes is characterized via unconstrained molecular dynamics (MD) simulations. Although the overall water dynamics corresponds well to literature data, namely, the efficient braking near polar head groups of lipids, a number of interesting and biologically relevant details observed in this work have not been sufficiently discussed so far; for instance, the fact that waters "sense" the membrane unexpectedly early, before water density begins to decrease. In this "transitional zone" the velocity distributions of water and their H-bonding patterns deviate from those in the bulk solution. The boundaries of this zone are well preserved even despite the local (<1 nm size) perturbation of the lipid bilayer, thus indicating a decoupling of the surface and bulk dynamics of water. This is in excellent agreement with recent experimental data. Near the membrane surface, water movement becomes anisotropic, that is, solvent molecules preferentially move outward the bilayer. Deep in the membrane interior, the velocities can even exceed those in the bulk solvent and undergo large-scale fluctuations. The analysis of MD trajectories of individual waters in the middle part of the acyl chain region of lipids reveals a number of interesting rare phenomena, such as the fast (ca. 50 ps) breakthrough across the membrane or long-time (up to 750 ps) "roaming" between lipid leaflets. The analysis of these events was accomplished to delineate the mechanisms of spontaneous water permeation inside the hydrophobic membrane core. It was shown that such nontrivial dynamics of water in an "alien" environment is driven by the dynamic heterogeneities of the local bilayer structure and the formation of transient atomic-scale "defects" in it. The picture observed in lipid bilayers is drastically different from that in a primitive membrane mimic, a hydrated cyclohexane slab. The possible biological impact of such phenomena in equilibrated lipid bilayers is discussed.

Incorporation of Hydrogen Bond Angle Dependency into the Generalized Solvation Free Energy Density Model.

PubMed

Ma, Songling; Hwang, Sungbo; Lee, Sehan; Acree, William E; No, Kyoung Tai

2018-04-23

To describe the physically realistic solvation free energy surface of a molecule in a solvent, a generalized version of the solvation free energy density (G-SFED) calculation method has been developed. In the G-SFED model, the contribution from the hydrogen bond (HB) between a solute and a solvent to the solvation free energy was calculated as the product of the acidity of the donor and the basicity of the acceptor of an HB pair. The acidity and basicity parameters of a solute were derived using the summation of acidities and basicities of the respective acidic and basic functional groups of the solute, and that of the solvent was experimentally determined. Although the contribution of HBs to the solvation free energy could be evenly distributed to grid points on the surface of a molecule, the G-SFED model was still inadequate to describe the angle dependency of the HB of a solute with a polarizable continuum solvent. To overcome this shortcoming of the G-SFED model, the contribution of HBs was formulated using the geometric parameters of the grid points described in the HB coordinate system of the solute. We propose an HB angle dependency incorporated into the G-SFED model, i.e., the G-SFED-HB model, where the angular-dependent acidity and basicity densities are defined and parametrized with experimental data. The G-SFED-HB model was then applied to calculate the solvation free energies of organic molecules in water, various alcohols and ethers, and the log P values of diverse organic molecules, including peptides and a protein. Both the G-SFED model and the G-SFED-HB model reproduced the experimental solvation free energies with similar accuracy, whereas the distributions of the SFED on the molecular surface calculated by the G-SFED and G-SFED-HB models were quite different, especially for molecules having HB donors or acceptors. Since the angle dependency of HBs was included in the G-SFED-HB model, the SFED distribution of the G-SFED-HB model is well described as compared to that of the G-SFED model.

Molecular structure and interactions in the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide.

PubMed

Dhumal, Nilesh R; Noack, Kristina; Kiefer, Johannes; Kim, Hyung J

2014-04-03

Electronic structure theory (density functional and Møller-Plesset perturbation theory) and vibrational spectroscopy (FT-IR and Raman) are employed to study molecular interactions in the room-temperature ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide. Different conformers of a cation-anion pair based on their molecular interactions are simulated in the gas phase and in a dielectric continuum solvent environment. Although the ordering of conformers in energy varies with theoretical methods, their predictions for three lowest energy conformers in the gas phase are similar. Strong C-H---N interactions between the acidic hydrogen atom of the cation imidazole ring and the nitrogen atom of the anion are predicted for either the lowest or second lowest energy conformer. In a continuum solvent, different theoretical methods yield the same ion-pair conformation for the lowest energy state. In both phases, the density functional method predicts that the anion is in a trans conformation in the lowest energy ion pair state. The theoretical results are compared with experimental observations from Raman scattering and IR absorption spectroscopies and manifestations of the molecular interactions in the vibrational spectra are discussed. The directions of the frequency shifts of the characteristic vibrations relative to the free anion and cation are explained by calculating the difference electron density coupled with electron density topography.

Use of limonene in countercurrent chromatography: a green alkane substitute.

PubMed

Faure, Karine; Bouju, Elodie; Suchet, Pauline; Berthod, Alain

2013-05-07

Counter-current chromatography (CCC) is a preparative separation technique working with the two liquid phases of a biphasic liquid system. One phase is used as the mobile phase when the other, the stationary phase, is held in place by centrifugal fields. Limonene is a biorenewable cycloterpene solvent coming from orange peel waste. It was evaluated as a possible substitute for heptane in CCC separations. The limonene/methanol/water and heptane/methanol/water phase diagrams are very similar at room temperature. The double bonds of the limonene molecule allows for possible π-π interactions with solutes rendering limonene slightly more polar than heptane giving small differences in solute partition coefficients in the two systems. The 24% higher limonene density is a difference with heptane that has major consequences in CCC. The polar and apolar phases of the limonene/methanol/water 10/9/1 v/v have -0.025 g/cm(3) density difference (lower limonene phase) compared to +0.132 g/cm(3) with heptane (upper heptane phase). This precludes the use of this limonene system with hydrodynamic CCC columns that need significant density difference to retain a liquid stationary phase. It is an advantage with hydrostatic CCC columns because density difference is related to the working pressure drop: limonene allows one to work with high centrifugal fields and moderate pressure drop. Limonene has the capability to be a "green" alternative to petroleum-based solvents in CCC applications.

Synthesis and Properties of Cross-Linked Polyamide Aerogels

NASA Technical Reports Server (NTRS)

Williams, Jarrod; Meador, Mary Ann; McCorkle, Linda

2014-01-01

We report our ongoing research on polyamide aerogels made by step growth polymerization using a combination of terephthaloyl chloride, isophthaloyl chloride and m-phenylenediamine. Crosslinking of the amine capped polymer chains with 1,3,5-benzenetricarbonyl trichloride causes gelation in as little as two to five minutes. Removing the reaction solvent is accomplished through solvent exchange, followed by drying using supercritical CO2 extraction to give colorless aerogels with densities ranging from 0.07 to 0.33 grams per cubic centimeter and surface areas as high as 440 square meters per gram. Statistical experimental design methodology has been utilized to investigate dependence of properties of these aerogels, such as density, compressive modulus, and surface area, on changes in fabrication parameters including formulated number of amide oligomer repeat units (n-value), acid chloride (meta, para or combination), and solids concentration of solution used for gelation. For example, the density of these materials was found to be dependent on the acid chloride type and the solids concentration, but n was not a significant variable. However, surface area was significantly influenced by all three parameters. The polyamide aerogels represent a potential cost savings over previously reported polyimide aerogels, since monomers are all inexpensive and commercially available. Surface area and density were both highest when 100 terephthaloyl chloride was used but a combination of 5 solid concentration, 100 terephthaloyl chloride and n of 20 gave the best combination of properties.

Structural characterization, solvent effects on nuclear magnetic shielding tensors, experimental and theoretical DFT studies on the vibrational and NMR spectra of 3-(acrylamido)phenylboronic acid

NASA Astrophysics Data System (ADS)

Alver, Özgür; Kaya, Mehmet Fatih; Dikmen, Gökhan

2015-12-01

Structural elucidation of 3-(acrylamido)phenylboronic acid (C9H10BNO3) was carried out with 1H, 13C and HETCOR NMR techniques. Solvent effects on nuclear magnetic shielding tensors were examined with deuterated dimethyl sulfoxide, acetone, methanol and water solvents. The correct order of appearance of carbon and hydrogen atoms on NMR scale from highest magnetic field region to the lowest one were investigated using different types of theoretical levels and the details of the levels were presented in this study. Stable structural conformers and vibrational band analysis of the title molecule (C9H10BNO3) were studied both experimental and theoretical viewpoints using FT-IR, Raman spectroscopic methods and density functional theory (DFT). FT-IR and Raman spectra were obtained in the region of 4000-400 cm-1, and 3700-10 cm-1, respectively. Becke-3-Lee-Yang-Parr (B3LYP) hybrid density functional theory method with 6-31++G(d, p) basis set was included in the search for optimized structures and vibrational wavenumbers. Experimental and theoretical results show that after application of a suitable scaling factor density functional B3LYP method resulted in acceptable results for predicting vibrational wavenumbers except OH and NH stretching modes which is most likely arising from increasing unharmonicity in the high wave number region and possible intra and inter molecular interaction at OH edges those of which are not fully taken into consideration in theoretical processes. To make a more quantitative vibrational assignments, potential energy distribution (PED) values were calculated using VEDA 4 (Vibrational Energy Distribution Analysis) program.

Low-density solvent based ultrasound-assisted emulsification microextraction and on-column derivatization combined with gas chromatography-mass spectrometry for the determination of carbamate pesticides in environmental water samples.

PubMed

Guo, Liang; Lee, Hian Kee

2012-04-27

A fast and efficient method for the determination of trace level of carbamate pesticides using a lower-density-than-water solvent for ultrasound-assisted emulsification microextraction coupled to on-column derivatization and analysis by GC-MS has been developed and studied. In this approach, a soft plastic Pasteur pipette was employed as a convenient extraction device. Fifty microliters of extraction solvent, of lower density than water, was injected into the sample solution held in the pipette. The latter was immediately immersed in an ultrasound water bath to form an emulsion. After 2 min extraction, the emulsion was fractionated into two layers by centrifugation. The upper layer (organic extract) could be collected conveniently by squeezing the bulb of the pipette, now held upside down, to move it into the narrow stem of the device, facilitating its retrieval for analysis. The extract was then combined with trimethylphenylammonium hydroxide and directly injected into a gas chromatography-mass spectrometry (GC-MS) system for on-column derivatization and analysis. The on-column derivatization provided an added convenience (since a separate step was not necessary). Parameters affecting the derivatization and extraction were investigated. Under the most favorable conditions, the method demonstrated high extraction efficiency with low limits of detection of between 0.01 and 0.1 μg/L, good linearity in the range of 0.05-50 μg/L, to 0.5-100 μg/L, and good repeatability (RSD below 9.2%, n=5). The proposed method was evaluated by determining carbamate pesticides in river water samples. Copyright © 2012 Elsevier B.V. All rights reserved.

Reverse Non-Equilibrium Molecular Dynamics Demonstrate That Surface Passivation Controls Thermal Transport at Semiconductor-Solvent Interfaces.

PubMed

Hannah, Daniel C; Gezelter, J Daniel; Schaller, Richard D; Schatz, George C

2015-06-23

We examine the role played by surface structure and passivation in thermal transport at semiconductor/organic interfaces. Such interfaces dominate thermal transport in semiconductor nanomaterials owing to material dimensions much smaller than the bulk phonon mean free path. Utilizing reverse nonequilibrium molecular dynamics simulations, we calculate the interfacial thermal conductance (G) between a hexane solvent and chemically passivated wurtzite CdSe surfaces. In particular, we examine the dependence of G on the CdSe slab thickness, the particular exposed crystal facet, and the extent of surface passivation. Our results indicate a nonmonotonic dependence of G on ligand-grafting density, with interfaces generally exhibiting higher thermal conductance for increasing surface coverage up to ∼0.08 ligands/Å(2) (75-100% of a monolayer, depending on the particular exposed facet) and decreasing for still higher coverages. By analyzing orientational ordering and solvent penetration into the ligand layer, we show that a balance of competing effects is responsible for this nonmonotonic dependence. Although the various unpassivated CdSe surfaces exhibit similar G values, the crystal structure of an exposed facet nevertheless plays an important role in determining the interfacial thermal conductance of passivated surfaces, as the density of binding sites on a surface determines the ligand-grafting densities that may ultimately be achieved. We demonstrate that surface passivation can increase G relative to a bare surface by roughly 1 order of magnitude and that, for a given extent of passivation, thermal conductance can vary by up to a factor of ∼2 between different surfaces, suggesting that appropriately tailored nanostructures may direct heat flow in an anisotropic fashion for interface-limited thermal transport.

Tuning Solvatochromism of Azo Dyes with Intramolecular Hydrogen Bonding in Solution and on Titanium Dioxide Nanoparticles

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

Zhang, Lei; Cole, Jacqueline M.; Liu, Xiaogang

2013-11-25

“Smart tuning” of optical properties in three azo dyes containing intramolecular hydrogen bonding is realized by the judicious control of solvents, when the dyes are in solution or adsorbed onto titanium dioxide nanoparticles. In solution, certain solvents destabilizing intramolecular hydrogen bonding induce a distinctive ≈70 nm “blue-shifted” absorption peak, compared with other solvents. In parallel, the optical properties of azo dye/TiO2 nanocomposites can be tuned using solvents with different hydrogen-bond accepting/donating abilities, giving insights into smart materials and dye-sensitized solar cell device design. It is proposed that intramolecular hydrogen bonding alone plays the leading role in such phenomena, which ismore » fundamentally different to other mechanisms, such as tautomerism and cis–trans isomerization, that explain the optical control of azo dyes. Hybrid density functional theory (DFT) is employed in order to trace the origin of this optical control, and these calculations support the mechanism involving intramolecular hydrogen bonding. Two complementary studies are also reported: 1H NMR spectroscopy is conducted in order to further understand the solvent effects on intramolecular hydrogen bonding; crystal structure analysis from associated research indicates the importance of intramolecular hydrogen bonding on intramolecular charge transfer.« less

Unveiling the mechanism of the promising two-dimensional photoswitch - Hemithioindigo

NASA Astrophysics Data System (ADS)

Li, Donglin; Yang, Yonggang; Li, Chaozheng; Liu, Yufang

2018-07-01

The control of internal molecular motions by outside stimuli is a decisive task in the construction of functional molecules and molecular machines. Light-induced intramolecular rotations of photoswitches have attracted increasing research interests because of the high stability and high reversibility of photoswitches. Recently, Henry et al. reported an unprecedented two-dimensional controlled photoswitch, the hemithioindigo (HTI) derivative Z1, whose single bond rotation in dimethyl sulphoxide (DMSO) solvent and double bond rotation in cyclohexane solvent can be induced by visible light (J. Am. Chem. Soc. 2016, 138, 12,219). Here we investigate the intramolecular rotations of the HTI and Z1 in different polar solvents by time-dependent density functional theory (TDDFT) and Nonadiabatic dynamic simulations. Due to the steric hindrance between methyl and thioindigo fragment, the rotations of Z1 in the excited state are obstructed. Interestingly, the HTI exhibits two distinct rotation paths in DMSO and cyclohexane solvents at about 50 fs. The intermolecular hydrogen bonds between HTI and DMSO play an important role in the rotation of HTI in DMSO solvent. Therefore, the HTI is a more promising two-dimensional photoswitch compared with the Z1. Our finding is thus of fundamental importance to understand the mechanisms of this class of photoswitches and design complex molecular behavior.

Enhanced performance of ferroelectric-based all organic transistors and capacitors through choice of solvent

NASA Astrophysics Data System (ADS)

Knotts, Grant; Bhaumik, Anagh; Ghosh, Kartik; Guha, Suchismita

2014-03-01

We examine the role of solvents in the performance of pentacene devices using the ferroelectric copolymer poly(vinylidene fluoride-co-trifluoroethylene) (PVDF-TrFe) as a gate insulating layer. High dipole moment solvents such as dimethyl sulfoxide used to dissolve the copolymer for spin casting increase the charge carrier mobility in field-effect transistors by nearly an order of magnitude as compared to lower dipole moment solvents. The polarization in Al/PVDF-TrFe/Au metal-ferroelectric-metal devices is also investigated. An increase in remnant polarization of ~ 20% is observed in the sample using dimethyl sulfoxide as the ferroelectric solvent. Interestingly, at low applied electric fields of ~ 100 MV/m a remnant polarization is seen in the high dipole moment device that is nearly 3.5 times larger than the value observed in the lower dipole moment samples, suggesting that the degree of dipolar order is higher at low operating voltages for the high dipole moment device. Detailed analysis of the capacitance characteristics of metal-insulator-semiconductor structure is performed. The density of interface trap states is nearly an order of magnitude lower for the high dipole moment device. This work was supported by National Science Foundation under Grant No. ECCS-1305642.

Molecular surface mesh generation by filtering electron density map.

PubMed

Giard, Joachim; Macq, Benoît

2010-01-01

Bioinformatics applied to macromolecules are now widely spread and in continuous expansion. In this context, representing external molecular surface such as the Van der Waals Surface or the Solvent Excluded Surface can be useful for several applications. We propose a fast and parameterizable algorithm giving good visual quality meshes representing molecular surfaces. It is obtained by isosurfacing a filtered electron density map. The density map is the result of the maximum of Gaussian functions placed around atom centers. This map is filtered by an ideal low-pass filter applied on the Fourier Transform of the density map. Applying the marching cubes algorithm on the inverse transform provides a mesh representation of the molecular surface.

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

Modulation of Folding Internal Friction by Local and Global Barrier Heights.

PubMed

Zheng, Wenwei; de Sancho, David; Best, Robert B

2016-03-17

Recent experiments have revealed an unexpected deviation from a first power dependence of protein relaxation times on solvent viscosity, an effect that has been attributed to "internal friction". One clear source of internal friction in protein dynamics is the isomerization of dihedral angles. A key outstanding question is whether the global folding barrier height influences the measured internal friction, based on the observation that the folding rates of fast-folding proteins, with smaller folding free energy barriers, tend to exhibit larger internal friction. Here, by studying two alanine-based peptides, we find that systematic variation of global folding barrier heights has little effect on the internal friction for folding rates. On the other hand, increasing local torsion angle barriers leads to increased internal friction, which is consistent with solvent memory effects being the origin of the viscosity dependence. Thus, it appears that local torsion transitions determine the viscosity dependence of the diffusion coefficient on the global coordinate and, in turn, internal friction effects on the folding rate.

Low Density Solvent-Based Dispersive Liquid-Liquid Microextraction for the Determination of Synthetic Antioxidants in Beverages by High-Performance Liquid Chromatography

PubMed Central

Çabuk, Hasan; Köktürk, Mustafa

2013-01-01

A simple and efficient method was established for the determination of synthetic antioxidants in beverages by using dispersive liquid-liquid microextraction combined with high-performance liquid chromatography with ultraviolet detection. Butylated hydroxy toluene, butylated hydroxy anisole, and tert-butylhydroquinone were the antioxidants evaluated. Experimental parameters including extraction solvent, dispersive solvent, pH of sample solution, salt concentration, and extraction time were optimized. Under optimal conditions, the extraction recoveries ranged from 53 to 96%. Good linearity was observed by the square of correlation coefficients ranging from 0.9975 to 0.9997. The relative standard deviations ranged from 1.0 to 5.2% for all of the analytes. Limits of detection ranged from 0.85 to 2.73 ng mL−1. The method was successfully applied for determination of synthetic antioxidants in undiluted beverage samples with satisfactory recoveries. PMID:23853535

Effect of solvent on crystallization behavior of xylitol

NASA Astrophysics Data System (ADS)

Hao, Hongxun; Hou, Baohong; Wang, Jing-Kang; Lin, Guangyu

2006-04-01

Effect of organic solvents content on crystallization behavior of xylitol was studied. Solubility and crystallization kinetics of xylitol in methanol-water system were experimentally determined. It was found that the solubility of xylitol at various methanol content all increases with increase of temperature. But it decreases when increasing methanol content at constant temperature. Based on the theory of population balance, the nucleation and growth rates of xylitol in methanol-water mixed solvents were calculated by moments method. From a series of experimental population density data of xylitol gotten from a batch-operated crystallizer, parameters of crystal nucleation and growth rate equations at different methanol content were got by the method of nonlinear least-squares. By analyzing, it was found that the content of methanol had an apparent effect on nucleation and growth rate of xylitol. At constant temperature, the nucleation and growth rate of xylitol all decrease with increase of methanol content.

Manufacturing Methods and Technology. Project Summary Reports

DTIC Science & Technology

1979-06-01

Specification grade Composition C-4 was successfully made in the laboratory using n-octane as the lacquer solvent. A modification of the Wabash method was...lifetime. This is a significant milestone for sealed metal dewar systems for high density mercury- cadmium -tellurium detectors. Such dewars are

Modeling solvation effects in real-space and real-time within density functional approaches

NASA Astrophysics Data System (ADS)

Delgado, Alain; Corni, Stefano; Pittalis, Stefano; Rozzi, Carlo Andrea

2015-10-01

The Polarizable Continuum Model (PCM) can be used in conjunction with Density Functional Theory (DFT) and its time-dependent extension (TDDFT) to simulate the electronic and optical properties of molecules and nanoparticles immersed in a dielectric environment, typically liquid solvents. In this contribution, we develop a methodology to account for solvation effects in real-space (and real-time) (TD)DFT calculations. The boundary elements method is used to calculate the solvent reaction potential in terms of the apparent charges that spread over the van der Waals solute surface. In a real-space representation, this potential may exhibit a Coulomb singularity at grid points that are close to the cavity surface. We propose a simple approach to regularize such singularity by using a set of spherical Gaussian functions to distribute the apparent charges. We have implemented the proposed method in the Octopus code and present results for the solvation free energies and solvatochromic shifts for a representative set of organic molecules in water.

Modeling solvation effects in real-space and real-time within density functional approaches

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

Delgado, Alain; Centro de Aplicaciones Tecnológicas y Desarrollo Nuclear, Calle 30 # 502, 11300 La Habana; Corni, Stefano

2015-10-14

The Polarizable Continuum Model (PCM) can be used in conjunction with Density Functional Theory (DFT) and its time-dependent extension (TDDFT) to simulate the electronic and optical properties of molecules and nanoparticles immersed in a dielectric environment, typically liquid solvents. In this contribution, we develop a methodology to account for solvation effects in real-space (and real-time) (TD)DFT calculations. The boundary elements method is used to calculate the solvent reaction potential in terms of the apparent charges that spread over the van der Waals solute surface. In a real-space representation, this potential may exhibit a Coulomb singularity at grid points that aremore » close to the cavity surface. We propose a simple approach to regularize such singularity by using a set of spherical Gaussian functions to distribute the apparent charges. We have implemented the proposed method in the OCTOPUS code and present results for the solvation free energies and solvatochromic shifts for a representative set of organic molecules in water.« less

Non-radiative decay paths in rhodamines: new theoretical insights.

PubMed

Savarese, Marika; Raucci, Umberto; Adamo, Carlo; Netti, Paolo A; Ciofini, Ilaria; Rega, Nadia

2014-10-14

We individuate a photoinduced electron transfer (PeT) as a quenching mechanism affecting rhodamine B photophysics in solvent. The PeT involves an electron transfer from the carboxylate group to the xanthene ring of rhodamine B. This is finely modulated by the subtle balance of coulombic and non-classical interactions between the carboxyphenyl and xanthene rings, also mediated by the solvent. We propose the use of an electronic density based index, the so called DCT index, as a new tool to assess and quantify the nature of the excited states involved in non-radiative decays near the region of their intersection. In the present case, this analysis allows us to gain insight on the interconversion process from the bright state to the dark state responsible for the quenching of rhodamine B fluorescence. Our findings encourage the use of density based indices to study the processes affecting excited state reactions that are characterized by a drastic change in the excitation nature, in order to rationalize the photophysical behavior of complex molecular systems.

“Breakthrough” osmosis and unusually high power densities in Pressure-Retarded Osmosis in non-ideally semi-permeable supported membranes

PubMed Central

Yaroshchuk, Andriy

2017-01-01

Osmosis is the movement of solvent across a membrane induced by a solute-concentration gradient. It is very important for cell biology. Recently, it has started finding technological applications in the emerging processes of Forward Osmosis and Pressure-Retarded Osmosis. They use ultrathin and dense membranes supported mechanically by much thicker porous layers. Until now, these processes have been modelled by assuming the membrane to be ideally-semipermeable. We show theoretically that allowing for even minor deviations from ideal semipermeability to solvent can give rise to a previously overlooked mode of “breakthrough” osmosis. Here the rate of osmosis is very large (compared to the conventional mode) and practically unaffected by the so-called Internal Concentration Polarization. In Pressure-Retarded Osmosis, the power densities can easily exceed the conventional mode by one order of magnitude. Much more robust support layers can be used, which is an important technical advantage (reduced membrane damage) in Pressure-Retarded Osmosis. PMID:28332607

Chemical recycling of plastic wastes made from polyethylene (LDPE and HDPE) and polypropylene (PP).

PubMed

Achilias, D S; Roupakias, C; Megalokonomos, P; Lappas, A A; Antonakou, Epsilon V

2007-11-19

The recycling of either model polymers or waste products based on low-density polyethylene (LDPE), high-density polyethylene (HDPE) or polypropylene (PP) is examined using the dissolution/reprecipitation method, as well as pyrolysis. In the first technique, different solvents/non-solvents were examined at different weight percent amounts and temperatures using as raw material both model polymers and commercial products (packaging film, bags, pipes, food-retail outlets). The recovery of polymer in every case was greater than 90%. FT-IR spectra and tensile mechanical properties of the samples before and after recycling were measured. Furthermore, catalytic pyrolysis was carried out in a laboratory fixed bed reactor with an FCC catalyst using again model polymers and waste products as raw materials. Analysis of the derived gases and oils showed that pyrolysis gave a mainly aliphatic composition consisting of a series of hydrocarbons (alkanes and alkenes), with a great potential to be recycled back into the petrochemical industry as a feedstock for the production of new plastics or refined fuels.

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.

Conformation and hydration of surface grafted and free polyethylene oxide chains in solutions

NASA Astrophysics Data System (ADS)

Dahal, Udaya; Wang, Zilu; Dormidontova, Elena

Due to the wide application of polyethylene oxide (PEO), ranging from biomedicine to fuel cells, it is one of the most studied polymers in the scientific world. In order to elucidate detailed molecular-level insights on the impact of surface grafting on PEO conformation, we performed atomistic molecular dynamics simulations of PEO chains in solution and grafted to a flat gold surface in different solvents. We examined the hydration as well as conformation of the free chain compared to the grafted polymer in pure water and mixed solvents. We find that grafted chains are stiffer and have a stronger tendency to form helical structures in isobutyric acid or mixture of isobutyric acid and water solution than the free chains in corresponding solutions. For grafted chains exposed to pure water the random coil conformation is retained at low grafting density, but becomes stretched and more dehydrated as the grafting density or temperature increases. This research is supported by NSF (DMR-1410928).

AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models.

PubMed

Poitevin, Frédéric; Orland, Henri; Doniach, Sebastian; Koehl, Patrice; Delarue, Marc

2011-07-01

Small Angle X-ray Scattering (SAXS) techniques are becoming more and more useful for structural biologists and biochemists, thanks to better access to dedicated synchrotron beamlines, better detectors and the relative easiness of sample preparation. The ability to compute the theoretical SAXS profile of a given structural model, and to compare this profile with the measured scattering intensity, yields crucial structural informations about the macromolecule under study and/or its complexes in solution. An important contribution to the profile, besides the macromolecule itself and its solvent-excluded volume, is the excess density due to the hydration layer. AquaSAXS takes advantage of recently developed methods, such as AquaSol, that give the equilibrium solvent density map around macromolecules, to compute an accurate SAXS/WAXS profile of a given structure and to compare it to the experimental one. Here, we describe the interface architecture and capabilities of the AquaSAXS web server (http://lorentz.dynstr.pasteur.fr/aquasaxs.php).

Inhibiting Polysulfide Shuttle in Lithium-Sulfur Batteries through Low-Ion-Pairing Salts and a Triflamide Solvent.

PubMed

Shyamsunder, Abhinandan; Beichel, Witali; Klose, Petra; Pang, Quan; Scherer, Harald; Hoffmann, Anke; Murphy, Graham K; Krossing, Ingo; Nazar, Linda F

2017-05-22

The step-change in gravimetric energy density needed for electrochemical energy storage devices to power unmanned autonomous vehicles, electric vehicles, and enable low-cost clean grid storage is unlikely to be provided by conventional lithium ion batteries. Lithium-sulfur batteries comprising lightweight elements provide a promising alternative, but the associated polysulfide shuttle in typical ether-based electrolytes generates loss in capacity and low coulombic efficiency. The first new electrolyte based on a unique combination of a relatively hydrophobic sulfonamide solvent and a low ion-pairing salt, which inhibits the polysulfide shuttle, is presented. This system behaves as a sparingly solvating electrolyte at slightly elevated temperatures, where it sustains reversible capacities as high as 1200-1500 mAh g -1 over a wide range of current density (2C-C/5, respectively) when paired with a lithium metal anode, with a coulombic efficiency of >99.7 % in the absence of LiNO 3 additive. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis of 1,3-Dimethylimidazolium Chloride and Volumetric Property Investigations of Its Aqueous Solution

NASA Astrophysics Data System (ADS)

Dong, L.; Zheng, D. X.; Wei, Z.; Wu, X. H.

2009-10-01

By investigating the vapor pressure of the solvent and the affinity between ionic liquids (ILs) and the solvent, it is proposed that 1,3-dimethylimidazolium chloride ([Mmim]Cl) has the potential to be used as a novel absorbent species with the absorption cycle working fluid. Adopting a high-pressure reaction kettle, the method of gas-liquid phase reaction was used to synthesize [Mmim]Cl under the conditions of 348.15 K and 0.7 MPa. The densities of [Mmim]Cl aqueous solutions were measured for mass fractions in the range from 20% to 90% at 293.15 K, 298.15 K, 303.15 K, 308.15 K, 313.15 K, and 318.15 K with a digital vibrating-tube densimeter. The excess volume, the apparent molar volume, the partial molar volume, and the apparent molar expansibility of this system were investigated, and the influences of variations of the cation and anion on the density of several IL aqueous solutions are discussed.

Ab initio modeling of CW-ESR spectra of the double spin labeled peptide Fmoc-(Aib-Aib-TOAC)2-Aib-OMe in acetonitrile.

PubMed

Zerbetto, Mirco; Carlotto, Silvia; Polimeno, Antonino; Corvaja, Carlo; Franco, Lorenzo; Toniolo, Claudio; Formaggio, Fernando; Barone, Vincenzo; Cimino, Paola

2007-03-15

In this work we address the interpretation, via an ab initio integrated computational approach, of the CW-ESR spectra of the double spin labeled, 310-helical, peptide Fmoc-(Aib-Aib-TOAC)2-Aib-OMe dissolved in acetonitrile. Our approach is based on the determination of geometric and local magnetic parameters of the heptapeptide by quantum mechanical density functional calculations taking into account solvent and, when needed, vibrational averaging contributions. The system is then described by a stochastic Liouville equation for the two electron spins interacting with each other and with two 14N nuclear spins, in the presence of diffusive rotational dynamics. Parametrization of the diffusion rotational tensor is provided by a hydrodynamic model. CW-ESR spectra are simulated with minimal resorting to fitting procedures, proving that the combination of sensitive ESR spectroscopy and sophisticated modeling can be highly helpful in providing 3D structural and dynamic information on molecular systems.

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

Method of preparation of removable syntactic foam

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

Arnold, C. Jr.; Derzon, D.K.; Nelson, J.S.

1995-07-11

Easily removable, environmentally safe, low-density, syntactic foams are disclosed which are prepared by mixing insoluble microballoons with a solution of water and/or alcohol-soluble polymer to produce a pourable slurry, optionally vacuum filtering the slurry in varying degrees to remove unwanted solvent and solute polymer, and drying to remove residual solvent. The properties of the foams can be controlled by the concentration and physical properties of the polymer, and by the size and properties of the microballoons. The suggested solute polymers are non-toxic and soluble in environmentally safe solvents such as water or low-molecular weight alcohols. The syntactic foams produced bymore » this process are particularly useful in those applications where ease of removability is beneficial, and could find use in packaging recoverable electronic components, in drilling and mining applications, in building trades, in art works, in the entertainment industry for special effects, in manufacturing as temporary fixtures, in agriculture as temporary supports and containers and for delivery of fertilizer, in medicine as casts and splints, as temporary thermal barriers, as temporary protective covers for fragile objects, as filters for particulate matter, which matter may be easily recovered upon exposure to a solvent, as in-situ valves (for one-time use) which go from maximum to minimum impedance when solvent flows through, and for the automatic opening or closing of spring-loaded, mechanical switches upon exposure to a solvent, among other applications. 1 fig.« less

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.

Delivery of drugs from laminar co-extrudates manufactured by a solvent-free process at room temperature.

PubMed

Oliveira, Gonçalo; Wahl, Martin A; Pinto, JoãO F

2014-11-01

This work aims to design and manufacture laminar co-extrudates as a new dosage form for the delivery of drugs. Co-extrudates made of lipid-based materials with a laminar shape were manufactured at room temperature in the absence of solvents and assessed over time for their mechanical properties (bending strength, deformation, stiffness, and elasticity), density, porosity, thermal behavior and main mechanism of drug release. The study has shown that the extrusion force at steady state increased with the extrusion rate and with the number of layers. The bending strength and stiffness of extrudates increased over time. Laminar co-extrudates with higher number of layers presented a decreasing dissolution efficiency of 38.3 ± 0.6%, 23.0 ± 0.2%, and 12.3 ± 0.2%, for mono-, bi-, and trilayer, respectively. After 90 days, the density, the deformation, and elasticity decreased: trilayer extrudates were the denser and the ones to present the lowest ability to deform and the highest elasticity, whereas monolayer extrudates were the less dense presenting the highest ability to deform. Changes were more evident in the first days after manufacture leading to stabilization over time. Laminar (co-)extrudates have been confirmed as an innovative dosage form for tailored delivery of drugs made without solvents at room temperature. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Influence of physical properties and operating parameters on hydrodynamics in Centrifugal Partition Chromatography.

PubMed

Adelmann, S; Schembecker, G

2011-08-12

Besides the selection of a suitable biphasic solvent system the separation efficiency in Centrifugal Partition Chromatography (CPC) is mainly influenced by the hydrodynamics in the chambers. The flow pattern, the stationary phase retention and the interfacial area for mass transfer strongly depend on physical properties of the solvent system and operating parameters. In order to measure these parameters we visualized the hydrodynamics in a FCPC-chamber for five different solvent systems with an optical measurement system and calculated the stationary phase retention, interfacial area and the distribution of mobile phase thickness in the chamber. Although inclined chambers were used we found that the Coriolis force always deflected the mobile phase towards the chamber wall reducing the interfacial area. This effect increased for systems with low density difference. We also have shown that the stability of phase systems (stationary phase retention) and its tendency to disperse increased for smaller values of the ratio of interfacial tension and density difference. But also the viscosity ratio and the flow pattern itself had a significant effect on retention and dispersion of the mobile phase. As a result operating parameters should be chosen carefully with respect to physical properties for a CPC system. In order to reduce the effect of the Coriolis force CPC devices with greater rotor radius are desirable. Copyright © 2011 Elsevier B.V. All rights reserved.

Theoretical Insight into the Influences of Molecular Ratios on Stabilities and Mechanical Properties, Solvent Effect of HMX/FOX-7 Cocrystal Explosive

NASA Astrophysics Data System (ADS)

Wei, Yan-Ju; Ren, Fu-De; Shi, Wen-Jing; Zhao, Qi

2016-10-01

A molecular dynamics method was employed to study the binding energies of the selected crystal planes of the 1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane/1,1-diamino-2,2-dinitroethylene (HMX/FOX-7) cocrystal in different molecular molar ratios. Mechanical properties, densities, and detonation velocities of the cocrystals in different ratios were estimated. The intermolecular interactions and bond dissociation energies (BDEs) of the N-NO2 bond in the HMX:FOX-7 (1:1) complex were calculated using the B3LYP and MP2(full) methods at the 6-311++G (d,p) and 6-311++G(2df,2p) basis sets. Solvent effects on stability are discussed. The results indicate that HMX/FOX-7 cocrystals prefer cocrystalizing in a 1:1 molar ratio, which has good mechanical properties. The N-NO2 bond becomes strong upon the formation of a complex and the sensitivity of HMX might decrease in cocrystals. The sensitivity change of HMX/FOX-7 originates from not only the formation of intermolecular interaction but also the increment in the N-NO2 BDE. HMX/FOX-7 cocrystals exhibit good detonation performance and meet the requirements of high-density energetic materials. Solvents with low dielectric constants may be chosen to obtain stable HMX/FOX-7 cocrystals.

A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility

PubMed Central

2014-01-01

Background Protein sites evolve at different rates due to functional and biophysical constraints. It is usually considered that the main structural determinant of a site’s rate of evolution is its Relative Solvent Accessibility (RSA). However, a recent comparative study has shown that the main structural determinant is the site’s Local Packing Density (LPD). LPD is related with dynamical flexibility, which has also been shown to correlate with sequence variability. Our purpose is to investigate the mechanism that connects a site’s LPD with its rate of evolution. Results We consider two models: an empirical Flexibility Model and a mechanistic Stress Model. The Flexibility Model postulates a linear increase of site-specific rate of evolution with dynamical flexibility. The Stress Model, introduced here, models mutations as random perturbations of the protein’s potential energy landscape, for which we use simple Elastic Network Models (ENMs). To account for natural selection we assume a single active conformation and use basic statistical physics to derive a linear relationship between site-specific evolutionary rates and the local stress of the mutant’s active conformation. We compare both models on a large and diverse dataset of enzymes. In a protein-by-protein study we found that the Stress Model outperforms the Flexibility Model for most proteins. Pooling all proteins together we show that the Stress Model is strongly supported by the total weight of evidence. Moreover, it accounts for the observed nonlinear dependence of sequence variability on flexibility. Finally, when mutational stress is controlled for, there is very little remaining correlation between sequence variability and dynamical flexibility. Conclusions We developed a mechanistic Stress Model of evolution according to which the rate of evolution of a site is predicted to depend linearly on the local mutational stress of the active conformation. Such local stress is proportional to LPD, so that this model explains the relationship between LPD and evolutionary rate. Moreover, the model also accounts for the nonlinear dependence between evolutionary rate and dynamical flexibility. PMID:24716445

Vibrational coherence in polar solutions of Zn(II) tetrakis(N-methylpyridyl)porphyrin with Soret-band excitation: rapidly damped intermolecular modes with clustered solvent molecules and slowly damped intramolecular modes from the porphyrin macrocycle.

PubMed

Dillman, Kevin L; Shelly, Katherine R; Beck, Warren F

2009-04-30

Ground-state coherent wavepacket motions arising from intermolecular modes with clustered, first-shell solvent molecules were observed using the femtosecond dynamic absorption technique in polar solutions of Zn(II) meso-tetrakis(N-methylpyridyl)porphyrin (ZnTMPyP) with excitation in the Soret absorption band. As was observed previously in bacteriochlorophyll a solution, the pump-probe transients in ZnTMPyP solutions are weakly modulated by slowly damped (effective damping time gamma > 1 ps) features that are assigned to intramolecular modes, the skeletal normal modes of vibration of the porphyrin. The 40 cm(-1) and 215 cm(-1) modes from the metal-doming and metal-solvent-ligand modes, respectively, are members of this set of modulation components. A slowly damped 2-4 cm(-1) component is assigned to the internal rotation of the N-methylpyridyl rings with respect to the porphyrin macrocycle; this mode obtains strong resonance Raman intensity enhancement from an extensive delocalization of pi-electron density from the porphyrin in the ground state onto the rings in the pi* excited states. The dominant features observed in the pump-probe transients are a pair of rapidly damped (gamma < 250 fs) modulation components arising from intermolecular modes with solvent molecules. This structural assignment is supported by an isotope-dependent shift of the average mode frequencies in methanol and perdeuterated methanol. The solvent dependence of the mean intermolecular mode frequency is consistent with a van der Waals intermolecular potential that has significant contributions only from the London dispersion and induction interactions; ion-dipole or ion-induced-dipole terms do not make large contributions because the pi-electron density is not extensively delocalized onto the N-methylpyridyl rings. The modulation depth associated with the intermolecular modes exhibits a marked dependence on the electronic structure of the solvent that is probably related to the degree of covalency; the strongest modulations are observed in acetonitrile and dimethylsulfoxide. The results strongly support a structural assignment of the low-frequency modes that are coupled to the primary and secondary electron-transfer reactions in photosynthetic reaction centers to intermolecular modes between the redox-active chromophores and first-solvation shell groups from the surrounding protein, and an important additional function of the intermolecular modes in the stabilization of charged intermediates is suggested.

The Role of Residual Casting Solvent in Determining the Lithographic and Dissolution Behavior of Poly(methyl Methacrylate), a Positive Electron Beam Resist.

NASA Astrophysics Data System (ADS)

Criss, Robert Randolph, Jr.

The effect of the pre-exposure bake and the choice of casting solvent on the sensitivity and contrast of PMMA has been documented to an extent not previously reported in the literature. PMMA films were spin cast onto clean silicon substrates from chlorobenzene and tri-chloroethylene solutions. The temperature of the pre-bake was varied over the range of 59^circ to 170^circC using a convection oven with pre-bake times ranging from 30 to 90 minutes. At the end of the designated bake time, the films were removed from the oven and allowed to cool in a temperature and humidity controlled environment. They were promptly exposed to a 15 KeV electron beam, then developed, with mild agitation, in a 1:1 mixture of MIBK and IPA at 22.5^ circC. Film thickness profiles were determined with an alpha-step profilometer. Films baked at temperatures below T_{rm glass} (the temperature which marks the onset of long-range, coordinated molecular motion), exhibited improved sensitivity and poorer contrast when compared to those baked above T_{rm glass }. Unique to this work is the finding that the lithographic performance depends on the choice of casting solvent, even at pre-bake temperatures significantly above T_{rm glass}. The relative concentrations of the casting solvents remaining in the baked films was determined from UV absorption spectra. The dissolution rates of exposed films were also measured and compared to the fragmented molecular weight model of development. Energy depositions were calculated from the empirical model of Everhart and Hoff. Cross-correlation of these results indicate that the pre-bake temperature more strongly correlates with the observed improvement in sensitivity than the presence of residual casting solvent. Residual casting solvent changes the density of the film, thus changing the energy deposition and dissolution behavior. Calculations based on the aforementioned models indicate that the observed lithographic and dissolution behavior can not be accounted for by this change in density. Arguments are presented to support the conclusion that the observed behavior is associated with film morphology. Comparison of results from films cast from TCE and chlorobenzene and baked above T_{rm glass} further support this conclusion.

Concentration dependences of the density, viscosity, and refraction index of Cu(NO3)2 · 3H2O solutions in DMSO at 298 K

NASA Astrophysics Data System (ADS)

Mamyrbekova, A. K.

2013-03-01

Physicochemical properties (density, dynamic viscosity, refraction index) of the DMSO-Cu(NO3)2 · 3H2O system are studied in the concentration range of 0.01-2 M at 298 K. The refraction index of a solution of copper(II) nitrate in dimethylsulfoxide (DMSO) is measured at 288-318 K. The excess and partial molar volumes of the solvent and dissolved substance are calculated analytically.

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.

PubMed

Vaguine, A A; Richelle, J; Wodak, S J

1999-01-01

In this paper we present SFCHECK, a stand-alone software package that features a unified set of procedures for evaluating the structure-factor data obtained from X-ray diffraction experiments and for assessing the agreement of the atomic coordinates with these data. The evaluation is performed completely automatically, and produces a concise PostScript pictorial output similar to that of PROCHECK [Laskowski, MacArthur, Moss & Thornton (1993). J. Appl. Cryst. 26, 283-291], greatly facilitating visual inspection of the results. The required inputs are the structure-factor amplitudes and the atomic coordinates. Having those, the program summarizes relevant information on the deposited structure factors and evaluates their quality using criteria such as data completeness, structure-factor uncertainty and the optical resolution computed from the Patterson origin peak. The dependence of various parameters on the nominal resolution (d spacing) is also given. To evaluate the global agreement of the atomic model with the experimental data, the program recomputes the R factor, the correlation coefficient between observed and calculated structure-factor amplitudes and Rfree (when appropriate). In addition, it gives several estimates of the average error in the atomic coordinates. The local agreement between the model and the electron-density map is evaluated on a per-residue basis, considering separately the macromolecule backbone and side-chain atoms, as well as solvent atoms and heterogroups. Among the criteria are the normalized average atomic displacement, the local density correlation coefficient and the polymer chain connectivity. The possibility of computing these criteria using the omit-map procedure is also provided. The described software should be a valuable tool in monitoring the refinement procedure and in assessing structures deposited in databases.

The macromolecular properties of blood-group-specific glycoproteins. Characterization of a series of fractions obtained by solvent fractionation

PubMed Central

Creeth, J. Michael; Bhaskar, K. Ramakrishnan; Donald, Alastair S. R.; Morgan, Walter T. J.

1974-01-01

1. The glycoprotein components of a human ovarian-cyst fluid were isolated by a solvent [95% (w/w) phenol]-extraction procedure; the phenol-insoluble water-soluble glycoprotein was further fractionated by (NH4)2SO4 and by ethanol to yield eight fractions. 2. The fractions were analysed in terms of amino acids, fucose, galactose, N-acetylglucosamine, N-acetylgalactosamine and sialic acid. Variations occurred, particularly in the proportion of peptide; these were partly correlated with varying extent of serological activity. 3. The fractions were characterized physicochemically in terms of buoyant density and degree of spreading in a density gradient, sedimentation velocity and molecular weight; their partial specific volumes and specific refraction increments were also determined. 4. The fractions showed wide variations in their sedimentation-velocity and density-gradient patterns, and gave evidence of pauci-dispersity in density. The fraction regarded as the most typical blood-group-specific glycoprotein sedimented as a single rapidly spreading peak and was of high molecular weight. 5. Significant correlations were observed between the physical properties of the glycoprotein fractions and the amount of their peptide component. The buoyant densities and sedimentation coefficients varied in a manner that suggested the existence of two families of glycoproteins. 6. It is suggested that variability in the extent of glycosylation, or in the degree of cross-linking, might account for the two families of glycoproteins, and that the extent of cross-linkage might also be a factor determining the solubility of these glycoproteins in hot saturated (NH4)2SO4. ImagesFig. 1.PLATE 1 PMID:4219280

Exciplex-like emission from a closely-spaced, orthogonally-sited anthracenyl-boron dipyrromethene (Bodipy) molecular dyad.

PubMed

Benniston, Andrew C; Harriman, Anthony; Whittle, Victoria L; Zelzer, Mischa; Harrington, Ross W; Clegg, William

2010-07-30

A molecular dyad, , has been prepared that incorporates a boron dipyrromethene (Bodipy) group functionalized at the meso position with an anthracenyl unit. Emission from the dyad contains contributions from both localized fluorescence from the Bodipy unit and exciplex-like emission associated with an intramolecular charge-transfer state. The peak position, intensity and lifetime of this exciplex emission are solvent dependent and the shift in the emission maximum shows a linear relationship to the solvent polarity function (Deltaf). The calculated dipole moment for the exciplex is 22.5 +/- 2.2 D. The radiative rate constant (k(RAD)) for exciplex emission decreases progressively with increasing solvent polarity. In this latter case, k(RAD) shows an obvious dependence on the energy gap between the exciplex state and the first-excited singlet state resident on the Bodipy unit. The emission characteristics for dissolved in perfluorooctane are used to characterize the refractive index and dielectric constant of the solvent.

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.

High energy density battery based on complex hydrides

DOEpatents

Zidan, Ragaiy

2016-04-26

A battery and process of operating a battery system is provided using high hydrogen capacity complex hydrides in an organic non-aqueous solvent that allows the transport of hydride ions such as AlH.sub.4.sup.- and metal ions during respective discharging and charging steps.