KECSA-Movable Type Implicit Solvation Model (KMTISM)

PubMed Central

2015-01-01

Computation of the solvation free energy for chemical and biological processes has long been of significant interest. The key challenges to effective solvation modeling center on the choice of potential function and configurational sampling. Herein, an energy sampling approach termed the “Movable Type” (MT) method, and a statistical energy function for solvation modeling, “Knowledge-based and Empirical Combined Scoring Algorithm” (KECSA) are developed and utilized to create an implicit solvation model: KECSA-Movable Type Implicit Solvation Model (KMTISM) suitable for the study of chemical and biological systems. KMTISM is an implicit solvation model, but the MT method performs energy sampling at the atom pairwise level. For a specific molecular system, the MT method collects energies from prebuilt databases for the requisite atom pairs at all relevant distance ranges, which by its very construction encodes all possible molecular configurations simultaneously. Unlike traditional statistical energy functions, KECSA converts structural statistical information into categorized atom pairwise interaction energies as a function of the radial distance instead of a mean force energy function. Within the implicit solvent model approximation, aqueous solvation free energies are then obtained from the NVT ensemble partition function generated by the MT method. Validation is performed against several subsets selected from the Minnesota Solvation Database v2012. Results are compared with several solvation free energy calculation methods, including a one-to-one comparison against two commonly used classical implicit solvation models: MM-GBSA and MM-PBSA. Comparison against a quantum mechanics based polarizable continuum model is also discussed (Cramer and Truhlar’s Solvation Model 12). PMID:25691832

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.

Explicitly Representing the Solvation Shell in Continuum Solvent Calculations

PubMed Central

Svendsen, Hallvard F.; Merz, Kenneth M.

2009-01-01

A method is presented to explicitly represent the first solvation shell in continuum solvation calculations. Initial solvation shell geometries were generated with classical molecular dynamics simulations. Clusters consisting of solute and 5 solvent molecules were fully relaxed in quantum mechanical calculations. The free energy of solvation of the solute was calculated from the free energy of formation of the cluster and the solvation free energy of the cluster calculated with continuum solvation models. The method has been implemented with two continuum solvation models, a Poisson-Boltzmann model and the IEF-PCM model. Calculations were carried out for a set of 60 ionic species. Implemented with the Poisson-Boltzmann model the method gave an unsigned average error of 2.1 kcal/mol and a RMSD of 2.6 kcal/mol for anions, for cations the unsigned average error was 2.8 kcal/mol and the RMSD 3.9 kcal/mol. Similar results were obtained with the IEF-PCM model. PMID:19425558

Differential geometry based solvation model. III. Quantum formulation

PubMed Central

Chen, Zhan; Wei, Guo-Wei

2011-01-01

Solvation is of fundamental importance to biomolecular systems. Implicit solvent models, particularly those based on the Poisson-Boltzmann equation for electrostatic analysis, are established approaches for solvation analysis. However, ad hoc solvent-solute interfaces are commonly used in the implicit solvent theory. Recently, we have introduced differential geometry based solvation models which allow the solvent-solute interface to be determined by the variation of a total free energy functional. Atomic fixed partial charges (point charges) are used in our earlier models, which depends on existing molecular mechanical force field software packages for partial charge assignments. As most force field models are parameterized for a certain class of molecules or materials, the use of partial charges limits the accuracy and applicability of our earlier models. Moreover, fixed partial charges do not account for the charge rearrangement during the solvation process. The present work proposes a differential geometry based multiscale solvation model which makes use of the electron density computed directly from the quantum mechanical principle. To this end, we construct a new multiscale total energy functional which consists of not only polar and nonpolar solvation contributions, but also the electronic kinetic and potential energies. By using the Euler-Lagrange variation, we derive a system of three coupled governing equations, i.e., the generalized Poisson-Boltzmann equation for the electrostatic potential, the generalized Laplace-Beltrami equation for the solvent-solute boundary, and the Kohn-Sham equations for the electronic structure. We develop an iterative procedure to solve three coupled equations and to minimize the solvation free energy. The present multiscale model is numerically validated for its stability, consistency and accuracy, and is applied to a few sets of molecules, including a case which is difficult for existing solvation models. Comparison is made to many other classic and quantum models. By using experimental data, we show that the present quantum formulation of our differential geometry based multiscale solvation model improves the prediction of our earlier models, and outperforms some explicit solvation model. PMID:22112067

SAMPL4 & DOCK3.7: lessons for automated docking procedures

NASA Astrophysics Data System (ADS)

Coleman, Ryan G.; Sterling, Teague; Weiss, Dahlia R.

2014-03-01

The SAMPL4 challenges were used to test current automated methods for solvation energy, virtual screening, pose and affinity prediction of the molecular docking pipeline DOCK 3.7. Additionally, first-order models of binding affinity were proposed as milestones for any method predicting binding affinity. Several important discoveries about the molecular docking software were made during the challenge: (1) Solvation energies of ligands were five-fold worse than any other method used in SAMPL4, including methods that were similarly fast, (2) HIV Integrase is a challenging target, but automated docking on the correct allosteric site performed well in terms of virtual screening and pose prediction (compared to other methods) but affinity prediction, as expected, was very poor, (3) Molecular docking grid sizes can be very important, serious errors were discovered with default settings that have been adjusted for all future work. Overall, lessons from SAMPL4 suggest many changes to molecular docking tools, not just DOCK 3.7, that could improve the state of the art. Future difficulties and projects will be discussed.

VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions.

PubMed

Kuechler, Erich R; Giese, Timothy J; York, Darrin M

2016-04-28

To better represent the solvation effects observed along reaction pathways, and of ionic species in general, a charge-dependent variable-radii smooth conductor-like screening model (VR-SCOSMO) is developed. This model is implemented and parameterized with a third order density-functional tight binding quantum model, DFTB3/3OB-OPhyd, a quantum method which was developed for organic and biological compounds, utilizing a specific parameterization for phosphate hydrolysis reactions. Unlike most other applications with the DFTB3/3OB model, an auxiliary set of atomic multipoles is constructed from the underlying DFTB3 density matrix which is used to interact the solute with the solvent response surface. The resulting method is variational, produces smooth energies, and has analytic gradients. As a baseline, a conventional SCOSMO model with fixed radii is also parameterized. The SCOSMO and VR-SCOSMO models shown have comparable accuracy in reproducing neutral-molecule absolute solvation free energies; however, the VR-SCOSMO model is shown to reduce the mean unsigned errors (MUEs) of ionic compounds by half (about 2-3 kcal/mol). The VR-SCOSMO model presents similar accuracy as a charge-dependent Poisson-Boltzmann model introduced by Hou et al. [J. Chem. Theory Comput. 6, 2303 (2010)]. VR-SCOSMO is then used to examine the hydrolysis of trimethylphosphate and seven other phosphoryl transesterification reactions with different leaving groups. Two-dimensional energy landscapes are constructed for these reactions and calculated barriers are compared to those obtained from ab initio polarizable continuum calculations and experiment. Results of the VR-SCOSMO model are in good agreement in both cases, capturing the rate-limiting reaction barrier and the nature of the transition state.

Water-enhanced solvation of organic solutes in ketone and ester solvents

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

Lee, J.H.; Brunt, V. van; King, C.J.

1994-05-01

Previous research has shown that the solubilities of dicarboxylic acids in certain electron-donor solvents are substantially increased in the presence of water. Information on solubilities, liquid-liquid equilibria and maximum-boiling ternary azeotropes was screened so as to identify other systems where codissolved water appears to enhance solvation of organic solutes in solvents. Several carboxylic acids, an alcohol, diols, and phenols were selected for examination as solutes in ketone and ester solvents. Effects of water upon solute solubilities and volatilities were measured. Results showed that water-enhanced solvation is greatest for carboxylic acids. Solute activity coefficients decreased by factors of 2--3, 6--8, andmore » 7--10 due to the presence of water for mono-, di and tricarboxylic acids, respectively. Activity coefficients decreased by a factor of about 1.5 for ethanol and 1,2-propanediol as solutes. Water-enhanced solvation of phenols is small, when existent.« less

Drug-drug cocrystals of antituberculous 4-aminosalicylic acid: Screening, crystal structures, thermochemical and solubility studies.

PubMed

Drozd, Ksenia V; Manin, Alex N; Churakov, Andrei V; Perlovich, German L

2017-03-01

Experimental multistage cocrystal screening of the antituberculous drug 4-aminosalicylic acid (PASA) has been conducted with a number of coformers (pyrazinamide (PYR), nicotinamide (NAM), isonicotinamide (iNAM), isoniazid (INH), caffeine (CAF) and theophylline (TPH)). The crystal structures of 4-aminosalicylic acid cocrystals with isonicotinamide ([PASA+iNAM] (2:1)) and methanol solvate with caffeine ([PASA+CAF+MeOH] (1:1:1)) have been determined by single X-ray diffraction experiments. For the first time for PASA cocrystals it has been found that the structural unit of the [PASA+iNAM] cocrystal (2:1) is formed by 2 types of heterosynthons: acid-pyridine and acid-amide. The desolvation study of the [PASA+CAF+MeOH] cocrystal solvate (1:1:1) has been conducted. The correlation models linking the melting points of the cocrystals with the melting points of the coformers used in this paper have been developed. The thermochemical and solubility properties for all the obtained cocrystals have been studied. Cocrystallization has been shown to lead not only to PASA solubility improving but also to its higher stability against the chemical decomposition. Copyright © 2016 Elsevier B.V. All rights reserved.

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.

The impact of surface area, volume, curvature, and Lennard-Jones potential to solvation modeling.

PubMed

Nguyen, Duc D; Wei, Guo-Wei

2017-01-05

This article explores the impact of surface area, volume, curvature, and Lennard-Jones (LJ) potential on solvation free energy predictions. Rigidity surfaces are utilized to generate robust analytical expressions for maximum, minimum, mean, and Gaussian curvatures of solvent-solute interfaces, and define a generalized Poisson-Boltzmann (GPB) equation with a smooth dielectric profile. Extensive correlation analysis is performed to examine the linear dependence of surface area, surface enclosed volume, maximum curvature, minimum curvature, mean curvature, and Gaussian curvature for solvation modeling. It is found that surface area and surfaces enclosed volumes are highly correlated to each other's, and poorly correlated to various curvatures for six test sets of molecules. Different curvatures are weakly correlated to each other for six test sets of molecules, but are strongly correlated to each other within each test set of molecules. Based on correlation analysis, we construct twenty six nontrivial nonpolar solvation models. Our numerical results reveal that the LJ potential plays a vital role in nonpolar solvation modeling, especially for molecules involving strong van der Waals interactions. It is found that curvatures are at least as important as surface area or surface enclosed volume in nonpolar solvation modeling. In conjugation with the GPB model, various curvature-based nonpolar solvation models are shown to offer some of the best solvation free energy predictions for a wide range of test sets. For example, root mean square errors from a model constituting surface area, volume, mean curvature, and LJ potential are less than 0.42 kcal/mol for all test sets. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

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

Biomolecular electrostatics and solvation: a computational perspective

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

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G.

2012-11-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. Thismore » review discusses the solvation of biomolecules with a computational biophysics view towards describing the phenomenon. While our main focus lies on the computational aspect of the models, we summarize the common characteristics of biomolecular solvation (e.g., solvent structure, polarization, ion binding, and nonpolar behavior) in order to provide reasonable backgrounds to understand the solvation models.« less

Biomolecular electrostatics and solvation: a computational perspective

PubMed Central

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G.; Schnieders, Michael J.; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A.

2012-01-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view towards describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g., solvent structure, polarization, ion binding, and nonpolar behavior) in order to provide a background to understand the different types of solvation models. PMID:23217364

Biomolecular electrostatics and solvation: a computational perspective.

PubMed

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G; Schnieders, Michael J; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A

2012-11-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

Water solvent effects using continuum and discrete models: The nitromethane molecule, CH3NO2.

PubMed

Modesto-Costa, Lucas; Uhl, Elmar; Borges, Itamar

2015-11-15

The first three valence transitions of the two nitromethane conformers (CH3NO2) are two dark n → π* transitions and a very intense π → π* transition. In this work, these transitions in gas-phase and solvated in water of both conformers were investigated theoretically. The polarizable continuum model (PCM), two conductor-like screening (COSMO) models, and the discrete sequential quantum mechanics/molecular mechanics (S-QM/MM) method were used to describe the solvation effect on the electronic spectra. Time dependent density functional theory (TDDFT), configuration interaction including all single substitutions and perturbed double excitations (CIS(D)), the symmetry-adapted-cluster CI (SAC-CI), the multistate complete active space second order perturbation theory (CASPT2), and the algebraic-diagrammatic construction (ADC(2)) electronic structure methods were used. Gas-phase CASPT2, SAC-CI, and ADC(2) results are in very good agreement with published experimental and theoretical spectra. Among the continuum models, PCM combined either with CASPT2, SAC-CI, or B3LYP provided good agreement with available experimental data. COSMO combined with ADC(2) described the overall trends of the transition energy shifts. The effect of increasing the number of explicit water molecules in the S-QM/MM approach was discussed and the formation of hydrogen bonds was clearly established. By including explicitly 24 water molecules corresponding to the complete first solvation shell in the S-QM/MM approach, the ADC(2) method gives more accurate results as compared to the TDDFT approach and with similar computational demands. The ADC(2) with S-QM/MM model is, therefore, the best compromise for accurate solvent calculations in a polar environment. © 2015 Wiley Periodicals, Inc.

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

Solvation structure of the halides from x-ray absorption spectroscopy

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

Antalek, Matthew; Hedman, Britt; Sarangi, Ritimukta, E-mail: ritis@slac.stanford.edu

2016-07-28

Three-dimensional models for the aqueous solvation structures of chloride, bromide, and iodide are reported. K-edge extended X-ray absorption fine structure (EXAFS) and Minuit X-ray absorption near edge (MXAN) analyses found well-defined single shell solvation spheres for bromide and iodide. However, dissolved chloride proved structurally distinct, with two solvation shells needed to explain its strikingly different X-ray absorption near edge structure (XANES) spectrum. Final solvation models were as follows: iodide, 8 water molecules at 3.60 ± 0.13 Å and bromide, 8 water molecules at 3.40 ± 0.14 Å, while chloride solvation included 7 water molecules at 3.15 ± 0.10 Å, andmore » a second shell of 7 water molecules at 4.14 ± 0.30 Å. Each of the three derived solvation shells is approximately uniformly disposed about the halides, with no global asymmetry. Time-dependent density functional theory calculations simulating the chloride XANES spectra following from alternative solvation spheres revealed surprising sensitivity of the electronic state to 6-, 7-, or 8-coordination, implying a strongly bounded phase space for the correct structure during an MXAN fit. MXAN analysis further showed that the asymmetric solvation predicted from molecular dynamics simulations using halide polarization can play no significant part in bulk solvation. Classical molecular dynamics used to explore chloride solvation found a 7-water solvation shell at 3.12 (−0.04/+0.3) Å, supporting the experimental result. These experiments provide the first fully three-dimensional structures presenting to atomic resolution the aqueous solvation spheres of the larger halide ions.« less

Improving accuracy of electrochemical capacitance and solvation energetics in first-principles calculations

NASA Astrophysics Data System (ADS)

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Schwarz, Kathleen A.

2018-04-01

Reliable first-principles calculations of electrochemical processes require accurate prediction of the interfacial capacitance, a challenge for current computationally efficient continuum solvation methodologies. We develop a model for the double layer of a metallic electrode that reproduces the features of the experimental capacitance of Ag(100) in a non-adsorbing, aqueous electrolyte, including a broad hump in the capacitance near the potential of zero charge and a dip in the capacitance under conditions of low ionic strength. Using this model, we identify the necessary characteristics of a solvation model suitable for first-principles electrochemistry of metal surfaces in non-adsorbing, aqueous electrolytes: dielectric and ionic nonlinearity, and a dielectric-only region at the interface. The dielectric nonlinearity, caused by the saturation of dipole rotational response in water, creates the capacitance hump, while ionic nonlinearity, caused by the compactness of the diffuse layer, generates the capacitance dip seen at low ionic strength. We show that none of the previously developed solvation models simultaneously meet all these criteria. We design the nonlinear electrochemical soft-sphere solvation model which both captures the capacitance features observed experimentally and serves as a general-purpose continuum solvation model.

Modeling ultrafast solvated electronic dynamics using time-dependent density functional theory and polarizable continuum model.

PubMed

Liang, Wenkel; Chapman, Craig T; Ding, Feizhi; Li, Xiaosong

2012-03-01

A first-principles solvated electronic dynamics method is introduced. Solvent electronic degrees of freedom are coupled to the time-dependent electronic density of a solute molecule by means of the implicit reaction field method, and the entire electronic system is propagated in time. This real-time time-dependent approach, incorporating the polarizable continuum solvation model, is shown to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution. © 2012 American Chemical Society

Differential geometry based solvation model II: Lagrangian formulation.

PubMed

Chen, Zhan; Baker, Nathan A; Wei, G W

2011-12-01

Solvation is an elementary process in nature and is of paramount importance to more sophisticated chemical, biological and biomolecular processes. The understanding of solvation is an essential prerequisite for the quantitative description and analysis of biomolecular systems. This work presents a Lagrangian formulation of our differential geometry based solvation models. The Lagrangian representation of biomolecular surfaces has a few utilities/advantages. First, it provides an essential basis for biomolecular visualization, surface electrostatic potential map and visual perception of biomolecules. Additionally, it is consistent with the conventional setting of implicit solvent theories and thus, many existing theoretical algorithms and computational software packages can be directly employed. Finally, the Lagrangian representation does not need to resort to artificially enlarged van der Waals radii as often required by the Eulerian representation in solvation analysis. The main goal of the present work is to analyze the connection, similarity and difference between the Eulerian and Lagrangian formalisms of the solvation model. Such analysis is important to the understanding of the differential geometry based solvation model. The present model extends the scaled particle theory of nonpolar solvation model with a solvent-solute interaction potential. The nonpolar solvation model is completed with a Poisson-Boltzmann (PB) theory based polar solvation model. The differential geometry theory of surfaces is employed to provide a natural description of solvent-solute interfaces. The optimization of the total free energy functional, which encompasses the polar and nonpolar contributions, leads to coupled potential driven geometric flow and PB equations. Due to the development of singularities and nonsmooth manifolds in the Lagrangian representation, the resulting potential-driven geometric flow equation is embedded into the Eulerian representation for the purpose of computation, thanks to the equivalence of the Laplace-Beltrami operator in the two representations. The coupled partial differential equations (PDEs) are solved with an iterative procedure to reach a steady state, which delivers desired solvent-solute interface and electrostatic potential for problems of interest. These quantities are utilized to evaluate the solvation free energies and protein-protein binding affinities. A number of computational methods and algorithms are described for the interconversion of Lagrangian and Eulerian representations, and for the solution of the coupled PDE system. The proposed approaches have been extensively validated. We also verify that the mean curvature flow indeed gives rise to the minimal molecular surface and the proposed variational procedure indeed offers minimal total free energy. Solvation analysis and applications are considered for a set of 17 small compounds and a set of 23 proteins. The salt effect on protein-protein binding affinity is investigated with two protein complexes by using the present model. Numerical results are compared to the experimental measurements and to those obtained by using other theoretical methods in the literature. © Springer-Verlag 2011

Differential geometry based solvation model II: Lagrangian formulation

PubMed Central

Chen, Zhan; Baker, Nathan A.; Wei, G. W.

2010-01-01

Solvation is an elementary process in nature and is of paramount importance to more sophisticated chemical, biological and biomolecular processes. The understanding of solvation is an essential prerequisite for the quantitative description and analysis of biomolecular systems. This work presents a Lagrangian formulation of our differential geometry based solvation model. The Lagrangian representation of biomolecular surfaces has a few utilities/advantages. First, it provides an essential basis for biomolecular visualization, surface electrostatic potential map and visual perception of biomolecules. Additionally, it is consistent with the conventional setting of implicit solvent theories and thus, many existing theoretical algorithms and computational software packages can be directly employed. Finally, the Lagrangian representation does not need to resort to artificially enlarged van der Waals radii as often required by the Eulerian representation in solvation analysis. The main goal of the present work is to analyze the connection, similarity and difference between the Eulerian and Lagrangian formalisms of the solvation model. Such analysis is important to the understanding of the differential geometry based solvation model. The present model extends the scaled particle theory (SPT) of nonpolar solvation model with a solvent-solute interaction potential. The nonpolar solvation model is completed with a Poisson-Boltzmann (PB) theory based polar solvation model. The differential geometry theory of surfaces is employed to provide a natural description of solvent-solute interfaces. The minimization of the total free energy functional, which encompasses the polar and nonpolar contributions, leads to coupled potential driven geometric flow and Poisson-Boltzmann equations. Due to the development of singularities and nonsmooth manifolds in the Lagrangian representation, the resulting potential-driven geometric flow equation is embedded into the Eulerian representation for the purpose of computation, thanks to the equivalence of the Laplace-Beltrami operator in the two representations. The coupled partial differential equations (PDEs) are solved with an iterative procedure to reach a steady state, which delivers desired solvent-solute interface and electrostatic potential for problems of interest. These quantities are utilized to evaluate the solvation free energies and protein-protein binding affinities. A number of computational methods and algorithms are described for the interconversion of Lagrangian and Eulerian representations, and for the solution of the coupled PDE system. The proposed approaches have been extensively validated. We also verify that the mean curvature flow indeed gives rise to the minimal molecular surface (MMS) and the proposed variational procedure indeed offers minimal total free energy. Solvation analysis and applications are considered for a set of 17 small compounds and a set of 23 proteins. The salt effect on protein-protein binding affinity is investigated with two protein complexes by using the present model. Numerical results are compared to the experimental measurements and to those obtained by using other theoretical methods in the literature. PMID:21279359

Implicit solvation model for density-functional study of nanocrystal surfaces and reaction pathways

NASA Astrophysics Data System (ADS)

Mathew, Kiran; Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Arias, T. A.; Hennig, Richard G.

2014-02-01

Solid-liquid interfaces are at the heart of many modern-day technologies and provide a challenge to many materials simulation methods. A realistic first-principles computational study of such systems entails the inclusion of solvent effects. In this work, we implement an implicit solvation model that has a firm theoretical foundation into the widely used density-functional code Vienna ab initio Software Package. The implicit solvation model follows the framework of joint density functional theory. We describe the framework, our algorithm and implementation, and benchmarks for small molecular systems. We apply the solvation model to study the surface energies of different facets of semiconducting and metallic nanocrystals and the SN2 reaction pathway. We find that solvation reduces the surface energies of the nanocrystals, especially for the semiconducting ones and increases the energy barrier of the SN2 reaction.

Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects.

PubMed

Lomize, Andrei L; Pogozheva, Irina D; Mosberg, Henry I

2011-04-25

A new implicit solvation model was developed for calculating free energies of transfer of molecules from water to any solvent with defined bulk properties. The transfer energy was calculated as a sum of the first solvation shell energy and the long-range electrostatic contribution. The first term was proportional to solvent accessible surface area and solvation parameters (σ(i)) for different atom types. The electrostatic term was computed as a product of group dipole moments and dipolar solvation parameter (η) for neutral molecules or using a modified Born equation for ions. The regression coefficients in linear dependencies of solvation parameters σ(i) and η on dielectric constant, solvatochromic polarizability parameter π*, and hydrogen-bonding donor and acceptor capacities of solvents were optimized using 1269 experimental transfer energies from 19 organic solvents to water. The root-mean-square errors for neutral compounds and ions were 0.82 and 1.61 kcal/mol, respectively. Quantification of energy components demonstrates the dominant roles of hydrophobic effect for nonpolar atoms and of hydrogen-bonding for polar atoms. The estimated first solvation shell energy outweighs the long-range electrostatics for most compounds including ions. The simplicity and computational efficiency of the model allows its application for modeling of macromolecules in anisotropic environments, such as biological membranes.

Performance of the SMD and SM8 models for predicting solvation free energy of neutral solutes in methanol, dimethyl sulfoxide and acetonitrile.

PubMed

Zanith, Caroline C; Pliego, Josefredo R

2015-03-01

The continuum solvation models SMD and SM8 were developed using 2,346 solvation free energy values for 318 neutral molecules in 91 solvents as reference. However, no solvation data of neutral solutes in methanol was used in the parametrization, while only few solvation free energy values of solutes in dimethyl sulfoxide and acetonitrile were used. In this report, we have tested the performance of the models for these important solvents. Taking data from literature, we have generated solvation free energy, enthalpy and entropy values for 37 solutes in methanol, 21 solutes in dimethyl sulfoxide and 19 solutes in acetonitrile. Both SMD and SM8 models have presented a good performance in methanol and acetonitrile, with mean unsigned error equal or less than 0.66 and 0.55 kcal mol(-1) in methanol and acetonitrile, respectively. However, the correlation is worse in dimethyl sulfoxide, where the SMD and SM8 methods present mean unsigned error of 1.02 and 0.95 kcal mol(-1), respectively. Our results point out the SMx family of models need be improved for dimethyl sulfoxide solvent.

Performance of the SMD and SM8 models for predicting solvation free energy of neutral solutes in methanol, dimethyl sulfoxide and acetonitrile

NASA Astrophysics Data System (ADS)

Zanith, Caroline C.; Pliego, Josefredo R.

2015-03-01

The continuum solvation models SMD and SM8 were developed using 2,346 solvation free energy values for 318 neutral molecules in 91 solvents as reference. However, no solvation data of neutral solutes in methanol was used in the parametrization, while only few solvation free energy values of solutes in dimethyl sulfoxide and acetonitrile were used. In this report, we have tested the performance of the models for these important solvents. Taking data from literature, we have generated solvation free energy, enthalpy and entropy values for 37 solutes in methanol, 21 solutes in dimethyl sulfoxide and 19 solutes in acetonitrile. Both SMD and SM8 models have presented a good performance in methanol and acetonitrile, with mean unsigned error equal or less than 0.66 and 0.55 kcal mol-1 in methanol and acetonitrile, respectively. However, the correlation is worse in dimethyl sulfoxide, where the SMD and SM8 methods present mean unsigned error of 1.02 and 0.95 kcal mol-1, respectively. Our results point out the SMx family of models need be improved for dimethyl sulfoxide solvent.

Molecular Dynamics based on a Generalized Born solvation model: application to protein folding

NASA Astrophysics Data System (ADS)

Onufriev, Alexey

2004-03-01

An accurate description of the aqueous environment is essential for realistic biomolecular simulations, but may become very expensive computationally. We have developed a version of the Generalized Born model suitable for describing large conformational changes in macromolecules. The model represents the solvent implicitly as continuum with the dielectric properties of water, and include charge screening effects of salt. The computational cost associated with the use of this model in Molecular Dynamics simulations is generally considerably smaller than the cost of representing water explicitly. Also, compared to traditional Molecular Dynamics simulations based on explicit water representation, conformational changes occur much faster in implicit solvation environment due to the absence of viscosity. The combined speed-up allow one to probe conformational changes that occur on much longer effective time-scales. We apply the model to folding of a 46-residue three helix bundle protein (residues 10-55 of protein A, PDB ID 1BDD). Starting from an unfolded structure at 450 K, the protein folds to the lowest energy state in 6 ns of simulation time, which takes about a day on a 16 processor SGI machine. The predicted structure differs from the native one by 2.4 A (backbone RMSD). Analysis of the structures seen on the folding pathway reveals details of the folding process unavailable form experiment.

The Generalized Born solvation model: What is it?

NASA Astrophysics Data System (ADS)

Onufriev, Alexey

2004-03-01

Implicit solvation models provide, for many applications, an effective way of describing the electrostatic effects of aqueous solvation. Here we outline the main approximations behind the popular Generalized Born solvation model. We show how its accuracy, relative to the Poisson-Boltzmann treatment, can be significantly improved in a computationally inexpensive manner to make the model useful in the studies of large-scale conformational transitions at the atomic level. The improved model is tested in a molecular dynamics simulation of folding of a 46-residue (three helix bundle) protein. Starting from an extended structure at 450K, the protein folds to the lowest energy conformation within 6 ns of simulation time, and the predicted structure differs from the native one by 2.4 A (backbone RMSD).

Relative complexation energies for Li(+) ion in solution: molecular level solvation versus polarizable continuum model study.

PubMed

Eilmes, Andrzej; Kubisiak, Piotr

2010-01-21

Relative complexation energies for the lithium cation in acetonitrile and diethyl ether have been studied. Quantum-chemical calculations explicitly describing the solvation of Li(+) have been performed based on structures obtained from molecular dynamics simulations. The effect of an increasing number of solvent molecules beyond the first solvation shell has been found to consist in reduction of the differences in complexation energies for different coordination numbers. Explicit-solvation data have served as a benchmark to the results of polarizable continuum model (PCM) calculations. It has been demonstrated that the PCM approach can yield relative complexation energies comparable to the predictions based on molecular-level solvation, but at significantly lower computational cost. The best agreement between the explicit-solvation and the PCM results has been obtained when the van der Waals surface was adopted to build the molecular cavity.

Standard electrode potential, Tafel equation, and the solvation thermodynamics.

PubMed

Matyushov, Dmitry V

2009-06-21

Equilibrium in the electronic subsystem across the solution-metal interface is considered to connect the standard electrode potential to the statistics of localized electronic states in solution. We argue that a correct derivation of the Nernst equation for the electrode potential requires a careful separation of the relevant time scales. An equation for the standard metal potential is derived linking it to the thermodynamics of solvation. The Anderson-Newns model for electronic delocalization between the solution and the electrode is combined with a bilinear model of solute-solvent coupling introducing nonlinear solvation into the theory of heterogeneous electron transfer. We therefore are capable of addressing the question of how nonlinear solvation affects electrochemical observables. The transfer coefficient of electrode kinetics is shown to be equal to the derivative of the free energy, or generalized force, required to shift the unoccupied electronic level in the bulk. The transfer coefficient thus directly quantifies the extent of nonlinear solvation of the redox couple. The current model allows the transfer coefficient to deviate from the value of 0.5 of the linear solvation models at zero electrode overpotential. The electrode current curves become asymmetric in respect to the change in the sign of the electrode overpotential.

Atomic decomposition of the protein solvation free energy and its application to amyloid-beta protein in water

NASA Astrophysics Data System (ADS)

Chong, Song-Ho; Ham, Sihyun

2011-07-01

We report the development of an atomic decomposition method of the protein solvation free energy in water, which ascribes global change in the solvation free energy to local changes in protein conformation as well as in hydration structure. So far, empirical decomposition analyses based on simple continuum solvation models have prevailed in the study of protein-protein interactions, protein-ligand interactions, as well as in developing scoring functions for computer-aided drug design. However, the use of continuum solvation model suffers serious drawbacks since it yields the protein free energy landscape which is quite different from that of the explicit solvent model and since it does not properly account for the non-polar hydrophobic effects which play a crucial role in biological processes in water. Herein, we develop an exact and general decomposition method of the solvation free energy that overcomes these hindrances. We then apply this method to elucidate the molecular origin for the solvation free energy change upon the conformational transitions of 42-residue amyloid-beta protein (Aβ42) in water, whose aggregation has been implicated as a primary cause of Alzheimer's disease. We address why Aβ42 protein exhibits a great propensity to aggregate when transferred from organic phase to aqueous phase.

Calculating pKa values for substituted phenols and hydration energies for other compounds with the first-order Fuzzy-Border continuum solvation model

PubMed Central

Sharma, Ity; Kaminski, George A.

2012-01-01

We have computed pKa values for eleven substituted phenol compounds using the continuum Fuzzy-Border (FB) solvation model. Hydration energies for 40 other compounds, including alkanes, alkenes, alkynes, ketones, amines, alcohols, ethers, aromatics, amides, heterocycles, thiols, sulfides and acids have been calculated. The overall average unsigned error in the calculated acidity constant values was equal to 0.41 pH units and the average error in the solvation energies was 0.076 kcal/mol. We have also reproduced pKa values of propanoic and butanoic acids within ca. 0.1 pH units from the experimental values by fitting the solvation parameters for carboxylate ion carbon and oxygen atoms. The FB model combines two distinguishing features. First, it limits the amount of noise which is common in numerical treatment of continuum solvation models by using fixed-position grid points. Second, it employs either second- or first-order approximation for the solvent polarization, depending on a particular implementation. These approximations are similar to those used for solute and explicit solvent fast polarization treatment which we developed previously. This article describes results of employing the first-order technique. This approximation places the presented methodology between the Generalized Born and Poisson-Boltzmann continuum solvation models with respect to their accuracy of reproducing the many-body effects in modeling a continuum solvent. PMID:22815192

Prediction of solvation enthalpy of gaseous organic compounds in propanol

NASA Astrophysics Data System (ADS)

Golmohammadi, Hassan; Dashtbozorgi, Zahra

2016-09-01

The purpose of this paper is to present a novel way for developing quantitative structure-property relationship (QSPR) models to predict the gas-to-propanol solvation enthalpy (Δ H solv) of 95 organic compounds. Different kinds of descriptors were calculated for each compound using the Dragon software package. The variable selection technique of replacement method (RM) was employed to select the optimal subset of solute descriptors. Our investigation reveals that the dependence of physical chemistry properties of solution on solvation enthalpy is nonlinear and that the RM method is unable to model the solvation enthalpy accurately. The results established that the calculated Δ H solv values by SVM were in good agreement with the experimental ones, and the performances of the SVM models were superior to those obtained by RM model.

Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models.

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

Kamerlin, Shina C. L.; Haranczyk, Maciej; Warshel, Arieh

2009-05-01

Phosphate hydrolysis is ubiquitous in biology. However, despite intensive research on this class of reactions, the precise nature of the reaction mechanism remains controversial. In this work, we have examined the hydrolysis of three homologous phosphate diesters. The solvation free energy was simulated by means of either an implicit solvation model (COSMO), hybrid quantum mechanical / molecular mechanical free energy perturbation (QM/MM-FEP) or a mixed solvation model in which N water molecules were explicitly included in the ab initio description of the reacting system (where N=1-3), with the remainder of the solvent being implicitly modelled as a continuum. Here, bothmore » COSMO and QM/MM-FEP reproduce Delta Gobs within an error of about 2kcal/mol. However, we demonstrate that in order to obtain any form of reliable results from a mixed model, it is essential to carefully select the explicit water molecules from short QM/MM runs that act as a model for the true infinite system. Additionally, the mixed models tend to be increasingly inaccurate the more explicit water molecules are placed into the system. Thus, our analysis indicates that this approach provides an unreliable way for modelling phosphate hydrolysis in solution.« less

Evaluation of DNA Force Fields in Implicit Solvation

PubMed Central

Gaillard, Thomas; Case, David A.

2011-01-01

DNA structural deformations and dynamics are crucial to its interactions in the cell. Theoretical simulations are essential tools to explore the structure, dynamics, and thermodynamics of biomolecules in a systematic way. Molecular mechanics force fields for DNA have benefited from constant improvements during the last decades. Several studies have evaluated and compared available force fields when the solvent is modeled by explicit molecules. On the other hand, few systematic studies have assessed the quality of duplex DNA models when implicit solvation is employed. The interest of an implicit modeling of the solvent consists in the important gain in the simulation performance and conformational sampling speed. In this study, respective influences of the force field and the implicit solvation model choice on DNA simulation quality are evaluated. To this end, extensive implicit solvent duplex DNA simulations are performed, attempting to reach both conformational and sequence diversity convergence. Structural parameters are extracted from simulations and statistically compared to available experimental and explicit solvation simulation data. Our results quantitatively expose the respective strengths and weaknesses of the different DNA force fields and implicit solvation models studied. This work can lead to the suggestion of improvements to current DNA theoretical models. PMID:22043178

Breaking the polar-nonpolar division in solvation free energy prediction.

PubMed

Wang, Bao; Wang, Chengzhang; Wu, Kedi; Wei, Guo-Wei

2018-02-05

Implicit solvent models divide solvation free energies into polar and nonpolar additive contributions, whereas polar and nonpolar interactions are inseparable and nonadditive. We present a feature functional theory (FFT) framework to break this ad hoc division. The essential ideas of FFT are as follows: (i) representability assumption: there exists a microscopic feature vector that can uniquely characterize and distinguish one molecule from another; (ii) feature-function relationship assumption: the macroscopic features, including solvation free energy, of a molecule is a functional of microscopic feature vectors; and (iii) similarity assumption: molecules with similar microscopic features have similar macroscopic properties, such as solvation free energies. Based on these assumptions, solvation free energy prediction is carried out in the following protocol. First, we construct a molecular microscopic feature vector that is efficient in characterizing the solvation process using quantum mechanics and Poisson-Boltzmann theory. Microscopic feature vectors are combined with macroscopic features, that is, physical observable, to form extended feature vectors. Additionally, we partition a solvation dataset into queries according to molecular compositions. Moreover, for each target molecule, we adopt a machine learning algorithm for its nearest neighbor search, based on the selected microscopic feature vectors. Finally, from the extended feature vectors of obtained nearest neighbors, we construct a functional of solvation free energy, which is employed to predict the solvation free energy of the target molecule. The proposed FFT model has been extensively validated via a large dataset of 668 molecules. The leave-one-out test gives an optimal root-mean-square error (RMSE) of 1.05 kcal/mol. FFT predictions of SAMPL0, SAMPL1, SAMPL2, SAMPL3, and SAMPL4 challenge sets deliver the RMSEs of 0.61, 1.86, 1.64, 0.86, and 1.14 kcal/mol, respectively. Using a test set of 94 molecules and its associated training set, the present approach was carefully compared with a classic solvation model based on weighted solvent accessible surface area. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Solvated dissipative electro-elastic network model of hydrated proteins

NASA Astrophysics Data System (ADS)

Martin, Daniel

2013-03-01

Elastic network models coarse grain proteins into a network of residue beads connected by springs. We add dissipative dynamics to this mechanical system by applying overdamped Langevin equations of motion to normal-mode vibrations of the network. In addition, the network is made heterogeneous and softened at the protein surface by accounting for hydration of the ionized residues. Solvation changes the network Hessian in two ways. Diagonal solvation terms soften the spring constants and off-diagonal dipole-dipole terms correlate displacements of the ionized residues. The model is used to formulate the response functions of the electrostatic potential and electric field appearing in theories of redox reactions and spectroscopy. We also formulate the dielectric response of the protein and find that solvation of the surface ionized residues leads to a slow relaxation peak in the dielectric loss spectrum, about two orders of magnitude slower than the main peak of protein relaxation. Finally, the solvated network is used to formulate the allosteric response of the protein to ion binding. The global thermodynamics of ion binding is not strongly affected by the network solvation, but it dramatically enhances conformational changes in response to placing a charge at the a the active site.

Solvated dissipative electro-elastic network model of hydrated proteins

NASA Astrophysics Data System (ADS)

Martin, Daniel R.; Matyushov, Dmitry V.

2012-10-01

Elastic network models coarse grain proteins into a network of residue beads connected by springs. We add dissipative dynamics to this mechanical system by applying overdamped Langevin equations of motion to normal-mode vibrations of the network. In addition, the network is made heterogeneous and softened at the protein surface by accounting for hydration of the ionized residues. Solvation changes the network Hessian in two ways. Diagonal solvation terms soften the spring constants and off-diagonal dipole-dipole terms correlate displacements of the ionized residues. The model is used to formulate the response functions of the electrostatic potential and electric field appearing in theories of redox reactions and spectroscopy. We also formulate the dielectric response of the protein and find that solvation of the surface ionized residues leads to a slow relaxation peak in the dielectric loss spectrum, about two orders of magnitude slower than the main peak of protein relaxation. Finally, the solvated network is used to formulate the allosteric response of the protein to ion binding. The global thermodynamics of ion binding is not strongly affected by the network solvation, but it dramatically enhances conformational changes in response to placing a charge at the active site of the protein.

Coformer screening using thermal analysis based on binary phase diagrams.

PubMed

Yamashita, Hiroyuki; Hirakura, Yutaka; Yuda, Masamichi; Terada, Katsuhide

2014-08-01

The advent of cocrystals has demonstrated a growing need for efficient and comprehensive coformer screening in search of better development forms, including salt forms. Here, we investigated a coformer screening system for salts and cocrystals based on binary phase diagrams using thermal analysis and examined the effectiveness of the method. Indomethacin and tenoxicam were used as models of active pharmaceutical ingredients (APIs). Physical mixtures of an API and 42 kinds of coformers were analyzed using Differential Scanning Calorimetry (DSC) and X-ray DSC. We also conducted coformer screening using a conventional slurry method and compared these results with those from the thermal analysis method and previous studies. Compared with the slurry method, the thermal analysis method was a high-performance screening system, particularly for APIs with low solubility and/or propensity to form solvates. However, this method faced hurdles for screening coformers combined with an API in the presence of kinetic hindrance for salt or cocrystal formation during heating or if there is degradation near the metastable eutectic temperature. The thermal analysis and slurry methods are considered complementary to each other for coformer screening. Feasibility of the thermal analysis method in drug discovery practice is ensured given its small scale and high throughput.

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.

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models.

PubMed

Genheden, Samuel

2017-10-01

We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

Water Lone Pair Delocalization in Classical and Quantum Descriptions of the Hydration of Model Ions

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

Remsing, Richard C.; Duignan, Timothy T.; Baer, Marcel D.

Understanding the nature of ionic hydration at a fundamental level has eluded scientists despite intense interest for nearly a century. In particular, the microscopic origins of the asymmetry of ion solvation thermodynamics with respect to the sign of the ionic charge remains a mystery. Here, we determine the response of accurate quantum mechanical water models to strong nanoscale solvation forces arising from excluded volumes and ionic electrostatic fields. This is compared to the predictions of two important limiting classes of classical models of water with fixed point changes, differing in their treatment of "lone-pair" electrons. Using the quantum water modelmore » as our standard of accuracy, we find that a single fixed classical treatment of lone pair electrons cannot accurately describe solvation of both apolar and cationic solutes, underlining the need for a more flexible description of local electronic effects in solvation processes. However, we explicitly show that all water models studied respond to weak long-ranged electrostatic perturbations in a manner that follows macroscopic dielectric continuum models, as would be expected. We emphasize the importance of these findings in the context of realistic ion models, using density functional theory and empirical models, and discuss the implications of our results for quantitatively accurate reduced descriptions of solvation in dielectric media.« less

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models

NASA Astrophysics Data System (ADS)

Genheden, Samuel

2017-10-01

We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

Comparative assessment of computational methods for the determination of solvation free energies in alcohol-based molecules.

PubMed

Martins, Silvia A; Sousa, Sergio F

2013-06-05

The determination of differences in solvation free energies between related drug molecules remains an important challenge in computational drug optimization, when fast and accurate calculation of differences in binding free energy are required. In this study, we have evaluated the performance of five commonly used polarized continuum model (PCM) methodologies in the determination of solvation free energies for 53 typical alcohol and alkane small molecules. In addition, the performance of these PCM methods, of a thermodynamic integration (TI) protocol and of the Poisson-Boltzmann (PB) and generalized Born (GB) methods, were tested in the determination of solvation free energies changes for 28 common alkane-alcohol transformations, by the substitution of an hydrogen atom for a hydroxyl substituent. The results show that the solvation model D (SMD) performs better among the PCM-based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane-alcohol transformations, with an average error below 1 kcal/mol for both quantities. However, for the determination of solvation free energy changes on alkane-alcohol transformation, PB and TI yielded better results. TI was particularly accurate in the treatment of hydroxyl groups additions to aromatic rings (0.53 kcal/mol), a common transformation when optimizing drug-binding in computer-aided drug design. Copyright © 2013 Wiley Periodicals, Inc.

Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms

PubMed Central

Wagoner, Jason A.; Baker, Nathan A.

2006-01-01

Continuum solvation models provide appealing alternatives to explicit solvent methods because of their ability to reproduce solvation effects while alleviating the need for expensive sampling. Our previous work has demonstrated that Poisson-Boltzmann methods are capable of faithfully reproducing polar explicit solvent forces for dilute protein systems; however, the popular solvent-accessible surface area model was shown to be incapable of accurately describing nonpolar solvation forces at atomic-length scales. Therefore, alternate continuum methods are needed to reproduce nonpolar interactions at the atomic scale. In the present work, we address this issue by supplementing the solvent-accessible surface area model with additional volume and dispersion integral terms suggested by scaled particle models and Weeks–Chandler–Andersen theory, respectively. This more complete nonpolar implicit solvent model shows very good agreement with explicit solvent results and suggests that, although often overlooked, the inclusion of appropriate dispersion and volume terms are essential for an accurate implicit solvent description of atomic-scale nonpolar forces. PMID:16709675

Long-ranged contributions to solvation free energies from theory and short-ranged models

PubMed Central

Remsing, Richard C.; Liu, Shule; Weeks, John D.

2016-01-01

Long-standing problems associated with long-ranged electrostatic interactions have plagued theory and simulation alike. Traditional lattice sum (Ewald-like) treatments of Coulomb interactions add significant overhead to computer simulations and can produce artifacts from spurious interactions between simulation cell images. These subtle issues become particularly apparent when estimating thermodynamic quantities, such as free energies of solvation in charged and polar systems, to which long-ranged Coulomb interactions typically make a large contribution. In this paper, we develop a framework for determining very accurate solvation free energies of systems with long-ranged interactions from models that interact with purely short-ranged potentials. Our approach is generally applicable and can be combined with existing computational and theoretical techniques for estimating solvation thermodynamics. We demonstrate the utility of our approach by examining the hydration thermodynamics of hydrophobic and ionic solutes and the solvation of a large, highly charged colloid that exhibits overcharging, a complex nonlinear electrostatic phenomenon whereby counterions from the solvent effectively overscreen and locally invert the integrated charge of the solvated object. PMID:26929375

On the different roles of anions and cations in the solvation of enzymes in ionic liquids.

PubMed

Klähn, Marco; Lim, Geraldine S; Seduraman, Abirami; Wu, Ping

2011-01-28

The solvation of the enzyme Candida antarctica lipase B (CAL-B) was studied in eight different ionic liquids (ILs). The influence of enzyme-ion interactions on the solvation of CAL-B and the structure of the enzyme-IL interface are analyzed. CAL-B and ILs are described with molecular dynamics (MD) simulations in combination with an atomistic empirical force field. The considered cations are based on imidazolium or guanidinium that are paired with nitrate, tetrafluoroborate or hexafluorophosphate anions. The interactions of CAL-B with ILs are dominated by Coulomb interactions with anions, while the second largest contribution stems from van der Waals interactions with cations. The enzyme-ion interaction strength is determined by the ion size and the magnitude of the ion surface charge. The solvation of CAL-B in ILs is unfavorable compared to water because of large formation energies for the CAL-B solute cages in ILs. The internal energy in the IL and of CAL-B increases linearly with the enzyme-ion interaction strength. The average electrostatic potential on the surface of CAL-B is larger in ILs than in water, due to a weaker screening of charged enzyme residues. Ion densities increased moderately in the vicinity of charged residues and decreased close to non-polar residues. An aggregation of long alkyl chains close to non-polar regions and the active site entrance of CAL-B are observed in one IL that involved long non-polar decyl groups. In ILs that contain 1-butyl-3-methylimidazolium cations, the diffusion of one or two cations into the active site of CAL-B occurs during MD simulations. This suggests a possible obstruction of the active site in these ILs. Overall, the results indicate that small ions lead to a stronger electrostatic screening within the solvent and stronger interactions with the enzyme. Also a large ion surface charge, when more hydrophilic ions are used, increases enzyme-IL interactions. An increase of these interactions destabilizes the enzyme and impedes enzyme solvation due to an increase in solute cage formation energies.

Estimation of Solvation Quantities from Experimental Thermodynamic Data: Development of the Comprehensive CompSol Databank for Pure and Mixed Solutes

NASA Astrophysics Data System (ADS)

Moine, Edouard; Privat, Romain; Sirjean, Baptiste; Jaubert, Jean-Noël

2017-09-01

The Gibbs energy of solvation measures the affinity of a solute for its solvent and is thus a key property for the selection of an appropriate solvent for a chemical synthesis or a separation process. More fundamentally, Gibbs energies of solvation are choice data for developing and benchmarking molecular models predicting solvation effects. The Comprehensive Solvation—CompSol—database was developed with the ambition to propose very large sets of new experimental solvation chemical-potential, solvation entropy, and solvation enthalpy data of pure and mixed components, covering extended temperature ranges. For mixed compounds, the solvation quantities were generated in infinite-dilution conditions by combining experimental values of pure-component and binary-mixture thermodynamic properties. Three types of binary-mixture properties were considered: partition coefficients, activity coefficients at infinite dilution, and Henry's-law constants. A rigorous methodology was implemented with the aim to select data at appropriate conditions of temperature, pressure, and concentration for the estimation of solvation data. Finally, our comprehensive CompSol database contains 21 671 data associated with 1969 pure species and 70 062 data associated with 14 102 binary mixtures (including 760 solvation data related to the ionic-liquid class of solvents). On the basis of the very large amount of experimental data contained in the CompSol database, it is finally discussed how solvation energies are influenced by hydrogen-bonding association effects.

Recent Developments and Applications of the MMPBSA Method

PubMed Central

Wang, Changhao; Greene, D'Artagnan; Xiao, Li; Qi, Ruxi; Luo, Ray

2018-01-01

The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method. PMID:29367919

Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations

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

Yang, Xiu; Lei, Huan; Gao, Peiyuan

Atomic radii and charges are two major parameters used in implicit solvent electrostatics and energy calculations. The optimization problem for charges and radii is under-determined, leading to uncertainty in the values of these parameters and in the results of solvation energy calculations using these parameters. This paper presents a method for quantifying this uncertainty in solvation energies using surrogate models based on generalized polynomial chaos (gPC) expansions. There are relatively few atom types used to specify radii parameters in implicit solvation calculations; therefore, surrogate models for these low-dimensional spaces could be constructed using least-squares fitting. However, there are many moremore » types of atomic charges; therefore, construction of surrogate models for the charge parameter space required compressed sensing combined with an iterative rotation method to enhance problem sparsity. We present results for the uncertainty in small molecule solvation energies based on these approaches. Additionally, we explore the correlation between uncertainties due to radii and charges which motivates the need for future work in uncertainty quantification methods for high-dimensional parameter spaces.« less

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

Kuechler, Erich R.; Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431; Giese, Timothy J.

To better represent the solvation effects observed along reaction pathways, and of ionic species in general, a charge-dependent variable-radii smooth conductor-like screening model (VR-SCOSMO) is developed. This model is implemented and parameterized with a third order density-functional tight binding quantum model, DFTB3/3OB-OPhyd, a quantum method which was developed for organic and biological compounds, utilizing a specific parameterization for phosphate hydrolysis reactions. Unlike most other applications with the DFTB3/3OB model, an auxiliary set of atomic multipoles is constructed from the underlying DFTB3 density matrix which is used to interact the solute with the solvent response surface. The resulting method is variational,more » produces smooth energies, and has analytic gradients. As a baseline, a conventional SCOSMO model with fixed radii is also parameterized. The SCOSMO and VR-SCOSMO models shown have comparable accuracy in reproducing neutral-molecule absolute solvation free energies; however, the VR-SCOSMO model is shown to reduce the mean unsigned errors (MUEs) of ionic compounds by half (about 2-3 kcal/mol). The VR-SCOSMO model presents similar accuracy as a charge-dependent Poisson-Boltzmann model introduced by Hou et al. [J. Chem. Theory Comput. 6, 2303 (2010)]. VR-SCOSMO is then used to examine the hydrolysis of trimethylphosphate and seven other phosphoryl transesterification reactions with different leaving groups. Two-dimensional energy landscapes are constructed for these reactions and calculated barriers are compared to those obtained from ab initio polarizable continuum calculations and experiment. Results of the VR-SCOSMO model are in good agreement in both cases, capturing the rate-limiting reaction barrier and the nature of the transition state.« less

Predicting solvation free energies and thermodynamics in polar solvents and mixtures using a solvation-layer interface condition

PubMed Central

Goossens, Spencer; Mehdizadeh Rahimi, Ali

2017-01-01

We demonstrate that with two small modifications, the popular dielectric continuum model is capable of predicting, with high accuracy, ion solvation thermodynamics (Gibbs free energies, entropies, and heat capacities) in numerous polar solvents. We are also able to predict ion solvation free energies in water–co-solvent mixtures over available concentration series. The first modification to the classical dielectric Poisson model is a perturbation of the macroscopic dielectric-flux interface condition at the solute–solvent interface: we add a nonlinear function of the local electric field, giving what we have called a solvation-layer interface condition (SLIC). The second modification is including the microscopic interface potential (static potential) in our model. We show that the resulting model exhibits high accuracy without the need for fitting solute atom radii in a state-dependent fashion. Compared to experimental results in nine water–co-solvent mixtures, SLIC predicts transfer free energies to within 2.5 kJ/mol. The co-solvents include both protic and aprotic species, as well as biologically relevant denaturants such as urea and dimethylformamide. Furthermore, our results indicate that the interface potential is essential to reproduce entropies and heat capacities. These and previous tests of the SLIC model indicate that it is a promising dielectric continuum model for accurate predictions in a wide range of conditions.

Predicting solvation free energies and thermodynamics in polar solvents and mixtures using a solvation-layer interface condition

NASA Astrophysics Data System (ADS)

Molavi Tabrizi, Amirhossein; Goossens, Spencer; Mehdizadeh Rahimi, Ali; Knepley, Matthew; Bardhan, Jaydeep P.

2017-03-01

We demonstrate that with two small modifications, the popular dielectric continuum model is capable of predicting, with high accuracy, ion solvation thermodynamics (Gibbs free energies, entropies, and heat capacities) in numerous polar solvents. We are also able to predict ion solvation free energies in water-co-solvent mixtures over available concentration series. The first modification to the classical dielectric Poisson model is a perturbation of the macroscopic dielectric-flux interface condition at the solute-solvent interface: we add a nonlinear function of the local electric field, giving what we have called a solvation-layer interface condition (SLIC). The second modification is including the microscopic interface potential (static potential) in our model. We show that the resulting model exhibits high accuracy without the need for fitting solute atom radii in a state-dependent fashion. Compared to experimental results in nine water-co-solvent mixtures, SLIC predicts transfer free energies to within 2.5 kJ/mol. The co-solvents include both protic and aprotic species, as well as biologically relevant denaturants such as urea and dimethylformamide. Furthermore, our results indicate that the interface potential is essential to reproduce entropies and heat capacities. These and previous tests of the SLIC model indicate that it is a promising dielectric continuum model for accurate predictions in a wide range of conditions.

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

NASA Astrophysics Data System (ADS)

Yang, Pei-Kun

2014-10-01

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

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

DOE PAGES

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.; ...

2017-07-26

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. In this paper, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing tomore » the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. Finally, this suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.« less

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

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

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. In this paper, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing tomore » the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. Finally, this suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.« less

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

NASA Astrophysics Data System (ADS)

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.; Mundy, Chistopher J.

2017-10-01

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. Here, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.

Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas.

PubMed

Santos-Martins, Diogo; Fernandes, Pedro Alexandrino; Ramos, Maria João

2016-11-01

In the context of SAMPL5, we submitted blind predictions of the cyclohexane/water distribution coefficient (D) for a series of 53 drug-like molecules. Our method is purely empirical and based on the additive contribution of each solute atom to the free energy of solvation in water and in cyclohexane. The contribution of each atom depends on the atom type and on the exposed surface area. Comparatively to similar methods in the literature, we used a very small set of atomic parameters: only 10 for solvation in water and 1 for solvation in cyclohexane. As a result, the method is protected from overfitting and the error in the blind predictions could be reasonably estimated. Moreover, this approach is fast: it takes only 0.5 s to predict the distribution coefficient for all 53 SAMPL5 compounds, allowing its application in virtual screening campaigns. The performance of our approach (submission 49) is modest but satisfactory in view of its efficiency: the root mean square error (RMSE) was 3.3 log D units for the 53 compounds, while the RMSE of the best performing method (using COSMO-RS) was 2.1 (submission 16). Our method is implemented as a Python script available at https://github.com/diogomart/SAMPL5-DC-surface-empirical .

Heterogeneous nucleation of polymorphs on polymer surfaces: polymer-molecule interactions using a heterogeneous dielectric solvation model.

PubMed

Wahlberg, Nanna; Madsen, Anders Ø; Mikkelsen, Kurt V

2018-06-09

We have investigated the mechanism of the nucleation of acetaminophen on poly(methyl-methacrylate) and poly(vinyl-acetate) utilizing a combination of quantum mechanical computations and electrostatic models. We have used a heterogeneous dielectric solvation model to determine the stability of different orientations of acetaminophen on polymer surfaces. We find that for the nucleation of acetaminophen on the polymer surfaces in vacuum, the most stable orientation is a flat orientation. For the nucleation process in solution where acetaminophen and the polymer surface are surrounded by a solvent, we find that the heterogeneous dielectric solvation model predicts that a sideways orientation is the most stable orientation.

Microcalorimetric study of thermal unfolding of lysozyme in water/glycerol mixtures: An analysis by solvent exchange model

NASA Astrophysics Data System (ADS)

Spinozzi, Francesco; Ortore, Maria Grazia; Sinibaldi, Raffaele; Mariani, Paolo; Esposito, Alessandro; Cinelli, Stefania; Onori, Giuseppe

2008-07-01

Folded protein stabilization or destabilization induced by cosolvent in mixed aqueous solutions has been studied by differential scanning microcalorimetry and related to difference in preferential solvation of native and denatured states. In particular, the thermal denaturation of a model system formed by lysozyme dissolved in water in the presence of the stabilizing cosolvent glycerol has been considered. Transition temperatures and enthalpies, heat capacity, and standard free energy changes have been determined when applying a two-state denaturation model to microcalorimetric data. Thermodynamic parameters show an unexpected, not linear, trend as a function of solvent composition; in particular, the lysozyme thermodynamic stability shows a maximum centered at water molar fraction of about 0.6. Using a thermodynamic hydration model based on the exchange equilibrium between glycerol and water molecules from the protein solvation layer to the bulk, the contribution of protein-solvent interactions to the unfolding free energy and the changes of this contribution with solvent composition have been derived. The preferential solvation data indicate that lysozyme unfolding involves an increase in the solvation surface, with a small reduction of the protein-preferential hydration. Moreover, the derived changes in the excess solvation numbers at denaturation show that only few solvent molecules are responsible for the variation of lysozyme stability in relation to the solvent composition.

Residue length and solvation model dependency of elastinlike polypeptides

NASA Astrophysics Data System (ADS)

Bilsel, Mustafa; Arkin, Handan

2010-05-01

We have performed exhaustive multicanonical Monte Carlo simulations of elastinlike polypeptides with a chain including amino acids (valine-proline-glycine-valine-glycine)n or in short (VPGVG)n , where n changes from 1 to 4, in order to investigate the thermodynamic and structural properties. To predict the characteristic secondary structure motifs of the molecules, Ramachandran plots were prepared and analyzed as well. In these studies, we utilized a realistic model where the interactions between all types of atoms were taken into account. Effects of solvation were also simulated by using an implicit-solvent model with two commonly used solvation parameter sets and compared with the vacuum case.

Absolute single-ion solvation free energy scale in methanol determined by the lithium cluster-continuum approach.

PubMed

Pliego, Josefredo R; Miguel, Elizabeth L M

2013-05-02

Absolute solvation free energy of the lithium cation in methanol was calculated by the cluster-continuum quasichemical theory of solvation. Clusters with up to five methanol molecules were investigated using X3LYP, MP2, and MP4 methods with DZVP, 6-311+G(2df,2p), TZVPP+diff, and QZVPP+diff basis sets and including the cluster solvation through the PCM and SMD continuum models. Our calculations have determined a value of -118.1 kcal mol(-1) for the solvation free energy of the lithium, in close agreement with a value of -116.6 kcal mol(-1) consistent with the TATB assumption. Using data of solvation and transfer free energy of a pair of ions, electrode potentials and pKa, we have obtained the solvation free energy of 25 ions in methanol. Our analysis leads to a value of -253.6 kcal mol(-1) for the solvation free energy of the proton, which can be compared with the value of -263.5 kcal mol(-1) obtained by Kelly et al. using the cluster pair approximation. Considering that this difference is due to the methanol surface potential, we have estimated that it corresponds to -0.429 V.

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

PubMed

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

2010-12-09

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

Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling.

PubMed

Chakravorty, Arghya; Jia, Zhe; Li, Lin; Zhao, Shan; Alexov, Emil

2018-02-13

Typically, the ensemble average polar component of solvation energy (ΔG polar solv ) of a macromolecule is computed using molecular dynamics (MD) or Monte Carlo (MC) simulations to generate conformational ensemble and then single/rigid conformation solvation energy calculation is performed on each snapshot. The primary objective of this work is to demonstrate that Poisson-Boltzmann (PB)-based approach using a Gaussian-based smooth dielectric function for macromolecular modeling previously developed by us (Li et al. J. Chem. Theory Comput. 2013, 9 (4), 2126-2136) can reproduce that ensemble average (ΔG polar solv ) of a protein from a single structure. We show that the Gaussian-based dielectric model reproduces the ensemble average ΔG polar solv (⟨ΔG polar solv ⟩) from an energy-minimized structure of a protein regardless of the minimization environment (structure minimized in vacuo, implicit or explicit waters, or crystal structure); the best case, however, is when it is paired with an in vacuo-minimized structure. In other minimization environments (implicit or explicit waters or crystal structure), the traditional two-dielectric model can still be selected with which the model produces correct solvation energies. Our observations from this work reflect how the ability to appropriately mimic the motion of residues, especially the salt bridge residues, influences a dielectric model's ability to reproduce the ensemble average value of polar solvation free energy from a single in vacuo-minimized structure.

Solvation effect on isomer stability and electronic structures of protonated serotonin

NASA Astrophysics Data System (ADS)

Omidyan, Reza; Amanollahi, Zohreh; Azimi, Gholamhassan

2017-07-01

Microsolvation effect on geometry and transition energies of protonated serotonin has been investigated by MP2 and CC2 quantum chemical methods. Also, conductor-like screening model, implemented recently in the MP2 and ADC(2) methods, was examined to address the bulk water environment's effect on the isomer stability and electronic transition energies of protonated serotonin. It has been predicted that the dipole moment of gas phase isomers plays the main role on the isomer stabilization in water solution and electronic transition shifts. Also, both red- and blue-shift effects have been predicted to take place on electronic transition energies, upon hydration.

Atomistic characterization of the active-site solvation dynamics of a model photocatalyst

DOE PAGES

van Driel, Tim B.; Kjær, Kasper S.; Hartsock, Robert W.; ...

2016-11-28

The interactions between the reactive excited state of molecular photocatalysts and surrounding solvent dictate reaction mechanisms and pathways, but are not readily accessible to conventional optical spectroscopic techniques. Here we report an investigation of the structural and solvation dynamics following excitation of a model photocatalytic molecular system [Ir 2(dimen) 4] 2+, where dimen is para-diisocyanomenthane. The time-dependent structural changes in this model photocatalyst, as well as the changes in the solvation shell structure, have been measured with ultrafast diffuse X-ray scattering and simulated with Born-Oppenheimer Molecular Dynamics. Both methods provide direct access to the solute–solvent pair distribution function, enabling themore » solvation dynamics around the catalytically active iridium sites to be robustly characterized. Our results provide evidence for the coordination of the iridium atoms by the acetonitrile solvent and demonstrate the viability of using diffuse X-ray scattering at free-electron laser sources for studying the dynamics of photocatalysis.« less

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.

Mechanistic Design of Chemically Diverse Polymers with Applications in Oral Drug Delivery.

PubMed

Mosquera-Giraldo, Laura I; Borca, Carlos H; Meng, Xiangtao; Edgar, Kevin J; Slipchenko, Lyudmila V; Taylor, Lynne S

2016-11-14

Polymers play a key role in stabilizing amorphous drug formulations, a recent strategy employed to improve solubility and bioavailability of drugs delivered orally. However, the molecular mechanism of stabilization is unclear, therefore, the rational design of new crystallization-inhibiting excipients remains a substantial challenge. This article presents a combined experimental and computational approach to elucidate the molecular features that improve the effectiveness of cellulose polymers as solution crystallization inhibitors, a crucial first step toward their rational design. Polymers with chemically diverse substituents including carboxylic acids, esters, ethers, alcohols, amides, amines, and sulfides were synthesized. Measurements of nucleation induction times of the model drug, telaprevir, show that the only effective polymers contained carboxylate groups in combination with an optimal hydrocarbon chain length. Computational results indicate that polymer conformation as well as solvation free energy are important determinants of effectiveness at inhibiting crystallization and show that simulations are a promising predictive tool in the screening of polymers. This study suggests that polymers need to have an adequate hydrophilicity to promote solvation in an aqueous environment, and sufficient hydrophobic regions to drive interactions with the drug. Particularly, the right balance between key substituent groups and lengths of hydrocarbon side chains is needed to create effective materials.

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

PubMed

Carvalho, Nathalia F; Pliego, Josefredo R

2015-10-28

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

Solvation of decane and benzene in mixtures of 1-octanol and N, N-dimethylformamide

NASA Astrophysics Data System (ADS)

Kustov, A. V.; Smirnova, N. L.

2016-09-01

The heats of dissolution of decane and benzene in a model system of octanol-1 (OctOH) and N, N-dimethylformamide (DMF) at 308 K are measured using a variable temperature calorimeter equipped with an isothermal shell. Standard enthalpies are determined and standard heat capacities of dissolution in the temperature range of 298-318 K are calculated using data obtained in [1, 2]. The state of hydrocarbon molecules in a binary mixture is studied in terms of the enhanced coordination model (ECM). Benzene is shown to be preferentially solvated by DMF over the range of physiological temperatures. The solvation shell of decane is found to be strongly enriched with 1-octanol. It is obvious that although both hydrocarbons are nonpolar, the presence of the aromatic π-system in benzene leads to drastic differences in their solvation in a lipid-protein medium.

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

Modeling Free Energies of Solvation in Olive Oil

PubMed Central

Chamberlin, Adam C.; Levitt, David G.; Cramer, Christopher J.; Truhlar, Donald G.

2009-01-01

Olive oil partition coefficients are useful for modeling the bioavailability of drug-like compounds. We have recently developed an accurate solvation model called SM8 for aqueous and organic solvents (Marenich, A. V.; Olson, R. M.; Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Chem. Theory Comput. 2007, 3, 2011) and a temperature-dependent solvation model called SM8T for aqueous solution (Chamberlin, A. C.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B 2008, 112, 3024). Here we describe an extension of SM8T to predict air–olive oil and water–olive oil partitioning for drug-like solutes as functions of temperature. We also describe the database of experimental partition coefficients used to parameterize the model; this database includes 371 entries for 304 compounds spanning the 291–310 K temperature range. PMID:19434923

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

Liu, Maoyuan; Besford, Quinn Alexander; Mulvaney, Thomas

The entropy of hydrophobic solvation has been explained as the result of ordered solvation structures, of hydrogen bonds, of the small size of the water molecule, of dispersion forces, and of solvent density fluctuations. We report a new approach to the calculation of the entropy of hydrophobic solvation, along with tests of and comparisons to several other methods. The methods are assessed in the light of the available thermodynamic and spectroscopic information on the effects of temperature on hydrophobic solvation. Five model hydrophobes in SPC/E water give benchmark solvation entropies via Widom’s test-particle insertion method, and other methods and modelsmore » are tested against these particle-insertion results. Entropies associated with distributions of tetrahedral order, of electric field, and of solvent dipole orientations are examined. We find these contributions are small compared to the benchmark particle-insertion entropy. Competitive with or better than other theories in accuracy, but with no free parameters, is the new estimate of the entropy contributed by correlations between dipole moments. Dipole correlations account for most of the hydrophobic solvation entropy for all models studied and capture the distinctive temperature dependence seen in thermodynamic and spectroscopic experiments. Entropies based on pair and many-body correlations in number density approach the correct magnitudes but fail to describe temperature and size dependences, respectively. Hydrogen-bond definitions and free energies that best reproduce entropies from simulations are reported, but it is difficult to choose one hydrogen bond model that fits a variety of experiments. The use of information theory, scaled-particle theory, and related methods is discussed briefly. Our results provide a test of the Frank-Evans hypothesis that the negative solvation entropy is due to structured water near the solute, complement the spectroscopic detection of that solvation structure by identifying the structural feature responsible for the entropy change, and point to a possible explanation for the observed dependence on length scale. Our key results are that the hydrophobic effect, i.e. the signature, temperature-dependent, solvation entropy of nonpolar molecules in water, is largely due to a dispersion force arising from correlations between rotating permanent dipole moments, that the strength of this force depends on the Kirkwood g-factor, and that the strength of this force may be obtained exactly without simulation.« less

Absorption and fluorescence spectra of heterocyclic isomers from long-range-corrected density functional theory in polarizable continuum approach.

PubMed

Kityk, Andriy V

2012-03-22

Long-range-corrected (LC) DFT/TDDFT methods may provide adequate description of ground and excited state properties; however, accuracy of such an approach depends much on a range separation (exchange screening) representing adjustable model parameter. Its relation to a size or specific of molecular systems has been explored in numerous studies, whereas the effect of solvent environment is usually ignored during the evaluation of state properties. To benchmark and assess the quality of the LC-DFT/TDDFT formalism, we report the optical absorption and fluorescence emission energies of organic heterocyclic isomers, DPIPQ and PTNA, calculated by LC-BLYP DFT/TDDFT method in the polarizable continuum (PCM) approach. The calculations are compared with the optical absorption and fluorescence spectra measured in organic solvents of different polarity. Despite a considerable structural difference, both dyes exhibit quite similar range separations being somewhat different for the optical absorption and fluorescence emission processes. Properly parametrized LC-BLYP xc-potential well reproduces basic features of the optical absorption spectra including the electronic transitions to higher excited states. The DFT/TDDFT/PCM analysis correctly predicts the solvation trends although solvatochromic shifts of the electronic transition energies appear to be evidently underestimated in most cases, especially for the fluorescence emission. Considering the discrepancy between the experiment and theory, evaluated state dipole moments and solvation corrections to the exchange screening are analyzed. The results of the present study emphasize the importance of a solvent-dependent range separation in DFT/TDDFT/PCM calculations for investigating excited state properties. © 2012 American Chemical Society

Quantum chemical approach for condensed-phase thermochemistry (IV): Solubility of gaseous molecules

NASA Astrophysics Data System (ADS)

Ishikawa, Atsushi; Kamata, Masahiro; Nakai, Hiromi

2016-07-01

The harmonic solvation model (HSM) was applied to the solvation of gaseous molecules and compared to a procedure based on the ideal gas model (IGM). Examination of 25 molecules showed that (i) the accuracy of ΔGsolv was similar for both methods, but the HSM shows advantages for calculating ΔHsolv and TΔSsolv; (ii) TΔSsolv contributes more than ΔHsolv to ΔGsolv in the HSM, i.e. the solvation of gaseous molecules is entropy-driven, which agrees well with experimental understanding (the IGM does not show this); (iii) the temperature dependence of Henry's law coefficient was correctly reproduced with the HSM.

Generalized Born Models of Macromolecular Solvation Effects

NASA Astrophysics Data System (ADS)

Bashford, Donald; Case, David A.

2000-10-01

It would often be useful in computer simulations to use a simple description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson equation are attractive because of their computational efficiency. Here we give an overview of one such approximation, the generalized Born model, which is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids. We discuss its strengths and weaknesses, both for its fidelity to the underlying continuum model and for its ability to replace explicit consideration of solvent molecules in macromolecular simulations. We focus particularly on versions of the generalized Born model that have a pair-wise analytical form, and therefore fit most naturally into conventional molecular mechanics calculations.

Water's hydrogen bonds in the hydrophobic effect: a simple model.

PubMed

Xu, Huafeng; Dill, Ken A

2005-12-15

We propose a simple analytical model to account for water's hydrogen bonds in the hydrophobic effect. It is based on computing a mean-field partition function for a water molecule in the first solvation shell around a solute molecule. The model treats the orientational restrictions from hydrogen bonding, and utilizes quantities that can be obtained from bulk water simulations. We illustrate the principles in a 2-dimensional Mercedes-Benz-like model. Our model gives good predictions for the heat capacity of hydrophobic solvation, reproduces the solvation energies and entropies at different temperatures with only one fitting parameter, and accounts for the solute size dependence of the hydrophobic effect. Our model supports the view that water's hydrogen bonding propensity determines the temperature dependence of the hydrophobic effect. It explains the puzzling experimental observation that dissolving a nonpolar solute in hot water has positive entropy.

Charge-dependent non-bonded interaction methods for use in quantum mechanical modeling of condensed phase reactions

NASA Astrophysics Data System (ADS)

Kuechler, Erich R.

Molecular modeling and computer simulation techniques can provide detailed insight into biochemical phenomena. This dissertation describes the development, implementation and parameterization of two methods for the accurate modeling of chemical reactions in aqueous environments, with a concerted scientific effort towards the inclusion of charge-dependent non-bonded non-electrostatic interactions into currently used computational frameworks. The first of these models, QXD, modifies interactions in a hybrid quantum mechanical/molecular (QM/MM) mechanical framework to overcome the current limitations of 'atom typing' QM atoms; an inaccurate and non-intuitive practice for chemically active species as these static atom types are dictated by the local bonding and electrostatic environment of the atoms they represent, which will change over the course of the simulation. The efficacy QXD model is demonstrated using a specific reaction parameterization (SRP) of the Austin Model 1 (AM1) Hamiltonian by simultaneously capturing the reaction barrier for chloride ion attack on methylchloride in solution and the solvation free energies of a series of compounds including the reagents of the reaction. The second, VRSCOSMO, is an implicit solvation model for use with the DFTB3/3OB Hamiltonian for biochemical reactions; allowing for accurate modeling of ionic compound solvation properties while overcoming the discontinuous nature of conventional PCM models when chemical reaction coordinates. The VRSCOSMO model is shown to accurately model the solvation properties of over 200 chemical compounds while also providing smooth, continuous reaction surfaces for a series of biologically motivated phosphoryl transesterification reactions. Both of these methods incorporate charge-dependent behavior into the non-bonded interactions variationally, allowing the 'size' of atoms to change in meaningful ways with respect to changes in local charge state, as to provide an accurate, predictive and transferable models for the interactions between the quantum mechanical system and their solvated surroundings.

Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite

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

Jurrus, Elizabeth; Engel, Dave; Star, Keith

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suitemore » of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.« less

Improvements to the APBS biomolecular solvation software suite.

PubMed

Jurrus, Elizabeth; Engel, Dave; Star, Keith; Monson, Kyle; Brandi, Juan; Felberg, Lisa E; Brookes, David H; Wilson, Leighton; Chen, Jiahui; Liles, Karina; Chun, Minju; Li, Peter; Gohara, David W; Dolinsky, Todd; Konecny, Robert; Koes, David R; Nielsen, Jens Erik; Head-Gordon, Teresa; Geng, Weihua; Krasny, Robert; Wei, Guo-Wei; Holst, Michael J; McCammon, J Andrew; Baker, Nathan A

2018-01-01

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pK a values, and an improved web-based visualization tool for viewing electrostatics. © 2017 The Protein Society.

Excess electron localization in solvated DNA bases.

PubMed

Smyth, Maeve; Kohanoff, Jorge

2011-06-10

We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.

Excess Electron Localization in Solvated DNA Bases

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

Smyth, Maeve; Kohanoff, Jorge

2011-06-10

We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.

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

PubMed

Li, Bo; Zhao, Yanxiang

2013-01-01

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

Going full circle: phase-transition thermodynamics of ionic liquids.

PubMed

Preiss, Ulrich; Verevkin, Sergey P; Koslowski, Thorsten; Krossing, Ingo

2011-05-27

We present the full enthalpic phase transition cycle for ionic liquids (ILs) as examples of non-classical salts. The cycle was closed for the lattice, solvation, dissociation, and vaporization enthalpies of 30 different ILs, relying on as much experimental data as was available. High-quality dissociation enthalpies were calculated at the G3 MP2 level. From the cycle, we could establish, for the first time, the lattice and solvation enthalpies of ILs with imidazolium ions. For vaporization, lattice, and dissociation enthalpies, we also developed new prediction methods in the course of our investigations. Here, as only single-ion values need to be calculated and the tedious optimization of an ion pair can be circumvented, the computational time is short. For the vaporization enthalpy, a very simple approach was found, using a surface term and the calculated enthalpic correction to the total gas-phase energy. For the lattice enthalpy, the most important constituent proved to be the calculated conductor-like screening model (COSMO) solvation enthalpy in the ideal electric conductor. A similar model was developed for the dissociation enthalpy. According to our assessment, the typical error of the lattice enthalpy would be 9.4 kJ mol(-1), which is less than half the deviation we get when using the (optimized) Kapustinskii equation or the recent volume-based thermodynamics (VBT) theory. In contrast, the non-optimized VBT formula gives lattice enthalpies 20 to 140 kJ mol(-1) lower than the ones we assessed in the cycle, because of the insufficient description of dispersive interactions. Our findings show that quantum-chemical calculations can greatly improve the VBT approaches, which were parameterized for simple, inorganic salts with ideally point-shaped charges. In conclusion, we suggest the term "augmented VBT", or "aVBT", to describe this kind of theoretical approach. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

SISGR: Linking Ion Solvation and Lithium Battery Electrolyte Properties

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

Trulove, Paul C.; Foley, Matthew P.

2012-09-30

The solvation and phase behavior of the model battery electrolyte salt lithium trifluoromethanesulfonate (LiCF 3SO 3) in commonly used organic solvents; ethylene carbonate (EC), gamma-butyrolactone (GBL), and propylene carbonate (PC) was explored. Data from differential scanning calorimetry (DSC), Raman spectroscopy, and X-ray diffraction were correlated to provide insight into the solvation states present within a sample mixture. Data from DSC analyses allowed the construction of phase diagrams for each solvent system. Raman spectroscopy enabled the determination of specific solvation states present within a solvent-salt mixture, and X-ray diffraction data provided exact information concerning the structure of a solvates that couldmore » be isolated Thermal analysis of the various solvent-salt mixtures revealed the phase behavior of the model electrolytes was strongly dependent on solvent symmetry. The point groups of the solvents were (in order from high to low symmetry): C2V for EC, CS for GBL, and C1 for PC(R). The low symmetry solvents exhibited a crystallinity gap that increased as solvent symmetry decreased; no gap was observed for EC-LiTf, while a crystallinity gap was observed spanning 0.15 to 0.3 mole fraction for GBL-LiTf, and 0.1 to 0.33 mole fraction for PC(R)-LiTf mixtures. Raman analysis demonstrated the dominance of aggregated species in almost all solvent compositions. The AGG and CIP solvates represent the majority of the species in solutions for the more concentrated mixtures, and only in very dilute compositions does the SSIP solvate exist in significant amounts. Thus, the poor charge transport characteristics of CIP and AGG account for the low conductivity and transport properties of LiTf and explain why is a poor choice as a source of Li + ions in a Li-ion battery.« less

C–IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids

DOE PAGES

de Oliveira, Tiago E.; Netz, Paulo A.; Kremer, Kurt; ...

2016-05-03

We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination iterative Boltzmann inversion (C–IBI). While the underlying coarse-grained model is still structure based and, thus, preserves pair-wise solution structure, our method also reproduces solvation thermodynamics of binary and/or ternary mixtures. In addition, we observe much faster convergence within C–IBI compared to IBI. To validate the robustness, we apply C–IBI to study test cases of solvation thermodynamics of aqueous urea and a triglycine solvation in aqueous urea.

Nonlinear Poisson Equation for Heterogeneous Media

PubMed Central

Hu, Langhua; Wei, Guo-Wei

2012-01-01

The Poisson equation is a widely accepted model for electrostatic analysis. However, the Poisson equation is derived based on electric polarizations in a linear, isotropic, and homogeneous dielectric medium. This article introduces a nonlinear Poisson equation to take into consideration of hyperpolarization effects due to intensive charges and possible nonlinear, anisotropic, and heterogeneous media. Variational principle is utilized to derive the nonlinear Poisson model from an electrostatic energy functional. To apply the proposed nonlinear Poisson equation for the solvation analysis, we also construct a nonpolar solvation energy functional based on the nonlinear Poisson equation by using the geometric measure theory. At a fixed temperature, the proposed nonlinear Poisson theory is extensively validated by the electrostatic analysis of the Kirkwood model and a set of 20 proteins, and the solvation analysis of a set of 17 small molecules whose experimental measurements are also available for a comparison. Moreover, the nonlinear Poisson equation is further applied to the solvation analysis of 21 compounds at different temperatures. Numerical results are compared to theoretical prediction, experimental measurements, and those obtained from other theoretical methods in the literature. A good agreement between our results and experimental data as well as theoretical results suggests that the proposed nonlinear Poisson model is a potentially useful model for electrostatic analysis involving hyperpolarization effects. PMID:22947937

Discrete and continuum modeling of solvent effects in a twisted intramolecular charge transfer system: The 4-N,N-dimethylaminobenzonitrile (DMABN) molecule.

PubMed

Modesto-Costa, Lucas; Borges, Itamar

2018-08-05

The 4-N,N-dimethylaminobenzonitrile (DMABN) molecule is a prototypical system displaying twisted intramolecular (TICT) charge transfer effects. The ground and the first four electronic excited states (S 1 -S 4 ) in gas phase and upon solvation were studied. Charge transfer values as function of the torsion angle between the donor group (dimethylamine) and the acceptor moiety (benzonitrile) were explicitly computed. Potential energy curves were also obtained. The algebraic diagrammatic construction method at the second-order [ADC(2)] ab initio wave function was employed. Three solvents of increased polarities (benzene, DMSO and water) were investigated using discrete (average solvent electrostatic configuration - ASEC) and continuum (conductor-like screening model - COSMO) models. The results for the S 3 and S 4 excited states and the S 1 -S 4 charge transfer curves were not previously available in the literature. Electronic gas phase and solvent vertical spectra are in good agreement with previous theoretical and experimental results. In the twisted (90°) geometry the optical oscillator strengths have negligible values even for the S 2 bright state. Potential energy curves show two distinct pairs of curves intersecting at decreasing angles or not crossing in the more polar solvents. Charge transfer and electric dipole values allowed the rationalization of these results. The former effects are mostly independent of the solvent model and polarity. Although COSMO and ASEC solvent models mostly lead to similar results, there is an important difference: some crossings of the excitation energy curves appear only in the ASEC solvation model, which has important implications to the photochemistry of DMABN. Copyright © 2018 Elsevier B.V. All rights reserved.

Continuum electromechanical modeling of protein-membrane interactions

NASA Astrophysics Data System (ADS)

Zhou, Y. C.; Lu, Benzhuo; Gorfe, Alemayehu A.

2010-10-01

A continuum electromechanical model is proposed to describe the membrane curvature induced by electrostatic interactions in a solvated protein-membrane system. The model couples the macroscopic strain energy of membrane and the electrostatic solvation energy of the system, and equilibrium membrane deformation is obtained by minimizing the electroelastic energy functional with respect to the dielectric interface. The model is illustrated with the systems with increasing geometry complexity and captures the sensitivity of membrane curvature to the permanent and mobile charge distributions.

DESTRUCTION OF HALOGENATED HYDROCARBONS WITH SOLVATED ELECTRONS IN THE PRESENCE OF WATER. (R826180)

EPA Science Inventory

Model halogenated aromatic and aliphatic hydrocarbons and halogenated phenols were dehalogenated in seconds by solvated electrons generated from sodium in both anhydrous liquid ammonia and ammonia/water solutions. The minimum sodium required to completely dehalogenate these mo...

Analytical theory of the hydrophobic effect of solutes in water.

PubMed

Urbic, Tomaz; Dill, Ken A

2017-09-01

We develop an analytical statistical-mechanical model for hydrophobic solvation in water. In this three-dimensional Mercedes-Benz-like model, two neighboring waters have three possible interaction states: a radial van der Waals interaction, a tetrahedral orientation-dependent hydrogen-bonding interaction, or no interaction. Nonpolar solutes are modeled as van der Waals particles of different radii. The model is sufficiently simple that we can calculate the partition function and thermal and volumetric properties of solvation versus temperature, pressure, and solute radius. Predictions are in good agreement with results of Monte Carlo simulations. And their trends agree with experiments on hydrophobic solute insertion. The theory shows that first-shell waters are more highly structured than bulk waters, because of hydrogen bonding, and that that structure melts out faster with temperature than it does in bulk waters. Because the theory is analytical, it can explore a broad range of solvation properties and anomalies of water, at minimal computational expense.

Analytical theory of the hydrophobic effect of solutes in water

NASA Astrophysics Data System (ADS)

Urbic, Tomaz; Dill, Ken A.

2017-09-01

We develop an analytical statistical-mechanical model for hydrophobic solvation in water. In this three-dimensional Mercedes-Benz-like model, two neighboring waters have three possible interaction states: a radial van der Waals interaction, a tetrahedral orientation-dependent hydrogen-bonding interaction, or no interaction. Nonpolar solutes are modeled as van der Waals particles of different radii. The model is sufficiently simple that we can calculate the partition function and thermal and volumetric properties of solvation versus temperature, pressure, and solute radius. Predictions are in good agreement with results of Monte Carlo simulations. And their trends agree with experiments on hydrophobic solute insertion. The theory shows that first-shell waters are more highly structured than bulk waters, because of hydrogen bonding, and that that structure melts out faster with temperature than it does in bulk waters. Because the theory is analytical, it can explore a broad range of solvation properties and anomalies of water, at minimal computational expense.

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm.

PubMed

Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael

2016-11-01

Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology.

Extrapolating Single Organic Ion Solvation Thermochemistry from Simulated Water Nanodroplets.

PubMed

Coles, Jonathan P; Houriez, Céline; Meot-Ner Mautner, Michael; Masella, Michel

2016-09-08

We compute the ion/water interaction energies of methylated ammonium cations and alkylated carboxylate anions solvated in large nanodroplets of 10 000 water molecules using 10 ns molecular dynamics simulations and an all-atom polarizable force-field approach. Together with our earlier results concerning the solvation of these organic ions in nanodroplets whose molecular sizes range from 50 to 1000, these new data allow us to discuss the reliability of extrapolating absolute single-ion bulk solvation energies from small ion/water droplets using common power-law functions of cluster size. We show that reliable estimates of these energies can be extrapolated from a small data set comprising the results of three droplets whose sizes are between 100 and 1000 using a basic power-law function of droplet size. This agrees with an earlier conclusion drawn from a model built within the mean spherical framework and paves the road toward a theoretical protocol to systematically compute the solvation energies of complex organic ions.

"Martinizing" the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins.

PubMed

Ricci, Clarisse G; Li, Bo; Cheng, Li-Tien; Dzubiella, Joachim; McCammon, J Andrew

2017-07-13

Solvation is a fundamental driving force in many biological processes including biomolecular recognition and self-assembly, not to mention protein folding, dynamics, and function. The variational implicit solvent method (VISM) is a theoretical tool currently developed and optimized to estimate solvation free energies for systems of very complex topology, such as biomolecules. VISM's theoretical framework makes it unique because it couples hydrophobic, van der Waals, and electrostatic interactions as a functional of the solvation interface. By minimizing this functional, VISM produces the solvation interface as an output of the theory. In this work, we push VISM to larger scale applications by combining it with coarse-grained solute Hamiltonians adapted from the MARTINI framework, a well-established mesoscale force field for modeling large-scale biomolecule assemblies. We show how MARTINI-VISM ( M VISM) compares with atomistic VISM ( A VISM) for a small set of proteins differing in size, shape, and charge distribution. We also demonstrate M VISM's suitability to study the solvation properties of an interesting encounter complex, barnase-barstar. The promising results suggest that coarse-graining the protein with the MARTINI force field is indeed a valuable step to broaden VISM's and MARTINI's applications in the near future.

Protons in non-ionic aqueous reverse micelles.

PubMed

Rodriguez, Javier; Martí, Jordi; Guàrdia, Elvira; Laria, Daniel

2007-05-03

Using molecular dynamics techniques, we investigate the solvation of an excess proton within an aqueous reverse micelle in vacuo, with the neutral surfactant diethylene glycol monodecyl ether [CH3(CH2)11(OC2H4)2OH]. The simulation experiments were performed using a multistate empirical valence bond Hamiltonian model. Our results show that the stable solvation environments for the excess proton are located in the water-surfactant interface and that its first solvation shell is composed exclusively by water molecules. The relative prevalence of Eigen- versus Zundel-like solvation structures is investigated; compared to bulk results, Zundel-like structures in micelles become somewhat more stable. Characteristic times for the proton translocation jumps have been computed using population relaxation time correlation functions. The micellar rate for proton transfer is approximately 40x smaller than that found in bulk water at ambient conditions. Differences in the computed rates are examined in terms of the hydrogen-bond connectivity involving the first solvation shell of the excess charge with the rest of the micellar environment. Simulation results would indicate that proton transfers are correlated with rare episodes during which the HB connectivity between the first and second solvation shells suffers profound modifications.

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

NASA Astrophysics Data System (ADS)

Wang, Yuan; Liang, Zuozhong

2017-12-01

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

MTS-MD of Biomolecules Steered with 3D-RISM-KH Mean Solvation Forces Accelerated with Generalized Solvation Force Extrapolation.

PubMed

Omelyan, Igor; Kovalenko, Andriy

2015-04-14

We developed a generalized solvation force extrapolation (GSFE) approach to speed up multiple time step molecular dynamics (MTS-MD) of biomolecules steered with mean solvation forces obtained from the 3D-RISM-KH molecular theory of solvation (three-dimensional reference interaction site model with the Kovalenko-Hirata closure). GSFE is based on a set of techniques including the non-Eckart-like transformation of coordinate space separately for each solute atom, extension of the force-coordinate pair basis set followed by selection of the best subset, balancing the normal equations by modified least-squares minimization of deviations, and incremental increase of outer time step in motion integration. Mean solvation forces acting on the biomolecule atoms in conformations at successive inner time steps are extrapolated using a relatively small number of best (closest) solute atomic coordinates and corresponding mean solvation forces obtained at previous outer time steps by converging the 3D-RISM-KH integral equations. The MTS-MD evolution steered with GSFE of 3D-RISM-KH mean solvation forces is efficiently stabilized with our optimized isokinetic Nosé-Hoover chain (OIN) thermostat. We validated the hybrid MTS-MD/OIN/GSFE/3D-RISM-KH integrator on solvated organic and biomolecules of different stiffness and complexity: asphaltene dimer in toluene solvent, hydrated alanine dipeptide, miniprotein 1L2Y, and protein G. The GSFE accuracy and the OIN efficiency allowed us to enlarge outer time steps up to huge values of 1-4 ps while accurately reproducing conformational properties. Quasidynamics steered with 3D-RISM-KH mean solvation forces achieves time scale compression of conformational changes coupled with solvent exchange, resulting in further significant acceleration of protein conformational sampling with respect to real time dynamics. Overall, this provided a 50- to 1000-fold effective speedup of conformational sampling for these systems, compared to conventional MD with explicit solvent. We have been able to fold the miniprotein from a fully denatured, extended state in about 60 ns of quasidynamics steered with 3D-RISM-KH mean solvation forces, compared to the average physical folding time of 4-9 μs observed in experiment.

Air-water partition coefficients for a suite of polycyclic aromatic and other C10 through C20 unsaturated hydrocarbons.

PubMed

Rayne, Sierra; Forest, Kaya

2016-09-18

The air-water partition coefficients (Kaw) for 86 large polycyclic aromatic hydrocarbons and their unsaturated relatives were estimated using high-level G4(MP2) gas and aqueous phase calculations with the SMD, IEFPCM-UFF, and CPCM solvation models. An extensive method validation effort was undertaken which involved confirming that, via comparisons to experimental enthalpies of formation, gas-phase energies at the G4(MP2) level for the compounds of interest were at or near thermochemical accuracy. Investigations of the three solvation models using a range of neutral and ionic compounds suggested that while no clear preferential solvation model could be chosen in advance for accurate Kaw estimates of the target compounds, the employment of increasingly higher levels of theory would result in lower Kaw errors. Subsequent calculations on the polycyclic aromatic and unsaturated hydrocarbons at the G4(MP2) level revealed excellent agreement for the IEFPCM-UFF and CPCM models against limited available experimental data. The IEFPCM-UFF-G4(MP2) and CPCM-G4(MP2) solvation energy calculation approaches are anticipated to give Kaw estimates within typical experimental ranges, each having general Kaw errors of less than 0.5 log10 units. When applied to other large organic compounds, the method should allow development of a broad and reliable Kaw database for multimedia environmental modeling efforts on various contaminants.

Nonlinear Poisson equation for heterogeneous media.

PubMed

Hu, Langhua; Wei, Guo-Wei

2012-08-22

The Poisson equation is a widely accepted model for electrostatic analysis. However, the Poisson equation is derived based on electric polarizations in a linear, isotropic, and homogeneous dielectric medium. This article introduces a nonlinear Poisson equation to take into consideration of hyperpolarization effects due to intensive charges and possible nonlinear, anisotropic, and heterogeneous media. Variational principle is utilized to derive the nonlinear Poisson model from an electrostatic energy functional. To apply the proposed nonlinear Poisson equation for the solvation analysis, we also construct a nonpolar solvation energy functional based on the nonlinear Poisson equation by using the geometric measure theory. At a fixed temperature, the proposed nonlinear Poisson theory is extensively validated by the electrostatic analysis of the Kirkwood model and a set of 20 proteins, and the solvation analysis of a set of 17 small molecules whose experimental measurements are also available for a comparison. Moreover, the nonlinear Poisson equation is further applied to the solvation analysis of 21 compounds at different temperatures. Numerical results are compared to theoretical prediction, experimental measurements, and those obtained from other theoretical methods in the literature. A good agreement between our results and experimental data as well as theoretical results suggests that the proposed nonlinear Poisson model is a potentially useful model for electrostatic analysis involving hyperpolarization effects. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Establishing linear solvation energy relationships between VOCs and monolayer-protected gold nanoclusters using quartz crystal microbalance.

PubMed

Li, Chi-Lin; Lu, Chia-Jung

2009-08-15

Linear solvation energy relationships (LSERs) have been recognized as a useful model for investigating the chemical forces behind the partition coefficients between vapor molecules and absorbents. This study is the first to determine the solvation properties of monolayer-protected gold nanoclusters (MPCs) with different surface ligands. The ratio of partition coefficients/MPC density (K/rho) of 18 volatile organic compounds (VOCs) for four different MPCs obtained through quartz crystal microbalance (QCM) experiments were used for the LSER model calculations. LSER modeling results indicate that all MPC surfaces showed a statistically significant (p<0.05) preference to hydrogen-bond acidic molecules. Through dipole-dipole attraction, 4-methoxythiophenol-capped MPCs can also interact with polar organics (s=1.04). Showing a unique preference for the hydrogen bond basicity of vapors (b=1.11), 2-benzothiazolethiol-capped MPCs provide evidence of an intra-molecular, proton-shift mechanism on surface of nano-gold.

Quantitative prediction of solvation free energy in octanol of organic compounds.

PubMed

Delgado, Eduardo J; Jaña, Gonzalo A

2009-03-01

The free energy of solvation, DeltaGS0, in octanol of organic compounds is quantitatively predicted from the molecular structure. The model, involving only three molecular descriptors, is obtained by multiple linear regression analysis from a data set of 147 compounds containing diverse organic functions, namely, halogenated and non-halogenated alkanes, alkenes, alkynes, aromatics, alcohols, aldehydes, ketones, amines, ethers and esters; covering a DeltaGS0 range from about -50 to 0 kJ.mol(-1). The model predicts the free energy of solvation with a squared correlation coefficient of 0.93 and a standard deviation, 2.4 kJ.mol(-1), just marginally larger than the generally accepted value of experimental uncertainty. The involved molecular descriptors have definite physical meaning corresponding to the different intermolecular interactions occurring in the bulk liquid phase. The model is validated with an external set of 36 compounds not included in the training set.

Quantitative Prediction of Solvation Free Energy in Octanol of Organic Compounds

PubMed Central

Delgado, Eduardo J.; Jaña, Gonzalo A.

2009-01-01

The free energy of solvation, ΔGS0, in octanol of organic compunds is quantitatively predicted from the molecular structure. The model, involving only three molecular descriptors, is obtained by multiple linear regression analysis from a data set of 147 compounds containing diverse organic functions, namely, halogenated and non-halogenated alkanes, alkenes, alkynes, aromatics, alcohols, aldehydes, ketones, amines, ethers and esters; covering a ΔGS0 range from about −50 to 0 kJ·mol−1. The model predicts the free energy of solvation with a squared correlation coefficient of 0.93 and a standard deviation, 2.4 kJ·mol−1, just marginally larger than the generally accepted value of experimental uncertainty. The involved molecular descriptors have definite physical meaning corresponding to the different intermolecular interactions occurring in the bulk liquid phase. The model is validated with an external set of 36 compounds not included in the training set. PMID:19399236

Differential geometry based solvation model I: Eulerian formulation

NASA Astrophysics Data System (ADS)

Chen, Zhan; Baker, Nathan A.; Wei, G. W.

2010-11-01

This paper presents a differential geometry based model for the analysis and computation of the equilibrium property of solvation. Differential geometry theory of surfaces is utilized to define and construct smooth interfaces with good stability and differentiability for use in characterizing the solvent-solute boundaries and in generating continuous dielectric functions across the computational domain. A total free energy functional is constructed to couple polar and nonpolar contributions to the solvation process. Geometric measure theory is employed to rigorously convert a Lagrangian formulation of the surface energy into an Eulerian formulation so as to bring all energy terms into an equal footing. By optimizing the total free energy functional, we derive coupled generalized Poisson-Boltzmann equation (GPBE) and generalized geometric flow equation (GGFE) for the electrostatic potential and the construction of realistic solvent-solute boundaries, respectively. By solving the coupled GPBE and GGFE, we obtain the electrostatic potential, the solvent-solute boundary profile, and the smooth dielectric function, and thereby improve the accuracy and stability of implicit solvation calculations. We also design efficient second-order numerical schemes for the solution of the GPBE and GGFE. Matrix resulted from the discretization of the GPBE is accelerated with appropriate preconditioners. An alternative direct implicit (ADI) scheme is designed to improve the stability of solving the GGFE. Two iterative approaches are designed to solve the coupled system of nonlinear partial differential equations. Extensive numerical experiments are designed to validate the present theoretical model, test computational methods, and optimize numerical algorithms. Example solvation analysis of both small compounds and proteins are carried out to further demonstrate the accuracy, stability, efficiency and robustness of the present new model and numerical approaches. Comparison is given to both experimental and theoretical results in the literature.

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics

NASA Astrophysics Data System (ADS)

Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J. Andrew

2015-12-01

Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson-Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum-Chandler-Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods.

A Finite Element Solution of Lateral Periodic Poisson–Boltzmann Model for Membrane Channel Proteins

PubMed Central

Xu, Jingjie; Lu, Benzhuo

2018-01-01

Membrane channel proteins control the diffusion of ions across biological membranes. They are closely related to the processes of various organizational mechanisms, such as: cardiac impulse, muscle contraction and hormone secretion. Introducing a membrane region into implicit solvation models extends the ability of the Poisson–Boltzmann (PB) equation to handle membrane proteins. The use of lateral periodic boundary conditions can properly simulate the discrete distribution of membrane proteins on the membrane plane and avoid boundary effects, which are caused by the finite box size in the traditional PB calculations. In this work, we: (1) develop a first finite element solver (FEPB) to solve the PB equation with a two-dimensional periodicity for membrane channel proteins, with different numerical treatments of the singular charges distributions in the channel protein; (2) add the membrane as a dielectric slab in the PB model, and use an improved mesh construction method to automatically identify the membrane channel/pore region even with a tilt angle relative to the z-axis; and (3) add a non-polar solvation energy term to complete the estimation of the total solvation energy of a membrane protein. A mesh resolution of about 0.25 Å (cubic grid space)/0.36 Å (tetrahedron edge length) is found to be most accurate in linear finite element calculation of the PB solvation energy. Computational studies are performed on a few exemplary molecules. The results indicate that all factors, the membrane thickness, the length of periodic box, membrane dielectric constant, pore region dielectric constant, and ionic strength, have individually considerable influence on the solvation energy of a channel protein. This demonstrates the necessity to treat all of those effects in the PB model for membrane protein simulations. PMID:29495644

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics.

PubMed

Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J Andrew

2015-12-28

Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson-Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum-Chandler-Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods.

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson–Boltzmann electrostatics

PubMed Central

Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J. Andrew

2015-01-01

Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson–Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum–Chandler–Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods. PMID:26723595

A Finite Element Solution of Lateral Periodic Poisson-Boltzmann Model for Membrane Channel Proteins.

PubMed

Ji, Nan; Liu, Tiantian; Xu, Jingjie; Shen, Longzhu Q; Lu, Benzhuo

2018-02-28

Membrane channel proteins control the diffusion of ions across biological membranes. They are closely related to the processes of various organizational mechanisms, such as: cardiac impulse, muscle contraction and hormone secretion. Introducing a membrane region into implicit solvation models extends the ability of the Poisson-Boltzmann (PB) equation to handle membrane proteins. The use of lateral periodic boundary conditions can properly simulate the discrete distribution of membrane proteins on the membrane plane and avoid boundary effects, which are caused by the finite box size in the traditional PB calculations. In this work, we: (1) develop a first finite element solver (FEPB) to solve the PB equation with a two-dimensional periodicity for membrane channel proteins, with different numerical treatments of the singular charges distributions in the channel protein; (2) add the membrane as a dielectric slab in the PB model, and use an improved mesh construction method to automatically identify the membrane channel/pore region even with a tilt angle relative to the z -axis; and (3) add a non-polar solvation energy term to complete the estimation of the total solvation energy of a membrane protein. A mesh resolution of about 0.25 Å (cubic grid space)/0.36 Å (tetrahedron edge length) is found to be most accurate in linear finite element calculation of the PB solvation energy. Computational studies are performed on a few exemplary molecules. The results indicate that all factors, the membrane thickness, the length of periodic box, membrane dielectric constant, pore region dielectric constant, and ionic strength, have individually considerable influence on the solvation energy of a channel protein. This demonstrates the necessity to treat all of those effects in the PB model for membrane protein simulations.

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.

“Martinizing” the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins

PubMed Central

2017-01-01

Solvation is a fundamental driving force in many biological processes including biomolecular recognition and self-assembly, not to mention protein folding, dynamics, and function. The variational implicit solvent method (VISM) is a theoretical tool currently developed and optimized to estimate solvation free energies for systems of very complex topology, such as biomolecules. VISM’s theoretical framework makes it unique because it couples hydrophobic, van der Waals, and electrostatic interactions as a functional of the solvation interface. By minimizing this functional, VISM produces the solvation interface as an output of the theory. In this work, we push VISM to larger scale applications by combining it with coarse-grained solute Hamiltonians adapted from the MARTINI framework, a well-established mesoscale force field for modeling large-scale biomolecule assemblies. We show how MARTINI-VISM (MVISM) compares with atomistic VISM (AVISM) for a small set of proteins differing in size, shape, and charge distribution. We also demonstrate MVISM’s suitability to study the solvation properties of an interesting encounter complex, barnase–barstar. The promising results suggest that coarse-graining the protein with the MARTINI force field is indeed a valuable step to broaden VISM’s and MARTINI’s applications in the near future. PMID:28613904

Quantum mechanical/molecular mechanical/continuum style solvation model: linear response theory, variational treatment, and nuclear gradients.

PubMed

Li, Hui

2009-11-14

Linear response and variational treatment are formulated for Hartree-Fock (HF) and Kohn-Sham density functional theory (DFT) methods and combined discrete-continuum solvation models that incorporate self-consistently induced dipoles and charges. Due to the variational treatment, analytic nuclear gradients can be evaluated efficiently for these discrete and continuum solvation models. The forces and torques on the induced point dipoles and point charges can be evaluated using simple electrostatic formulas as for permanent point dipoles and point charges, in accordance with the electrostatic nature of these methods. Implementation and tests using the effective fragment potential (EFP, a polarizable force field) method and the conductorlike polarizable continuum model (CPCM) show that the nuclear gradients are as accurate as those in the gas phase HF and DFT methods. Using B3LYP/EFP/CPCM and time-dependent-B3LYP/EFP/CPCM methods, acetone S(0)-->S(1) excitation in aqueous solution is studied. The results are close to those from full B3LYP/CPCM calculations.

Extending the Solvation-Layer Interface Condition Continum Electrostatic Model to a Linearized Poisson-Boltzmann Solvent.

PubMed

Molavi Tabrizi, Amirhossein; Goossens, Spencer; Mehdizadeh Rahimi, Ali; Cooper, Christopher D; Knepley, Matthew G; Bardhan, Jaydeep P

2017-06-13

We extend the linearized Poisson-Boltzmann (LPB) continuum electrostatic model for molecular solvation to address charge-hydration asymmetry. Our new solvation-layer interface condition (SLIC)/LPB corrects for first-shell response by perturbing the traditional continuum-theory interface conditions at the protein-solvent and the Stern-layer interfaces. We also present a GPU-accelerated treecode implementation capable of simulating large proteins, and our results demonstrate that the new model exhibits significant accuracy improvements over traditional LPB models, while reducing the number of fitting parameters from dozens (atomic radii) to just five parameters, which have physical meanings related to first-shell water behavior at an uncharged interface. In particular, atom radii in the SLIC model are not optimized but uniformly scaled from their Lennard-Jones radii. Compared to explicit-solvent free-energy calculations of individual atoms in small molecules, SLIC/LPB is significantly more accurate than standard parametrizations (RMS error 0.55 kcal/mol for SLIC, compared to RMS error of 3.05 kcal/mol for standard LPB). On parametrizing the electrostatic model with a simple nonpolar component for total molecular solvation free energies, our model predicts octanol/water transfer free energies with an RMS error 1.07 kcal/mol. A more detailed assessment illustrates that standard continuum electrostatic models reproduce total charging free energies via a compensation of significant errors in atomic self-energies; this finding offers a window into improving the accuracy of Generalized-Born theories and other coarse-grained models. Most remarkably, the SLIC model also reproduces positive charging free energies for atoms in hydrophobic groups, whereas standard PB models are unable to generate positive charging free energies regardless of the parametrized radii. The GPU-accelerated solver is freely available online, as is a MATLAB implementation.

A linear solvation energy relationship model of organic chemical partitioning to dissolved organic carbon.

PubMed

Kipka, Undine; Di Toro, Dominic M

2011-09-01

Predicting the association of contaminants with both particulate and dissolved organic matter is critical in determining the fate and bioavailability of chemicals in environmental risk assessment. To date, the association of a contaminant to particulate organic matter is considered in many multimedia transport models, but the effect of dissolved organic matter is typically ignored due to a lack of either reliable models or experimental data. The partition coefficient to dissolved organic carbon (K(DOC)) may be used to estimate the fraction of a contaminant that is associated with dissolved organic matter. Models relating K(DOC) to the octanol-water partition coefficient (K(OW)) have not been successful for many types of dissolved organic carbon in the environment. Instead, linear solvation energy relationships are proposed to model the association of chemicals with dissolved organic matter. However, more chemically diverse K(DOC) data are needed to produce a more robust model. For humic acid dissolved organic carbon, the linear solvation energy relationship predicts log K(DOC) with a root mean square error of 0.43. Copyright © 2011 SETAC.

A comparison of the solvation structure and dynamics of the lithium ion in linear organic carbonates with different alkyl chain lengths.

PubMed

Fulfer, K D; Kuroda, D G

2017-09-20

The structure and dynamics of electrolytes composed of lithium hexafluorophosphate (LiPF 6 ) in dimethyl carbonate, ethyl methyl carbonate, and diethyl carbonate were investigated using a combination of linear and two-dimensional infrared spectroscopies. The solutions studied here have a LiPF 6 concentration of X(LiPF 6 ) = 0.09, which is typically found in commercial lithium ion batteries. This study focuses on comparing the differences in the solvation shell structure and dynamics produced by linear organic carbonates of different alkyl chain lengths. The IR experiments show that either linear carbonate forms a tetrahedral solvation shell (coordination number of 4) around the lithium ion irrespective of whether the solvation shell has anions in close proximity to the carbonates. Moreover, analysis of the absorption cross sections via FTIR and DFT computations reveals a distortion in the angle formed by Li + -O[double bond, length as m-dash]C which decreases from the expected 180° when the alkyl chains of the carbonate are lengthened. In addition, our findings also reveal that, likely due to its asymmetric structure, ethyl methyl carbonate has a significantly more distorted tetrahedral lithium ion solvation shell than either of the other two investigated carbonates. IR photon echo studies further demonstrate that the motions of the solvation shell have a time scale of a few picoseconds for all three linear carbonates. Interestingly, a slowdown of the in place-motions of the first solvation shell is observed when the carbonate has a longer alkyl chain length irrespective of the symmetry. In addition, vibrational energy transfer with a time scale of tens of picoseconds is observed between strongly coupled modes arising from the solvation shell structure of the Li + which corroborates the modeling of these solvation shells in terms of highly coupled vibrational states. Results of this study provide new insights into the molecular structure and dynamics of the lithium ion electrolyte components as a function of solvent structure.

Strong Stretching of Poly(ethylene glycol) Brushes Mediated by Ionic Liquid Solvation.

PubMed

Han, Mengwei; Espinosa-Marzal, Rosa M

2017-09-07

We have measured forces between mica surfaces coated with a poly(ethylene glycol) (PEG) brush solvated by a vacuum-dry ionic liquid, 1-ethyl-3-methyl imidazolium bis(trifluoromethylsulfonyl)imide, with a surface forces apparatus. At high grafting density, the solvation mediated by the ionic liquid causes the brush to stretch twice as much as in water. Modeling of the steric repulsion indicates that PEG behaves as a polyelectrolyte; the hydrogen bonding between ethylene glycol and the imidazolium cation seems to effectively charge the polymer brush, which justifies the strong stretching. Importantly, under strong polymer compression, solvation layers are squeezed out at a higher rate than for the neat ionic liquid. We propose that the thermal fluctuations of the PEG chains, larger in the brush than in the mushroom configuration, maintain the fluidity of the ionic liquid under strong compression, in contrast to the solid-like squeezing-out behavior of the neat ionic liquid. This is the first experimental study of the behavior of a polymer brush solvated by an ionic liquid under nanoconfinement.

Preparation and physicochemical characterization of 5 niclosamide solvates and 1 hemisolvate.

PubMed

van Tonder, Elsa C; Mahlatji, Mabatane D; Malan, Sarel F; Liebenberg, Wilna; Caira, Mino R; Song, Mingna; de Villiers, Melgardt M

2004-02-23

The purpose of the study was to characterize the physicochemical, structural, and spectral properties of the 1:1 niclosamide and methanol, diethyl ether, dimethyl sulfoxide, N,N' dimethylformamide, and tetrahydrofuran solvates and the 2:1 niclosamide and tetraethylene glycol hemisolvate prepared by recrystallization from these organic solvents. Structural, spectral, and thermal analysis results confirmed the presence of the solvents and differences in the structural properties of these solvates. In addition, differences in the activation energy of desolvation, batch solution calorimetry, and the aqueous solubility at 25 degrees C, 24 hours, showed the stability of the solvates to be in the order: anhydrate > diethyl ether solvate > tetraethylene glycol hemisolvate > methanol solvate > dimethyl sulfoxide solvate > N,N' dimethylformamide solvate. The intrinsic and powder dissolution rates of the solvates were in the order: anhydrate > diethyl ether solvate > tetraethylene glycol hemisolvate > N,N' dimethylformamide solvate > methanol solvate > dimethyl sulfoxide solvate. Although these nonaqueous solvates had higher solubility and dissolution rates than the monohydrous forms, they were unstable in aqueous media and rapidly transformed to one of the monohydrous forms.

Effects of nonadditive interactions on ion solvation at the water/vapor interface: a molecular dynamics study.

PubMed

Yagasaki, Takuma; Saito, Shinji; Ohmine, Iwao

2010-12-09

The solvation of halide ions at the water/vapor interface is investigated by using molecular dynamics simulations with nonpolarizable molecular mechanical (MM), polarizable MM, and quantum mechanical (QM)/MM methods. The free energy profile of the ion solvation is decomposed into the energy and the entropic contributions along the ion displacement from inside to the surface of water. It is found that the surface affinity of the ion, relative to the bulk value, is determined by a subtle balance between the energetic destabilization and the entropic stabilization with the ion displacement. The amount of energetic destabilization is found to be reduced when nonadditive interactions are included, as in the polarizable MM and QM/MM models. The structure of water around the ion at the interface is also largely modified when the higher order effects are considered. For example, the induced dipole effect enhances the solvation structure around the ion at the interface significantly and thus reduces the amount of entropic stabilization at the interface, relative to in the bulk. It is found that this induced dipole effect causes the slowing in the ion-water hydrogen bond dynamics at the interface. On the other hand, the higher order induced multipole effects in the QM/MM method suppress both the excessive enhancement of the solvation structure and the slowing of the ion-water hydrogen bond dynamics at the interface. The present study demonstrates that not only the induced dipole moment but also the higher order induced multipole moments, which are neglected in standard empirical models, are essential for the correct description of the ion solvation at the water/vapor interface.

Advanced dielectric continuum model of preferential solvation

NASA Astrophysics Data System (ADS)

Basilevsky, Mikhail; Odinokov, Alexey; Nikitina, Ekaterina; Grigoriev, Fedor; Petrov, Nikolai; Alfimov, Mikhail

2009-01-01

A continuum model for solvation effects in binary solvent mixtures is formulated in terms of the density functional theory. The presence of two variables, namely, the dimensionless solvent composition y and the dimensionless total solvent density z, is an essential feature of binary systems. Their coupling, hidden in the structure of the local dielectric permittivity function, is postulated at the phenomenological level. Local equilibrium conditions are derived by a variation in the free energy functional expressed in terms of the composition and density variables. They appear as a pair of coupled equations defining y and z as spatial distributions. We consider the simplest spherically symmetric case of the Born-type ion immersed in the benzene/dimethylsulfoxide (DMSO) solvent mixture. The profiles of y(R ) and z(R ) along the radius R, which measures the distance from the ion center, are found in molecular dynamics (MD) simulations. It is shown that for a given solute ion z(R ) does not depend significantly on the composition variable y. A simplified solution is then obtained by inserting z(R ), found in the MD simulation for the pure DMSO, in the single equation which defines y(R ). In this way composition dependences of the main solvation effects are investigated. The local density augmentation appears as a peak of z(R ) at the ion boundary. It is responsible for the fine solvation effects missing when the ordinary solvation theories, in which z =1, are applied. These phenomena, studied for negative ions, reproduce consistently the simulation results. For positive ions the simulation shows that z ≫1 (z =5-6 at the maximum of the z peak), which means that an extremely dense solvation shell is formed. In such a situation the continuum description fails to be valid within a consistent parametrization.

Linear solvation energy relationships in normal phase chromatography based on gradient separations.

PubMed

Wu, Di; Lucy, Charles A

2017-09-22

Coupling the modified Soczewiñski model and one gradient run, a gradient method was developed to build a linear solvation energy relationship (LSER) for normal phase chromatography. The gradient method was tested on dinitroanilinopropyl (DNAP) and silica columns with hexane/dichloromethane (DCM) mobile phases. LSER models built based on the gradient separation agree with those derived from a series of isocratic separations. Both models have similar LSER coefficients and comparable goodness of fit, but the LSER model based on gradient separation required fewer trial and error experiments. Copyright © 2017 Elsevier B.V. All rights reserved.

Design and application of implicit solvent models in biomolecular simulations.

PubMed

Kleinjung, Jens; Fraternali, Franca

2014-04-01

We review implicit solvent models and their parametrisation by introducing the concepts and recent devlopments of the most popular models with a focus on parametrisation via force matching. An overview of recent applications of the solvation energy term in protein dynamics, modelling, design and prediction is given to illustrate the usability and versatility of implicit solvation in reproducing the physical behaviour of biomolecular systems. Limitations of implicit modes are discussed through the example of more challenging systems like nucleic acids and membranes. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Modeling the color of natural dyes

NASA Astrophysics Data System (ADS)

Ge, Xiaochuan; Calzolari, Arrigo; Binnie, Simon; Baroni, Stefano

2013-03-01

We report on a theoretical study, based on time-dependent density-functional theory, of various factors affecting the optical properties of a few representative anthocyanins, a class of molecules responsible for the color of many fruits, flowers, and leaves, which have also aroused some interest for photovoltaic applications. We first address the influence of substituting different side groups in the phenyl ring of flavylium dyes. We find that these dyes can be classified into three broad classes, according to the number of peaks (1, 2, or 3) featured in the visible range, and give a rationale to this finding. We then examine the effects of solvent-induced thermal fluctuations and dielectric screening, by calculating the spectrum of a representative molecule in solution, for each one these classes. This is achieved by first running an ab initio molecular dynamics simulation of an explicit model for the water-solvated molecule, and then accumulating time averages of the optical spectra calculated on the fly. The effects of thermal fluctuations are shown to overshadow those of dielectric screening, and more dramatic the larger the number of peaks in the gas phase. The effects of different functionals (GGA vs. hybrids) on the calculated spectra are also addressed.

Structure and Dynamics of Solvated Polymers near a Silica Surface: On the Different Roles Played by Solvent.

PubMed

Perrin, Elsa; Schoen, Martin; Coudert, François-Xavier; Boutin, Anne

2018-04-26

Whereas it is experimentally known that the inclusion of nanoparticles in hydrogels can lead to a mechanical reinforcement, a detailed molecular understanding of the adhesion mechanism is still lacking. Here we use coarse-grained molecular dynamics simulations to investigate the nature of the interface between silica surfaces and solvated polymers. We show how differences in the nature of the polymer and the polymer-solvent interactions can lead to drastically different behavior of the polymer-surface adhesion. Comparing explicit and implicit solvent models, we conclude that this effect cannot be fully described in an implicit solvent. We highlight the crucial role of polymer solvation for the adsorption of the polymer chain on the silica surface, the significant dynamics of polymer chains on the surface, and details of the modifications in the structure solvated polymer close to the interface.

Solvation of o-hydroxybenzoic acid in pure and modified supercritical carbon dioxide, according to numerical modeling data

NASA Astrophysics Data System (ADS)

Antipova, M. L.; Gurina, D. L.; Odintsova, E. G.; Petrenko, V. E.

2015-08-01

The dissolution of an elementary fragment of crystal structure (an o-hydroxybenzoic acid ( o-HBA) dimer) in both pure and modified supercritical (SC) carbon dioxide by adding methanol (molar fraction, 0.035) at T = 318 K, ρ = 0.7 g/cm3 is simulated. Features of the solvation mechanism in each solvent are revealed. The solvation of o-HBA in pure SC CO2 is shown to occur via electron donor-acceptor interactions. o-HBA forms a solvate complex in modified SC CO2 through hydrogen bonds between the carboxyl group and methanol. The hydroxyl group of o-HBA participates in the formation of an intramolecular hydrogen bond, and not in interactions with the solvent. It is concluded that the o-HBA-methanol complex is a stable molecular structure, and its lifetime is one order of magnitude higher than those of other hydrogen bonds in fluids.

A quantum mechanical strategy to investigate the structure of liquids: the cases of acetonitrile, formamide, and their mixture.

PubMed

Mennucci, Benedetta; da Silva, Clarissa O

2008-06-05

A computational strategy based on quantum mechanical (QM) calculations and continuum solvation models is used to investigate the structure of liquids (either neat liquids or mixtures). The strategy is based on the comparison of calculated and experimental spectroscopic properties (IR-Raman vibrational frequencies and Raman intensities). In particular, neat formamide, neat acetonitrile, and their equimolar mixture are studied comparing isolated and solvated clusters of different nature and size. In all cases, the study seems to indicate that liquids, even when strongly associated, can be effectively modeled in terms of a shell-like system in which clusters of strongly interacting molecules (the microenvironments) are solvated by a polarizable macroenvironment represented by the rest of the molecules. Only taking into proper account both these effects can a correct picture of the liquid structure be achieved.

Theoretical Investigation of OCN(-) Charge Transfer Complexes in Condensed Phase Media: Spectroscopic Properties in Amorphous Ice

NASA Technical Reports Server (NTRS)

Park, Jin-Young; Woon, David E.

2004-01-01

Density functional theory (DFT) calculations of cyanate (OCN(-)) charge-transfer complexes were performed to model the "XCN" feature observed in interstellar icy grain mantles. OCN(-) charge-transfer complexes were formed from precursor combinations of HNCO or HOCN with either NH3 or H2O. Three different solvation strategies for realistically modeling the ice matrix environment were explored, including (1) continuum solvation, (2) pure DFT cluster calculations, and (3) an ONIOM DFT/PM3 cluster calculation. The model complexes were evaluated by their ability to reproduce seven spectroscopic measurements associated with XCN: the band origin of the OCN(-) asymmetric stretching mode, shifts in that frequency due to isotopic substitutions of C, N, O, and H, plus two weak features. The continuum solvent field method produced results consistent with some of the experimental data but failed to account for other behavior due to its limited capacity to describe molecular interactions with solvent. DFT cluster calculations successfully reproduced the available spectroscopic measurements very well. In particular, the deuterium shift showed excellent agreement in complexes where OCN(-) was fully solvated. Detailed studies of representative complexes including from two to twelve water molecules allowed the exploration of various possible solvation structures and provided insights into solvation trends. Moreover, complexes arising from cyanic or isocyanic acid in pure water suggested an alternative mechanism for the formation of OCN(-) charge-transfer complexes without the need for a strong base such as NH3 to be present. An extended ONIOM (B3LYP/PM3) cluster calculation was also performed to assess the impact of a more realistic environment on HNCO dissociation in pure water.

Four-component relativistic calculations in solution with the polarizable continuum model of solvation: theory, implementation, and application to the group 16 dihydrides H2X (X = O, S, Se, Te, Po).

PubMed

Remigio, Roberto Di; Bast, Radovan; Frediani, Luca; Saue, Trond

2015-05-28

We present a formulation of four-component relativistic self-consistent field (SCF) theory for a molecular solute described within the framework of the polarizable continuum model (PCM) for solvation. The linear response function for a four-component PCM-SCF state is also derived, as well as the explicit form of the additional contributions to the first-order response equations. The implementation of such a four-component PCM-SCF model, as carried out in a development version of the DIRAC program package, is documented. In particular, we present the newly developed application programming interface PCMSolver used in the actual implementation with DIRAC. To demonstrate the applicability of the approach, we present and analyze calculations of solvation effects on the geometries, electric dipole moments, and static electric dipole polarizabilities for the group 16 dihydrides H2X (X = O, S, Se, Te, Po).

Quantum chemical approach for condensed-phase thermochemistry (V): Development of rigid-body type harmonic solvation model

NASA Astrophysics Data System (ADS)

Tarumi, Moto; Nakai, Hiromi

2018-05-01

This letter proposes an approximate treatment of the harmonic solvation model (HSM) assuming the solute to be a rigid body (RB-HSM). The HSM method can appropriately estimate the Gibbs free energy for condensed phases even where an ideal gas model used by standard quantum chemical programs fails. The RB-HSM method eliminates calculations for intra-molecular vibrations in order to reduce the computational costs. Numerical assessments indicated that the RB-HSM method can evaluate entropies and internal energies with the same accuracy as the HSM method but with lower calculation costs.

Ion solvation in polymer blends and block copolymer melts: effects of chain length and connectivity on the reorganization of dipoles.

PubMed

Nakamura, Issei

2014-05-29

We studied the thermodynamic properties of ion solvation in polymer blends and block copolymer melts and developed a dipolar self-consistent field theory for polymer mixtures. Our theory accounts for the chain connectivity of polymerized monomers, the compressibility of the liquid mixtures under electrostriction, the permanent and induced dipole moments of monomers, and the resultant dielectric contrast among species. In our coarse-grained model, dipoles are attached to the monomers and allowed to rotate freely in response to electrostatic fields. We demonstrate that a strong electrostatic field near an ion reorganizes dipolar monomers, resulting in nonmonotonic changes in the volume fraction profile and the dielectric function of the polymers with respect to those of simple liquid mixtures. For the parameter sets used, the spatial variations near an ion can be in the range of 1 nm or larger, producing significant differences in the solvation energy among simple liquid mixtures, polymer blends, and block copolymers. The solvation energy of an ion depends substantially on the chain length in block copolymers; thus, our theory predicts the preferential solvation of ions arising from differences in chain length.

Preferential solvation of lithium cations and impacts on oxygen reduction in lithium–air batteries

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

Zheng, Dong; Qu, Deyu; Yang, Xiao -Qing

2015-09-16

The solvation of Li⁺ with eleven non-aqueous solvents commonly used as the electrolytes for Li batteries were studied. The solvation preferences of different solvents were compared by means of electrospray mass spectrometry and collision-induced dissociation. The relative strength of the solvent for the solvation of Li⁺ was determined. The Lewis acidity of the solvated Li⁺ cations was determined by the preferential solvation of the solvent in the solvation shell. The kinetics of the catalytic disproportionation of the O₂⁻ depends on the relative Lewis acidity of the solvated Li⁺ ion. The impact of the solvated Li⁺ cation on the O₂ redoxmore » reaction was also investigated.« less

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

PubMed Central

Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael

2016-01-01

Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology. DOI: http://dx.doi.org/10.7554/eLife.19274.001 PMID:27801646

Development of a methodology to compute solvation free energies on the basis of the theory of energy representation for solutions represented with a polarizable force field.

PubMed

Suzuoka, Daiki; Takahashi, Hideaki; Ishiyama, Tatsuya; Morita, Akihiro

2012-12-07

We have developed a method of molecular simulations utilizing a polarizable force field in combination with the theory of energy representation (ER) for the purpose of establishing an efficient and accurate methodology to compute solvation free energies. The standard version of the ER method is, however, based on the assumption that the solute-solvent interaction is pairwise additive for its construction. A crucial step in the present method is to introduce an intermediate state in the solvation process to treat separately the many-body interaction associated with the polarizable model. The intermediate state is chosen so that the solute-solvent interaction can be formally written in the pairwise form, though the solvent molecules are interacting with each other with polarizable charges dependent on the solvent configuration. It is, then, possible to extract the free energy contribution δμ due to the many-body interaction between solute and solvent from the total solvation free energy Δμ. It is shown that the free energy δμ can be computed by an extension of the recent development implemented in quantum mechanical∕molecular mechanical simulations. To assess the numerical robustness of the approach, we computed the solvation free energies of a water and a methanol molecule in water solvent, where two paths for the solvation processes were examined by introducing different intermediate states. The solvation free energies of a water molecule associated with the two paths were obtained as -5.3 and -5.8 kcal∕mol. Those of a methanol molecule were determined as -3.5 and -3.7 kcal∕mol. These results of the ER simulations were also compared with those computed by a numerically exact approach. It was demonstrated that the present approach produces the solvation free energies in comparable accuracies to simulations of thermodynamic integration (TI) method within a tenth of computational time used for the TI simulations.

Corrosion Thermodynamics of Magnesium and Alloys from First Principles as a Function of Solvation

NASA Astrophysics Data System (ADS)

Limmer, Krista; Williams, Kristen; Andzelm, Jan

Thermodynamics of corrosion processes occurring on magnesium surfaces, such as hydrogen evolution and water dissociation, have been examined with density functional theory (DFT) to evaluate the effect of impurities and dilute alloying additions. The modeling of corrosion thermodynamics requires examination of species in a variety of chemical and electronic states in order to accurately represent the complex electrochemical corrosion process. In this study, DFT calculations for magnesium corrosion thermodynamics were performed with two DFT codes (VASP and DMol3), with multiple exchange-correlation functionals for chemical accuracy, as well as with various levels of implicit and explicit solvation for surfaces and solvated ions. The accuracy of the first principles calculations has been validated against Pourbaix diagrams constructed from solid, gas and solvated charged ion calculations. For aqueous corrosion, it is shown that a well parameterized implicit solvent is capable of accurately representing all but the first coordinating layer of explicit water for charged ions.

Solvent-driven reductive activation of carbon dioxide by gold anions.

PubMed

Knurr, Benjamin J; Weber, J Mathias

2012-11-14

Catalytic activation and electrochemical reduction of CO(2) for the formation of chemically usable feedstock and fuel are central goals for establishing a carbon neutral fuel cycle. The role of solvent molecules in catalytic processes is little understood, although solvent-solute interactions can strongly influence activated intermediate species. We use vibrational spectroscopy of mass-selected Au(CO(2))(n)(-) cluster ions to probe the solvation of AuCO(2)(-) as a model for a reactive intermediate in the reductive activation of a CO(2) ligand by a single-atom catalyst. For the first few solvent molecules, solvation of the complex preferentially occurs at the CO(2) moiety, enhancing reductive activation through polarization of the excess charge onto the partially reduced ligand. At higher levels of solvation, direct interaction of additional solvent molecules with the Au atom diminishes reduction. The results show how the solvation environment can enhance or diminish the effects of a catalyst, offering design criteria for single-atom catalyst engineering.

How Anion Chaotrope Changes the Local Structure of Water. Insights from Photoelectron Spectroscopy and Theoretical Modeling of SCN - Water Clusters

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

Valiev, Marat; Deng, Shihu; Wang, Xue B.

2015-09-09

The behavior of charged solute molecules in aqueous solutions is often classified using the concept of kosmotropes (“structure makers”) and chaotropes (“structure breakers”). There is a growing consensus that the key to kosmotropic/chaotropic behaviors lies in the local solvent region, but the exact microscopic basis for such differentiation is not well understood. This issue is examined in this work by analyzing size selective solvation of a well-known chaotrope, negatively charged SCN - molecule. Combining experimental photoelectron spectroscopy measurements with theoretical modeling we examine evolution of solvation structure up to eight waters. We observe that SCN - indeed fits the descriptionmore » of weakly hydrated ion and its solvation is heavily driven by stabilization of water-water interaction network. However, the impact on water structure is more subtle than that associated with “structure breaker”. In particular, we observe that the solvation structure of SCN - preserves the “packing” structure of the water network but changes local directionality of hydrogen bonds in the local solvent region. The resulting effect closer to that of “structure weakener”, where solute can be readily accommodated into the native water network, at the cost of compromising its stability due to constraints on hydrogen bonding.« less

Differential solvation of intrinsically disordered linkers drives the formation of spatially organized droplets in ternary systems of linear multivalent proteins

NASA Astrophysics Data System (ADS)

Harmon, Tyler S.; Holehouse, Alex S.; Pappu, Rohit V.

2018-04-01

Intracellular biomolecular condensates are membraneless organelles that encompass large numbers of multivalent protein and nucleic acid molecules. The bodies assemble via a combination of liquid–liquid phase separation and gelation. A majority of condensates included multiple components and show multilayered organization as opposed to being well-mixed unitary liquids. Here, we put forward a simple thermodynamic framework to describe the emergence of spatially organized droplets in multicomponent systems comprising of linear multivalent polymers also known as associative polymers. These polymers, which mimic proteins and/or RNA have the architecture of domains or motifs known as stickers that are interspersed by flexible spacers known as linkers. Using a minimalist numerical model for a four-component system, we have identified features of linear multivalent molecules that are necessary and sufficient for generating spatially organized droplets. We show that differences in sequence-specific effective solvation volumes of disordered linkers between interaction domains enable the formation of spatially organized droplets. Molecules with linkers that are preferentially solvated are driven to the interface with the bulk solvent, whereas molecules that have linkers with negligible effective solvation volumes form cores in the core–shell architectures that emerge in the minimalist four-component systems. Our modeling has relevance for understanding the physical determinants of spatially organized membraneless organelles.

Comparison of the Marcus and Pekar partitions in the context of non-equilibrium, polarizable-continuum solvation models

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

You, Zhi-Qiang; Herbert, John M., E-mail: herbert@chemistry.ohio-state.edu; Mewes, Jan-Michael

2015-11-28

The Marcus and Pekar partitions are common, alternative models to describe the non-equilibrium dielectric polarization response that accompanies instantaneous perturbation of a solute embedded in a dielectric continuum. Examples of such a perturbation include vertical electronic excitation and vertical ionization of a solution-phase molecule. Here, we provide a general derivation of the accompanying polarization response, for a quantum-mechanical solute described within the framework of a polarizable continuum model (PCM) of electrostatic solvation. Although the non-equilibrium free energy is formally equivalent within the two partitions, albeit partitioned differently into “fast” versus “slow” polarization contributions, discretization of the PCM integral equations failsmore » to preserve certain symmetries contained in these equations (except in the case of the conductor-like models or when the solute cavity is spherical), leading to alternative, non-equivalent matrix equations. Unlike the total equilibrium solvation energy, however, which can differ dramatically between different formulations, we demonstrate that the equivalence of the Marcus and Pekar partitions for the non-equilibrium solvation correction is preserved to high accuracy. Differences in vertical excitation and ionization energies are <0.2 eV (and often <0.01 eV), even for systems specifically selected to afford a large polarization response. Numerical results therefore support the interchangeability of the Marcus and Pekar partitions, but also caution against relying too much on the fast PCM charges for interpretive value, as these charges differ greatly between the two partitions, especially in polar solvents.« less

The effect of concentration- and temperature-dependent dielectric constant on the activity coefficient of NaCl electrolyte solutions

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

Valiskó, Mónika; Boda, Dezső, E-mail: boda@almos.vein.hu

2014-06-21

Our implicit-solvent model for the estimation of the excess chemical potential (or, equivalently, the activity coefficient) of electrolytes is based on using a dielectric constant that depends on the thermodynamic state, namely, the temperature and concentration of the electrolyte, ε(c, T). As a consequence, the excess chemical potential is split into two terms corresponding to ion-ion (II) and ion-water (IW) interactions. The II term is obtained from computer simulation using the Primitive Model of electrolytes, while the IW term is estimated from the Born treatment. In our previous work [J. Vincze, M. Valiskó, and D. Boda, “The nonmonotonic concentration dependencemore » of the mean activity coefficient of electrolytes is a result of a balance between solvation and ion-ion correlations,” J. Chem. Phys. 133, 154507 (2010)], we showed that the nonmonotonic concentration dependence of the activity coefficient can be reproduced qualitatively with this II+IW model without using any adjustable parameter. The Pauling radii were used in the calculation of the II term, while experimental solvation free energies were used in the calculation of the IW term. In this work, we analyze the effect of the parameters (dielectric constant, ionic radii, solvation free energy) on the concentration and temperature dependence of the mean activity coefficient of NaCl. We conclude that the II+IW model can explain the experimental behavior using a concentration-dependent dielectric constant and that we do not need the artificial concept of “solvated ionic radius” assumed by earlier studies.« less

A thermodynamic model to predict electron mobility in superfluid helium.

PubMed

Aitken, Frédéric; Volino, Ferdinand; Mendoza-Luna, Luis Guillermo; Haeften, Klaus von; Eloranta, Jussi

2017-06-21

Electron mobility in superfluid helium is modeled between 0.1 and 2.2 K by a van der Waals-type thermodynamic equation of state, which relates the free volume of solvated electrons to temperature, density, and phase dependent internal pressure. The model is first calibrated against known electron mobility reference data along the saturated vapor pressure line and then validated to reproduce the existing mobility literature values as a function of pressure and temperature with at least 10% accuracy. Four different electron mobility regimes are identified: (1) Landau critical velocity limit (T ≈ 0), (2) mobility limited by thermal phonons (T < 0.6 K), (3) thermal phonon and discrete roton scattering ("roton gas") limited mobility (0.6 K < T < 1.2 K), and (4) the viscous liquid ("roton continuum") limit (T > 1.2 K) where the ion solvation structure directly determines the mobility. In the latter regime, the Stokes equation can be used to estimate the hydrodynamic radius of the solvated electron based on its mobility and fluid viscosity. To account for the non-continuum behavior appearing below 1.2 K, the temperature and density dependent Millikan-Cunningham factor is introduced. The hydrodynamic electron bubble radii predicted by the present model appear generally larger than the solvation cavity interface barycenter values obtained from density functional theory (DFT) calculations. Based on the classical Stokes law, this difference can arise from the variation of viscosity and flow characteristics around the electron. The calculated DFT liquid density profiles show distinct oscillations at the vacuum/liquid interface, which increase the interface rigidity.

Concentration Fluctuations and Capacitive Response in Dense Ionic Solutions.

PubMed

Uralcan, Betul; Aksay, Ilhan A; Debenedetti, Pablo G; Limmer, David T

2016-07-07

We use molecular dynamics simulations in a constant potential ensemble to study the effects of solution composition on the electrochemical response of a double layer capacitor. We find that the capacitance first increases with ion concentration following its expected ideal solution behavior but decreases upon approaching a pure ionic liquid in agreement with recent experimental observations. The nonmonotonic behavior of the capacitance as a function of ion concentration results from the competition between the independent motion of solvated ions in the dilute regime and solvation fluctuations in the concentrated regime. Mirroring the capacitance, we find that the characteristic decay length of charge density correlations away from the electrode is also nonmonotonic. The correlation length first decreases with ion concentration as a result of better electrostatic screening but increases with ion concentration as a result of enhanced steric interactions. When charge fluctuations induced by correlated ion-solvent fluctuations are large relative to those induced by the pure ionic liquid, such capacitive behavior is expected to be generic.

Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

PubMed Central

2012-01-01

Implicit solvation is a mean force approach to model solvent forces acting on a solute molecule. It is frequently used in molecular simulations to reduce the computational cost of solvent treatment. In the first instance, the free energy of solvation and the associated solvent–solute forces can be approximated by a function of the solvent-accessible surface area (SASA) of the solute and differentiated by an atom–specific solvation parameter σiSASA. A procedure for the determination of values for the σiSASA parameters through matching of explicit and implicit solvation forces is proposed. Using the results of Molecular Dynamics simulations of 188 topologically diverse protein structures in water and in implicit solvent, values for the σiSASA parameters for atom types i of the standard amino acids in the GROMOS force field have been determined. A simplified representation based on groups of atom types σgSASA was obtained via partitioning of the atom–type σiSASA distributions by dynamic programming. Three groups of atom types with well separated parameter ranges were obtained, and their performance in implicit versus explicit simulations was assessed. The solvent forces are available at http://mathbio.nimr.mrc.ac.uk/wiki/Solvent_Forces. PMID:23180979

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

Bond-valence methods for pKa prediction. II. Bond-valence, electrostatic, molecular geometry, and solvation effects

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

Bickmore, Barry R.; Rosso, Kevin M.; Tadanier, Christopher J.

2006-08-15

In a previous contribution, we outlined a method for predicting (hydr)oxy-acid and oxide surface acidity constants based on three main factors: bond valence, Me?O bond ionicity, and molecular shape. Here electrostatics calculations and ab initio molecular dynamics simulations are used to qualitatively show that Me?O bond ionicity controls the extent to which the electrostatic work of proton removal departs from ideality, bond valence controls the extent of solvation of individual functional groups, and bond valence and molecular shape controls local dielectric response. These results are consistent with our model of acidity, but completely at odds with other methods of predictingmore » acidity constants for use in multisite complexation models. In particular, our ab initio molecular dynamics simulations of solvated monomers clearly indicate that hydrogen bonding between (hydr)oxo-groups and water molecules adjusts to obey the valence sum rule, rather than maintaining a fixed valence based on the coordination of the oxygen atom as predicted by the standard MUSIC model.« less

Hydroxide Solvation and Transport in Anion Exchange Membranes

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

Chen, Chen; Tse, Ying-Lung Steve; Lindberg, Gerrick E.

Understanding hydroxide solvation and transport in anion exchange membranes (AEMs) can provide important insight into the design principles of these new membranes. To accurately model hydroxide solvation and transport, we developed a new multiscale reactive molecular dynamics model for hydroxide in aqueous solution, which was then subsequently modified for an AEM material. With this model, we investigated the hydroxide solvation structure and transport mechanism in the membrane. We found that a relatively even separation of the rigid side chains produces a continuous overlapping region for hydroxide transport that is made up of the first hydration shell of the tethered cationicmore » groups. Our results show that hydroxide has a significant preference for this overlapping region, transporting through it and between the AEM side chains with substantial contributions from both vehicular (standard diffusion) and Grotthuss (proton hopping) mechanisms. Comparison of the AEM with common proton exchange membranes (PEMs) showed that the excess charge is less delocalized in the AEM than the PEMs, which is correlated with a higher free energy barrier for proton transfer reactions. The vehicular mechanism also contributes considerably more than the Grotthuss mechanism for hydroxide transport in the AEM, while our previous studies of PEM systems showed a larger contribution from the Grotthuss mechanism than the vehicular mechanism for proton transport. The activation energy barrier for hydroxide diffusion in the AEM is greater than that for proton diffusion in PEMs, implying a more significant enhancement of ion transport in the AEM at elevated temperatures.« less

Hydroxide Solvation and Transport in Anion Exchange Membranes.

PubMed

Chen, Chen; Tse, Ying-Lung Steve; Lindberg, Gerrick E; Knight, Chris; Voth, Gregory A

2016-01-27

Understanding hydroxide solvation and transport in anion exchange membranes (AEMs) can provide important insight into the design principles of these new membranes. To accurately model hydroxide solvation and transport, we developed a new multiscale reactive molecular dynamics model for hydroxide in aqueous solution, which was then subsequently modified for an AEM material. With this model, we investigated the hydroxide solvation structure and transport mechanism in the membrane. We found that a relatively even separation of the rigid side chains produces a continuous overlapping region for hydroxide transport that is made up of the first hydration shell of the tethered cationic groups. Our results show that hydroxide has a significant preference for this overlapping region, transporting through it and between the AEM side chains with substantial contributions from both vehicular (standard diffusion) and Grotthuss (proton hopping) mechanisms. Comparison of the AEM with common proton exchange membranes (PEMs) showed that the excess charge is less delocalized in the AEM than the PEMs, which is correlated with a higher free energy barrier for proton transfer reactions. The vehicular mechanism also contributes considerably more than the Grotthuss mechanism for hydroxide transport in the AEM, while our previous studies of PEM systems showed a larger contribution from the Grotthuss mechanism than the vehicular mechanism for proton transport. The activation energy barrier for hydroxide diffusion in the AEM is greater than that for proton diffusion in PEMs, implying a more significant enhancement of ion transport in the AEM at elevated temperatures.

Multiscale Multiphysics and Multidomain Models I: Basic Theory

PubMed Central

Wei, Guo-Wei

2013-01-01

This work extends our earlier two-domain formulation of a differential geometry based multiscale paradigm into a multidomain theory, which endows us the ability to simultaneously accommodate multiphysical descriptions of aqueous chemical, physical and biological systems, such as fuel cells, solar cells, nanofluidics, ion channels, viruses, RNA polymerases, molecular motors and large macromolecular complexes. The essential idea is to make use of the differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain of solvent from the microscopic domain of solute, and dynamically couple continuum and discrete descriptions. Our main strategy is to construct energy functionals to put on an equal footing of multiphysics, including polar (i.e., electrostatic) solvation, nonpolar solvation, chemical potential, quantum mechanics, fluid mechanics, molecular mechanics, coarse grained dynamics and elastic dynamics. The variational principle is applied to the energy functionals to derive desirable governing equations, such as multidomain Laplace-Beltrami (LB) equations for macromolecular morphologies, multidomain Poisson-Boltzmann (PB) equation or Poisson equation for electrostatic potential, generalized Nernst-Planck (NP) equations for the dynamics of charged solvent species, generalized Navier-Stokes (NS) equation for fluid dynamics, generalized Newton's equations for molecular dynamics (MD) or coarse-grained dynamics and equation of motion for elastic dynamics. Unlike the classical PB equation, our PB equation is an integral-differential equation due to solvent-solute interactions. To illustrate the proposed formalism, we have explicitly constructed three models, a multidomain solvation model, a multidomain charge transport model and a multidomain chemo-electro-fluid-MD-elastic model. Each solute domain is equipped with distinct surface tension, pressure, dielectric function, and charge density distribution. In addition to long-range Coulombic interactions, various non-electrostatic solvent-solute interactions are considered in the present modeling. We demonstrate the consistency between the non-equilibrium charge transport model and the equilibrium solvation model by showing the systematical reduction of the former to the latter at equilibrium. This paper also offers a brief review of the field. PMID:25382892

Multiscale Multiphysics and Multidomain Models I: Basic Theory.

PubMed

Wei, Guo-Wei

2013-12-01

This work extends our earlier two-domain formulation of a differential geometry based multiscale paradigm into a multidomain theory, which endows us the ability to simultaneously accommodate multiphysical descriptions of aqueous chemical, physical and biological systems, such as fuel cells, solar cells, nanofluidics, ion channels, viruses, RNA polymerases, molecular motors and large macromolecular complexes. The essential idea is to make use of the differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain of solvent from the microscopic domain of solute, and dynamically couple continuum and discrete descriptions. Our main strategy is to construct energy functionals to put on an equal footing of multiphysics, including polar (i.e., electrostatic) solvation, nonpolar solvation, chemical potential, quantum mechanics, fluid mechanics, molecular mechanics, coarse grained dynamics and elastic dynamics. The variational principle is applied to the energy functionals to derive desirable governing equations, such as multidomain Laplace-Beltrami (LB) equations for macromolecular morphologies, multidomain Poisson-Boltzmann (PB) equation or Poisson equation for electrostatic potential, generalized Nernst-Planck (NP) equations for the dynamics of charged solvent species, generalized Navier-Stokes (NS) equation for fluid dynamics, generalized Newton's equations for molecular dynamics (MD) or coarse-grained dynamics and equation of motion for elastic dynamics. Unlike the classical PB equation, our PB equation is an integral-differential equation due to solvent-solute interactions. To illustrate the proposed formalism, we have explicitly constructed three models, a multidomain solvation model, a multidomain charge transport model and a multidomain chemo-electro-fluid-MD-elastic model. Each solute domain is equipped with distinct surface tension, pressure, dielectric function, and charge density distribution. In addition to long-range Coulombic interactions, various non-electrostatic solvent-solute interactions are considered in the present modeling. We demonstrate the consistency between the non-equilibrium charge transport model and the equilibrium solvation model by showing the systematical reduction of the former to the latter at equilibrium. This paper also offers a brief review of the field.

Examination of the formation process of pre-solvated and solvated electron in n-alcohol using femtosecond pulse radiolysis

NASA Astrophysics Data System (ADS)

Toigawa, Tomohiro; Gohdo, Masao; Norizawa, Kimihiro; Kondoh, Takafumi; Kan, Koichi; Yang, Jinfeng; Yoshida, Yoichi

2016-06-01

The formation process of pre-solvated and solvated electron in methanol (MeOH), ethanol (EtOH), n-butanol (BuOH), and n-octanol (OcOH) were investigated using a fs-pulse radiolysis technique by observing the pre-solvated electron at 1400 nm. The formation time constants of the pre-solvated electrons were determined to be 1.2, 2.2, 3.1, and 6.3 ps for MeOH, EtOH, BuOH, and OcOH, respectively. The formation time constants of the solvated electrons were determined to be 6.7, 13.6, 22.2, and 32.9 ps for MeOH, EtOH, BuOH, and OcOH, respectively. The formation dynamics and structure of the pre-solvated and solvated electrons in n-alcohols were discussed based on relation between the obtained time constant and dielectric relaxation time constant from the view point of kinetics. The observed formation time constants of the solvated electrons seemed to be strongly correlated with the second component of the dielectric relaxation time constants, which are related to single molecule motion. On the other hand, the observed formation time constants of the pre-solvated electrons seemed to be strongly correlated with the third component of the dielectric relaxation time constants, which are related to dynamics of hydrogen bonds.

Ionic size effects to molecular solvation energy and to ion current across a channel resulted from the nonuniform size-modified PNP equations.

PubMed

Qiao, Yu; Tu, Bin; Lu, Benzhuo

2014-05-07

Ionic finite size can impose considerable effects to both the equilibrium and non-equilibrium properties of a solvated molecular system, such as the solvation energy, ionic concentration, and transport in a channel. As discussed in our former work [B. Lu and Y. C. Zhou, Biophys. J. 100, 2475 (2011)], a class of size-modified Poisson-Boltzmann (PB)/Poisson-Nernst-Planck (PNP) models can be uniformly studied through the general nonuniform size-modified PNP (SMPNP) equations deduced from the extended free energy functional of Borukhov et al. [I. Borukhov, D. Andelman, and H. Orland, Phys. Rev. Lett. 79, 435 (1997)] This work focuses on the nonuniform size effects to molecular solvation energy and to ion current across a channel for real biomolecular systems. The main contributions are: (1) we prove that for solvation energy calculation with nonuniform size effects (through equilibrium SMPNP simulation), there exists a simplified approximation formulation which is the same as the widely used one in PB community. This approximate form avoids integration over the whole domain and makes energy calculations convenient. (2) Numerical calculations show that ionic size effects tend to negate the solvation effects, which indicates that a higher molecular solvation energy (lower absolute value) is to be predicted when ionic size effects are considered. For both calculations on a protein and a DNA fragment systems in a 0.5M 1:1 ionic solution, a difference about 10 kcal/mol in solvation energies is found between the PB and the SMPNP predictions. Moreover, it is observed that the solvation energy decreases as ionic strength increases, which behavior is similar as those predicted by the traditional PB equation (without size effect) and by the uniform size-modified Poisson-Boltzmann equation. (3) Nonequilibrium SMPNP simulations of ion permeation through a gramicidin A channel show that the ionic size effects lead to reduced ion current inside the channel compared with the results without considering size effects. As a component of the current, the drift term is the main contribution to the total current. The ionic size effects to the total current almost come through the drift term, and have little influence on the diffusion terms in SMPNP.

Competitive lithium solvation of linear and cyclic carbonates from quantum chemistry

DOE PAGES

Kent, Paul R. C.; Ganesh, Panchapakesan; Borodin, Oleg; ...

2015-11-17

The composition of the lithium cation (Li+) solvation shell in mixed linear and cyclic carbonate-based electrolytes has been re-examined using Born–Oppenheimer molecular dynamics (BOMD) as a function of salt concentration and cluster calculations with ethylene carbonate:dimethyl carbonate (EC:DMC)–LiPF 6 as a model system. A coordination preference for EC over DMC to a Li+ was found at low salt concentrations, while a slightly higher preference for DMC over EC was found at high salt concentrations. Analysis of the relative binding energies of the (EC) n(DMC) m–Li+ and (EC) n(DMC) m–LiPF 6 solvates in the gas-phase and for an implicit solvent (asmore » a function of the solvent dielectric constant) indicated that the DMC-containing Li+ solvates were stabilized relative to (EC 4)–Li+ and (EC) 3–LiPF 6 by immersing them in the implicit solvent. Such stabilization was more pronounced in the implicit solvents with a high dielectric constant. Results from previous Raman and IR experiments were reanalyzed and reconciled by correcting them for changes of the Raman activities, IR intensities and band shifts for the solvents which occur upon Li+ coordination. After these correction factors were applied to the results of BOMD simulations, the composition of the Li+ solvation shell from the BOMD simulations was found to agree well with the solvation numbers extracted from Raman experiments. Finally, the mechanism of the Li+ diffusion in the dilute (EC:DMC)LiPF 6 mixed solvent electrolyte was studied using the BOMD simulations.« 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.

Real single ion solvation free energies with quantum mechanical simulation

DOE PAGES

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.; ...

2017-07-04

Single ion solvation free energies are one of the most important properties of electrolyte solutions and yet there is ongoing debate about what these values are. Only the values for neutral ion pairs are known. Here, we use DFT interaction potentials with molecular dynamics simulation (DFT-MD) combined with a modified version of the quasi-chemical theory (QCT) to calculate these energies for the lithium and fluoride ions. A method to correct for the error in the DFT functional is developed and very good agreement with the experimental value for the lithium fluoride pair is obtained. Moreover, this method partitions the energiesmore » into physically intuitive terms such as surface potential, cavity and charging energies which are amenable to descriptions with reduced models. Here, our research suggests that lithium's solvation free energy is dominated by the free energetics of a charged hard sphere, whereas fluoride exhibits significant quantum mechanical behavior that cannot be simply described with a reduced model.« less

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

Real single ion solvation free energies with quantum mechanical simulation

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

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.

Single ion solvation free energies are one of the most important properties of electrolyte solutions and yet there is ongoing debate about what these values are. Only the values for neutral ion pairs are known. Here, we use DFT interaction potentials with molecular dynamics simulation (DFT-MD) combined with a modified version of the quasi-chemical theory (QCT) to calculate these energies for the lithium and fluoride ions. A method to correct for the error in the DFT functional is developed and very good agreement with the experimental value for the lithium fluoride pair is obtained. Moreover, this method partitions the energiesmore » into physically intuitive terms such as surface potential, cavity and charging energies which are amenable to descriptions with reduced models. Here, our research suggests that lithium's solvation free energy is dominated by the free energetics of a charged hard sphere, whereas fluoride exhibits significant quantum mechanical behavior that cannot be simply described with a reduced model.« less

The SAMPL5 challenge for embedded-cluster integral equation theory: solvation free energies, aqueous p K a, and cyclohexane-water log D

NASA Astrophysics Data System (ADS)

Tielker, Nicolas; Tomazic, Daniel; Heil, Jochen; Kloss, Thomas; Ehrhart, Sebastian; Güssregen, Stefan; Schmidt, K. Friedemann; Kast, Stefan M.

2016-11-01

We predict cyclohexane-water distribution coefficients (log D 7.4) for drug-like molecules taken from the SAMPL5 blind prediction challenge by the "embedded cluster reference interaction site model" (EC-RISM) integral equation theory. This task involves the coupled problem of predicting both partition coefficients (log P) of neutral species between the solvents and aqueous acidity constants (p K a) in order to account for a change of protonation states. The first issue is addressed by calibrating an EC-RISM-based model for solvation free energies derived from the "Minnesota Solvation Database" (MNSOL) for both water and cyclohexane utilizing a correction based on the partial molar volume, yielding a root mean square error (RMSE) of 2.4 kcal mol-1 for water and 0.8-0.9 kcal mol-1 for cyclohexane depending on the parametrization. The second one is treated by employing on one hand an empirical p K a model (MoKa) and, on the other hand, an EC-RISM-derived regression of published acidity constants (RMSE of 1.5 for a single model covering acids and bases). In total, at most 8 adjustable parameters are necessary (2-3 for each solvent and two for the p K a) for training solvation and acidity models. Applying the final models to the log D 7.4 dataset corresponds to evaluating an independent test set comprising other, composite observables, yielding, for different cyclohexane parametrizations, 2.0-2.1 for the RMSE with the first and 2.2-2.8 with the combined first and second SAMPL5 data set batches. Notably, a pure log P model (assuming neutral species only) performs statistically similarly for these particular compounds. The nature of the approximations and possible perspectives for future developments are discussed.

The SAMPL5 challenge for embedded-cluster integral equation theory: solvation free energies, aqueous pK a, and cyclohexane-water log D.

PubMed

Tielker, Nicolas; Tomazic, Daniel; Heil, Jochen; Kloss, Thomas; Ehrhart, Sebastian; Güssregen, Stefan; Schmidt, K Friedemann; Kast, Stefan M

2016-11-01

We predict cyclohexane-water distribution coefficients (log D 7.4 ) for drug-like molecules taken from the SAMPL5 blind prediction challenge by the "embedded cluster reference interaction site model" (EC-RISM) integral equation theory. This task involves the coupled problem of predicting both partition coefficients (log P) of neutral species between the solvents and aqueous acidity constants (pK a ) in order to account for a change of protonation states. The first issue is addressed by calibrating an EC-RISM-based model for solvation free energies derived from the "Minnesota Solvation Database" (MNSOL) for both water and cyclohexane utilizing a correction based on the partial molar volume, yielding a root mean square error (RMSE) of 2.4 kcal mol -1 for water and 0.8-0.9 kcal mol -1 for cyclohexane depending on the parametrization. The second one is treated by employing on one hand an empirical pK a model (MoKa) and, on the other hand, an EC-RISM-derived regression of published acidity constants (RMSE of 1.5 for a single model covering acids and bases). In total, at most 8 adjustable parameters are necessary (2-3 for each solvent and two for the pK a ) for training solvation and acidity models. Applying the final models to the log D 7.4 dataset corresponds to evaluating an independent test set comprising other, composite observables, yielding, for different cyclohexane parametrizations, 2.0-2.1 for the RMSE with the first and 2.2-2.8 with the combined first and second SAMPL5 data set batches. Notably, a pure log P model (assuming neutral species only) performs statistically similarly for these particular compounds. The nature of the approximations and possible perspectives for future developments are discussed.

"Bligh and Dyer" and Folch Methods for Solid-Liquid-Liquid Extraction of Lipids from Microorganisms. Comprehension of Solvatation Mechanisms and towards Substitution with Alternative Solvents.

PubMed

Breil, Cassandra; Abert Vian, Maryline; Zemb, Thomas; Kunz, Werner; Chemat, Farid

2017-03-27

Bligh and Dyer (B & D) or Folch procedures for the extraction and separation of lipids from microorganisms and biological tissues using chloroform/methanol/water have been used tens of thousands of times and are "gold standards" for the analysis of extracted lipids. Based on the Conductor-like Screening MOdel for realistic Solvatation (COSMO-RS), we select ethanol and ethyl acetate as being potentially suitable for the substitution of methanol and chloroform. We confirm this by performing solid-liquid extraction of yeast ( Yarrowia lipolytica IFP29 ) and subsequent liquid-liquid partition-the two steps of routine extraction. For this purpose, we consider similar points in the ternary phase diagrams of water/methanol/chloroform and water/ethanol/ethyl acetate, both in the monophasic mixtures and in the liquid-liquid miscibility gap. Based on high performance thin-layer chromatography (HPTLC) to obtain the distribution of lipids classes, and gas chromatography coupled with a flame ionisation detector (GC/FID) to obtain fatty acid profiles, this greener solvents pair is found to be almost as effective as the classic methanol-chloroform couple in terms of efficiency and selectivity of lipids and non-lipid material. Moreover, using these bio-sourced solvents as an alternative system is shown to be as effective as the classical system in terms of the yield of lipids extracted from microorganism tissues, independently of their apparent hydrophilicity.

“Bligh and Dyer” and Folch Methods for Solid–Liquid–Liquid Extraction of Lipids from Microorganisms. Comprehension of Solvatation Mechanisms and towards Substitution with Alternative Solvents

PubMed Central

Breil, Cassandra; Abert Vian, Maryline; Zemb, Thomas; Kunz, Werner; Chemat, Farid

2017-01-01

Bligh and Dyer (B & D) or Folch procedures for the extraction and separation of lipids from microorganisms and biological tissues using chloroform/methanol/water have been used tens of thousands of times and are “gold standards” for the analysis of extracted lipids. Based on the Conductor-like Screening MOdel for realistic Solvatation (COSMO-RS), we select ethanol and ethyl acetate as being potentially suitable for the substitution of methanol and chloroform. We confirm this by performing solid–liquid extraction of yeast (Yarrowia lipolytica IFP29) and subsequent liquid–liquid partition—the two steps of routine extraction. For this purpose, we consider similar points in the ternary phase diagrams of water/methanol/chloroform and water/ethanol/ethyl acetate, both in the monophasic mixtures and in the liquid–liquid miscibility gap. Based on high performance thin-layer chromatography (HPTLC) to obtain the distribution of lipids classes, and gas chromatography coupled with a flame ionisation detector (GC/FID) to obtain fatty acid profiles, this greener solvents pair is found to be almost as effective as the classic methanol–chloroform couple in terms of efficiency and selectivity of lipids and non-lipid material. Moreover, using these bio-sourced solvents as an alternative system is shown to be as effective as the classical system in terms of the yield of lipids extracted from microorganism tissues, independently of their apparent hydrophilicity. PMID:28346372

Testing inhomogeneous solvation theory in structure-based ligand discovery.

PubMed

Balius, Trent E; Fischer, Marcus; Stein, Reed M; Adler, Thomas B; Nguyen, Crystal N; Cruz, Anthony; Gilson, Michael K; Kurtzman, Tom; Shoichet, Brian K

2017-08-15

Binding-site water is often displaced upon ligand recognition, but is commonly neglected in structure-based ligand discovery. Inhomogeneous solvation theory (IST) has become popular for treating this effect, but it has not been tested in controlled experiments at atomic resolution. To do so, we turned to a grid-based version of this method, GIST, readily implemented in molecular docking. Whereas the term only improves docking modestly in retrospective ligand enrichment, it could be added without disrupting performance. We thus turned to prospective docking of large libraries to investigate GIST's impact on ligand discovery, geometry, and water structure in a model cavity site well-suited to exploring these terms. Although top-ranked docked molecules with and without the GIST term often overlapped, many ligands were meaningfully prioritized or deprioritized; some of these were selected for testing. Experimentally, 13/14 molecules prioritized by GIST did bind, whereas none of the molecules that it deprioritized were observed to bind. Nine crystal complexes were determined. In six, the ligand geometry corresponded to that predicted by GIST, for one of these the pose without the GIST term was wrong, and three crystallographic poses differed from both predictions. Notably, in one structure, an ordered water molecule with a high GIST displacement penalty was observed to stay in place. Inclusion of this water-displacement term can substantially improve the hit rates and ligand geometries from docking screens, although the magnitude of its effects can be small and its impact in drug binding sites merits further controlled studies.

Outer-sphere interaction of aluminum and gallium solvates with competitive anions in 1,2-propanediol solutions

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

Petrosyants, S.P.; Buslaeva, E.R.

1986-04-01

The interaction of aluminum and gallium solvates with ..pi..-acid ligand in 1,2-propanediol solutions has been investigated. The formation of associates of hexacoordinate aluminum solvates depends on the solvation of the anions in the bulk of the solution or on the faces of the solvento complexes. In the case of gallium the association of the solvates with the anions is determined by two factors: the existence of a configurational equilibrium for the solvento complexes and the preferential solvation of the competitive ..pi..-acid ligands.

Necessity of capillary modes in a minimal model of nanoscale hydrophobic solvation

PubMed Central

Vaikuntanathan, Suriyanarayanan; Rotskoff, Grant; Hudson, Alexander; Geissler, Phillip L.

2016-01-01

Modern theories of the hydrophobic effect highlight its dependence on length scale, emphasizing the importance of interfaces in the vicinity of sizable hydrophobes. We recently showed that a faithful treatment of such nanoscale interfaces requires careful attention to the statistics of capillary waves, with significant quantitative implications for the calculation of solvation thermodynamics. Here, we show that a coarse-grained lattice model like that of Chandler [Chandler D (2005) Nature 437(7059):640–647], when informed by this understanding, can capture a broad range of hydrophobic behaviors with striking accuracy. Specifically, we calculate probability distributions for microscopic density fluctuations that agree very well with results of atomistic simulations, even many SDs from the mean and even for probe volumes in highly heterogeneous environments. This accuracy is achieved without adjustment of free parameters, because the model is fully specified by well-known properties of liquid water. As examples of its utility, we compute the free-energy profile for a solute crossing the air–water interface, as well as the thermodynamic cost of evacuating the space between extended nanoscale surfaces. These calculations suggest that a highly reduced model for aqueous solvation can enable efficient multiscale modeling of spatial organization driven by hydrophobic and interfacial forces. PMID:26957607

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

NASA Astrophysics Data System (ADS)

Sadigh Vishkaee, Teherh; Fazaeli, Reza

2018-06-01

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

Conformational analysis of cellobiose by electronic structure theories.

PubMed

French, Alfred D; Johnson, Glenn P; Cramer, Christopher J; Csonka, Gábor I

2012-03-01

Adiabatic Φ/ψ maps for cellobiose were prepared with B3LYP density functional theory. A mixed basis set was used for minimization, followed with 6-31+G(d) single-point calculations, with and without SMD continuum solvation. Different arrangements of the exocyclic groups (38 starting geometries) were considered for each Φ/ψ point. The vacuum calculations agreed with earlier computational and experimental results on the preferred gas phase conformation (anti-Φ(H), syn-ψ(H)), and the results from the solvated calculations were consistent with the (syn Φ(H)/ψ(H) conformations from condensed phases (crystals or solutions). Results from related studies were compared, and there is substantial dependence on the solvation model as well as arrangements of exocyclic groups. New stabilizing interactions were revealed by Atoms-In-Molecules theory. Published by Elsevier Ltd.

Alternative Bio-Based Solvents for Extraction of Fat and Oils: Solubility Prediction, Global Yield, Extraction Kinetics, Chemical Composition and Cost of Manufacturing

PubMed Central

Sicaire, Anne-Gaëlle; Vian, Maryline; Fine, Frédéric; Joffre, Florent; Carré, Patrick; Tostain, Sylvain; Chemat, Farid

2015-01-01

The present study was designed to evaluate the performance of alternative bio-based solvents, more especially 2-methyltetrahydrofuran, obtained from crop’s byproducts for the substitution of petroleum solvents such as hexane in the extraction of fat and oils for food (edible oil) and non-food (bio fuel) applications. First a solvent selection as well as an evaluation of the performance was made with Hansen Solubility Parameters and the COnductor-like Screening MOdel for Realistic Solvation (COSMO-RS) simulations. Experiments were performed on rapeseed oil extraction at laboratory and pilot plant scale for the determination of lipid yields, extraction kinetics, diffusion modeling, and complete lipid composition in term of fatty acids and micronutrients (sterols, tocopherols and tocotrienols). Finally, economic and energetic evaluations of the process were conducted to estimate the cost of manufacturing using 2-methyltetrahydrofuran (MeTHF) as alternative solvent compared to hexane as petroleum solvent. PMID:25884332

Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. II. Fullerenes.

PubMed

Calvo, F; Yurtsever, E

2016-08-28

The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C60 (+) and C70 (+) are close to 49 and 51, respectively, and agree with mass spectrometry experiments.

Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. II. Fullerenes

NASA Astrophysics Data System (ADS)

Calvo, F.; Yurtsever, E.

2016-08-01

The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C 60+ and C 70+ are close to 49 and 51, respectively, and agree with mass spectrometry experiments.

Differential geometry based solvation model I: Eulerian formulation

PubMed Central

Chen, Zhan; Baker, Nathan A.; Wei, G. W.

2010-01-01

This paper presents a differential geometry based model for the analysis and computation of the equilibrium property of solvation. Differential geometry theory of surfaces is utilized to define and construct smooth interfaces with good stability and differentiability for use in characterizing the solvent-solute boundaries and in generating continuous dielectric functions across the computational domain. A total free energy functional is constructed to couple polar and nonpolar contributions to the salvation process. Geometric measure theory is employed to rigorously convert a Lagrangian formulation of the surface energy into an Eulerian formulation so as to bring all energy terms into an equal footing. By minimizing the total free energy functional, we derive coupled generalized Poisson-Boltzmann equation (GPBE) and generalized geometric flow equation (GGFE) for the electrostatic potential and the construction of realistic solvent-solute boundaries, respectively. By solving the coupled GPBE and GGFE, we obtain the electrostatic potential, the solvent-solute boundary profile, and the smooth dielectric function, and thereby improve the accuracy and stability of implicit solvation calculations. We also design efficient second order numerical schemes for the solution of the GPBE and GGFE. Matrix resulted from the discretization of the GPBE is accelerated with appropriate preconditioners. An alternative direct implicit (ADI) scheme is designed to improve the stability of solving the GGFE. Two iterative approaches are designed to solve the coupled system of nonlinear partial differential equations. Extensive numerical experiments are designed to validate the present theoretical model, test computational methods, and optimize numerical algorithms. Example solvation analysis of both small compounds and proteins are carried out to further demonstrate the accuracy, stability, efficiency and robustness of the present new model and numerical approaches. Comparison is given to both experimental and theoretical results in the literature. PMID:20938489

Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model

NASA Astrophysics Data System (ADS)

Bordner, Andrew J.; Zorman, Barry; Abagyan, Ruben

2011-10-01

Membrane proteins comprise a significant fraction of the proteomes of sequenced organisms and are the targets of approximately half of marketed drugs. However, in spite of their prevalence and biomedical importance, relatively few experimental structures are available due to technical challenges. Computational simulations can potentially address this deficit by providing structural models of membrane proteins. Solvation within the spatially heterogeneous membrane/solvent environment provides a major component of the energetics driving protein folding and association within the membrane. We have developed an implicit solvation model for membranes that is both computationally efficient and accurate enough to enable molecular mechanics predictions for the folding and association of peptides within the membrane. We derived the new atomic solvation model parameters using an unbiased fitting procedure to experimental data and have applied it to diverse problems in order to test its accuracy and to gain insight into membrane protein folding. First, we predicted the positions and orientations of peptides and complexes within the lipid bilayer and compared the simulation results with solid-state NMR structures. Additionally, we performed folding simulations for a series of host-guest peptides with varying propensities to form alpha helices in a hydrophobic environment and compared the structures with experimental measurements. We were also able to successfully predict the structures of amphipathic peptides as well as the structures for dimeric complexes of short hexapeptides that have experimentally characterized propensities to form beta sheets within the membrane. Finally, we compared calculated relative transfer energies with data from experiments measuring the effects of mutations on the free energies of translocon-mediated insertion of proteins into lipid bilayers and of combined folding and membrane insertion of a beta barrel protein.

Screening-level models to estimate partition ratios of organic chemicals between polymeric materials, air and water.

PubMed

Reppas-Chrysovitsinos, Efstathios; Sobek, Anna; MacLeod, Matthew

2016-06-15

Polymeric materials flowing through the technosphere are repositories of organic chemicals throughout their life cycle. Equilibrium partition ratios of organic chemicals between these materials and air (KMA) or water (KMW) are required for models of fate and transport, high-throughput exposure assessment and passive sampling. KMA and KMW have been measured for a growing number of chemical/material combinations, but significant data gaps still exist. We assembled a database of 363 KMA and 910 KMW measurements for 446 individual compounds and nearly 40 individual polymers and biopolymers, collected from 29 studies. We used the EPI Suite and ABSOLV software packages to estimate physicochemical properties of the compounds and we employed an empirical correlation based on Trouton's rule to adjust the measured KMA and KMW values to a standard reference temperature of 298 K. Then, we used a thermodynamic triangle with Henry's law constant to calculate a complete set of 1273 KMA and KMW values. Using simple linear regression, we developed a suite of single parameter linear free energy relationship (spLFER) models to estimate KMA from the EPI Suite-estimated octanol-air partition ratio (KOA) and KMW from the EPI Suite-estimated octanol-water (KOW) partition ratio. Similarly, using multiple linear regression, we developed a set of polyparameter linear free energy relationship (ppLFER) models to estimate KMA and KMW from ABSOLV-estimated Abraham solvation parameters. We explored the two LFER approaches to investigate (1) their performance in estimating partition ratios, and (2) uncertainties associated with treating all different polymers as a single "bulk" polymeric material compartment. The models we have developed are suitable for screening assessments of the tendency for organic chemicals to be emitted from materials, and for use in multimedia models of the fate of organic chemicals in the indoor environment. In screening applications we recommend that KMA and KMW be modeled as 0.06 ×KOA and 0.06 ×KOW respectively, with an uncertainty range of a factor of 15.

Investigation of Solvation Effects on Optical Rotatory Dispersion Using the Polarizable Continuum Model

NASA Astrophysics Data System (ADS)

Aharon, Tal; Lemler, Paul M.; Vaccaro, Patrick; Caricato, Marco

2017-06-01

The Optical Rotatory Dispersion (ORD) of a chiral solute is heavily affected by solvation, but this effect does not follow the usual correlation with the solvent polarity, i.e., larger solvent polarity does not imply a larger change in the solute's property. Therefore, a great deal of experimental and theoretical effort has been directed towards correlating the solvation effect on the ORD and the solvent properties. This discovery followed from the development of cavity ring down polarimetry (CRPD), which allows measurements of gas-phase ORD. In order to investigate this phenomenon, we chose a set of five rigid molecules to limit the effect of molecular vibrations and isolate the role of solvation. The latter was investigated with the Polarizable Continuum Model (PCM), and compared to experimental results. We used Bondi radii to build the PCM cavity, and performed extensive calculations at multiple frequencies using density functional theory (DFT) with two functionals: B3LYP and CAM-B3LYP, together with the aug-cc-pVDZ basis set. We also performed coupled cluster singles and doubles (CCSD/aug-cc-pVDZ) calculations at the wavelengths where gas-phase data are available, all of which are augmented with zero point vibrational corrections. These results are compared to experimental data and seem to indicate that PCM does not entirely account for the environmental effects on the ORD.

Nonlinear functional for solvation in Density Functional Theory

NASA Astrophysics Data System (ADS)

Gunceler, Deniz; Sundararaman, Ravishankar; Schwarz, Kathleen; Letchworth-Weaver, Kendra; Arias, T. A.

2013-03-01

Density functional calculations of molecules and surfaces in a liquid can accelerate the development of many technologies ranging from solar energy harvesting to lithium batteries. Such studies require the development of robust functionals describing the liquid. Polarizable continuum models (PCM's) have been applied to some solvated systems; but they do not sufficiently capture solvation effects to describe highly polar systems like surfaces of ionic solids. In this work, we present a nonlinear fluid functional within the framework of Joint Density Functional Theory. The fluid is treated not as a linear dielectric, but as a distribution of dipoles that responds to the solute, which we describe starting from the exact free energy functional for point dipoles. We also show PCM's can be recovered as the linear limit of our functional. Our description is of similar computational cost to PCM's, and captures complex solvation effects like dielectric saturation without requiring new fit parameters. For polar and nonpolar molecules, it achieves millihartree level agreement with experimental solvation energies. Furthermore, our functional now makes it possible to investigate chemistry on the surface of lithium battery materials, which PCM's predict to be unstable. Supported as part of the Energy Materials Center at Cornell, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001086

Binding selectivity of dibenzo-18-crown-6 for alkali metal cations in aqueous solution: A density functional theory study using a continuum solvation model.

PubMed

Choi, Chang Min; Heo, Jiyoung; Kim, Nam Joon

2012-08-08

Dibenzo-18-crown-6 (DB18C6) exhibits the binding selectivity for alkali metal cations in solution phase. In this study, we investigate the main forces that determine the binding selectivity of DB18C6 for the metal cations in aqueous solution using the density functional theory (DFT) and the conductor-like polarizable continuum model (CPCM). The bond dissociation free energies (BDFE) of DB18C6 complexes with alkali metal cations (M+-DB18C6, M = Li, Na, K, Rb, and Cs) in aqueous solution are calculated at the B3LYP/6-311++G(d,p)//B3LYP/6-31 + G(d) level using the CPCM. It is found that the theoretical BDFE is the largest for K+-DB18C6 and decreases as the size of the metal cation gets larger or smaller than that of K+, which agrees well with previous experimental results. The solvation energy of M+-DB18C6 in aqueous solution plays a key role in determining the binding selectivity of DB18C6. In particular, the non-electrostatic dispersion interaction between the solute and solvent, which depends strongly on the complex structure, is largely responsible for the different solvation energies of M+-DB18C6. This study shows that the implicit solvation model like the CPCM works reasonably well in predicting the binding selectivity of DB18C6 in aqueous solution.

A density functional theory based approach for predicting melting points of ionic liquids

DOE PAGES

Chen, Lihua; Bryantsev, Vyacheslav S.

2017-01-17

Accurate prediction of melting points of ILs is important both from the fundamental point of view and from the practical perspective for screening ILs with low melting points and broadening their utilization in a wider temperature range. In this work, we present an ab initio approach to calculating melting points of ILs with known crystal structures and illustrate its application for a series of 11 ILs containing imidazolium/pyrrolidinium cations and halide/polyatomic fluoro-containing anions. The melting point is determined as a temperature at which the Gibbs free energy of fusion is zero. The Gibbs free energy of fusion can be expressedmore » through the use of the Born-Fajans-Haber cycle via the lattice free energy of forming a solid IL from gaseous phase ions and the sum of the solvation free energies of ions comprising IL. Dispersion-corrected density functional theory (DFT) involving (semi)local (PBE-D3) and hybrid exchange-correlation (HSE06-D3) functionals is applied to estimate the lattice enthalpy, entropy, and free energy. The ions solvation free energies are calculated with the SMD-generic-IL solvation model at the M06-2X/6-31+G(d) level of theory under standard conditions. The melting points of ILs computed with the HSE06-D3 functional are in good agreement with the experimental data, with a mean absolute error of 30.5 K and a mean relative error of 8.5%. The model is capable of accurately reproducing the trends in melting points upon variation of alkyl substituents in organic cations and replacement one anion by another. The results verify that the lattice energies of ILs containing polyatomic fluoro-containing anions can be approximated reasonably well using the volume-based thermodynamic approach. However, there is no correlation of the computed lattice energies with molecular volume for ILs containing halide anions. Moreover, entropies of solid ILs follow two different linear relationships with molecular volume for halides and polyatomic fluoro-containing anions. As a result, continuous progress in predicting crystal structures of organic salts with halide anions will be a key factor for successful prediction of melting points with no prior knowledge of the crystal structure.« less

A density functional theory based approach for predicting melting points of ionic liquids

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

Chen, Lihua; Bryantsev, Vyacheslav S.

Accurate prediction of melting points of ILs is important both from the fundamental point of view and from the practical perspective for screening ILs with low melting points and broadening their utilization in a wider temperature range. In this work, we present an ab initio approach to calculating melting points of ILs with known crystal structures and illustrate its application for a series of 11 ILs containing imidazolium/pyrrolidinium cations and halide/polyatomic fluoro-containing anions. The melting point is determined as a temperature at which the Gibbs free energy of fusion is zero. The Gibbs free energy of fusion can be expressedmore » through the use of the Born-Fajans-Haber cycle via the lattice free energy of forming a solid IL from gaseous phase ions and the sum of the solvation free energies of ions comprising IL. Dispersion-corrected density functional theory (DFT) involving (semi)local (PBE-D3) and hybrid exchange-correlation (HSE06-D3) functionals is applied to estimate the lattice enthalpy, entropy, and free energy. The ions solvation free energies are calculated with the SMD-generic-IL solvation model at the M06-2X/6-31+G(d) level of theory under standard conditions. The melting points of ILs computed with the HSE06-D3 functional are in good agreement with the experimental data, with a mean absolute error of 30.5 K and a mean relative error of 8.5%. The model is capable of accurately reproducing the trends in melting points upon variation of alkyl substituents in organic cations and replacement one anion by another. The results verify that the lattice energies of ILs containing polyatomic fluoro-containing anions can be approximated reasonably well using the volume-based thermodynamic approach. However, there is no correlation of the computed lattice energies with molecular volume for ILs containing halide anions. Moreover, entropies of solid ILs follow two different linear relationships with molecular volume for halides and polyatomic fluoro-containing anions. As a result, continuous progress in predicting crystal structures of organic salts with halide anions will be a key factor for successful prediction of melting points with no prior knowledge of the crystal structure.« less

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

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

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for coarse grained models of electrolyte solution. Here, we provide rigorous definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation (DFT-MD) and isolate the effects of charge and cavitation,more » comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to highly unphysical values for the solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry (CHA) for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation. We would like to thank Thomas Beck, Shawn Kathmann, Richard Remsing and John Weeks for helpful discussions. Computing resources were generously allocated by PNNL's Institutional Computing program. This research also used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. TTD, GKS, and CJM were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative, a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated by Battelle for the U.S. Department of Energy.« less

Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation

PubMed Central

Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E.

2014-01-01

This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand the structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as means to sample conformational space for a better understanding of the relevance of a given model. From this discussion, the major limitations with modeling, in general, were highlighted. These are the difficult issues in sampling conformational space effectively—the multiple minima or conformational sampling problems—and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These are discussed in detail in this unit. PMID:18428877

Molecular modeling of nucleic Acid structure: electrostatics and solvation.

PubMed

Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E

2014-12-19

This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. Copyright © 2014 John Wiley & Sons, Inc.

Solvation thermodynamics and the physical-chemical meaning of the constant in Abraham solvation equations.

PubMed

van Noort, Paul C M

2012-04-01

Abraham solvation equations find widespread use in environmental chemistry. Until now, the intercept in these equations was determined by fitting experimental data. To simplify the determination of the coefficients in Abraham solvation equations, this study derives theoretical expressions for the value of the intercept for various partition processes. To that end, a modification of the description of the Ben-Naim standard state into the van der Waals volume is proposed. Differences between predicted and fitted values of the Abraham solvation equation intercept for the enthalpy of solvation, the entropy of solvation, solvent-water partitioning, air-solvent partitioning, partitioning into micelles, partitioning into lipid membranes and lipids, and chromatographic retention indices are comparable to experimental uncertainties in these values. Copyright © 2011 Elsevier Ltd. All rights reserved.

Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein

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

Kuffel, Anna; Czapiewski, Dariusz; Zielkiewicz, Jan, E-mail: jaz@chem.pg.gda.pl

2015-10-07

The dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties of solvation water of ice around its two crystallographic planes: basal and prism. Three main conclusions are inferred from our investigations. The first one is that the solvation shell of CfAFP does not seem to be particularlymore » far-ranged, at least not beyond what is usually observed for proteins that do not interact with ice. Therefore, it does not appear to us that the antifreeze activity is enhanced by a long-ranged retardation of water mobility. Also the correlation between the collective mobility of water and the collective mobility of protein atoms highly resembles the one measured for the protein that does not interact with ice. Our second conclusion is that the dynamical properties of solvation water of CfAFP are non-uniform. The dynamics of solvation water of ice-binding plane is, in some respects, different from the dynamics of solvation water of the two remaining planes. The feature that distinguishes the dynamics of solvation water of the three planes is the activation energy of diffusion process. The third conclusion is that—from the three analyzed solvation shells of CfAFP—the dynamical properties of solvation water of the ice-binding plane resemble the most the properties of solvation water of ice; note, however, that these properties still clearly differ from the dynamic properties of solvation water of ice.« less

Thermodynamic-ensemble independence of solvation free energy.

PubMed

Chong, Song-Ho; Ham, Sihyun

2015-02-10

Solvation free energy is the fundamental thermodynamic quantity in solution chemistry. Recently, it has been suggested that the partial molar volume correction is necessary to convert the solvation free energy determined in different thermodynamic ensembles. Here, we demonstrate ensemble-independence of the solvation free energy on general thermodynamic grounds. Theoretical estimates of the solvation free energy based on the canonical or grand-canonical ensemble are pertinent to experiments carried out under constant pressure without any conversion.

Predictive Multiscale Modeling of Nanocellulose Based Materials and Systems

NASA Astrophysics Data System (ADS)

Kovalenko, Andriy

2014-08-01

Cellulose Nanocrysals (CNC) is a renewable biodegradable biopolymer with outstanding mechanical properties made from highly abundant natural source, and therefore is very attractive as reinforcing additive to replace petroleum-based plastics in biocomposite materials, foams, and gels. Large-scale applications of CNC are currently limited due to its low solubility in non-polar organic solvents used in existing polymerization technologies. The solvation properties of CNC can be improved by chemical modification of its surface. Development of effective surface modifications has been rather slow because extensive chemical modifications destabilize the hydrogen bonding network of cellulose and deteriorate the mechanical properties of CNC. We employ predictive multiscale theory, modeling, and simulation to gain a fundamental insight into the effect of CNC surface modifications on hydrogen bonding, CNC crystallinity, solvation thermodynamics, and CNC compatibilization with the existing polymerization technologies, so as to rationally design green nanomaterials with improved solubility in non-polar solvents, controlled liquid crystal ordering and optimized extrusion properties. An essential part of this multiscale modeling approach is the statistical- mechanical 3D-RISM-KH molecular theory of solvation, coupled with quantum mechanics, molecular mechanics, and multistep molecular dynamics simulation. The 3D-RISM-KH theory provides predictive modeling of both polar and non-polar solvents, solvent mixtures, and electrolyte solutions in a wide range of concentrations and thermodynamic states. It properly accounts for effective interactions in solution such as steric effects, hydrophobicity and hydrophilicity, hydrogen bonding, salt bridges, buffer, co-solvent, and successfully predicts solvation effects and processes in bulk liquids, solvation layers at solid surface, and in pockets and other inner spaces of macromolecules and supramolecular assemblies. This methodology enables rational design of CNC-based bionanocomposite materials and systems. Furthermore, the 3D-RISM-KH based multiscale modeling addresses the effect of hemicellulose and lignin composition on nanoscale forces that control cell wall strength towards overcoming plant biomass recalcitrance. It reveals molecular forces maintaining the cell wall structure and provides directions for genetic modulation of plants and pretreatment design to render biomass more amenable to processing. We envision integrated biomass valorization based on extracting and decomposing the non-cellulosic components to low molecular weight chemicals and utilizing the cellulose microfibrils to make CNC. This is an important alternative to approaches of full conversion of lignocellulose to biofuels that face challenges arising from the deleterious impact of cellulose crystallinity on enzymatic processing.

Simple model of hydrophobic hydration.

PubMed

Lukšič, Miha; Urbic, Tomaz; Hribar-Lee, Barbara; Dill, Ken A

2012-05-31

Water is an unusual liquid in its solvation properties. Here, we model the process of transferring a nonpolar solute into water. Our goal was to capture the physical balance between water's hydrogen bonding and van der Waals interactions in a model that is simple enough to be nearly analytical and not heavily computational. We develop a 2-dimensional Mercedes-Benz-like model of water with which we compute the free energy, enthalpy, entropy, and the heat capacity of transfer as a function of temperature, pressure, and solute size. As validation, we find that this model gives the same trends as Monte Carlo simulations of the underlying 2D model and gives qualitative agreement with experiments. The advantages of this model are that it gives simple insights and that computational time is negligible. It may provide a useful starting point for developing more efficient and more realistic 3D models of aqueous solvation.

Calculation of the Gibbs Free Energy of Solvation and Dissociation of HCl in Water via Monte Carlo Simulations and Continuum Solvation Models

DTIC Science & Technology

2013-01-01

Narten, J. Chem. Phys., 1975, 63, 3624–3631. 10 A. Botti, F. Bruni, S. Imberti, M. A. Ricci and A. K. Soper , J. Chem. Phys., 2004, 121, 7840–7848. 11 D...10478. 48 I. Harsányi and L. Pusztai, J. Phys.: Condens. Matter, 2005, 17, S59–S65. 49 A. Botti, F. Bruni, M. A. Ricci and A. K. Soper , J. Chem. Phys

Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions

PubMed Central

Deng, Shaozhong; Xue, Changfeng; Baumketner, Andriy; Jacobs, Donald; Cai, Wei

2013-01-01

This paper extends the image charge solvation model (ICSM) [J. Chem. Phys. 131, 154103 (2009)], a hybrid explicit/implicit method to treat electrostatic interactions in computer simulations of biomolecules formulated for spherical cavities, to prolate spheroidal and triaxial ellipsoidal cavities, designed to better accommodate non-spherical solutes in molecular dynamics (MD) simulations. In addition to the utilization of a general truncated octahedron as the MD simulation box, central to the proposed extension is an image approximation method to compute the reaction field for a point charge placed inside such a non-spherical cavity by using a single image charge located outside the cavity. The resulting generalized image charge solvation model (GICSM) is tested in simulations of liquid water, and the results are analyzed in comparison with those obtained from the ICSM simulations as a reference. We find that, for improved computational efficiency due to smaller simulation cells and consequently a less number of explicit solvent molecules, the generalized model can still faithfully reproduce known static and dynamic properties of liquid water at least for systems considered in the present paper, indicating its great potential to become an accurate but more efficient alternative to the ICSM when bio-macromolecules of irregular shapes are to be simulated. PMID:23913979

Single-Ion Solvation Free Energies and the Normal Hydrogen Electrode Potential in Methanol, Acetonitrile, and Dimethyl Sulfoxide

PubMed Central

Kelly, Casey P.; Cramer, Christopher J.; Truhlar, Donald G.

2008-01-01

The division of thermodynamic solvation free energies of electrolytes into ionic constituents is conventionally accomplished by using the single-ion solvation free energy of one reference ion, conventionally the proton, to set the single-ion scales. Thus the determination of the free energy of solvation of the proton in various solvents is a fundamental issue of central importance in solution chemistry. In the present article, relative solvation free energies of ions and ion-solvent clusters in methanol, acetonitrile, and dimethyl sulfoxide (DMSO) have been determined using a combination of experimental and theoretical gas-phase free energies of formation, solution-phase reduction potentials and acid dissociation constants, and gas-phase clustering free energies. Applying the cluster pair approximation to differences between these relative solvation free energies leads to values of −263.5, −260.2, and −273.3 kcal/mol for the absolute solvation free energy of the proton in methanol, acetonitrile, and DMSO, respectively. The final absolute proton solvation free energies are used to assign absolute values for the normal hydrogen electrode potential and the solvation free energies of other single ions in the above solvents. PMID:17214493

An explicitly solvated full atomistic model of the cardiac thin filament and application on the calcium binding affinity effects from familial hypertrophic cardiomyopathy linked mutations

NASA Astrophysics Data System (ADS)

Williams, Michael; Schwartz, Steven

2015-03-01

The previous version of our cardiac thin filament (CTF) model consisted of the troponin complex (cTn), two coiled-coil dimers of tropomyosin (Tm), and 29 actin units. We now present the newest revision of the model to include explicit solvation. The model was developed to continue our study of genetic mutations in the CTF proteins which are linked to familial hypertrophic cardiomyopathies. Binding of calcium to the cTnC subunit causes subtle conformational changes to propagate through the cTnC to the cTnI subunit which then detaches from actin. Conformational changes propagate through to the cTnT subunit, which allows Tm to move into the open position along actin, leading to muscle contraction. Calcium disassociation allows for the reverse to occur, which results in muscle relaxation. The inclusion of explicit TIP3 water solvation allows for the model to get better individual local solvent to protein interactions; which are important when observing the N-lobe calcium binding pocket of the cTnC. We are able to compare in silica and in vitro experimental results to better understand the physiological effects from mutants, such as the R92L/W and F110V/I of the cTnT, on the calcium binding affinity compared to the wild type.

Ions in water: Free energies, surface effects, and geometrical constraints

NASA Astrophysics Data System (ADS)

Herce, Henry David

In this work, we present our results for ion solvation in finite and infinite water clusters. Molecular Dynamic simulations are used to connect the fundamental macroscopic quantities such as free energy, internal energy and entropy with the underlying microscopic description. Molecular dynamics studies complement experimental results and lead to a deeper insight into the solvation and diffusion of ionic species. Beyond its intrinsic interest, the ion solvation problem has practical relevance because of its role as ideal model system with which to construct and test ion-water interaction potentials. The ionic charging free energy is a very sensitive probe for the treatment of electrostatics in any given simulation setting. In this work, we present methods to compute the ionic charging free energy in systems characterized by atomic charges, and higher-order multipoles, mainly dipoles and quadrupoles. The results of these methods under periodic boundary conditions and spherical boundary conditions are then compared. For the treatment of spherical boundary conditions, we introduce a generalization of Gauss' law that links the microscopic variables to the relevant thermodynamic quantities. Ionic solvation in finite clusters is a problem relevant for many areas of chemistry and biology, such as the gas-liquid interface of tropospheric aerosol particles, or the interphase between water and proteins, membranes, etc. Careful evaluations of the free energy, internal energy and entropy are used to address controversial or unresolved issues, related to the underlying physical cause of surface solvation, and the basic assumptions that go with it. Our main conclusions are the following: (i) The main cause of surface solvation of a single ion in a water cluster is both water and ion polarization, coupled to the charge and size of the ion. Interestingly, the total energy of the ion increases near the cluster surface, while the total energy of water decreases. Also, our analysis clearly shows that the cause of surface solvation is not the size of the total water dipole (unless this is too small). (ii) The entropic contribution is the same order of magnitude as the energetic contribution, and therefore cannot be neglected for quantitative results. (iii) A pure energetic analysis can give a qualitative description of the ion position at room temperature. (iv) We have observed surface solvation of a large positive iodine-like ion in a polarizable water cluster, but not in a non-polarizable water cluster.

Extended solvent-contact model approach to blind SAMPL5 prediction challenge for the distribution coefficients of drug-like molecules

NASA Astrophysics Data System (ADS)

Chung, Kee-Choo; Park, Hwangseo

2016-11-01

The performance of the extended solvent-contact model has been addressed in the SAMPL5 blind prediction challenge for distribution coefficient (LogD) of drug-like molecules with respect to the cyclohexane/water partitioning system. All the atomic parameters defined for 41 atom types in the solvation free energy function were optimized by operating a standard genetic algorithm with respect to water and cyclohexane solvents. In the parameterizations for cyclohexane, the experimental solvation free energy (Δ G sol ) data of 15 molecules for 1-octanol were combined with those of 77 molecules for cyclohexane to construct a training set because Δ G sol values of the former were unavailable for cyclohexane in publicly accessible databases. Using this hybrid training set, we established the LogD prediction model with the correlation coefficient ( R), average error (AE), and root mean square error (RMSE) of 0.55, 1.53, and 3.03, respectively, for the comparison of experimental and computational results for 53 SAMPL5 molecules. The modest accuracy in LogD prediction could be attributed to the incomplete optimization of atomic solvation parameters for cyclohexane. With respect to 31 SAMPL5 molecules containing the atom types for which experimental reference data for Δ G sol were available for both water and cyclohexane, the accuracy in LogD prediction increased remarkably with the R, AE, and RMSE values of 0.82, 0.89, and 1.60, respectively. This significant enhancement in performance stemmed from the better optimization of atomic solvation parameters by limiting the element of training set to the molecules with experimental Δ G sol data for cyclohexane. Due to the simplicity in model building and to low computational cost for parameterizations, the extended solvent-contact model is anticipated to serve as a valuable computational tool for LogD prediction upon the enrichment of experimental Δ G sol data for organic solvents.

A unified perspective on preferential solvation and adsorption based on inhomogeneous solvation theory

NASA Astrophysics Data System (ADS)

Shimizu, Seishi; Matubayasi, Nobuyuki

2018-02-01

How cosolvents affects solvation has been revealed through the independent determination of solute-solvent and solute-cosolvent interactions guaranteed by the phase rule. Based on the first principles of inhomogeneous solvation theory, we present here a general matrix theory encompassing both preferential solvation and surface adsorption. The central role of the stability conditions, that govern how many excess numbers (surface excesses) are independently determinable, have been clarified from the first principles. The advantage of the inhomogeneous approach has been demonstrated to be in its ease in treating solvation and adsorption in a unified manner, while its disadvantage, for example in membrane dialysis experiments, can be overcome by the inhomogeneous-homogeneous conversion.

Calculating Water Thermodynamics in the Binding Site of Proteins - Applications of WaterMap to Drug Discovery.

PubMed

Cappel, Daniel; Sherman, Woody; Beuming, Thijs

2017-01-01

The ability to accurately characterize the solvation properties (water locations and thermodynamics) of biomolecules is of great importance to drug discovery. While crystallography, NMR, and other experimental techniques can assist in determining the structure of water networks in proteins and protein-ligand complexes, most water molecules are not fully resolved and accurately placed. Furthermore, understanding the energetic effects of solvation and desolvation on binding requires an analysis of the thermodynamic properties of solvent involved in the interaction between ligands and proteins. WaterMap is a molecular dynamics-based computational method that uses statistical mechanics to describe the thermodynamic properties (entropy, enthalpy, and free energy) of water molecules at the surface of proteins. This method can be used to assess the solvent contributions to ligand binding affinity and to guide lead optimization. In this review, we provide a comprehensive summary of published uses of WaterMap, including applications to lead optimization, virtual screening, selectivity analysis, ligand pose prediction, and druggability assessment. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Solvation structures of water in trihexyltetradecylphosphonium-orthoborate ionic liquids

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

Wang, Yong-Lei, E-mail: wangyonl@gmail.com; System and Component Design, Department of Machine Design, KTH Royal Institute of Technology, SE-100 44 Stockholm; Sarman, Sten

2016-08-14

Atomistic molecular dynamics simulations have been performed to investigate effective interactions of isolated water molecules dispersed in trihexyltetradecylphosphonium-orthoborate ionic liquids (ILs). The intrinsic free energy changes in solvating one water molecule from gas phase into bulk IL matrices were estimated as a function of temperature, and thereafter, the calculations of potential of mean force between two dispersed water molecules within different IL matrices were performed using umbrella sampling simulations. The systematic analyses of local ionic microstructures, orientational preferences, probability and spatial distributions of dispersed water molecules around neighboring ionic species indicate their preferential coordinations to central polar segments in orthoboratemore » anions. The effective interactions between two dispersed water molecules are partially or totally screened as their separation distance increases due to interference of ionic species in between. These computational results connect microscopic anionic structures with macroscopically and experimentally observed difficulty in completely removing water from synthesized IL samples and suggest that the introduction of hydrophobic groups to central polar segments and the formation of conjugated ionic structures in orthoborate anions can effectively reduce residual water content in the corresponding IL samples.« less

Interfacial ion solvation: Obtaining the thermodynamic limit from molecular simulations

NASA Astrophysics Data System (ADS)

Cox, Stephen J.; Geissler, Phillip L.

2018-06-01

Inferring properties of macroscopic solutions from molecular simulations is complicated by the limited size of systems that can be feasibly examined with a computer. When long-ranged electrostatic interactions are involved, the resulting finite size effects can be substantial and may attenuate very slowly with increasing system size, as shown by previous work on dilute ions in bulk aqueous solution. Here we examine corrections for such effects, with an emphasis on solvation near interfaces. Our central assumption follows the perspective of Hünenberger and McCammon [J. Chem. Phys. 110, 1856 (1999)]: Long-wavelength solvent response underlying finite size effects should be well described by reduced models like dielectric continuum theory, whose size dependence can be calculated straightforwardly. Applied to an ion in a periodic slab of liquid coexisting with vapor, this approach yields a finite size correction for solvation free energies that differs in important ways from results previously derived for bulk solution. For a model polar solvent, we show that this new correction quantitatively accounts for the variation of solvation free energy with volume and aspect ratio of the simulation cell. Correcting periodic slab results for an aqueous system requires an additional accounting for the solvent's intrinsic charge asymmetry, which shifts electric potentials in a size-dependent manner. The accuracy of these finite size corrections establishes a simple method for a posteriori extrapolation to the thermodynamic limit and also underscores the realism of dielectric continuum theory down to the nanometer scale.

Lithium ion solvation and diffusion in bulk organic electrolytes from first-principles and classical reactive molecular dynamics.

PubMed

Ong, Mitchell T; Verners, Osvalds; Draeger, Erik W; van Duin, Adri C T; Lordi, Vincenzo; Pask, John E

2015-01-29

Lithium-ion battery performance is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact both the solvation and diffusivity of Li ions. In this work, we used first-principles molecular dynamics to examine the solvation and diffusion of Li ions in the bulk organic solvents ethylene carbonate (EC), ethyl methyl carbonate (EMC), and a mixture of EC and EMC. We found that Li ions are solvated by either carbonyl or ether oxygen atoms of the solvents and sometimes by the PF6(-) anion. Li(+) prefers a tetrahedrally coordinated first solvation shell regardless of which species are involved, with the specific preferred solvation structure dependent on the organic solvent. In addition, we calculated Li diffusion coefficients in each electrolyte, finding slightly larger diffusivities in the linear carbonate EMC compared to the cyclic carbonate EC. The magnitude of the diffusion coefficient correlates with the strength of Li(+) solvation. Corresponding analysis for the PF6(-) anion shows greater diffusivity associated with a weakly bound, poorly defined first solvation shell. These results can be used to aid in the design of new electrolytes to improve Li-ion battery performance.

Nonpolar Solvation Free Energy from Proximal Distribution Functions

PubMed Central

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

2017-01-01

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

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

Probing solvation decay length in order to characterize hydrophobicity-induced bead-bead attractive interactions in polymer chains.

PubMed

Das, Siddhartha; Chakraborty, Suman

2011-08-01

In this paper, we quantitatively demonstrate that exponentially decaying attractive potentials can effectively mimic strong hydrophobic interactions between monomer units of a polymer chain dissolved in aqueous solvent. Classical approaches to modeling hydrophobic solvation interactions are based on invariant attractive length scales. However, we demonstrate here that the solvation interaction decay length may need to be posed as a function of the relative separation distances and the sizes of the interacting species (or beads or monomers) to replicate the necessary physical interactions. As an illustrative example, we derive a universal scaling relationship for a given solute-solvent combination between the solvation decay length, the bead radius, and the distance between the interacting beads. With our formalism, the hydrophobic component of the net attractive interaction between monomer units can be synergistically accounted for within the unified framework of a simple exponentially decaying potential law, where the characteristic decay length incorporates the distinctive and critical physical features of the underlying interaction. The present formalism, even in a mesoscopic computational framework, is capable of incorporating the essential physics of the appropriate solute-size dependence and solvent-interaction dependence in the hydrophobic force estimation, without explicitly resolving the underlying molecular level details.

Solvation of carbonaceous molecules by para-H{sub 2} and ortho-D{sub 2} clusters. I. Polycyclic aromatic hydrocarbons

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

Calvo, F., E-mail: florent.calvo@univ-grenoble-alpes.fr; Yurtsever, E.

This work theoretically examines the progressive coating of planar polycyclic aromatic hydrocarbon (PAH) molecules ranging from benzene to circumcoronene (C{sub 54}H{sub 18}) by para-hydrogen and ortho-deuterium. The coarse-grained Silvera-Goldman potential has been extended to model the interactions between hydrogen molecules and individual atoms of the PAH and parametrized against quantum chemical calculations for benzene-H{sub 2}. Path-integral molecular dynamics simulations at 2 K were performed for increasingly large amounts of hydrogen coating the PAH up to the first solvation shell and beyond. From the simulations, various properties were determined such as the size of the first shell and its thickness asmore » well as the solvation energy. The degree of delocalization was notably quantified from an energy landscape perspective, by monitoring the fluctuations among inherent structures sampled by the trajectories. Our results generally demonstrate a high degree of localization owing to relatively strong interactions between hydrogen and the PAH, and qualitatively minor isotopic effects. In the limit of large hydrogen amounts, the shell size and solvation energy both follow approximate linear relations with the numbers of carbon and hydrogen in the PAH.« less

Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. I. Polycyclic aromatic hydrocarbons.

PubMed

Calvo, F; Yurtsever, E

2016-06-14

This work theoretically examines the progressive coating of planar polycyclic aromatic hydrocarbon (PAH) molecules ranging from benzene to circumcoronene (C54H18) by para-hydrogen and ortho-deuterium. The coarse-grained Silvera-Goldman potential has been extended to model the interactions between hydrogen molecules and individual atoms of the PAH and parametrized against quantum chemical calculations for benzene-H2. Path-integral molecular dynamics simulations at 2 K were performed for increasingly large amounts of hydrogen coating the PAH up to the first solvation shell and beyond. From the simulations, various properties were determined such as the size of the first shell and its thickness as well as the solvation energy. The degree of delocalization was notably quantified from an energy landscape perspective, by monitoring the fluctuations among inherent structures sampled by the trajectories. Our results generally demonstrate a high degree of localization owing to relatively strong interactions between hydrogen and the PAH, and qualitatively minor isotopic effects. In the limit of large hydrogen amounts, the shell size and solvation energy both follow approximate linear relations with the numbers of carbon and hydrogen in the PAH.

Solvent induced conformational fluctuation of alanine dipeptide studied by using vibrational probes

NASA Astrophysics Data System (ADS)

Cai, Kaicong; Du, Fenfen; Liu, Jia; Su, Tingting

2015-02-01

The solvation effect on the three dimensional structure and the vibrational feature of alanine dipeptide (ALAD) was evaluated by applying the implicit solvents from polarizable continuum solvent model (PCM) through ab initio calculations, by using molecular dynamic (MD) simulations with explicit solvents, and by combining these two approaches. The implicit solvent induced potential energy fluctuations of ALAD in CHCl3, DMSO and H2O are revealed by means of ab initio calculations, and a global view of conformational and solvation environmental dependence of amide I frequencies is achieved. The results from MD simulations with explicit solvents show that ALAD trends to form PPII, αL, αR, and C5 in water, PPII and C5 in DMSO, and C5 in CHCl3, ordered by population, and the demonstration of the solvated structure, the solute-solvent interaction and hydrogen bonding is therefore enhanced. Representative ALAD-solvent clusters were sampled from MD trajectories and undergone ab initio calculations. The explicit solvents reveal the hydrogen bonding between ALAD and solvents, and the correlation between amide I frequencies and the Cdbnd O bond length is built. The implicit solvents applied to the ALAD-solvent clusters further compensate the solvation effect from the bulk, and thus enlarge the degree of structural distortion and the amide I frequency red shift. The combination of explicit solvent in the first hydration shell and implicit solvent in the bulk is helpful for our understanding about the conformational fluctuation of solvated polypeptides through vibrational probes.

Natural abundance 17O, 6Li NMR and molecular modeling studies of the solvation structures of lithium bis(fluorosulfonyl)imide/1,2-dimethoxyethane liquid electrolytes

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

Wan, Chuan; Hu, Mary Y.; Borodin, Oleg

2016-03-01

Natural abundance 17O and 6Li NMR experiments, quantum chemistry and molecular dynamics studies were employed to investigate the solvation structures of Li+ at various concentrations of LiFSI in DME electrolytes in an effort to solve this puzzle. It was found that the chemical shifts of both 17O and 6Li changed with the concentration of LiFSI, indicating the changes of solvation structures with concentration. For the quantum chemistry calculations, the coordinated cluster LiFSI(DME)2 forms at first, and its relative ratio increases with increasing LiFSI concentration to 1 M. Then the solvation structure LiFSI(DME) become the dominant component. As a result, themore » coordination of forming contact ion pairs between Li+ and FSI- ion increases, but the association between Li+ and DME molecule decreases. Furthermore, at LiFSI concentration of 4 M the solvation structures associated with Li+(FSI-)2(DME), Li+2(FSI-)(DME)4 and (LiFSI)2(DME)3 become the dominant components. For the molecular dynamics simulation, with increasing concentration, the association between DME and Li+ decreases, and the coordinated number of FSI- increases, which is in perfect accord with the DFT results. These results provide more insight on the fundamental mechanism on the very high CE of Li deposition in these electrolytes, especially at high current density conditions.« less

Tools for identifying gelator scaffolds and solvents.

PubMed

Zurcher, Danielle M; McNeil, Anne J

2015-03-06

Small molecule gelators are serendipitously discovered more often than they are designed. As a consequence, it has been challenging to develop applications based on the limited set of known materials. This synopsis highlights recent strategies to streamline the process of gelator discovery, with a focus on the role of unidirectional intermolecular interactions and solvation. We present these strategies as a series of tools that can be employed to help identify gelator scaffolds and solvents for gel formation. Overall, we suggest that this guided approach is more efficient than random derivatization and screening.

Preparation of cerium halide solvate complexes

DOEpatents

Vasudevan, Kalyan V; Smith, Nickolaus A; Gordon, John C; McKigney, Edward A; Muenchaussen, Ross E

2013-08-06

Crystals of a solvated cerium(III) halide solvate complex resulted from a process of forming a paste of a cerium(III) halide in an ionic liquid, adding a solvent to the paste, removing any undissolved solid, and then cooling the liquid phase. Diffusing a solvent vapor into the liquid phase also resulted in crystals of a solvated cerium(III) halide complex.

Difference rule-a new thermodynamic principle: prediction of standard thermodynamic data for inorganic solvates.

PubMed

Jenkins, H Donald Brooke; Glasser, Leslie

2004-12-08

We present a quite general thermodynamic "difference" rule, derived from thermochemical first principles, quantifying the difference between the standard thermodynamic properties, P, of a solid n-solvate (or n-hydrate), n-S, containing n molecules of solvate, S (water or other) and the corresponding solid parent (unsolvated) salt: [P[n-solvate] - P[parent

Role of Solvation Effects in Protein Denaturation: From Thermodynamics to Single Molecules and Back

PubMed Central

England, Jeremy L.; Haran, Gilad

2011-01-01

Protein stability often is studied in vitro through the use of urea and guanidinium chloride, chemical cosolvents that disrupt protein native structure. Much controversy still surrounds the underlying mechanism by which these molecules denature proteins. Here we review current thinking on various aspects of chemical denaturation. We begin by discussing classic models of protein folding and how the effects of denaturants may fit into this picture through their modulation of the collapse, or coil-globule transition, which typically precedes folding. Subsequently, we examine recent molecular dynamics simulations that have shed new light on the possible microscopic origins of the solvation effects brought on by denaturants. It seems likely that both denaturants operate by facilitating solvation of hydrophobic regions of proteins. Finally, we present recent single-molecule fluorescence studies of denatured proteins, the analysis of which corroborates the role of denaturants in shifting the equilibrium of the coil-globule transition. PMID:21219136

Simple Models for Tough Concepts

ERIC Educational Resources Information Center

Cavagnoi, Richard M.; Barnett, Thomas

1976-01-01

Describes the construction of teaching models made from a variety of materials such as poker chips and cardboard that illustrate many chemical phenomena, including subatomic particles, molecular structure, solvation and dissociation, and enzyme-substrate interactions. (MLH)

Comparative study of solvation parameter models accounting the effects of mobile phase composition in reversed-phase liquid chromatography.

PubMed

Torres-Lapasió, J R; Ruiz-Angel, M J; García-Alvarez-Coque, M C

2007-09-28

Solvation parameter models relate linearly compound properties with five fundamental solute descriptors (excess molar refraction, dipolarity/polarizability, effective hydrogen-bond acidity and basicity, and McGowan volume). These models are widely used, due to the availability of protocols to obtain the descriptors, good performance, and general applicability. Several approaches to predict retention in reversed-phase liquid chromatography (RPLC) as a function of these descriptors and mobile phase composition are compared, assaying the performance with a set of 146 organic compounds of diverse nature, eluted with acetonitrile and methanol. The approaches are classified in two groups: those that only allow predictions of retention for the mobile phases used to build the models, and those valid at any other mobile phase composition. The first group includes the use of ratios between the regressed coefficients of the solvation models that are assumed to be characteristic for a column/solvent system, and the application of offsets to transfer the retention from a reference mobile phase to any other. Maximal accuracy in predictions corresponded, however, to the approaches in the second group, which were based on models that describe the retention as a function of mobile phase composition (expressed as the solvent volume fraction or a normalised polarity measurement), where the coefficients were made dependent on the solvent descriptors. The study revealed the properties that influence the retention and distinguish the particular behaviour of acetonitrile and methanol in RPLC.

Predicting drug loading in PLA-PEG nanoparticles.

PubMed

Meunier, M; Goupil, A; Lienard, P

2017-06-30

Polymer nanoparticles present advantageous physical and biopharmaceutical properties as drug delivery systems compared to conventional liquid formulations. Active pharmaceutical ingredients (APIs) are often hydrophobic, thus not soluble in conventional liquid delivery. Encapsulating the drugs in polymer nanoparticles can improve their pharmacological and bio-distribution properties, preventing rapid clearance from the bloodstream. Such nanoparticles are commonly made of non-toxic amphiphilic self-assembling block copolymers where the core (poly-[d,l-lactic acid] or PLA) serves as a reservoir for the API and the external part (Poly-(Ethylene-Glycol) or PEG) serves as a stealth corona to avoid capture by macrophage. The present study aims to predict the drug affinity for PLA-PEG nanoparticles and their effective drug loading using in silico tools in order to virtually screen potential drugs for non-covalent encapsulation applications. To that end, different simulation methods such as molecular dynamics and Monte-Carlo have been used to estimate the binding of actives on model polymer surfaces. Initially, the methods and models are validated against a series of pigments molecules for which experimental data exist. The drug affinity for the core of the nanoparticles is estimated using a Monte-Carlo "docking" method. Drug miscibility in the polymer matrix, using the Hildebrand solubility parameter (δ), and the solvation free energy of the drug in the PLA polymer model is then estimated. Finally, existing published ALogP quantitative structure-property relationships (QSPR) are compared to this method. Our results demonstrate that adsorption energies modelled by docking atomistic simulations on PLA surfaces correlate well with experimental drug loadings, whereas simpler approaches based on Hildebrand solubility parameters and Flory-Huggins interaction parameters do not. More complex molecular dynamics techniques which use estimation of the solvation free energies both in PLA and in water led to satisfactory predictive models. In addition, experimental drug loadings and Log P are found to correlate well. This work can be used to improve the understanding of drug-polymer interactions, a key component to designing better delivery systems. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantum mechanical/molecular mechanical/continuum style solvation model: second order Møller-Plesset perturbation theory.

PubMed

Thellamurege, Nandun M; Si, Dejun; Cui, Fengchao; Li, Hui

2014-05-07

A combined quantum mechanical/molecular mechanical/continuum (QM/MM/C) style second order Møller-Plesset perturbation theory (MP2) method that incorporates induced dipole polarizable force field and induced surface charge continuum solvation model is established. The Z-vector method is modified to include induced dipoles and induced surface charges to determine the MP2 response density matrix, which can be used to evaluate MP2 properties. In particular, analytic nuclear gradient is derived and implemented for this method. Using the Assisted Model Building with Energy Refinement induced dipole polarizable protein force field, the QM/MM/C style MP2 method is used to study the hydrogen bonding distances and strengths of the photoactive yellow protein chromopore in the wild type and the Glu46Gln mutant.

Lithium Ion Solvation and Diffusion in Bulk Organic Electrolytes from First-Principles and Classical Reactive Molecular Dynamics

DOE PAGES

Ong, Mitchell T.; Verners, Osvalds; Draeger, Erik W.; ...

2014-12-19

We report that lithium-ion battery performance is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact both the solvation and diffusivity of Li ions. In this work, we used first-principles molecular dynamics to examine the solvation and diffusion of Li ions in the bulk organic solvents ethylene carbonate (EC), ethyl methyl carbonate (EMC), and a mixture of EC and EMC. We found that Li ions are solvated by either carbonyl or ether oxygen atoms of the solvents and sometimes by the PF more » $$\\bar{6}$$ anion. Li + prefers a tetrahedrally coordinated first solvation shell regardless of which species are involved, with the specific preferred solvation structure dependent on the organic solvent. In addition, we calculated Li diffusion coefficients in each electrolyte, finding slightly larger diffusivities in the linear carbonate EMC compared to the cyclic carbonate EC. The magnitude of the diffusion coefficient correlates with the strength of Li + solvation. Corresponding analysis for the PF $$\\bar{6}$$ anion shows greater diffusivity associated with a weakly bound, poorly defined first solvation shell. In conclusion, these results can be used to aid in the design of new electrolytes to improve Li-ion battery performance.« less

Incorporating Born solvation energy into the three-dimensional Poisson-Nernst-Planck model to study ion selectivity in KcsA K+ channels

NASA Astrophysics Data System (ADS)

Liu, Xuejiao; Lu, Benzhuo

2017-12-01

Potassium channels are much more permeable to potassium than sodium ions, although potassium ions are larger and both carry the same positive charge. This puzzle cannot be solved based on the traditional Poisson-Nernst-Planck (PNP) theory of electrodiffusion because the PNP model treats all ions as point charges, does not incorporate ion size information, and therefore cannot discriminate potassium from sodium ions. The PNP model can qualitatively capture some macroscopic properties of certain channel systems such as current-voltage characteristics, conductance rectification, and inverse membrane potential. However, the traditional PNP model is a continuum mean-field model and has no or underestimates the discrete ion effects, in particular the ion solvation or self-energy (which can be described by Born model). It is known that the dehydration effect (closely related to ion size) is crucial to selective permeation in potassium channels. Therefore, we incorporated Born solvation energy into the PNP model to account for ion hydration and dehydration effects when passing through inhomogeneous dielectric channel environments. A variational approach was adopted to derive a Born-energy-modified PNP (BPNP) model. The model was applied to study a cylindrical nanopore and a realistic KcsA channel, and three-dimensional finite element simulations were performed. The BPNP model can distinguish different ion species by ion radius and predict selectivity for K+ over Na+ in KcsA channels. Furthermore, ion current rectification in the KcsA channel was observed by both the PNP and BPNP models. The I -V curve of the BPNP model for the KcsA channel indicated an inward rectifier effect for K+ (rectification ratio of ˜3 /2 ) but indicated an outward rectifier effect for Na+ (rectification ratio of ˜1 /6 ) .

Numerical solution of boundary-integral equations for molecular electrostatics.

PubMed

Bardhan, Jaydeep P

2009-03-07

Numerous molecular processes, such as ion permeation through channel proteins, are governed by relatively small changes in energetics. As a result, theoretical investigations of these processes require accurate numerical methods. In the present paper, we evaluate the accuracy of two approaches to simulating boundary-integral equations for continuum models of the electrostatics of solvation. The analysis emphasizes boundary-element method simulations of the integral-equation formulation known as the apparent-surface-charge (ASC) method or polarizable-continuum model (PCM). In many numerical implementations of the ASC/PCM model, one forces the integral equation to be satisfied exactly at a set of discrete points on the boundary. We demonstrate in this paper that this approach to discretization, known as point collocation, is significantly less accurate than an alternative approach known as qualocation. Furthermore, the qualocation method offers this improvement in accuracy without increasing simulation time. Numerical examples demonstrate that electrostatic part of the solvation free energy, when calculated using the collocation and qualocation methods, can differ significantly; for a polypeptide, the answers can differ by as much as 10 kcal/mol (approximately 4% of the total electrostatic contribution to solvation). The applicability of the qualocation discretization to other integral-equation formulations is also discussed, and two equivalences between integral-equation methods are derived.

Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model.

PubMed

Muddana, Hari S; Gilson, Michael K

2012-06-12

The prediction of protein-ligand binding affinities is of central interest in computer-aided drug discovery, but it is still difficult to achieve a high degree of accuracy. Recent studies suggesting that available force fields may be a key source of error motivate the present study, which reports the first mining minima (M2) binding affinity calculations based on a quantum mechanical energy model, rather than an empirical force field. We apply a semi-empirical quantum-mechanical energy function, PM6-DH+, coupled with the COSMO solvation model, to 29 host-guest systems with a wide range of measured binding affinities. After correction for a systematic error, which appears to derive from the treatment of polar solvation, the computed absolute binding affinities agree well with experimental measurements, with a mean error 1.6 kcal/mol and a correlation coefficient of 0.91. These calculations also delineate the contributions of various energy components, including solute energy, configurational entropy, and solvation free energy, to the binding free energies of these host-guest complexes. Comparison with our previous calculations, which used empirical force fields, point to significant differences in both the energetic and entropic components of the binding free energy. The present study demonstrates successful combination of a quantum mechanical Hamiltonian with the M2 affinity method.

Teaching Ionic Solvation Structure with a Monte Carlo Liquid Simulation Program

NASA Astrophysics Data System (ADS)

Serrano, Agostinho; Santos, Flávia M. T.; Greca, Ileana M.

2004-09-01

It is shown how basic aspects of ionic solvation structure, a fundamental topic for understanding different concepts and levels of representations of chemical structure and transformation, can be taught with the help of a Monte Carlo simulation package for molecular liquids. By performing a pair distribution function analysis of the solvation of Na + , Cl , and Ar in water, it is shown that it is feasible to explain the differences in solvation for these differently charged solutes. Visual representations of the solvated ions can also be employed to help the teaching activity. This may serve as an introduction to the study of solvation structure in chemistry undergraduate courses. The advantages of using tested, up-to-date scientific simulation programs as the fundamental bricks in the construction of virtual laboratories is also discussed.

A fast method for the determination of fractional contributions to solvation in proteins

PubMed Central

Talavera, David; Morreale, Antonio; Meyer, Tim; Hospital, Adam; Ferrer-Costa, Carles; Gelpi, Josep Lluis; de la Cruz, Xavier; Soliva, Robert; Luque, F. Javier; Orozco, Modesto

2006-01-01

A fast method for the calculation of residue contributions to protein solvation is presented. The approach uses the exposed polar and apolar surface of protein residues and has been parametrized from the fractional contributions to solvation determined from linear response theory coupled to molecular dynamics simulations. Application of the method to a large subset of proteins taken from the Protein Data Bank allowed us to compute the expected fractional solvation of residues. This information is used to discuss when a residue or a group of residues presents an uncommon solvation profile. PMID:17001031

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.

Effect of Hydrofluoroether Cosolvent Addition on Li Solvation in Acetonitrile-Based Solvate Electrolytes and Its Influence on S Reduction in a Li–S Battery

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

See, Kimberly A.; Wu, Heng -Liang; Lau, Kah Chun

Li-S batteries are a promising next-generation battery technology. Due to the formation of soluble polysulfides during cell operation, the electrolyte composition of the cell plays an active role in directing the formation and speciation of the soluble lithium polysulfides. Recently, new classes of electrolytes termed "solvates" that contain stoichiometric quantities of salt and solvent and form a liquid at room temperature have been explored due to their sparingly solvating properties with respect to polysulfides. The viscosity of the solvate electrolytes is understandably high limiting their viability; however, hydrofluoroether cosolvents, thought to be inert to the solvate structure itself, can bemore » introduced to reduce viscosity and enhance diffusion. Nazar and co-workers previously reported that addition of 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether (TTE) to the LiTFSI in acetonitrile solvate, (MeCN) 2-LiTFSI, results in enhanced capacity retention compared to the neat solvate. Here, we evaluate the effect of TTE addition on both the electrochemical behavior of the Li-S cell and the solvation structure of the (MeCN) 2-LiTFSI electrolyte. Contrary to previous suggestions, Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that TTE coordinates to Li + at the expense of MeCN coordination, thereby producing a higher content of free MeCN, a good polysulfide solvent, in the electrolyte. Furthermore, the electrolytes containing a higher free MeCN content facilitate faster polysulfide formation kinetics during the electrochemical reduction of S in a Li-S cell likely as a result of the solvation power of the free MeCN.« less

Effect of Hydrofluoroether Cosolvent Addition on Li Solvation in Acetonitrile-Based Solvate Electrolytes and Its Influence on S Reduction in a Li–S Battery

DOE PAGES

See, Kimberly A.; Wu, Heng -Liang; Lau, Kah Chun; ...

2016-11-16

Li-S batteries are a promising next-generation battery technology. Due to the formation of soluble polysulfides during cell operation, the electrolyte composition of the cell plays an active role in directing the formation and speciation of the soluble lithium polysulfides. Recently, new classes of electrolytes termed "solvates" that contain stoichiometric quantities of salt and solvent and form a liquid at room temperature have been explored due to their sparingly solvating properties with respect to polysulfides. The viscosity of the solvate electrolytes is understandably high limiting their viability; however, hydrofluoroether cosolvents, thought to be inert to the solvate structure itself, can bemore » introduced to reduce viscosity and enhance diffusion. Nazar and co-workers previously reported that addition of 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether (TTE) to the LiTFSI in acetonitrile solvate, (MeCN) 2-LiTFSI, results in enhanced capacity retention compared to the neat solvate. Here, we evaluate the effect of TTE addition on both the electrochemical behavior of the Li-S cell and the solvation structure of the (MeCN) 2-LiTFSI electrolyte. Contrary to previous suggestions, Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that TTE coordinates to Li + at the expense of MeCN coordination, thereby producing a higher content of free MeCN, a good polysulfide solvent, in the electrolyte. Furthermore, the electrolytes containing a higher free MeCN content facilitate faster polysulfide formation kinetics during the electrochemical reduction of S in a Li-S cell likely as a result of the solvation power of the free MeCN.« less

Effect of Hydrofluoroether Cosolvent Addition on Li Solvation in Acetonitrile-Based Solvate Electrolytes and Its Influence on S Reduction in a Li-S Battery.

PubMed

See, Kimberly A; Wu, Heng-Liang; Lau, Kah Chun; Shin, Minjeong; Cheng, Lei; Balasubramanian, Mahalingam; Gallagher, Kevin G; Curtiss, Larry A; Gewirth, Andrew A

2016-12-21

Li-S batteries are a promising next-generation battery technology. Due to the formation of soluble polysulfides during cell operation, the electrolyte composition of the cell plays an active role in directing the formation and speciation of the soluble lithium polysulfides. Recently, new classes of electrolytes termed "solvates" that contain stoichiometric quantities of salt and solvent and form a liquid at room temperature have been explored due to their sparingly solvating properties with respect to polysulfides. The viscosity of the solvate electrolytes is understandably high limiting their viability; however, hydrofluoroether cosolvents, thought to be inert to the solvate structure itself, can be introduced to reduce viscosity and enhance diffusion. Nazar and co-workers previously reported that addition of 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether (TTE) to the LiTFSI in acetonitrile solvate, (MeCN) 2 -LiTFSI, results in enhanced capacity retention compared to the neat solvate. Here, we evaluate the effect of TTE addition on both the electrochemical behavior of the Li-S cell and the solvation structure of the (MeCN) 2 -LiTFSI electrolyte. Contrary to previous suggestions, Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that TTE coordinates to Li + at the expense of MeCN coordination, thereby producing a higher content of free MeCN, a good polysulfide solvent, in the electrolyte. The electrolytes containing a higher free MeCN content facilitate faster polysulfide formation kinetics during the electrochemical reduction of S in a Li-S cell likely as a result of the solvation power of the free MeCN.

Microsolvation of the potassium ion with aromatic rings: comparison between hexafluorobenzene and benzene.

PubMed

Marques, J M C; Llanio-Trujillo, J L; Albertí, M; Aguilar, A; Pirani, F

2013-08-22

We employ a recently developed methodology to study structural and energetic properties of the first solvation shells of the potassium ion in nonpolar environments due to aromatic rings, which is important to understand the selectivity of several biochemical phenomena. Our evolutionary algorithm is used in the global optimization study of clusters formed of K(+) solvated with hexafluorobenzene (HFBz) molecules. The global intermolecular interaction for these clusters has been decomposed in HFBz-HFBz and in K(+)-HFBz contributions, using a potential model based on different decompositions of the molecular polarizability of hexafluorobenzene. Putative global minimum structures of microsolvation clusters up to 21 hexafluorobenzene molecules were obtained and compared with the analogous K(+)-benzene clusters reported in our previous work (J. Phys. Chem. A 2012, 116, 4947-4956). We have found that both K(+)-(Bz)n and K(+)-(HFBz)n clusters show a strong magic number around the closure of the first solvation shell. Nonetheless, all K(+)-benzene clusters have essentially the same first solvation shell geometry with four solvent molecules around the ion, whereas the corresponding one for K(+)-(HFBz)n is completed with nine HFBz species, and its structural motif varies as n increases. This is attributed to the ion-solvent interaction that has a larger magnitude for K(+)-Bz than in the case of K(+)-HFBz. In addition, the ability of having more HFBz than Bz molecules around K(+) in the first solvation shell is intimately related to the inversion in the sign of the quadrupole moment of the two solvent species, which leads to a distinct ion-solvent geometry of approach.

In silico insights into the solvation characteristics of the ionic liquid 1-methyltriethoxy-3-ethylimidazolium acetate for cellulosic biomass.

PubMed

Schutt, Timothy C; Bharadwaj, Vivek S; Hegde, Govind A; Johns, Adam J; Mark Maupin, C

2016-09-14

Lignocellulosic biomass is a domestically grown, sustainable, and potentially carbon-neutral feedstock for the production of liquid fuels and other value added chemicals. This underutilized renewable feedstock has the potential to alleviate some of the current socio-economic dependence on foreign petroleum supplies while stimulating rural economies. Unfortunately, the potential of biomass has largely been underdeveloped due to the recalcitrant nature of lignocellulosic materials. Task-specific ionic liquids (ILs) have shown considerable promise as an alternative non-aqueous solvent for solvation and deconstruction of lignocellulose in the presence of metal chloride catalyst or enzymes. Recently it has been hypothesized that adding oxygen atoms to the tail of an imidazolium cation would alleviate some of the negative characteristics of the ILs by increasing mass transport properties, and decreasing IL deactivation of enzymes, while at the same time retaining favorable solvation characteristics for lignocellulose. Reported here are fully atomistic molecular dynamic simulations of 1-methyltriethoxy-3-ethylimidazolium acetate ([Me-(OEt)3-Et-IM(+)] [OAc(-)]) that elucidate promising molecular-level details pertaining to the solvation characteristics of model compounds of cellulose, and IL-induced side-chain and ring puckering conformations. It is found that the anion interactions with the saccharide induce alternate ring puckering conformations from those seen in aqueous environments (i.e.(1)C4), while the cation interactions are found to influence the conformation of the ω dihedral. These perturbations in saccharide structures are discussed in the context of their contribution to the disruption of hydrogen bonding in cellulosic architecture and their role in solvation.

How to study picosecond solvation dynamics using fluorescent probes with small Stokes shifts

NASA Astrophysics Data System (ADS)

Silori, Yogita; Dey, Shivalee; De, Arijit K.

2018-02-01

Xanthene dyes have wide ranging applications as fluorescent probes in analytical, biochemical and medical contexts. Being cationic/anionic in nature, the solvation dynamics of xanthene dyes confined within a negatively/positively charged interface are very interesting. Unfortunately, the floppy structure and small Stokes shift render any xanthene dye unsuitable for use as a solvation probe. Using di-sodium fluorescein, we present our work on the picosecond solvation dynamics of bulk and confined water (at pH = 9.2). We also propose a new methodology for studying picosecond solvation dynamics using any fluorescent dye with a small Stokes shift. We discuss how scattering contributions can be effectively removed, and propose an alternative way of defining zero time of solvation. Finally, we demonstrate the tuning location of the probe within confinement.

Controls over δ44/40Ca and Sr/Ca variations in coccoliths: New perspectives from laboratory cultures and cellular models

NASA Astrophysics Data System (ADS)

Mejía, Luz María; Paytan, Adina; Eisenhauer, Anton; Böhm, Florian; Kolevica, Ana; Bolton, Clara; Méndez-Vicente, Ana; Abrevaya, Lorena; Isensee, Kirsten; Stoll, Heather

2018-01-01

Coccoliths comprise a major fraction of the global carbonate sink. Therefore, changes in coccolithophores' Ca isotopic fractionation could affect seawater Ca isotopic composition, affecting interpretations of the global Ca cycle and related changes in seawater chemistry and climate. Despite this, a quantitative interpretation of coccolith Ca isotopic fractionation and a clear understanding of the mechanisms driving it are not yet available. Here, we address this gap in knowledge by developing a simple model (CaSri-Co) to track coccolith Ca isotopic fractionation during cellular Ca uptake and allocation to calcification. We then apply it to published and new δ 44 / 40 Ca and Sr/Ca data of cultured coccolithophores of the species Emiliania huxleyi and Gephyrocapsa oceanica. We identify changes in calcification rates, Ca retention efficiency and solvation-desolvation rates as major drivers of the Ca isotopic fractionation and Sr/Ca variations observed in cultures. Higher calcification rates, higher Ca retention efficiencies and lower solvation-desolvation rates increase both coccolith Ca isotopic fractionation and Sr/Ca. Coccolith Ca isotopic fractionation is most sensitive to changes in solvation-desolvation rates. Changes in Ca retention efficiency may be a major driver of coccolith Sr/Ca variations in cultures. We suggest that substantial changes in the water structure strength caused by past changes in temperature could have induced significant changes in coccolithophores' Ca isotopic fractionation, potentially having some influence on seawater Ca isotopic composition. We also suggest a potential effect on Ca isotopic fractionation via modification of the solvation environment through cellular exudates, a hypothesis that remains to be tested.

The effect of co-solvent addition on Li-solvation in solvate electrolytes in Li-S batteries

NASA Astrophysics Data System (ADS)

Lau, Kah Chun; See, Kimberly A.; Wu, Heng-Liang; Shin, Minjeong; Curtiss, Larry A.; Gewirth, Andrew A.

Li?S batteries are a promising next-generation battery technology. Due to the formation of soluble polysulfides during cell operation, the electrolyte composition of the cell plays an active role in directing the formation and speciation of the soluble lithium polysulfides. Recently, new classes of electrolytes termed `solvates' that contain stoichiometric quantities of salt and solvent and form a liquid at room temperature have been explored due to their sparingly solvating properties with respect to polysulfides. The viscosity of the solvate electrolytes is understandably high limiting their viability, however, cosolvents that thought to be inert to the solvate structure itself, can be introduced to reduce viscosity and enhance diffusion. In this work, Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations are used to study the unique solvation structure of 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether as co-solvent in solvate (MeCN)2?LiTFSI electrolyte that used in Li-S battery. The underlying design rules and implications to Li-S battery performance will be discussed. This work was supported as part of the Joint Center for Energy Storage Research, an Energy Innovation Hub funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences.

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.

Potentials of Mean Force With Ab Initio Mixed Hamiltonian Models of Solvation

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

Dupuis, Michel; Schenter, Gregory K.; Garrett, Bruce C.

2003-08-01

We give an account of a computationally tractable and efficient procedure for the calculation of potentials of mean force using mixed Hamiltonian models of electronic structure where quantum subsystems are described with computationally intensive ab initio wavefunctions. The mixed Hamiltonian is mapped into an all-classical Hamiltonian that is amenable to a thermodynamic perturbation treatment for the calculation of free energies. A small number of statistically uncorrelated (solute-solvent) configurations are selected from the Monte Carlo random walk generated with the all-classical Hamiltonian approximation. Those are used in the averaging of the free energy using the mixed quantum/classical Hamiltonian. The methodology ismore » illustrated for the micro-solvated SN2 substitution reaction of methyl chloride by hydroxide. We also compare the potential of mean force calculated with the above protocol with an approximate formalism, one in which the potential of mean force calculated with the all-classical Hamiltonian is simply added to the energy of the isolated (non-solvated) solute along the reaction path. Interestingly the latter approach is found to be in semi-quantitative agreement with the full mixed Hamiltonian approximation.« less

Hydrolysis of Nerve Agents by Model Nucleophiles: A Computational Study

PubMed Central

Beck, Jeremy M.

2008-01-01

Density functional theory calculations were employed to study the reaction of five nerve agents with model nucleophiles, including EtX− and EtXH (X = O, S, Se) for serine, cysteine and selenocysteine, respectively. Calculations at the B3LYP/6-311++G(2d,p) level of theory predict an exothermic reaction between ethoxide and all of the nerve agents studied. As compared to EtO− as a nucleophile, these reactions become ~30 kcal/mol more endothermic for EtS−, and by ~40 kcal/mol for EtSe−. The equivalent reactions with the neutral nucleophiles (EtXH) were more endothermic. The effect of solvation on the reaction thermochemistry was determined using a polarizable continuum model simulating the dielectric constant of chloroform. While there was a large exothermic shift for reactions involving charged nucleophiles with solvation modeling, the corresponding shift was minimal for the reaction with neutral nucleophiles. PMID:18538754

Modeling the Hydration Layer around Proteins: Applications to Small- and Wide-Angle X-Ray Scattering

PubMed Central

Virtanen, Jouko Juhani; Makowski, Lee; Sosnick, Tobin R.; Freed, Karl F.

2011-01-01

Small-/wide-angle x-ray scattering (SWAXS) experiments can aid in determining the structures of proteins and protein complexes, but success requires accurate computational treatment of solvation. We compare two methods by which to calculate SWAXS patterns. The first approach uses all-atom explicit-solvent molecular dynamics (MD) simulations. The second, far less computationally expensive method involves prediction of the hydration density around a protein using our new HyPred solvation model, which is applied without the need for additional MD simulations. The SWAXS patterns obtained from the HyPred model compare well to both experimental data and the patterns predicted by the MD simulations. Both approaches exhibit advantages over existing methods for analyzing SWAXS data. The close correspondence between calculated and observed SWAXS patterns provides strong experimental support for the description of hydration implicit in the HyPred model. PMID:22004761

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.

Theory of competitive solvation of polymers by two solvents and entropy-enthalpy compensation in the solvation free energy upon dilution with the second solvent.

PubMed

Dudowicz, Jacek; Freed, Karl F; Douglas, Jack F

2015-06-07

We develop a statistical mechanical lattice theory for polymer solvation by a pair of relatively low molar mass solvents that compete for binding to the polymer backbone. A theory for the equilibrium mixture of solvated polymer clusters {AiBCj} and free unassociated molecules A, B, and C is formulated in the spirit of Flory-Huggins mean-field approximation. This theoretical framework enables us to derive expressions for the boundaries for phase stability (spinodals) and other basic properties of these polymer solutions: the internal energy U, entropy S, specific heat CV, extent of solvation Φsolv, average degree of solvation 〈Nsolv〉, and second osmotic virial coefficient B2 as functions of temperature and the composition of the mixture. Our theory predicts many new phenomena, but the current paper applies the theory to describe the entropy-enthalpy compensation in the free energy of polymer solvation, a phenomenon observed for many years without theoretical explanation and with significant relevance to liquid chromatography and other polymer separation methods.

Effect of the Hydrofluoroether Cosolvent Structure in Acetonitrile-Based Solvate Electrolytes on the Li+ Solvation Structure and Li-S Battery Performance.

PubMed

Shin, Minjeong; Wu, Heng-Liang; Narayanan, Badri; See, Kimberly A; Assary, Rajeev S; Zhu, Lingyang; Haasch, Richard T; Zhang, Shuo; Zhang, Zhengcheng; Curtiss, Larry A; Gewirth, Andrew A

2017-11-15

We evaluate hydrofluoroether (HFE) cosolvents with varying degrees of fluorination in the acetonitrile-based solvate electrolyte to determine the effect of the HFE structure on the electrochemical performance of the Li-S battery. Solvates or sparingly solvating electrolytes are an interesting electrolyte choice for the Li-S battery due to their low polysulfide solubility. The solvate electrolyte with a stoichiometric ratio of LiTFSI salt in acetonitrile, (MeCN) 2 -LiTFSI, exhibits limited polysulfide solubility due to the high concentration of LiTFSI. We demonstrate that the addition of highly fluorinated HFEs to the solvate yields better capacity retention compared to that of less fluorinated HFE cosolvents. Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that HFEs exhibiting a higher degree of fluorination coordinate to Li + at the expense of MeCN coordination, resulting in higher free MeCN content in solution. However, the polysulfide solubility remains low, and no crossover of polysulfides from the S cathode to the Li anode is observed.

Effect of the Hydrofluoroether Cosolvent Structure in Acetonitrile-Based Solvate Electrolytes on the Li+ Solvation Structure and Li-S Battery Performance.

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

Shin, Minjeong; Wu, Heng-Liang; Narayanan, Badri

We evaluate hydrofluoroether (HFE) cosolvents with varying degrees of fluorination in the acetonitrile-based solvate electrolyte to determine the effect of the HFE structure on the electrochemical performance of the Li-S battery. Solvates or sparingly solvating electrolytes are an interesting electrolyte choice for the Li-S battery due to their low polysulfide solubility. The solvate electrolyte with a stoichiometric ratio of LiTFSI salt in acetonitrile, (MeCN)(2)-LiTFSI, exhibits limited polysulfide solubility due to the high concentration of LiTFSI. We demonstrate that the addition of highly fluorinated HFEs to the solvate yields better capacity retention compared to that of less fluorinated HFE cosolvents. Ramanmore » and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that HFEs exhibiting a higher degree of fluorination coordinate to Li+ at the expense of MeCN coordination, resulting in higher free MeCN content in solution. However, the polysulfide solubility remains low, and no crossover of polysulfides from the S cathode to the Li anode is observed.« less

Combining frozen-density embedding with the conductor-like screening model using Lagrangian techniques for response properties.

PubMed

Schieschke, Nils; Di Remigio, Roberto; Frediani, Luca; Heuser, Johannes; Höfener, Sebastian

2017-07-15

We present the explicit derivation of an approach to the multiscale description of molecules in complex environments that combines frozen-density embedding (FDE) with continuum solvation models, in particular the conductor-like screening model (COSMO). FDE provides an explicit atomistic description of molecule-environment interactions at reduced computational cost, while the outer continuum layer accounts for the effect of long-range isotropic electrostatic interactions. Our treatment is based on a variational Lagrangian framework, enabling rigorous derivations of ground- and excited-state response properties. As an example of the flexibility of the theoretical framework, we derive and discuss FDE + COSMO analytical molecular gradients for excited states within the Tamm-Dancoff approximation (TDA) and for ground states within second-order Møller-Plesset perturbation theory (MP2) and a second-order approximate coupled cluster with singles and doubles (CC2). It is shown how this method can be used to describe vertical electronic excitation (VEE) energies and Stokes shifts for uracil in water and carbostyril in dimethyl sulfoxide (DMSO), respectively. In addition, VEEs for some simplified protein models are computed, illustrating the performance of this method when applied to larger systems. The interaction terms between the FDE subsystem densities and the continuum can influence excitation energies up to 0.3 eV and, thus, cannot be neglected for general applications. We find that the net influence of the continuum in presence of the first FDE shell on the excitation energy amounts to about 0.05 eV for the cases investigated. The present work is an important step toward rigorously derived ab initio multilayer and multiscale modeling approaches. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Quantum mechanical/molecular mechanical/continuum style solvation model: Second order Møller-Plesset perturbation theory

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

Thellamurege, Nandun M.; Si, Dejun; Cui, Fengchao

A combined quantum mechanical/molecular mechanical/continuum (QM/MM/C) style second order Møller-Plesset perturbation theory (MP2) method that incorporates induced dipole polarizable force field and induced surface charge continuum solvation model is established. The Z-vector method is modified to include induced dipoles and induced surface charges to determine the MP2 response density matrix, which can be used to evaluate MP2 properties. In particular, analytic nuclear gradient is derived and implemented for this method. Using the Assisted Model Building with Energy Refinement induced dipole polarizable protein force field, the QM/MM/C style MP2 method is used to study the hydrogen bonding distances and strengths ofmore » the photoactive yellow protein chromopore in the wild type and the Glu46Gln mutant.« less

Contact Forces between Single Metal Oxide Nanoparticles in Gas-Phase Applications and Processes.

PubMed

Salameh, Samir; van der Veen, Monique A; Kappl, Michael; van Ommen, J Ruud

2017-03-14

In this work we present a comprehensive experimental study to determine the contact forces between individual metal oxide nanoparticles in the gas-phase using atomic force microscopy. In addition, we determined the amount of physisorbed water for each type of particle surface. By comparing our results with mathematical models of the interaction forces, we could demonstrate that classical continuum models of van der Waals and capillary forces alone cannot sufficiently describe the experimental findings. Rather, the discrete nature of the molecules has to be considered, which leads to ordering at the interface and the occurrence of solvation forces. We demonstrate that inclusion of solvation forces in the model leads to quantitative agreement with experimental data and that tuning of the molecular order by addition of isopropanol vapor allows us to control the interaction forces between the nanoparticles.

Using low-field NMR to infer the physical properties of glassy oligosaccharide/water mixtures.

PubMed

Aeberhardt, Kasia; Bui, Quang D; Normand, Valéry

2007-03-01

Low-field NMR (LF-NMR) is usually used as an analytical technique, for instance, to determine water and oil contents. For this application, no attempt is made to understand the physical origin of the data. Here we build a physical model to explain the five fit parameters of the conventional free induction decay (FID) for glassy oligosaccharide/water mixtures. The amplitudes of the signals from low-mobility and high-mobility protons correspond to the density of oligosaccharide protons and water protons, respectively. The relaxation time of the high-mobility protons is described using a statistical model for the probability that oligosaccharide hydroxyl groups form multiple hydrogen bonds. The variation of energy of the hydrogen bond is calculated from the average bond distance and the average angle contribution. Applying the model to experimental data shows that hydrogen atoms screen the water oxygen atoms when two water molecules solvate a single hydroxyl group. Furthermore, the relaxation time of the oligosaccharide protons is independent of its molecular weight and the water content. Finally, inversion of the FID using the inverse Laplace transform gives the continuous spectrum of relaxation times, which is a fingerprint of the oligosaccharide.

25 Mg NMR and computational modeling studies of the solvation structures and molecular dynamics in magnesium based liquid electrolytes

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

Hu, Jian Zhi; Rajput, Nav Nidhi; Wan, Chuan

There is increasing evidence that the solvation structure of the active components in a liquid electrolyte solution strongly impacts the performance in electrochemical applications. In this work, the nanoscale solvation structures and dynamics of Mg(BH4)2 and Mg(TFSI)2 dissolved in diglyme (DGM) at various concentrations and ratios of Mg(BH4)2/Mg(TFSI)2 were investigated using a combination of natural abundance 25Mg NMR, quantum chemistry calculations of 25Mg NMR chemical shifts, classical molecular dynamics (MD) calculations, and electrochemical performance tests. By mixing two competing Mg salts, we were able to reduce the strong covalent interactions between Mg2+ and BH4– anions. A small increase is observedmore » in the coordination number of Mg-TFSI and a significant increase in the interaction of Mg2+ ions with glymes. Through a combination of NMR, DFT and MD simulations, various stable species around 1 nm in size were detected in the mixed salt solution, which play key roles in the enhanced electrochemical performance of the mixed electrolyte. It is established that for the neat Mg(TFSI)2 in DGM electrolyte at dilute concentrations the TFSI- is fully dissociated from Mg2+. At higher concentrations, Mg2+ and TFSI- are only partially dissociated as contact ion pairs are formed. In contrast, at 0.01 M Mg(BH4)2 (saturated concentration) in DGM, the first solvation shell of a Mg2+ ion contains two BH4- anions and one DGM molecule, while the second solvation shell consists of five to six DGM molecules. An exchange mechanism between the solvation structures in the combined electrolyte containing both Mg(BH4)2 and Mg(TFSI)2 in DGM was found to result in the observation of a single 25Mg NMR peak. This exchange is responsible for an increase in uncoordinated anions, as well as improved stability and ionic conductivity as compared to single anion solution. Solvent molecule rearrangement and direct Mg-ion exchange between the basic solvation structures are hypothesized as likely reasons for the exchange. We elucidate that the solvent rearrangement is energetically much more favorable than direct Mg-ion hopping and is thus suggested as the dominant exchange mechanism.« less

Extraction of tryptophan with ionic liquids studied with molecular dynamics simulations.

PubMed

Seduraman, Abirami; Wu, Ping; Klähn, Marco

2012-01-12

Extraction of amino acids from aqueous solutions with ionic liquids (ILs) in biphasic systems is analyzed with molecular dynamics (MD) simulations. Extraction of tryptophan (TRP) with the imidazolium-based ILs [C(4)mim][PF(6)], [C(8)mim][PF(6)], and [C(8)mim][BF(4)] are considered as model cases. Solvation free energies of TRP are calculated with MD simulations and thermodynamic integration in combination with an empirical force field, whose parametrization is based on the liquid-phase charge distribution of the ILs. Calculated solvation free energies reproduce successfully all observed experimental trends according to the previously reported partition of TRP between water and IL phases. Water is present in ILs as a cosolvent, due to direct contact with the aqueous phase during extraction, and is found to play a major role in the extraction of TRP. Water improves solvation of cationic TRP by 7.8 and 5.1 kcal/mol in [C(4)mim][PF(6)] and [C(8)mim][PF(6)], respectively, which is in the case of [C(4)mim][PF(6)] sufficient to extract TRP. Extraction in [C(8)mim][PF(6)] is not feasible, since the hydrophobic octyl groups of the cations limit the water concentration in the IL. The solvation of cationic TRP is 2.4 kcal/mol less favorable in [C(8)mim][PF(6)] than in [C(4)mim][PF(6)]. Water improves the solvation of TRP in ILs mostly through dipole-dipole interactions with the polar backbone of TRP. Extraction is most efficient with [C(8)mim][BF(4)], where hydrophilic BF(4)(-) anions substantially increase the water concentration in the IL. Additionally, stronger direct electrostatic interactions of TRP with BF(4)(-) anions improve its solvation in the IL further. The solvation of cationic TRP in [C(8)mim][BF(4)] is 3.4 kcal/mol more favorable than in [C(8)mim][PF(6)]. Overall, the extractive power of the ILs correlates with the water saturation concentration of the IL phase, which in turn is determined by the hydrophilicity of the constituting ions. The results of this work identify relations between the extraction performance of ILs and the basic chemical properties of the ions, which provide guidelines that could contribute to the design of improved novel ILs for amino acid extraction.

25Mg NMR and Computational Modeling Studies of the Solvation Structures and Molecular Dynamics in Magnesium Based Liquid Electrolytes

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

Hu, Jian Z.; Rajput, Nav Nidhi; Wan, Chuan

There is increasing evidence that the solvation structure of the active components in a liquid electrolyte solution strongly impacts the performance in electrochemical applications. In this work, the nanoscale solvation structures and dynamics of Mg(BH4)2 and Mg(TFSI)2 dissolved in diglyme (DGM) at various concentrations and ratios of Mg(BH4)2/Mg(TFSI)2 were investigated using a combination of natural abundance 25Mg NMR, quantum chemistry calculations of 25Mg NMR chemical shifts, classical molecular dynamics (MD) calculations, and electrochemical performance tests. By mixing two competing Mg salts, we were able to reduce the strong covalent interactions between Mg2+ and BH4– anions. A small increase is observedmore » in the coordination number of Mg-TFSI and a significant increase in the interaction of Mg2+ ions with glymes. Through a combination of NMR, DFT and MD simulations, various stable species around 1 nm in size were detected in the mixed salt solution, which play key roles in the enhanced electrochemical performance of the mixed electrolyte. It is established that for the neat Mg(TFSI)2 in DGM electrolyte at dilute concentrations the TFSI- is fully dissociated from Mg2+. At higher concentrations, Mg2+ and TFSI- are only partially dissociated as contact ion pairs are formed. In contrast, at 0.01 M Mg(BH4)2 (saturated concentration) in DGM, the first solvation shell of a Mg2+ ion contains two BH4- anions and one DGM molecule, while the second solvation shell consists of five to six DGM molecules. An exchange mechanism between the solvation structures in the combined electrolyte containing both Mg(BH4)2 and Mg(TFSI)2 in DGM was found to result in the observation of a single 25Mg NMR peak. This exchange is responsible for an increase in uncoordinated anions, as well as improved stability and ionic conductivity as compared to single anion solution. Solvent molecule rearrangement and direct Mg-ion exchange between the basic solvation structures are hypothesized as likely reasons for the exchange. We elucidate that the solvent rearrangement is energetically much more favorable than direct Mg-ion hopping and is thus suggested as the dominant exchange mechanism.« less

Impact of various lipophilic substituents on ruthenium(II), rhodium(III) and iridium(III) salicylaldimine-based complexes: synthesis, in vitro cytotoxicity studies and DNA interactions.

PubMed

Cassells, Irwin; Stringer, Tameryn; Hutton, Alan T; Prince, Sharon; Smith, Gregory S

2018-05-30

A series of bidentate salicylaldimine ligands was prepared and reacted with either [RuCl(µ-Cl)(p-cymene)] 2 , [RhCl(µ-Cl)(Cp*)] 2 or [IrCl(µ-Cl)(Cp*)] 2 . All of the compounds were characterised using an array of spectroscopic and analytical techniques, namely, nuclear magnetic resonance (NMR) spectroscopy, infrared (IR) spectroscopy and mass spectrometry. Single crystal X-ray diffraction (XRD) was used to confirm the bidentate coordination mode of the salicylaldimine ligand to the metal centre. The platinum group metal (PGM) complexes were screened against the MCF7 breast cancer cell line. The ruthenium and iridium salicylaldimine complexes showed comparable or greater cytotoxicity than cisplatin against the MCF7 cancer cells, as well as greater cytotoxicity than their rhodium counterparts. Three of the salicylaldimine complexes showed potent activity in the range 18-21 µM. Two of these complexes had a greater affinity for cancerous cells than for CHO non-cancerous cells (SI > 4). Preliminary mechanistic studies suggest that the ruthenium complexes undergo solvation prior to 5'-GMP binding, whereas the iridium complexes were inert to the solvation process.

Solvent friction effects propagate over the entire protein molecule through low-frequency collective modes.

PubMed

Moritsugu, Kei; Kidera, Akinori; Smith, Jeremy C

2014-07-24

Protein solvation dynamics has been investigated using atom-dependent Langevin friction coefficients derived directly from molecular dynamics (MD) simulations. To determine the effect of solvation on the atomic friction coefficients, solution and vacuum MD simulations were performed for lysozyme and staphylococcal nuclease and analyzed by Langevin mode analysis. The coefficients thus derived are roughly correlated with the atomic solvent-accessible surface area (ASA), as expected from the fact that friction occurs as the result of collisions with solvent molecules. However, a considerable number of atoms with higher friction coefficients are found inside the core region. Hence, the influence of solvent friction propagates into the protein core. The internal coefficients have large contributions from the low-frequency modes, yielding a simple picture of the surface-to-core long-range damping via solvation governed by collective low-frequency modes. To make use of these findings in implicit-solvent modeling, we compare the all-atom friction results with those obtained using Langevin dynamics (LD) with two empirical representations: the constant-friction and the ASA-dependent (Pastor-Karplus) friction models. The constant-friction model overestimates the core and underestimates the surface damping whereas the ASA-dependent friction model, which damps protein atoms only on the solvent-accessible surface, reproduces well the friction coefficients for both the surface and core regions observed in the explicit-solvent MD simulations. Therefore, in LD simulation, the solvent friction coefficients should be imposed only on the protein surface.

Electron detachment energies in high-symmetry alkali halide solvated-electron anions

NASA Astrophysics Data System (ADS)

Anusiewicz, Iwona; Berdys, Joanna; Simons, Jack; Skurski, Piotr

2003-07-01

We decompose the vertical electron detachment energies (VDEs) in solvated-electron clusters of alkali halides in terms of (i) an electrostatic contribution that correlates with the dipole moment (μ) of the individual alkali halide molecule and (ii) a relaxation component that is related to the polarizability (α) of the alkali halide molecule. Detailed numerical ab initio results for twelve species (MX)n- (M=Li,Na; X=F,Cl,Br; n=2,3) are used to construct an interpolation model that relates the clusters' VDEs to their μ and α values as well as a cluster size parameter r that we show is closely related to the alkali cation's ionic radius. The interpolation formula is then tested by applying it to predict the VDEs of four systems [i.e., (KF)2-, (KF)3-, (KCl)2-, and (KCl)3-] that were not used in determining the parameters of the model. The average difference between the model's predicted VDEs and the ab initio calculated electron binding energies is less than 4% (for the twelve species studied). It is concluded that one can easily estimate the VDE of a given high-symmetry solvated electron system by employing the model put forth here if the α, μ and cation ionic radii are known. Alternatively, if VDEs are measured for an alkali halide cluster and the α and μ values are known, one can estimate the r parameter, which, in turn, determines the "size" of the cluster anion.

Solvent friction effects propagate over the entire protein molecule through low-frequency collective modes

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

Moritsugu, Kei; Kidera, Akinori; Smith, Jeremy C.

2014-06-25

Protein solvation dynamics has been investigated using atom-dependent Langevin friction coefficients derived directly from molecular dynamics (MD) simulations. To determine the effect of solvation on the atomic friction coefficients, solution and vacuum MD simulations were performed for lysozyme and staphylococcal nuclease and analyzed by Langevin mode analysis. The coefficients thus derived are roughly correlated with the atomic solvent-accessible surface area (ASA), as expected from the fact that friction occurs as the result of collisions with solvent molecules. However, a considerable number of atoms with higher friction coefficients are found inside the core region. Hence, the influence of solvent friction propagatesmore » into the protein core. The internal coefficients have large contributions from the low-frequency modes, yielding a simple picture of the surface-to-core long-range damping via solvation governed by collective low-frequency modes. To make use of these findings in implicit-solvent modeling, we compare the all-atom friction results with those obtained using Langevin dynamics (LD) with two empirical representations: the constant-friction and the ASA-dependent (Pastor Karplus) friction models. The constant-friction model overestimates the core and underestimates the surface damping whereas the ASA-dependent friction model, which damps protein atoms only on the solvent-accessible surface, reproduces well the friction coefficients for both the surface and core regions observed in the explicit-solvent MD simulations. Furthermore, in LD simulation, the solvent friction coefficients should be imposed only on the protein surface.« less

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

PubMed

Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

2018-01-09

We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

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

PubMed

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

2011-05-26

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

On the solvation of hydronium by carbon dioxide: Structural and infrared spectroscopic study of (H3O+)(CO2)n

NASA Astrophysics Data System (ADS)

Yang, Jianpeng; Kong, Xiangtao; Jiang, Ling

2018-02-01

Hydronium (H3O+) is the smallest member of protonated water. In this work, we use quantum chemical calculations to explore the solvation of H3O+ by adding one CO2 molecule at a time. The effect of stepwise solvation on infrared spectroscopy, structure, and energetics has been systematically studied. It has been found that the first solvation shell of H3O+ is completed at n = 6. Besides the hydrogen-bond interaction, the CCO2-OCO2 intermolecular interaction is also responsible for the stabilization of the larger clusters. The transfer of the proton from H3O+ onto CO2 with the formation of the OCOH+ moiety is not observed in the early stage of solvation process. Calculated IR spectra suggest that vibrational frequencies of H-bonded Osbnd H stretching would afford a sensitive probe for exploring the early stage solvation of hydronium by carbon dioxide. IR spectra for the (H3O+)(CO2)n (n = 1-7) clusters could be measured by the infrared photodissociation spectroscopic technique and thus provide a vivid physical picture about how carbon dioxide solvates the hydronium.

Crystallization of toxic glycol solvates of rifampin from glycerin and propylene glycol contaminated with ethylene glycol or diethylene glycol.

PubMed

de Villiers, Melgardt M; Caira, Mino R; Li, Jinjing; Strydom, Schalk J; Bourne, Susan A; Liebenberg, Wilna

2011-06-06

This study was initiated when it was suspected that syringe blockage experienced upon administration of a compounded rifampin suspension was caused by the recrystallization of toxic glycol solvates of the drug. Single crystal X-ray structure analysis, powder X-ray diffraction, thermal analysis and gas chromatography were used to identify the ethylene glycol in the solvate crystals recovered from the suspension. Controlled crystallization and solubility studies were used to determine the ease with which toxic glycol solvates crystallized from glycerin and propylene glycol contaminated with either ethylene or diethylene glycol. The single crystal structures of two distinct ethylene glycol solvates of rifampin were solved while thermal analysis, GC analysis and solubility studies confirmed that diethylene glycol solvates of the drug also crystallized. Controlled crystallization studies showed that crystallization of the rifampin solvates from glycerin and propylene glycol depended on the level of contamination and changes in the solubility of the drug in the contaminated solvents. Although the exact source of the ethylene glycol found in the compounded rifampin suspension is not known, the results of this study show how important it is to ensure that the drug and excipients comply with pharmacopeial or FDA standards.

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.

Interactions of S-peptide analogue in aqueous urea and trimethylamine-N-oxide solutions: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Sarma, Rahul; Paul, Sandip

2013-07-01

The ability of the osmolyte, trimethylamine-N-oxide (TMAO), to protect proteins from deleterious effect of urea, another commonly available osmolyte, is well-established. However, the molecular mechanism of this counteraction is not understood yet. To provide a molecular level understanding of how TMAO protects proteins in highly concentrated urea solution, we report here molecular dynamics simulation results of a 15-residue model peptide in two different conformations: helix and extended. For both conformations, simulations are carried out in pure water as well as in binary and ternary aqueous solutions of urea and TMAO. Analysis of solvation characteristics reveals direct interactions of urea and TMAO with peptide residues. However, the number of TMAO molecules that enter in the first solvation shell of the peptide is significantly lower than that of urea, and, unlike water and urea, TMAO shows its inability to form hydrogen bond with backbone oxygen and negatively charged sidechains. Preferential accumulation of urea near the peptide surface and preferential exclusion of TMAO from the peptide surface are observed. Inclusion of osmolytes in the peptide solvation shell leads to dehydration of the peptide in binary and ternary solutions of urea and TMAO. Solvation of peptide residues are investigated more closely by calculating the number of hydrogen bonds between the peptide and solution species. It is found that number of hydrogen bonds formed by the peptide with solution species increases in binary urea solution (relative to pure water) and this relative enhancement in hydrogen bond number reduces upon addition of TMAO. Our simulation results also suggest that, in the ternary solution, the peptide solvation layer is better mixed in terms of water and urea as compared to binary urea solution. Implications of the results for counteraction mechanism of TMAO are discussed.

Hydrophobic Solvation: Aqueous Methane Solutions

ERIC Educational Resources Information Center

Konrod, Oliver; Lankau, Timm

2007-01-01

A basic introduction to concept of a solvation shell around an apolar solute as well as its detection is presented. The hydrophobic solvation of toluene is found to be a good teaching example which connects macroscopic, phenomenological thermodynamic results with an atomistic point of view.

Role of Dispersive Fluorous Interaction in the Solvation Dynamics of the Perfluoro Group Containing Molecules.

PubMed

Mondal, Saptarsi; Chaterjee, Soumit; Halder, Ritaban; Jana, Biman; Singh, Prashant Chandra

2017-08-17

Perfluoro group containing molecules possess an important self-aggregation property through the fluorous (F···F) interaction which makes them useful for diverse applications such as medicinal chemistry, separation techniques, polymer technology, and biology. In this article, we have investigated the solvation dynamics of coumarin-153 (C153) and coumarin-6H (C6H) in ethanol (ETH), 2-fluoroethanol (MFE), and 2,2,2-trifluoroethanol (TFE) using the femtosecond upconversion technique and molecular dynamics (MD) simulation to understand the role of fluorous interaction between the solute and solvent molecules in the solvation dynamics of perfluoro group containing molecules. The femtosecond upconversion data show that the time scales of solvation dynamics of C6H in ETH, MFE, and TFE are approximately the same whereas the solvation dynamics of C153 in TFE is slow as compared to that of ETH and MFE. It has also been observed that the time scale of solvation dynamics of C6H in ETH and MFE is higher than that of C153 in the same solvents. MD simulation results show a qualitative agreement with the experimental data in terms of the time scale of the slow components of the solvation for all the systems. The experimental and simulation studies combined lead to the conclusion that the solvation dynamics of C6H in all solvents as well as C153 in ETH and MFE is mostly governed by the charge distribution of ester moieties (C═O and O) of dye molecules whereas the solvation of C153 in TFE is predominantly due to the dispersive fluorous interaction (F···F) between the perfluoro groups of the C153 and solvent molecules.

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.

Impact of Water-Dilution on the Solvation Properties of the Ionic Liquid 1-Methyltriethoxy-3-ethylimidazolium Acetate for Model Biomass Molecules.

PubMed

Schutt, Timothy C; Hegde, Govind A; Bharadwaj, Vivek S; Johns, Adam J; Maupin, C Mark

2017-02-02

Many studies have suggested that the processing of lignocellulosic biomass could provide a renewable feedstock to supplant much of the current demand on petroleum sources. Currently, alkyl imidazolium-based ionic liquids (ILs) have shown considerable promise in the pretreatment, solvation, and hydrolysis of lignocellulosic materials although their high cost and unfavorable viscosity has limited their widespread use. Functionalizing these ILs with an oligo(ethoxy) tail has previously been shown through experiment to decrease the IL's viscosity resulting in enhanced mass transport characteristics, in addition to other favorable traits including decreased inhibition of some enzymes. Additionally, the use of cosolvents to mitigate the cost and unfavorable traits of ILs is an area of growing interest with particular attention on water as the presence of water in biomass processes is inevitable. Through the use of biased and unbiased molecular dynamics (MD) simulations, this study provides a molecular-level perspective of the various solvent-solvent and solvent-solute interactions in binary mixtures of water and 1-methyltriethoxy-3-ethylimidazolium acetate ([Me-(OEt) 3 -Et-IM + ] [OAc - ]) in the presence of model cellulose compounds (i.e., glucose and cellobiose). It is observed that at ∼75% w/w IL and water a transition in the nanostructure of the solvent occurs between water-like and IL-like solvation characteristics. It is shown that H-bonding interactions between the anion and water are a major driving force that significantly impacts the solvent properties of the IL as well as conformational preferences of the cellulosic model compound. In addition, it is found that the oligo(ethoxy) cation tail is responsible for the reduction in the propensity for tail aggregation as compared to alkyl tails of similar length, which, combined with increased ionic shielding, results in increased diffusion and enhanced water-like solvation characteristics.

The small impact of various partial charge distributions in ground and excited state on the computational Stokes shift of 1-methyl-6-oxyquinolinium betaine in diverse water models

NASA Astrophysics Data System (ADS)

Heid, Esther; Harringer, Sophia; Schröder, Christian

2016-10-01

The influence of the partial charge distribution obtained from quantum mechanics of the solute 1-methyl-6-oxyquinolinium betaine in the ground- and first excited state on the time-dependent Stokes shift is studied via molecular dynamics computer simulation. Furthermore, the effect of the employed solvent model — here the non-polarizable SPC, TIP4P and TIP4P/2005 and the polarizable SWM4 water model — on the solvation dynamics of the system is investigated. The use of different functionals and calculation methods influences the partial charge distribution and the magnitude of the dipole moment of the solute, but not the orientation of the dipole moment. Simulations based on the calculated charge distributions show nearly the same relaxation behavior. Approximating the whole solute molecule by a dipole results in the same relaxation behavior, but lower solvation energies, indicating that the time scale of the Stokes shift does not depend on peculiarities of the solute. However, the SPC and TIP4P water models show too fast dynamics which can be ascribed to a too large diffusion coefficient and too low viscosity. The calculated diffusion coefficient and viscosity for the SWM4 and TIP4P/2005 models coincide well with experimental values and the corresponding relaxation behavior is comparable to experimental values. Furthermore we found that for a quantitative description of the Stokes shift of the applied system at least two solvation shells around the solute have to be taken into account.

Crystal growth, structure and morphology of hydrocortisone methanol solvate

NASA Astrophysics Data System (ADS)

Chen, Jianxin; Wang, Jiangkang; Zhang, Ying; Wu, Hong; Chen, Wei; Guo, Zhichao

2004-04-01

Hydrocortisone (HC), an important grucocorticoid, was crystallized from methanol solvent in the form of its methanol solvate. Its crystal structure belongs to orthorhombic, space group P2 12 12 1, with the unit cell parameters a=7.712(3) Å, b=14.392(5) Å, c=18.408(6) Å, Z=4. The methanol takes part in intermolecular hydrogen bonding, so if we change the solvent, the crystal habit of HC maybe different. The long parallelepiped morphology was also predicted by Cerius 2TM simulation program. The influence of intermolecular interaction was taken into account in the attachment energy model. The morphology calculation performed on the potential energy minimized model using a generic DREIDING 2.21 force field and developed minimization protocol with derived partial charges fits the experimental crystal shape well.

Investigating the Effect of Charge Hydration Asymmetry and Incorporating it in Continuum Solvation Framework

NASA Astrophysics Data System (ADS)

Mukhopadhyay, Abhishek

One of the essential requirements of biomolecular modeling is an accurate description of water as a solvent. The challenge is to make this description computationally facile - reasonably fast, simple, robust and easy to incorporate into existing software packages, yet accurate. The most rigorous procedure to model the effect of aqueous solvent is to explicitly model every water molecule in the system. For many practical applications, this approach is computationally too intense, as the number of required water atoms is on an average at least one order of magnitude larger than the number of atoms of the molecule of interest. Implicit solvent models, in which solvent molecules are replaced by a continuous dielectric, have become a popular alternative to explicit solvent methods. However, implicit solvation models often lack various microscopic details which are crucial for accuracy. One such missing effect that is currently missing from popular implicit models is the so called effect of charge hydration asymmetry (CHA). The missing effect of charge hydration asymmetry - the asymmetric response of water upon the sign of solute charge - manifests a characteristic, strong dependence of solvation free energies on the sign of solute charge. Here, we incorporate this missing effect into the continuum solvation framework via the conceptually simplest Born equation and also in the generalized Born model. We identify the key electric multipole moments of model water molecules critical for the various degrees of CHA effect observed in studies based on molecular dynamics simulations using different rigid water models. We then use this gained insight to incorporate this effect first into the Born model and then into the generalized Born model. The proposed framework significantly improves accuracy of the hydration free energy estimates tested on a comprehensive set of varied molecular solutes - monovalent and divalent ions, small drug-like molecules, charged and uncharged amino acid dipeptides, and small proteins. We finally develop a methodology to resolve the issue with unacceptably large uncertainty that stems from a variety of fundamental and technical difficulties in experimental quantification of CHA from charged solutes. Using the proposed corrections in the continuum framework, we untangle the charge-asymmetric response of water from its symmetric response, and further circumvent the difficulties by extracting accurate estimate propensity of water to cause CHA from accurate experimental hydration free energies of neutral polar molecules. We show that the asymmetry in water's response is strong, about 50% of the symmetric response.

Structure and Dynamics of Highly PEG-ylated Sterically Stabilized Micelles in Aqueous Media

PubMed Central

Vuković, Lela; Khatib, Fatima A.; Drake, Stephanie P.; Madriaga, Antonett; Brandenburg, Kenneth S.; Král, Petr; Onyuksel, Hayat

2011-01-01

Molecular assemblies of highly PEG-ylated phospholipids are important in many biomedical applications. We study sterically stabilized micelles (SSM) of self-assembled DSPE-PEG2000 in pure water and isotonic HEPES buffered saline solution. The observed SSM sizes of 2 – 15 nm largely depend on the solvent and the lipid concentration used. The critical micelle concentration (CMC) of DSPE-PEG2000 is ≈ 10 times higher in water than in buffer and the viscosity of the dispersion dramatically increases with the lipid concentration. To explain the experimentally observed results, we perform atomistic molecular dynamics simulations of the solvated SSM. Our modeling reveal that the observed assemblies have very different aggregation numbers of Nagg ≈ 90 (saline solution) and Nagg < 8 (water), due to very different screening of their charged −PO4− groups. We also demonstrate that the micelle cores can inflate and their corona highly fluctuate, allowing thus storage and delivery of molecules with different chemistry. PMID:21780810

Structure and dynamics of highly PEG-ylated sterically stabilized micelles in aqueous media.

PubMed

Vuković, Lela; Khatib, Fatima A; Drake, Stephanie P; Madriaga, Antonett; Brandenburg, Kenneth S; Král, Petr; Onyuksel, Hayat

2011-08-31

Molecular assemblies of highly PEG-ylated phospholipids are important in many biomedical applications. We have studied sterically stabilized micelles (SSMs) of self-assembled DSPE–PEG2000 in pure water and isotonic HEPES-buffered saline solution. The observed SSM sizes of 2–15 nm largely depend on the solvent and the lipid concentration used. The critical micelle concentration of DSPE–PEG2000 is 10 times higher in water than in buffer, and the viscosity of the dispersion dramatically increases with the lipid concentration. To explain the experimentally observed results, we performed atomistic molecular dynamics simulations of solvated SSMs. Our modeling revealed that the observed assemblies have very different aggregation numbers (N(agg) ≈ 90 in saline solution and N(agg) < 8 in water) because of very different screening of their charged PO4(–) groups. We also demonstrate that the micelle cores can inflate and their coronas can fluctuate strongly, thus allowing storage and delivery of molecules with different chemistries.

Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory

DOE PAGES

Vukovic, Sinisa; Hay, Benjamin P.; Bryantsev, Vyacheslav S.

2015-04-02

The ability to predict the equilibrium constants for the formation of 1:1 uranyl:ligand complexes (log K 1 values) provides the essential foundation for the rational design of ligands with enhanced uranyl affinity and selectivity. We also use density functional theory (B3LYP) and the IEFPCM continuum solvation model to compute aqueous stability constants for UO 2 2+ complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K 1 values are significantly overestimated. Accurate predictions of the absolute log K 1 values (root mean square deviation from experiment < 1.0 for logmore » K 1 values ranging from 0 to 16.8) can be obtained by fitting the experimental data for two groups of mono and divalent negative oxygen donor ligands. The utility of correlations is demonstrated for amidoxime and imide dioxime ligands, providing a useful means of screening for new ligands with strong chelate capability to uranyl.« less

Self-consistent continuum solvation for optical absorption of complex molecular systems in solution

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

Timrov, Iurii; Biancardi, Alessandro; Andreussi, Oliviero

2015-01-21

We introduce a new method to compute the optical absorption spectra of complex molecular systems in solution, based on the Liouville approach to time-dependent density-functional perturbation theory and the revised self-consistent continuum solvation model. The former allows one to obtain the absorption spectrum over a whole wide frequency range, using a recently proposed Lanczos-based technique, or selected excitation energies, using the Casida equation, without having to ever compute any unoccupied molecular orbitals. The latter is conceptually similar to the polarizable continuum model and offers the further advantages of allowing an easy computation of atomic forces via the Hellmann-Feynman theorem andmore » a ready implementation in periodic-boundary conditions. The new method has been implemented using pseudopotentials and plane-wave basis sets, benchmarked against polarizable continuum model calculations on 4-aminophthalimide, alizarin, and cyanin and made available through the QUANTUM ESPRESSO distribution of open-source codes.« less

Solvation effects on like-charge attraction.

PubMed

Ghanbarian, Shahzad; Rottler, Jörg

2013-02-28

We present results of molecular dynamics simulations of the electrostatic interaction between two parallel charged rods in the presence of divalent counterions. Such polyelectrolytes have been considered as a simple model for understanding electrostatic interactions in highly charged biomolecules such as DNA. Since there are correlations between the free charge carriers, the phenomenon of like charge attraction appears for specific parameters. We explore the role of solvation effects and the resulting deviations from Coulomb's law on the nanoscale on this peculiar phenomenon. The behavior of the force between the charged rods in a simulation with atomistic representation of water molecules is completely different from a model in which water is modeled as a continuum dielectric. By calculating counterion-rodion pair correlation functions, we find that the presence of water molecules changes the structure of the counterion cloud and results in both qualitative and quantitative changes of the force between highly charged polyelectrolytes.

Hydrophobic potential of mean force as a solvation function for protein structure prediction.

PubMed

Lin, Matthew S; Fawzi, Nicolas Lux; Head-Gordon, Teresa

2007-06-01

We have developed a solvation function that combines a Generalized Born model for polarization of protein charge by the high dielectric solvent, with a hydrophobic potential of mean force (HPMF) as a model for hydrophobic interaction, to aid in the discrimination of native structures from other misfolded states in protein structure prediction. We find that our energy function outperforms other reported scoring functions in terms of correct native ranking for 91% of proteins and low Z scores for a variety of decoy sets, including the challenging Rosetta decoys. This work shows that the stabilizing effect of hydrophobic exposure to aqueous solvent that defines the HPMF hydration physics is an apparent improvement over solvent-accessible surface area models that penalize hydrophobic exposure. Decoys generated by thermal sampling around the native-state basin reveal a potentially important role for side-chain entropy in the future development of even more accurate free energy surfaces.

SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics.

PubMed

Darré, Leonardo; Machado, Matías Rodrigo; Brandner, Astrid Febe; González, Humberto Carlos; Ferreira, Sebastián; Pantano, Sergio

2015-02-10

Modeling of macromolecular structures and interactions represents an important challenge for computational biology, involving different time and length scales. However, this task can be facilitated through the use of coarse-grained (CG) models, which reduce the number of degrees of freedom and allow efficient exploration of complex conformational spaces. This article presents a new CG protein model named SIRAH, developed to work with explicit solvent and to capture sequence, temperature, and ionic strength effects in a topologically unbiased manner. SIRAH is implemented in GROMACS, and interactions are calculated using a standard pairwise Hamiltonian for classical molecular dynamics simulations. We present a set of simulations that test the capability of SIRAH to produce a qualitatively correct solvation on different amino acids, hydrophilic/hydrophobic interactions, and long-range electrostatic recognition leading to spontaneous association of unstructured peptides and stable structures of single polypeptides and protein-protein complexes.

Contact Forces between Single Metal Oxide Nanoparticles in Gas-Phase Applications and Processes

PubMed Central

2017-01-01

In this work we present a comprehensive experimental study to determine the contact forces between individual metal oxide nanoparticles in the gas-phase using atomic force microscopy. In addition, we determined the amount of physisorbed water for each type of particle surface. By comparing our results with mathematical models of the interaction forces, we could demonstrate that classical continuum models of van der Waals and capillary forces alone cannot sufficiently describe the experimental findings. Rather, the discrete nature of the molecules has to be considered, which leads to ordering at the interface and the occurrence of solvation forces. We demonstrate that inclusion of solvation forces in the model leads to quantitative agreement with experimental data and that tuning of the molecular order by addition of isopropanol vapor allows us to control the interaction forces between the nanoparticles. PMID:28186771

Femtosecond spectroscopic study of the solvation of amphiphilic molecules by water

NASA Astrophysics Data System (ADS)

Rezus, Y. L. A.; Bakker, H. J.

2008-06-01

We use polarization-resolved mid-infrared pump-probe spectroscopy to study the aqueous solvation of proline and N-methylacetamide. These molecules serve as models to study the solvation of proteins. We monitor the orientational dynamics of partly deuterated water molecules (HDO) that are present at a low concentration in the water. We find that the OD vibration of HDO relaxes via an intermediate level, that is characterized by a hydrogen-bond that is stronger than in the ground state. With increasing concentration the lifetime of the excited state increases from 1.8 ps to 2.4 ps and the lifetime of the intermediate level from 0.6 ps to 1.0 ps. Regarding the orientational dynamics we observe biexponential behavior, which finds its origin in the presence of two classes of water molecules. There is a fraction of water molecules that has bulk-like orientational dynamics ( τrot = 2.5 ps) and a fraction of immobilized water molecules ( τrot > 10 ps). The relative abundance of the two fractions is determined by the nature and concentration of the solute. We find that the hydrophobic solute groups are responsible for the immobilization of water molecules. Every methyl group causes the immobilization of approximately 4 water OH groups. The hydrophilic solute groups, on the other hand, do not hinder the reorientation and the water molecules solvating them reorient with the same rate as in the bulk liquid.

Chemistry in acetone complexes of metal dications: a remarkable ethylene production pathway.

PubMed

Wu, Jianhua; Liu, Dan; Zhou, Jian-Ge; Hagelberg, Frank; Park, Sung Soo; Shvartsburg, Alexandre A

2007-06-07

Electrospray ionization can generate microsolvated multiply charged metal ions for various metals and ligands, allowing exploration of chemistry within such clusters. The finite size of these systems permits comparing experimental results with accurate calculations, creating a natural laboratory to research ion solvation. Mass spectrometry has provided much insight into the stability and dissociation of ligated metal cations. While solvated singly charged ions tend to shrink by ligand evaporation, solvated polycations below a certain size exhibit charge reduction and/or ligand fragmentation due to organometallic reactions. Here we investigate the acetone complexes of representative divalent metals (Ca, Mn, Co, Ni, and Cu), comparing the results of collision-induced dissociation with the predictions of density functional theory. As for other solvated dications, channels involving proton or electron transfer compete with ligand loss and become dominant for smaller complexes. The heterolytic C-C bond cleavage is common, like in DMSO and acetonitrile complexes. Of primary interest is the unanticipated neutral ethylene loss, found for all metals studied except Cu and particularly intense for Ca and Mn. We focus on understanding that process in the context of competing dissociation pathways, as a function of metal identity and number of ligands. According to first-principles modeling, ethylene elimination proceeds along a complex path involving two intermediates. These results suggest that chemistry in microsolvated multiply charged ions may still hold major surprises.

Linear solvation energy relationships for toxicity of selected organic chemicals to Daphnia pulex and Daphnia magna

USGS Publications Warehouse

Passino, Dora R.M.; Hickey, James P.; Frank, Anthony M.

1988-01-01

In the Laurentian Great Lakes, more than 300 contaminants have been identified in fish, other biota, water, and sediment. Current hazard assessment of these chemicals by the National Fisheries Research Center-Great Lakes is based on their toxicity, occurrence in the environment, and source. Although scientists at the Center have tested over 70 chemicals with the crustacean Daphnia pulex, the number of experimental data needed to screen the huge array of chemicals in the Great Lakes exceeds the practical capabilities of conducting bioassays. This limitation can be partly circumvented, however, by using mathematical models based on quantitative structure-activity relationships (QSAR) to provide rapid, inexpensive estimates of toxicity. Many properties of chemicals, including toxicity, bioaccumulation and water solubility are well correlated and can be predicted by equations of the generalized linear solvation energy relationships (LSER). The equation we used to model solute toxicity is Toxicity = constant + mVI/100 + s (π* + dδ) + bβm + aαm where VI = intrinsic (Van der Waals) molar volume; π* = molecular dipolarity/polarizability; δ = polarizability 'correction term'; βm = solute hydrogen bond acceptor basicity; and αm = solute hydrogen bond donor acidity. The subscript m designates solute monomer values for α and β. We applied the LSER model to 48-h acute toxicity data (measured as immobilization) for six classes of chemicals detected in Great Lakes fish. The following regression was obtained for Daphnia pulex (concentration = μM): log EC50 = 4.86 - 4.35 VI/100; N = 38, r2 = 0.867, sd = 0.403 We also used the LSER modeling approach to analyze to a large published data set of 24-h acute toxicity for Daphnia magna; the following regression resulted, for eight classes of compounds (concentration = mM): log EC50 = 3.88 - 4.52 VI/100 - 1.62 π* + 1.66 βm - 0.916 αm; N = 62, r2 = 0.859, sd = 0.375 In addition we developed computer software that identifies chemical structures, estimates the LSER parameters, and predicts toxicity. The LSER models promise to be effective in differentiating between reactive and nonreactive toxicity behavior where other models have failed. Contaminants with reactive behavior are generally the most toxic and rank highest in hazard assessment of environmental chemicals.

Experimental cocrystal screening and solution based scale-up cocrystallization methods.

PubMed

Malamatari, Maria; Ross, Steven A; Douroumis, Dennis; Velaga, Sitaram P

2017-08-01

Cocrystals are crystalline single phase materials composed of two or more different molecular and/or ionic compounds generally in a stoichiometric ratio which are neither solvates nor simple salts. If one of the components is an active pharmaceutical ingredient (API), the term pharmaceutical cocrystal is often used. There is a growing interest among drug development scientists in exploring cocrystals, as means to address physicochemical, biopharmaceutical and mechanical properties and expand solid form diversity of the API. Conventionally, coformers are selected based on crystal engineering principles, and the equimolar mixtures of API and coformers are subjected to solution-based crystallization that are commonly employed in polymorph and salt screening. However, the availability of new knowledge on cocrystal phase behaviour in solid state and solutions has spurred the development and implementation of more rational experimental cocrystal screening as well as scale-up methods. This review aims to provide overview of commonly employed solid form screening techniques in drug development with an emphasis on cocrystal screening methodologies. The latest developments in understanding and the use of cocrystal phase diagrams in both screening and solution based scale-up methods are also presented. Final section is devoted to reviewing the state of the art research covering solution based scale-up cocrystallization process for different cocrystals besides more recent continuous crystallization methods. Copyright © 2017 Elsevier B.V. All rights reserved.

Solvation of actinide salts in water using a polarizable continuum model.

PubMed

Kumar, Narendra; Seminario, Jorge M

2015-01-29

In order to determine how actinide atoms are dressed when solvated in water, density functional theory calculations have been carried out to study the equilibrium structure of uranium plutonium and thorium salts (UO2(2+), PuO2(2+), Pu(4+), and Th(4+)) both in vacuum as well as in solution represented by a conductor-like polarizable continuum model. This information is of paramount importance for the development of sensitive nanosensors. Both UO2(2+) and PuO2(2+) ions show coordination number of 4-5 with counterions replacing one or two water molecules from the first coordination shell. On the other hand, Pu(4+), has a coordination number of 8 both when completely solvated and also in the presence of chloride and nitrate ions with counterions replacing water molecules in the first shell. Nitrates were found to bind more strongly to Pu(IV) than chloride anions. In the case of the Th(IV) ion, the coordination number was found to be 9 or 10 in the presence of chlorides. Moreover, the Pu(IV) ion shows greater affinity for chlorides than the Th(IV) ion. Adding dispersion and ZPE corrections to the binding energy does not alter the trends in relative stability of several conformers because of error cancelations. All structures and energetics of these complexes are reported.

A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation.

PubMed

Li, Yongxiu; Gao, Ya; Zhang, Xuqiang; Wang, Xingyu; Mou, Lirong; Duan, Lili; He, Xiao; Mei, Ye; Zhang, John Z H

2013-09-01

Main chain torsions of alanine dipeptide are parameterized into coupled 2-dimensional Fourier expansions based on quantum mechanical (QM) calculations at M06 2X/aug-cc-pvtz//HF/6-31G** level. Solvation effect is considered by employing polarizable continuum model. Utilization of the M06 2X functional leads to precise potential energy surface that is comparable to or even better than MP2 level, but with much less computational demand. Parameterization of the 2D expansions is against the full main chain torsion space instead of just a few low energy conformations. This procedure is similar to that for the development of AMBER03 force field, except unique weighting factor was assigned to all the grid points. To avoid inconsistency between quantum mechanical calculations and molecular modeling, the model peptide is further optimized at molecular mechanics level with main chain dihedral angles fixed before the calculation of the conformational energy on molecular mechanical level at each grid point, during which generalized Born model is employed. Difference in solvation models at quantum mechanics and molecular mechanics levels makes this parameterization procedure less straightforward. All force field parameters other than main chain torsions are taken from existing AMBER force field. With this new main chain torsion terms, we have studied the main chain dihedral distributions of ALA dipeptide and pentapeptide in aqueous solution. The results demonstrate that 2D main chain torsion is effective in delineating the energy variation associated with rotations along main chain dihedrals. This work is an implication for the necessity of more accurate description of main chain torsions in the future development of ab initio force field and it also raises a challenge to the development of quantum mechanical methods, especially the quantum mechanical solvation models.

Quantum mechanics/molecular mechanics modeling of photoelectron spectra: the carbon 1s core-electron binding energies of ethanol-water solutions.

PubMed

Löytynoja, T; Niskanen, J; Jänkälä, K; Vahtras, O; Rinkevicius, Z; Ågren, H

2014-11-20

Using ethanol-water solutions as illustration, we demonstrate the capability of the hybrid quantum mechanics/molecular mechanics (QM/MM) paradigm to simulate core photoelectron spectroscopy: the binding energies and the chemical shifts. An integrated approach with QM/MM binding energy calculations coupled to preceding molecular dynamics sampling is adopted to generate binding energies averaged over the solute-solvent configurations available at a particular temperature and pressure and thus allowing for a statistical assessment with confidence levels for the final binding energies. The results are analyzed in terms of the contributions in the molecular mechanics model-electrostatic, polarization, and van der Waals-with atom or bond granulation of the corresponding MM charge and polarizability force-fields. The role of extramolecular charge transfer screening of the core-hole and explicit hydrogen bonding is studied by extending the QM core to cover the first solvation shell. The results are compared to those obtained from pure electrostatic and polarizable continuum models. Particularly, the dependence of the carbon 1s binding energies with respect to the ethanol concentration is studied. Our results indicate that QM/MM can be used as an all-encompassing model to study photoelectron binding energies and chemical shifts in solvent environments.

Readily Made Solvated Electrons

ERIC Educational Resources Information Center

Ibanez, Jorge G.; Guerra-Millan, Francisco J.; Hugerat, Muhamad; Vazquez-Olavarrieta, Jorge L.; Basheer, Ahmad; Abu-Much, Riam

2011-01-01

The existence of solvated electrons has been known for a long time. Key methods for their production (i.e., photoionization of reducing ions, water radiolysis, and the reaction between H[middle dot] and OH[superscript -]) are unsuitable for most school laboratories. We describe a simple experiment to produce liquid ammonia and solvated electrons…

Solvated Electrons in Organic Chemistry Laboratory

ERIC Educational Resources Information Center

Ilich, Predrag-Peter; McCormick, Kathleen R.; Atkins, Adam D.; Mell, Geoffrey J.; Flaherty, Timothy J.; Bruck, Martin J.; Goodrich, Heather A.; Hefel, Aaron L.; Juranic, Nenad; Seleem, Suzanne

2010-01-01

A novel experiment is described in which solvated electrons in liquid ammonia reduce a benzyl alcohol carbon without affecting the aromatic ring. The reductive activity of solvated electrons can be partially or completely quenched through the addition of electron scavengers to the reaction mixture. The effectiveness of these scavengers was found…

How High Pressure Unifies Solvation Processes in Liquid Chromatography.

PubMed

Bocian, Szymon; Škrinjar, Tea; Bolanca, Tomislav; Buszewski, Bogusław

2017-11-01

A series of core-shell-based stationary phases of varying surface chemistry were subjected to solvent adsorption investigation under ultra-HPLC conditions. Acetonitrile and water excess isotherms were measured using a minor disturbance method. It was observed that adsorption of organic solvent is unified under high pressure. Preferential solvation due to specific interactions between the stationary phases and solvent molecules was limited. The obtained results showed that the solvation process is almost independent of surface chemistry, in contrast to HPLC conditions in which specific interactions differentiate solvation processes.

Solvation thermodynamics of amino acid side chains on a short peptide backbone

NASA Astrophysics Data System (ADS)

Hajari, Timir; van der Vegt, Nico F. A.

2015-04-01

The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvation free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side chain cavities in bulk water, in agreement with earlier work in the literature on analysis of cavity fluctuations at nonpolar molecular surfaces. The cavity and dispersion interaction contributions correlate quite well with the solvent accessible surface area of the nonpolar side chains attached to the backbone. This correlation however is weak for the overall solvation free energies owing to the fact that the cavity and dispersion free energy contributions are almost exactly cancelling each other.

Characterisation of different polymorphs of tris(8-hydroxyquinolinato)aluminium(III) using solid-state NMR and DFT calculations

PubMed Central

Goswami, Mithun; Nayak, Pabitra K; Periasamy, N; Madhu, PK

2009-01-01

Background Organic light emitting devices (OLED) are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato)-aluminium(III), known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR) is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. Results We report here 27Al one-dimensional (1D) and two-dimensional (2D) multiple-quantum magic-angle spinning (MQMAS) NMR studies of the meridional (α-phase) and the facial (δ-phase) isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory) quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the α-phase and the δ-phase, although the fluorescence emission shows no substantial difference between the α-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the α-phase. Conclusion The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the α-phase of Alq3 (containing meridional isomer) from the solid-state NMR studies. Solid-state NMR can hence be used as an effective complementary tool to XRD for characterisation and structural elucidation. PMID:19900275

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.

Characterisation of different polymorphs of tris(8-hydroxyquinolinato)aluminium(III) using solid-state NMR and DFT calculations.

PubMed

Goswami, Mithun; Nayak, Pabitra K; Periasamy, N; Madhu, P K

2009-11-09

Organic light emitting devices (OLED) are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato)-aluminium(III), known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR) is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. We report here 27Al one-dimensional (1D) and two-dimensional (2D) multiple-quantum magic-angle spinning (MQMAS) NMR studies of the meridional (alpha-phase) and the facial (delta-phase) isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory) quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the alpha-phase and the delta-phase, although the fluorescence emission shows no substantial difference between the alpha-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the alpha-phase. The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the alpha-phase of Alq3 (containing meridional isomer) from the solid-state NMR studies. Solid-state NMR can hence be used as an effective complementary tool to XRD for characterisation and structural elucidation.

Accuracy assessment of the linear Poisson-Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid-protein complexes.

PubMed

Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro

2015-04-05

The generalized Born model in the Onufriev, Bashford, and Case (Onufriev et al., Proteins: Struct Funct Genet 2004, 55, 383) implementation has emerged as one of the best compromises between accuracy and speed of computation. For simulations of nucleic acids, however, a number of issues should be addressed: (1) the generalized Born model is based on a linear model and the linearization of the reference Poisson-Boltmann equation may be questioned for highly charged systems as nucleic acids; (2) although much attention has been given to potentials, solvation forces could be much less sensitive to linearization than the potentials; and (3) the accuracy of the Onufriev-Bashford-Case (OBC) model for nucleic acids depends on fine tuning of parameters. Here, we show that the linearization of the Poisson Boltzmann equation has mild effects on computed forces, and that with optimal choice of the OBC model parameters, solvation forces, essential for molecular dynamics simulations, agree well with those computed using the reference Poisson-Boltzmann model. © 2015 Wiley Periodicals, Inc.

Pharmacophore modeling and conformational analysis in the gas phase and in aqueous solution of regioisomeric melatonin analogs. A theoretical and experimental study

NASA Astrophysics Data System (ADS)

Mendoza-Figueroa, Humberto; Martínez-Gudiño, Gelacio; Villanueva-Luna, Jorge E.; Trujillo-Serrato, Joel J.; Morales-Ríos, Martha S.

2017-04-01

In this work, 2-(N-acylaminoalkyl)indoles 1a-1d, that incorporate a pMeOBn group at the 3-position of the indole ring were virtual screened as potential melatoninergic ligands by analog-based design study using pharmacophore modeling. Pharmacophore models for melatoninergic agonist and antagonist activity were developed in order to identify the molecular constraints that define the geometric relationship among chemical features in each model. The best hypothesis consisted of six features for agonists and eight features for antagonists. The models suggest that the agonists and antagonists can share the same 3D arrangement for the six common pharmacophoric elements identified: two hydrogen bond acceptors (HBA), one hydrogen bond donor (HBD), one hydrophobic area (H), and two aromatic rings (AR). The extra hydrofobic interaction might be used as criterion for identified the pharmacological antagonist profile. Based on the pharmacophore fit, it was found that structures 1c and 1d show a good structural overlay that meets the requirements for the antagonistic pharmacophore hypothesis. Molecular modeling studies using the PCM solvation model predicted that the most stable conformers of 1a-1d match the antagonist pharmacophore hypothesis in contrast to those in the gas phase. Structures 1a-1c were synthesized only but the activities were not tested.

Structure of solvates of o-hydroxybenzoic acid in supercritical CO2-cosolvent media, according to molecular dynamics data

NASA Astrophysics Data System (ADS)

Petrenko, V. E.; Antipova, M. L.; Gurina, D. L.

2015-03-01

Three-component supercritical carbon dioxide-cosolvent (methanol, ethanol, water)- o-hydroxybenzoic acid ( o-HBA) mixtures at a density of 0.7 g/cm3 and temperatures of 318 and 348 K are simulated by means of molecular dynamics. The solvate structures are investigated. It is shown that the solvation mechanism of o-HBA (particularly the o-HBA molecule forming a stable solvate complex with one molecule of a cosolvent via a hydrogen bond through the carboxyl group) does not depend on the temperature or the cosolvent. It is noted that the form of the cosolvent in a supercritical fluid varies: alcohols are distributed in the bulk in the form of monomers and hydrogen-bonded dimers, and water molecules tend to form microclusters along with chained and spatially branched structures by means of hydrogen bonds. It is established that the local molar fraction of cosolvent around the solvate complexes grows. It is concluded that the solvation of o-HBA is determined by the behavior of cosolvent in media of supercritical CO2.

Anion Solvation in Carbonate-Based Electrolytes

DOE PAGES

von Wald Cresce, Arthur; Gobet, Mallory; Borodin, Oleg; ...

2015-11-16

The correlation between Li + solvation and interphasial chemistry on anodes firmly established in Li-ion batteries, the effect of cation–solvent interaction has gone beyond bulk thermodynamic and transport properties and become an essential element that determines the reversibility of electrochemistry and kinetics of Li-ion intercalation chemistries. Now, most studies are dedicated to the solvation of Li +, and the solvation of anions in carbonate-based electrolytes and its possible effect on the electrochemical stability of such electrolytes remains little understood. Moreover, as a mirror effort to prior Li + solvation studies, this work focuses on the interactions between carbonate-based solvents andmore » two anions (hexafluorophosphate, PF 6–, and tetrafluoroborate, BF 4–) that are most frequently used in Li-ion batteries. The possible correlation between such interaction and the interphasial chemistry on cathode surface is also explored.« less

Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: exact results for spherical inclusions.

PubMed

Bardhan, Jaydeep P; Knepley, Matthew G

2011-09-28

We analyze the mathematically rigorous BIBEE (boundary-integral based electrostatics estimation) approximation of the mixed-dielectric continuum model of molecular electrostatics, using the analytically solvable case of a spherical solute containing an arbitrary charge distribution. Our analysis, which builds on Kirkwood's solution using spherical harmonics, clarifies important aspects of the approximation and its relationship to generalized Born models. First, our results suggest a new perspective for analyzing fast electrostatic models: the separation of variables between material properties (the dielectric constants) and geometry (the solute dielectric boundary and charge distribution). Second, we find that the eigenfunctions of the reaction-potential operator are exactly preserved in the BIBEE model for the sphere, which supports the use of this approximation for analyzing charge-charge interactions in molecular binding. Third, a comparison of BIBEE to the recent GBε theory suggests a modified BIBEE model capable of predicting electrostatic solvation free energies to within 4% of a full numerical Poisson calculation. This modified model leads to a projection-framework understanding of BIBEE and suggests opportunities for future improvements. © 2011 American Institute of Physics

Novel dimer based descriptors with solvational computation for QSAR study of oxadiazoylbenzoyl-ureas as novel insect-growth regulators.

PubMed

Fan, Feng; Cheng, Jiagao; Li, Zhong; Xu, Xiaoyong; Qian, Xuhong

2010-02-01

Molecular aggregation state of bioactive compounds plays a key role in its bio-interactive procedure. In this article, based on the structure information of dimers, the simplest model of molecular aggregation state, and combined with solvational computation, total four descriptors (DeltaV, MR2, DeltaE(1), and DeltaE(2)) were calculated for QSAR study of a novel insect-growth regulator, N-(5-phenyl-1,3,4-oxadiazol-2-yl)-N'-benzoyl urea. Two QSAR models were constructed with r(2) = 0.671, q(2) = 0.516 and r(2) = 0.816, q(2) = 0.695, respectively. It implicates that the bioactivity may strongly depend on the characters of molecular aggregation state, especially on the dimeric transport ability from oil phase to water phase. Copyright 2009 Wiley Periodicals, Inc.

Computational SN 2-Type Mechanism for the Difluoromethylation of Lithium Enolate with Fluoroform through Bimetallic C-F Bond Dual Activation.

PubMed

Honda, Kazuya; Harris, Travis V; Hatanaka, Miho; Morokuma, Keiji; Mikami, Koichi

2016-06-20

The reaction mechanism for difluoromethylation of lithium enolates with fluoroform was analyzed computationally (DFT calculations with the artificial force induced reaction (AFIR) method and solvation model based on density (SMD) solvation model (THF)), showing an SN 2-type carbon-carbon bond formation; the "bimetallic" lithium enolate and lithium trifluoromethyl carbenoid exert the C-F bond "dual" activation, in contrast to the monometallic butterfly-shaped carbenoid in the Simmons-Smith reaction. Lithium enolates, generated by the reaction of 2 equiv. of lithium hexamethyldisilazide (rather than 1 or 3 equiv.) with the cheap difluoromethylating species fluoroform, are the most useful alkali metal intermediates for the synthesis of pharmaceutically important α-difluoromethylated carbonyl products. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The effect of macromolecular crowding on the electrostatic component of barnase-barstar binding: a computational, implicit solvent-based study.

PubMed

Qi, Helena W; Nakka, Priyanka; Chen, Connie; Radhakrishnan, Mala L

2014-01-01

Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder-protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein-protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase-barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders), this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered "effective" solvent dielectric to account for crowding, although the "best" effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the electrostatic component of protein binding, and it provides an initial framework for future analyses.

The Effect of Macromolecular Crowding on the Electrostatic Component of Barnase–Barstar Binding: A Computational, Implicit Solvent-Based Study

PubMed Central

Qi, Helena W.; Nakka, Priyanka; Chen, Connie; Radhakrishnan, Mala L.

2014-01-01

Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder–protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein–protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase–barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders), this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered “effective” solvent dielectric to account for crowding, although the “best” effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the electrostatic component of protein binding, and it provides an initial framework for future analyses. PMID:24915485

Effect of unsaturation on the absorption of ethane and ethylene in imidazolium-based ionic liquids.

PubMed

Moura, Leila; Mishra, Manas; Bernales, Varinia; Fuentealba, Patricio; Padua, Agilio A H; Santini, Catherine C; Costa Gomes, Margarida F

2013-06-20

The influence of the presence of imidazolium side chain unsaturation on the solubility of ethane and ethylene was studied in three ionic liquids: 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amide-saturated alkyl side-chain in the cation; 1-methyl-3-(buten-3-yl)imidazolium bis(trifluorosulfonyl)imide-double bond in the side-chain of the cation; and 1-methyl-3-benzylimidazolium bis(trifluorosulfonyl)imide-benzyl group in the side-chain of the cation. The solubility of both gases decreases when the side-chain of the cations is functionalized with an unsaturated group. This can be explained by a less favorable enthalpy of solvation. The difference of solubility between ethane and ethylene can be explained from a balance of enthalpic and entropic factors: for the ionic liquid with the saturated alkyl side-chain and the benzyl-substituted side-chain, it is the favorable entropy of solvation that explains the larger ethylene solubility, whereas in the case of the saturated side-chain, it is the more favorable enthalpy of solvation. Molecular simulation allowed the identification of the mechanisms of solvation and the preferential solvation sites for each gas in the different ionic liquids. Simulations have shown that the entropy of solvation is more favorable when the presence of the gas weakens the cation-anion interactions or when the gas can be solvated near different sites of the ionic liquid.

Niclosamide methanol solvate and niclosamide hydrate: structure, solvent inclusion mode and implications for properties.

PubMed

Harriss, Bethany I; Wilson, Claire; Radosavljevic Evans, Ivana

2014-08-01

Structural studies have been carried out of two solid forms of niclosamide [5-chloro-N-(2-chloro-4-nitrophenyl)-2-hydroxybenzamide, NCL], a widely used anthelmintic drug, namely niclosamide methanol monosolvate, C13H8Cl2N2O4·CH3OH or NCL·MeOH, and niclosamide monohydrate, denoted HA. The structure of the methanol solvate obtained from single-crystal X-ray diffraction is reported for the first time, elucidating the key host-guest hydrogen-bonding interactions which lead to solvate formation. The essentially planar NCL host molecules interact via π-stacking and pack in a herringbone-type arrangement, giving rise to channels along the crystallographic a axis in which the methanol guest molecules are located. The methanol and NCL molecules interact via short O-H...O hydrogen bonds. Laboratory powder X-ray diffraction (PXRD) measurements reveal that the initially phase-pure NCL·MeOH solvate readily transforms into NCL monohydrate within hours under ambient conditions. PXRD further suggests that the NCL monohydrate, HA, is isostructural with the NCL·MeOH solvate. This is consistent with the facile transformation of the methanol solvate into the hydrate when stored in air. The crystal packing and the topology of guest-molecule inclusion are compared with those of other NCL solvates for which the crystal structures are known, giving a consistent picture which correlates well with known experimentally observed desolvation properties.

Crystal structure and habit of dirithromycin acetone solvate: A combined experimental and simulative study

NASA Astrophysics Data System (ADS)

Yi, Qinhua; Chen, Jianfeng; Le, Yuan; Wang, Jiexin; Xue, Chunyu; Zhao, Hong

2013-06-01

Dirithromycin (DIR) was crystallized from acetone solvent in the form of an acetone solvate. Its crystal structure belongs to monoclinic, space group P21, with the unit cell parameters a=14.688(3) Å, b=11.6120(12) Å, c=14.9129(12) Å, β=94.794(10)°, and Z=2. Results of X-ray diffraction (XRD) and thermogravimetry-differential scanning calorimetry (TG-DSC) indicated that the solvent molecules could enter the crystal lattice and thus the solvate is formed. The molecular dynamics (MD) simulation method was applied to study the solvent effect. It revealed that the relative growth rates of the main crystal habit faces changed a lot, which made the most morphologically important habit face shift from (001) face to (100) face due to polar groups or atoms exposure and hence a large solvent interaction. The prism habit predicted by a modified attachment energy (AE) model agreed well with the observed experimental morphology grown from the acetone solution. This prediction method may help for a solvent selection to improve the morphology in the drug crystallization process.

Zero-point energy effects in anion solvation shells.

PubMed

Habershon, Scott

2014-05-21

By comparing classical and quantum-mechanical (path-integral-based) molecular simulations of solvated halide anions X(-) [X = F, Cl, Br and I], we identify an ion-specific quantum contribution to anion-water hydrogen-bond dynamics; this effect has not been identified in previous simulation studies. For anions such as fluoride, which strongly bind water molecules in the first solvation shell, quantum simulations exhibit hydrogen-bond dynamics nearly 40% faster than the corresponding classical results, whereas those anions which form a weakly bound solvation shell, such as iodide, exhibit a quantum effect of around 10%. This observation can be rationalized by considering the different zero-point energy (ZPE) of the water vibrational modes in the first solvation shell; for strongly binding anions, the ZPE of bound water molecules is larger, giving rise to faster dynamics in quantum simulations. These results are consistent with experimental investigations of anion-bound water vibrational and reorientational motion.

Optimization of Pore Structure of Cathodic Carbon Supports for Solvate Ionic Liquid Electrolytes Based Lithium-Sulfur Batteries.

PubMed

Zhang, Shiguo; Ikoma, Ai; Li, Zhe; Ueno, Kazuhide; Ma, Xiaofeng; Dokko, Kaoru; Watanabe, Masayoshi

2016-10-04

Lithium-sulfur (Li-S) batteries are a promising energy-storage technology owing to their high theoretical capacity and energy density. However, their practical application remains a challenge because of the serve shuttle effect caused by the dissolution of polysulfides in common organic electrolytes. Polysulfide-insoluble electrolytes, such as solvate ionic liquids (ILs), have recently emerged as alternative candidates and shown great potential in suppressing the shuttle effect and improving the cycle stability of Li-S batteries. Redox electrochemical reactions in polysulfide-insoluble electrolytes occur via a solid-state process at the interphase between the electrolyte and the composite cathode; therefore, creating an appropriate interface between sulfur and a carbon support is of great importance. Nevertheless, the porous carbon supports established for conventional organic electrolytes may not be suitable for polysulfide-insoluble electrolytes. In this work, we investigated the effect of the porous structure of carbon materials on the Li-S battery performance in polysulfide-insoluble electrolytes using solvate ILs as a model electrolyte. We determined that the pore volume (rather than the surface area) exerts a major influence on the discharge capacity of S composite cathodes. In particular, inverse opal carbons with three-dimensionally ordered interconnected macropores and a large pore volume deliver the highest discharge capacity. The battery performance in both polysulfide-soluble electrolytes and solvate ILs was used to study the effect of electrolytes. We propose a plausible mechanism to explain the different porous structure requirements in polysulfide-soluble and polysulfide-insoluble electrolytes.

Alkali-ion microsolvation with benzene molecules.

PubMed

Marques, J M C; Llanio-Trujillo, J L; Albertí, M; Aguilar, A; Pirani, F

2012-05-24

The target of this investigation is to characterize by a recently developed methodology, the main features of the first solvation shells of alkaline ions in nonpolar environments due to aromatic rings, which is of crucial relevance to understand the selectivity of several biochemical phenomena. We employ an evolutionary algorithm to obtain putative global minima of clusters formed with alkali-ions (M(+)) solvated with n benzene (Bz) molecules, i.e., M(+)-(Bz)(n). The global intermolecular interaction has been decomposed in Bz-Bz and in M(+)-Bz contributions, using a potential model based on different decompositions of the molecular polarizability of benzene. Specifically, we have studied the microsolvation of Na(+), K(+), and Cs(+) with benzene molecules. Microsolvation clusters up to n = 21 benzene molecules are involved in this work and the achieved global minimum structures are reported and discussed in detail. We observe that the number of benzene molecules allocated in the first solvation shell increases with the size of the cation, showing three molecules for Na(+) and four for both K(+) and Cs(+). The structure of this solvation shell keeps approximately unchanged as more benzene molecules are added to the cluster, which is independent of the ion. Particularly stable structures, so-called "magic numbers", arise for various nuclearities of the three alkali-ions. Strong "magic numbers" appear at n = 2, 3, and 4 for Na(+), K(+), and Cs(+), respectively. In addition, another set of weaker "magic numbers" (three per alkali-ion) are reported for larger nuclearities.

Using Q-Chem on the Peregrine System | High-Performance Computing | NREL

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A Comparison of Predictive Thermo and Water Solvation Property Prediction Tools and Experimental Data for Selected Traditional Chemical Warfare Agents and Simulants II: COSMO RS and COSMOTherm

DTIC Science & Technology

2017-04-01

A COMPARISON OF PREDICTIVE THERMO AND WATER SOLVATION PROPERTY PREDICTION TOOLS AND EXPERIMENTAL DATA FOR...4. TITLE AND SUBTITLE A Comparison of Predictive Thermo and Water Solvation Property Prediction Tools and Experimental Data for Selected...1  2.  EXPERIMENTAL PROCEDURE

Optimized multi-step NMR-crystallography approach for structural characterization of a stable quercetin solvate.

PubMed

Filip, Xenia; Miclaus, Maria; Martin, Flavia; Filip, Claudiu; Grosu, Ioana Georgeta

2017-05-10

Herein we report the preparation and solid state structural investigation of the 1,4-dioxane-quercetin solvate. NMR crystallography methods were employed for crystal structure determination of the solvate from microcrystalline powder. The stability of the compound relative to other reported quercetin solvates is discussed and found to be in perfect agreement with the hydrogen bonding networks/supra-molecular architectures formed in each case. It is also clearly shown that NMR crystallography represents an ideal analytical tool in such cases when hydrogen-bonding networks are required to be constrained at a high accuracy level. Copyright © 2017 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2010-09-01

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

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.

Hydrophilic Solvation Dominates the Terahertz Fingerprint of Amino Acids in Water.

PubMed

Esser, Alexander; Forbert, Harald; Sebastiani, Federico; Schwaab, Gerhard; Havenith, Martina; Marx, Dominik

2018-02-01

Spectroscopy in the terahertz frequency regime is a sensitive tool to probe solvation-induced effects in aqueous solutions. Yet, a systematic understanding of spectral lineshapes as a result of distinct solvation contributions remains terra incognita. We demonstrate that modularization of amino acids in terms of functional groups allows us to compute their distinct contributions to the total terahertz response. Introducing the molecular cross-correlation analysis method provides unique access to these site-specific contributions. Equivalent groups in different amino acids lead to look-alike spectral contributions, whereas side chains cause characteristic but additive complexities. Specifically, hydrophilic solvation of the zwitterionic groups in valine and glycine leads to similar terahertz responses which are fully decoupled from the side chain. The terahertz response due to H-bonding within the large hydrophobic solvation shell of valine turns out to be nearly indistinguishable from that in bulk water in direct comparison to the changes imposed by the charged functional groups that form strong H-bonds with their hydration shells. Thus, the hydrophilic groups and their solvation shells dominate the terahertz absorption difference, while on the same intensity scale, the influence of hydrophobic water can be neglected.

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.

Solvation thermodynamics of amino acid side chains on a short peptide backbone

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

Hajari, Timir; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de

The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvationmore » free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side chain cavities in bulk water, in agreement with earlier work in the literature on analysis of cavity fluctuations at nonpolar molecular surfaces. The cavity and dispersion interaction contributions correlate quite well with the solvent accessible surface area of the nonpolar side chains attached to the backbone. This correlation however is weak for the overall solvation free energies owing to the fact that the cavity and dispersion free energy contributions are almost exactly cancelling each other.« less

Effects of Electronic-State-Dependent Solute Polarizability: Application to Solute-Pump/Solvent-Probe Spectra.

PubMed

Sun, Xiang; Ladanyi, Branka M; Stratt, Richard M

2015-07-23

Experimental studies of solvation dynamics in liquids invariably ask how changing a solute from its electronic ground state to an electronically excited state affects a solution's dynamics. With traditional time-dependent-fluorescence experiments, that means looking for the dynamical consequences of the concomitant change in solute-solvent potential energy. But if one follows the shift in the dynamics through its effects on the macroscopic polarizability, as recent solute-pump/solvent-probe spectra do, there is another effect of the electronic excitation that should be considered: the jump in the solute's own polarizability. We examine the spectroscopic consequences of this solute polarizability change in the classic example of the solvation dye coumarin 153 dissolved in acetonitrile. After demonstrating that standard quantum chemical methods can be used to construct accurate multisite models for the polarizabilities of ground- and excited-state solvation dyes, we show via simulation that this polarizability change acts as a contrast agent, significantly enhancing the observable differences in optical-Kerr spectra between ground- and excited-state solutions. A comparison of our results with experimental solute-pump/solvent-probe spectra supports our interpretation and modeling of this spectroscopy. We predict, in particular, that solute-pump/solvent-probe spectra should be sensitive to changes in both the solvent dynamics near the solute and the electronic-state-dependence of the solute's own rotational dynamics.

Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility.

PubMed

Drake, Justin A; Harris, Robert C; Pettitt, B Montgomery

2016-08-23

Oligoglycine is a backbone mimic for all proteins and is prevalent in the sequences of intrinsically disordered proteins. We have computed the absolute chemical potential of glycine oligomers at infinite dilution by simulation with the CHARMM36 and Amber ff12SB force fields. We performed a thermodynamic decomposition of the solvation free energy (ΔG(sol)) of Gly2-5 into enthalpic (ΔH(sol)) and entropic (ΔS(sol)) components as well as their van der Waals and electrostatic contributions. Gly2-5 was either constrained to a rigid/extended conformation or allowed to be completely flexible during simulations to assess the effects of flexibility on these thermodynamic quantities. For both rigid and flexible oligoglycine models, the decrease in ΔG(sol) with chain length is enthalpically driven with only weak entropic compensation. However, the apparent rates of decrease of ΔG(sol), ΔH(sol), ΔS(sol), and their elec and vdw components differ for the rigid and flexible models. Thus, we find solvation entropy does not drive aggregation for this system and may not explain the collapse of long oligoglycines. Additionally, both force fields yield very similar thermodynamic scaling relationships with respect to chain length despite both force fields generating different conformational ensembles of various oligoglycine chains. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

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

PubMed

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

2018-06-14

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

Reactivity between biphenyl and precursor of solvated electrons in tetrahydrofuran measured by picosecond pulse radiolysis in near-ultraviolet, visible, and infrared.

PubMed

Saeki, Akinori; Kozawa, Takahiro; Ohnishi, Yuko; Tagawa, Seiichi

2007-02-22

The initial decrease of solvated electrons in tetrahydrofuran (THF) upon addition of biphenyl was investigated by picosecond pulse radiolysis. Transient absorption spectra derived from the biphenyl radical anion (centered at 408 and 655 nm) and solvated electrons of THF (infrared) were successfully measured in the wavelength region from 400 to 900 nm by the extension of a femtosecond continuum probe light to near-ultraviolet using a second harmonic generation of Ti:sapphire laser and a CaF2 plate. From the analysis of kinetic traces at 1300 nm considering the overlap of primary solvated electrons and partial biphenyl radical anion, C37, which is defined by the solute concentration to reduce the initial yield of solvated electrons to 1/e, was found to be 87 +/- 3 mM. The rate constant of solvated electrons with biphenyl was determined as 5.8 +/- 0.3 x 10(10) M(-1) s(-1). We demonstrate that the kinetic traces at both 408 nm mainly due to biphenyl radical anion and 1300 nm mainly due to solvated electrons are reproduced with high accuracy and consistency by a simple kinetic analysis. Much higher concentrations of biphenyl (up to 2 M) were examined, showing further increase of the initial yield of biphenyl radical anion accompanying a fast decay component. This observation is discussed in terms of geminate ion recombination, scavenging, delayed geminate ion recombination, and direct ionization of biphenyl at high concentration.

Investigation of rubidium(I) ion solvation in liquid ammonia using QMCF-MD simulation and NBO analysis of first solvation shell structure.

PubMed

Hidayat, Yuniawan; Armunanto, Ria; Pranowo, Harno Dwi

2018-04-27

Rb(I) ion solvation in liquid ammonia has been studied by an ab initio quantum mechanical charge field molecular dynamics simulation, and the first solvation shell structure has been analyzed using natural bond orbital. The simulation was performed for an ion and 593 ammonia molecules in a box with a length of 29.03 Å corresponding to a liquid ammonia density of 0.69 g/mL at 235.16 K. The quantum mechanical calculation was carried out for atomic interactions in the radius of 6.4 Å from the ion using LANL2DZ ECP and DZP (Dunning) basis sets for Rb(I) ion and ammonia respectively. The trajectories of the simulation were analyzed in terms of radial, angular, and coordination number distribution functions, vibration, and mean residence time (MRT). Two solvation shell regions are observed for the Rb(I)-N as well as the Rb(I)-H. The maximum distance of Rb(I)-N in the first solvation shell is in accordance with experimental data where a coordination number of 8 is favorable. A non-single coordination number of the first and second shell indicates dynamic solvation structure. It is confirmed by frequent exchange ligand processes observed within a simulation time of 15 ps. The low stabilization energy of donor acceptor ion-ligand interaction with a small Wiberg bond index affirms that the Rb(I)-NH 3 interaction is weak electrostatically.

Accurate pKa calculation of the conjugate acids of alkanolamines, alkaloids and nucleotide bases by quantum chemical methods.

PubMed

Gangarapu, Satesh; Marcelis, Antonius T M; Zuilhof, Han

2013-04-02

The pKa of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08-HX and M11-L) and ab initio methods (SCS-MP2, G3). Implicit solvent effects are included with a conductor-like polarizable continuum model (CPCM) and universal solvation models (SMD, SM8). G3, SCS-MP2 and M11-L methods coupled with SMD and SM8 solvation models perform well for alkanolamines with mean unsigned errors below 0.20 pKa units, in all cases. Extending this method to the pKa calculation of 35 nitrogen-containing compounds spanning 12 pKa units showed an excellent correlation between experimental and computational pKa values of these 35 amines with the computationally low-cost SM8/M11-L density functional approach. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Configurations of base-pair complexes in solutions. [nucleotide chemistry

NASA Technical Reports Server (NTRS)

Egan, J. T.; Nir, S.; Rein, R.; Macelroy, R.

1978-01-01

A theoretical search for the most stable conformations (i.e., stacked or hydrogen bonded) of the base pairs A-U and G-C in water, CCl4, and CHCl3 solutions is presented. The calculations of free energies indicate a significant role of the solvent in determining the conformations of the base-pair complexes. The application of the continuum method yields preferred conformations in good agreement with experiment. Results of the calculations with this method emphasize the importance of both the electrostatic interactions between the two bases in a complex, and the dipolar interaction of the complex with the entire medium. In calculations with the solvation shell method, the last term, i.e., dipolar interaction of the complex with the entire medium, was added. With this modification the prediction of the solvation shell model agrees both with the continuum model and with experiment, i.e., in water the stacked conformation of the bases is preferred.

Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models.

PubMed

Martínez-Fernández, L; Pepino, A J; Segarra-Martí, J; Banyasz, A; Garavelli, M; Improta, R

2016-09-13

The optical spectra of 5-methylcytidine in three different solvents (tetrahydrofuran, acetonitrile, and water) is measured, showing that both the absorption and the emission maximum in water are significantly blue-shifted (0.08 eV). The absorption spectra are simulated based on CAM-B3LYP/TD-DFT calculations but including solvent effects with three different approaches: (i) a hybrid implicit/explicit full quantum mechanical approach, (ii) a mixed QM/MM static approach, and (iii) a QM/MM method exploiting the structures issuing from molecular dynamics classical simulations. Ab-initio Molecular dynamics simulations based on CAM-B3LYP functionals have also been performed. The adopted approaches all reproduce the main features of the experimental spectra, giving insights on the chemical-physical effects responsible for the solvent shifts in the spectra of 5-methylcytidine and providing the basis for discussing advantages and limitations of the adopted solvation models.

Photoemission spectra and density functional theory calculations of 3d transition metal-aqua complexes (Ti-Cu) in aqueous solution.

PubMed

Yepes, Diana; Seidel, Robert; Winter, Bernd; Blumberger, Jochen; Jaque, Pablo

2014-06-19

Photoelectron spectroscopy measurements and density functional calculations are combined to determine the lowest electron binding energies of first-row transition-metal aqua ions, titanium through copper, with 3d(1) through 3d(9) electronic configurations, in their most common oxidation states. Vertical ionization energies are found to oscillate considerably between 6.76 and 9.65 eV for the dications and between 7.05 and 10.28 eV for the respective trivalent cations. The metal cations are modeled as [M(H2O)n](q+) clusters (q = 2, 3, and 4; n = 6 and 18) surrounded by continuum solvent. The performance of 10 exchange-correlation functionals, two GGAs, three MGGAs, two HGGAs and three HMGGAs, combined with the MDF10(ECP)/6-31+G(d,p) basis set is assessed for 11 M-O bond distances, 10 vertical ionization energies, 6 adiabatic ionization energies, and the associated reorganization free energies. We find that for divalent cations the HGGA and HMGGA functionals in combination with the 18 water model show the best agreement with experimental vertical ionization energies and geometries; for trivalent ions, the MGGA functionals perform best. The corresponding reorganization free energies (λo) of the oxidized ions are significantly underestimated with all DFT functionals and cluster models. This indicates that the structural reorganization of the solvation shell upon ionization is not adequately accounted for by the simple solvation models used, emphasizing the importance of extended sampling of thermally accessible solvation structures for an accurate computation of this quantity. The photoelectron spectroscopy measurements reported herein provide a comprehensive set of transition-metal redox energetic quantities for future electronic structure benchmarks.

Electron Tunneling in Lithium Ammonia Solutions Probed by Frequency-Dependent Electron-Spin Relaxation Studies

PubMed Central

Maeda, Kiminori; Lodge, Matthew T.J.; Harmer, Jeffrey; Freed, Jack H.; Edwards, Peter P.

2012-01-01

Electron transfer or quantum tunneling dynamics for excess or solvated electrons in dilute lithium-ammonia solutions have been studied by pulse electron paramagnetic resonance (EPR) spectroscopy at both X- (9.7 GHz) and W-band (94 GHz) frequencies. The electron spin-lattice (T1) and spin-spin (T2) relaxation data indicate an extremely fast transfer or quantum tunneling rate of the solvated electron in these solutions which serves to modulate the hyperfine (Fermi-contact) interaction with nitrogen nuclei in the solvation shells of ammonia molecules surrounding the localized, solvated electron. The donor and acceptor states of the solvated electron in these solutions are the initial and final electron solvation sites found before, and after, the transfer or tunneling process. To interpret and model our electron spin relaxation data from the two observation EPR frequencies requires a consideration of a multi-exponential correlation function. The electron transfer or tunneling process that we monitor through the correlation time of the nitrogen Fermi-contact interaction has a time scale of (1–10)×10−12 s over a temperature range 230–290K in our most dilute solution of lithium in ammonia. Two types of electron-solvent interaction mechanisms are proposed to account for our experimental findings. The dominant electron spin relaxation mechanism results from an electron tunneling process characterized by a variable donor-acceptor distance or range (consistent with such a rapidly fluctuating liquid structure) in which the solvent shell that ultimately accepts the transferring electron is formed from random, thermal fluctuations of the liquid structure in, and around, a natural hole or Bjerrum-like defect vacancy in the liquid. Following transfer and capture of the tunneling electron, further solvent-cage relaxation with a timescale of ca. 10−13 s results in a minor contribution to the electron spin relaxation times. This investigation illustrates the great potential of multi-frequency EPR measurements to interrogate the microscopic nature and dynamics of ultra fast electron transfer or quantum-tunneling processes in liquids. Our results also impact on the universal issue of the role of a host solvent (or host matrix, e.g. a semiconductor) in mediating long-range electron transfer processes and we discuss the implications of our results with a range of other materials and systems exhibiting the phenomenon of electron transfer. PMID:22568866

Spectrum of Slow and Super-Slow (Picosecond to Nanosecond) Water Dynamics around Organic and Biological Solutes.

PubMed

Ramakrishnan, Gopakumar; González-Jiménez, Mario; Lapthorn, Adrian J; Wynne, Klaas

2017-07-06

Water dynamics in the solvation shell of solutes plays a very important role in the interaction of biomolecules and in chemical reaction dynamics. However, a selective spectroscopic study of the solvation shell is difficult because of the interference of the solute dynamics. Here we report on the observation of heavily slowed down water dynamics in the solvation shell of different solutes by measuring the low-frequency spectrum of solvation water, free from the contribution of the solute. A slowdown factor of ∼50 is observed even for relatively low concentrations of the solute. We go on to show that the effect can be generalized to different solutes including proteins.

Kamlet-Taft solvent parameters, NMR spectroscopic analysis and thermoelectrochemistry of lithium-glyme solvate ionic liquids and their dilute solutions.

PubMed

Black, Jeffrey J; Dolan, Andrew; Harper, Jason B; Aldous, Leigh

2018-06-06

Solvate ionic liquids are a relatively new class of liquids produced by combining a coordinating solvent with a salt. They have a variety of uses and their suitability for such depends upon the ratio of salt to coordinating solvent. This work investigates the Kamlet-Taft solvent parameters of, NMR chemical shifts of nuclei in, and thermoelectrochemistry of a selected set of solvate ionic liquids produced from glymes (methyl terminated oligomers of ethylene glycol) and lithium bis(trifluoromethylsulfonyl)imide at two different compositions. The aim is to improve the understanding of the interactions occurring in these ionic liquids to help select suitable solvate ionic liquids for future applications.

Evidence for Reduced Hydrogen-Bond Cooperativity in Ionic Solvation Shells from Isotope-Dependent Dielectric Relaxation

NASA Astrophysics Data System (ADS)

Cota, Roberto; Ottosson, Niklas; Bakker, Huib J.; Woutersen, Sander

2018-05-01

We find that the reduction in dielectric response (depolarization) of water caused by solvated ions is different for H2O and D2O . This isotope dependence allows us to reliably determine the kinetic contribution to the depolarization, which is found to be significantly smaller than predicted by existing theory. The discrepancy can be explained from a reduced hydrogen-bond cooperativity in the solvation shell: we obtain quantitative agreement between theory and experiment by reducing the Kirkwood correlation factor of the solvating water from 2.7 (the bulk value) to ˜1.6 for NaCl and ˜1 (corresponding to completely uncorrelated motion of water molecules) for CsCl.

Calculating Free Energy Changes in Continuum Solvation Models

DOE PAGES

Ho, Junming; Ertem, Mehmed Z.

2016-02-27

We recently showed for a large dataset of pK as and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents (Phys. Chem. Chem. Phys. 2015, 17, 2859). In this paper, we significantly expand the scope of our study to examine the suitability of this approach for the calculation of general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMDM062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems and reaction types. This includes cluster-continuum schemes for pKmore » a calculations, as well as various neutral, radical and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and bimolecular SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar – the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 kJ mol -1 and 25 kJ mol -1 respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment. The results indicate that when appropriate combinations of electronic structure methods are employed, the direct approach provides a reliable alternative to the thermodynamic cycle calculations of solution phase kinetics and thermodynamics across a broad range of organic reactions.« less

A comparison between state-specific and linear-response formalisms for the calculation of vertical electronic transition energy in solution with the CCSD-PCM method.

PubMed

Caricato, Marco

2013-07-28

The calculation of vertical electronic transition energies of molecular systems in solution with accurate quantum mechanical methods requires the use of approximate and yet reliable models to describe the effect of the solvent on the electronic structure of the solute. The polarizable continuum model (PCM) of solvation represents a computationally efficient way to describe this effect, especially when combined with coupled cluster (CC) methods. Two formalisms are available to compute transition energies within the PCM framework: State-Specific (SS) and Linear-Response (LR). The former provides a more complete account of the solute-solvent polarization in the excited states, while the latter is computationally very efficient (i.e., comparable to gas phase) and transition properties are well defined. In this work, I review the theory for the two formalisms within CC theory with a focus on their computational requirements, and present the first implementation of the LR-PCM formalism with the coupled cluster singles and doubles method (CCSD). Transition energies computed with LR- and SS-CCSD-PCM are presented, as well as a comparison between solvation models in the LR approach. The numerical results show that the two formalisms provide different absolute values of transition energy, but similar relative solvatochromic shifts (from nonpolar to polar solvents). The LR formalism may then be used to explore the solvent effect on multiple states and evaluate transition probabilities, while the SS formalism may be used to refine the description of specific states and for the exploration of excited state potential energy surfaces of solvated systems.

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.

Modelling zwitterions in solution: 3-fluoro-γ-aminobutyric acid (3F-GABA).

PubMed

Cao, Jie; Bjornsson, Ragnar; Bühl, Michael; Thiel, Walter; van Mourik, Tanja

2012-01-02

The conformations and relative stabilities of folded and extended 3-fluoro-γ-aminobutyric acid (3F-GABA) conformers were studied using explicit solvation models. Geometry optimisations in the gas phase with one or two explicit water molecules favour folded and neutral structures containing intramolecular NH···O-C hydrogen bonds. With three or five explicit water molecules zwitterionic minima are obtained, with folded structures being preferred over extended conformers. The stability of folded versus extended zwitterionic conformers increases on going from a PCM continuum solvation model to the microsolvated complexes, though extended structures become less disfavoured with the inclusion of more water molecules. Full explicit solvation was studied with a hybrid quantum-mechanical/molecular-mechanical (QM/MM) scheme and molecular dynamics simulations, including more than 6000 TIP3P water molecules. According to free energies obtained from thermodynamic integration at the PM3/MM level and corrected for B3LYP/MM total energies, the fully extended conformer is more stable than folded ones by about -4.5 kJ mol(-1). B3LYP-computed (3)J(F,H) NMR spin-spin coupling constants, averaged over PM3/MM-MD trajectories, agree best with experiment for this fully extended form, in accordance with the original NMR analysis. The seeming discrepancy between static PCM calculations and experiment noted previously is now resolved. That the inexpensive semiempirical PM3 method performs so well for this archetypical zwitterion is encouraging for further QM/MM studies of biomolecular systems. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

How ions affect the structure of water.

PubMed

Hribar, Barbara; Southall, Noel T; Vlachy, Vojko; Dill, Ken A

2002-10-16

We model ion solvation in water. We use the MB model of water, a simple two-dimensional statistical mechanical model in which waters are represented as Lennard-Jones disks having Gaussian hydrogen-bonding arms. We introduce a charge dipole into MB waters. We perform (NPT) Monte Carlo simulations to explore how water molecules are organized around ions and around nonpolar solutes in salt solutions. The model gives good qualitative agreement with experiments, including Jones-Dole viscosity B coefficients, Samoilov and Hirata ion hydration activation energies, ion solvation thermodynamics, and Setschenow coefficients for Hofmeister series ions, which describe the salt concentration dependence of the solubilities of hydrophobic solutes. The two main ideas captured here are (1) that charge densities govern the interactions of ions with water, and (2) that a balance of forces determines water structure: electrostatics (water's dipole interacting with ions) and hydrogen bonding (water interacting with neighboring waters). Small ions (kosmotropes) have high charge densities so they cause strong electrostatic ordering of nearby waters, breaking hydrogen bonds. In contrast, large ions (chaotropes) have low charge densities, and surrounding water molecules are largely hydrogen bonded.

Theoretical prediction of pKa in methanol: testing SM8 and SMD models for carboxylic acids, phenols, and amines.

PubMed

Miguel, Elizabeth L M; Silva, Poliana L; Pliego, Josefredo R

2014-05-29

Methanol is a widely used solvent for chemical reactions and has solvation properties similar to those of water. However, the performance of continuum solvation models in this solvent has not been tested yet. In this report, we have investigated the performance of the SM8 and SMD models for pKa prediction of 26 carboxylic acids, 24 phenols, and 23 amines in methanol. The gas phase contribution was included at the X3LYP/TZVPP+diff//X3LYP/DZV+P(d) level. Using the proton exchange reaction with acetic acid, phenol, and ammonia as reference species leads to RMS error in the range of 1.4 to 3.6 pKa units. This finding suggests that the performance of the continuum models for methanol is similar to that found for aqueous solvent. Application of simple empirical correction through a linear equation leads to accurate pKa prediction, with uncertainty less than 0.8 units with the SM8 method. Testing with the less expensive PBE1PBE/6-311+G** method results in a slight improvement in the results.

Computational analysis of the solvation of coffee ingredients in aqueous ionic liquid mixtures.

PubMed

Zeindlhofer, Veronika; Khlan, Diana; Bica, Katharina; Schröder, Christian

2017-01-13

In this paper, we investigate the solvation of coffee ingredients including caffeine, gallic acid as representative for phenolic compounds and quercetin as representative for flavonoids in aqueous mixtures of the ionic liquid 1-ethyl-3-methylimidazolium acetate [C 2 mim][OAc] at various concentrations. Due to the anisotropy of the solutes we show that classical Kirkwood-Buff theory is not appropriate to study solvation effects with increasing ionic liquid content. However, excess coordination numbers as well as the mean residence time of solvent molecules at the surface of the solutes can be determined by Voronoi tessellation. Since the volume of the hydration shells is also available by this method, solvation free energies will be discussed as a function of the ionic liquid concentration to yield a physical meaningful picture of solvation for the anisotropic solutes. Hydrogen bonding capabilities of the solutes and their relevance for experimental extraction yields from spent coffee grounds are also discussed.

Elucidating Solvation Structures for Rational Design of Multivalent Electrolytes-A Review.

PubMed

Rajput, Nav Nidhi; Seguin, Trevor J; Wood, Brandon M; Qu, Xiaohui; Persson, Kristin A

2018-04-26

Fundamental molecular-level understanding of functional properties of liquid solutions provides an important basis for designing optimized electrolytes for numerous applications. In particular, exhaustive knowledge of solvation structure, stability, and transport properties is critical for developing stable electrolytes for fast-charging and high-energy-density next-generation energy storage systems. Accordingly, there is growing interest in the rational design of electrolytes for beyond lithium-ion systems by tuning the molecular-level interactions of solvate species present in the electrolytes. Here we present a review of the solvation structure of multivalent electrolytes and its impact on the electrochemical performance of these batteries. A direct correlation between solvate species present in the solution and macroscopic properties of electrolytes is sparse for multivalent electrolytes and contradictory results have been reported in the literature. This review aims to illustrate the current understanding, compare results, and highlight future needs and directions to enable the deep understanding needed for the rational design of improved multivalent electrolytes.

Stabilization of Quinapril by Incorporating Hydrogen Bonding Interactions

PubMed Central

Roy, B. N.; Singh, G. P.; Godbole, H. M.; Nehate, S. P.

2009-01-01

In the present study stability of various known solvates of quinapril hydrochloride has been compared with nitromethane solvate. Nitromethane solvate was found to be more stable compared to other known solvates. Single crystal X-ray diffraction analysis of quinapril nitromethane solvate shows intermolecular hydrogen bonding between quinapril molecule and nitromethane. Stabilization of quinapril by forming strong hydrogen bonding network as in case of co-crystals was further studied by forming co-crystal with tris(hydroxymethyl)amino methane. Quinapril free base forms a stable salt with tris(hydroxymethyl)amino methane not reported earlier. Quinapril tris(hydroxymethyl)amino methane salt found to be stable even at 80° for 72 h i.e. hardly any formation of diketopiperazine and diacid impurity. As expected single crystal X-ray diffraction analysis reveals tris(hydroxymethyl)amino methane salt of quinapril shows complex hydrogen bonding network between the two entities along with ionic bond. The properties of this stable salt - stable in solid as well as solution phase, might lead to an alternate highly stable formulation. PMID:20502545

Communication: Free-energy analysis of hydration effect on protein with explicit solvent: Equilibrium fluctuation of cytochrome c

NASA Astrophysics Data System (ADS)

Karino, Yasuhito; Matubayasi, Nobuyuki

2011-01-01

The relationship between the protein conformation and the hydration effect is investigated for the equilibrium fluctuation of cytochrome c. To elucidate the hydration effect with explicit solvent, the solvation free energy of the protein immersed in water was calculated using the molecular dynamics simulation coupled with the method of energy representation. The variations of the protein intramolecular energy and the solvation free energy are found to compensate each other in the course of equilibrium structural fluctuation. The roles of the attractive and repulsive components in the protein-water interaction are further examined for the solvation free energy. The attractive component represented as the average sum of protein-water interaction energy is dominated by the electrostatic effect and is correlated to the solvation free energy through the linear-response-type relationship. No correlation with the (total) solvation free energy is seen, on the other hand, for the repulsive component expressed as the excluded-volume effect.

Ultrafast Decay of the Solvated Electron in a Neat Polar Solvent: The Unusual Case of Propylene Carbonate.

PubMed

Le Caër, Sophie; Ortiz, Daniel; Marignier, Jean-Louis; Schmidhammer, Uli; Belloni, Jacqueline; Mostafavi, Mehran

2016-01-07

The behavior of carbonates is critical for a detailed understanding of aging phenomena in Li-ion batteries. Here we study the first reaction stages of propylene carbonate (PC), a cyclical carbonate, by picosecond pulse radiolysis. An absorption band with a maximum around 1360 nm is observed at 20 ps after the electron pulse and is shifted to 1310 nm after 50 ps. This band presents the features of a solvated electron absorption band, the solvation lasting up to 50 ps. Surprisingly, in this polar solvent, the solvated electron follows an ultrafast decay and disappears with a half time of 360 ps. This is attributed to the formation of a radical anion PC(-•). The yield of the solvated electron is low, suggesting that the radical anions are mainly directly produced from presolvated electrons. These results demonstrate that the initial electron transfers mechanisms are strongly different in linear compared with cyclical carbonates.

Electron solvation and localization at interfaces

NASA Astrophysics Data System (ADS)

Harris, Charles B.; Szymanski, Paul; Garrett-Roe, Sean; Miller, Andre D.; Gaffney, Kelly J.; Liu, Simon H.; Bezel, Ilya

2003-12-01

Two-photon photoemission of thiolate/Ag(111), nitrile/Ag(111), and alcohol/Ag(111) interfaces elucidates electron solvation and localization in two dimensions. For low coverages of thiolates on Ag(111), the occupied (HOMO) and unoccupied (LUMO) electronic states of the sulfer-silver bond are localized due to the lattice gas structure of the adsorbate. As the coverage saturates and the adsorbate-adsorbate nearest neighbor distance decreases, the HOMO and LUMO delocalize across many adsorbate molecules. Alcohol- and nitrile-covered Ag(111) surfaces solvate excess image potential state (IPS) electrons. In the case of alcohol-covered surfaces, this solvation is due to a shift in the local workfunction of the surface. For two-monolayer coverages of nitriles/Ag(111), localization accompanies solvation of the IPS. The size of the localized electron can be estimated by Fourier transformation of the wavefunction from momentum- to position-space. The IPS electron localizes to 15 +/- 4 angstroms full-width at half maximum in the plane of the surface, i.e., to a single lattice site.

Destruction of Energetic Materials in Supercritical Water

DTIC Science & Technology

2002-06-25

PHASE BEHAVIOR UNDER HYDROTHERMAL PROCESSING CONDITIONS...172 E. MODELING TOOLS FOR SOLVATION FREE ENERGIES IN HYDROTHERMAL SYSTEMS...potential equations of state of hydrothermal solutions. Figure 25 shows a schematic of the transient grating experiment. In this experiment, two laser

Solvation and Dynamics of Sodium and Potassium in Ethylene Carbonate from ab Initio Molecular Dynamics Simulations

DOE PAGES

Pham, Tuan Anh; Kweon, Kyoung E.; Samanta, Amit; ...

2017-09-18

The development of sodium and potassium batteries offers a promising way to meet the scaling and cost challenges of energy storage. However, compared to Li +, several intrinsic properties of Na + and K +, including their solvation and dynamics in typical organic electrolytes utilized in battery applications, are less well-understood. Here in this paper, we report a systematic investigation of Na + and K + in ethylene carbonate (EC) using first-principles molecular dynamics simulations. Our simulations reveal significant differences in the solvation structure and dynamical properties of Na + and K + compared to Li +. We find that,more » in contrast to Li + which exhibits a well-defined first solvation shell, the larger Na+ and K+ ions show more disordered and flexible solvation structures. These differences in solvation were found to significantly influence the ion dynamics, leading to larger diffusion coefficients of Na + and K + compared to Li +. Our simulations also reveal a clear and interesting analog in the behavior of the ions in EC and aqueous environments, particularly in the specific ion effects on the solvent dynamics. Lastly, this work provides fundamental understanding of the intrinsic properties of Na + and K + in organic electrolytes, which may ultimately influence the intercalation mechanism at the electrode–electrolyte interface and therefore battery performance, lifetime, and safety.« less

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.

Solvent-Induced Shift of Spectral Lines in Polar–Polarizable Solvents

DOE PAGES

Matyushov, Dmitry V.; Newton, Marshall D.

2017-03-09

Solvent-induced shift of optical transition lines is traditionally described by the Lippert- McRae equation given in terms of the Onsager theory for dipole solvation. It splits the overall shift into the equilibrium solvation by induced dipoles and the reaction field by the permanent dipoles in equilibrium with the chromophore in the ground state. Here we have reconsidered this classical problem from the perspective of microscopic solvation theories. A microscopic solvation functional is derived and continuum solvation is consistently introduced by taking the limit of zero wavevector in the reciprocal-space solvation susceptibility functions. We show that the phenomenological expression for themore » reaction field of permanent dipoles in the Lippert-McRae equation is not consistent with the microscopic theory. The main deficiency of the Lippert- McRae equation equation is the use of additivity of the response by permanent and induced dipoles of the liquid. An alternative closed-form equation for the spectral shift is derived. Its continuum limit allows a new, non-additive functionality for the solvent-induced shift in terms of the high-frequency and static dielectric constants. Finally, the main qualitative outcome of the theory is a significantly weaker dependence of the spectral shift on the polarizability of the solvent than predicted by the Lippert-McRae formula.« less

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

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

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

2014-12-01

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

Solvent-Induced Shift of Spectral Lines in Polar-Polarizable Solvents.

PubMed

Matyushov, Dmitry V; Newton, Marshall D

2017-03-23

Solvent-induced shift of optical transition lines is traditionally described by the Lippert-McRae equation given in terms of the Onsager theory for dipole solvation. It splits the overall shift into the equilibrium solvation by induced dipoles and the reaction field by the permanent dipoles in equilibrium with the chromophore in the ground state. We have reconsidered this classical problem from the perspective of microscopic solvation theories. A microscopic solvation functional is derived, and continuum solvation is consistently introduced by taking the limit of zero wavevector in the reciprocal-space solvation susceptibility functions. We show that the phenomenological expression for the reaction field of permanent dipoles in the Lippert-McRae equation is not consistent with the microscopic theory. The main deficiency of the Lippert-McRae equation is the use of additivity of the response by permanent and induced dipoles of the liquid. An alternative closed-form equation for the spectral shift is derived. Its continuum limit allows a new, nonadditive functionality for the solvent-induced shift in terms of the high-frequency and static dielectric constants. The main qualitative outcome of the theory is a significantly weaker dependence of the spectral shift on the polarizability of the solvent than predicted by the Lippert-McRae formula.

Understanding the influence of capillary waves on solvation at the liquid-vapor interface

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

Rane, Kaustubh, E-mail: rane@csi.tu-darmstadt.de; Vegt, Nico F. A. van der

2016-03-21

This work investigates the question if surface capillary waves (CWs) affect interfacial solvation thermodynamic properties that determine the propensity of small molecules toward the liquid-vapor interface. We focus on (1) the evaluation of these properties from molecular simulations in a practical manner and (2) understanding them from the perspective of theories in solvation thermodynamics, especially solvent reorganization effects. Concerning the former objective, we propose a computational method that exploits the relationship between an external field acting on the liquid-vapor interface and the magnitude of CWs. The system considered contains the solvent, an externally applied field (f) and the solute moleculemore » fixed at a particular location. The magnitude of f is selected to induce changes in CWs. The difference between the solvation free energies computed in the presence and in the absence of f is then shown to quantify the contribution of CWs to interfacial solvation. We describe the implementation of this method in the canonical ensemble by using a Lennard-Jones solvent and a non-ionic solute. Results are shown for three types of solutes that differ in the nature of short-ranged repulsive (hard-core) interactions. Overall, we observe that CWs have a negligible or very small effect on the interfacial solvation free energy of a solute molecule fixed near the liquid-vapor interface for the above systems. We also explain how the effects of pinning or dampening of CWs caused by a fixed solute are effectively compensated and do not contribute to the solvation free energy.« less

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

NASA Technical Reports Server (NTRS)

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

2017-01-01

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

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

PubMed

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

2017-04-06

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

Molecular basis for competitive solvation of the Burkholderia cepacia lipase by sorbitol and urea.

PubMed

Oliveira, Ivan P; Martínez, Leandro

2016-08-21

Increasing the stability of proteins is important for their application in industrial processes. In the intracellular environment many small molecules, called osmolytes, contribute to protein stabilization under physical or chemical stress. Understanding the nature of the interactions of these osmolytes with proteins can help the design of solvents and mutations to increase protein stability in extracellular media. One of the most common stabilizing osmolyes is sorbitol and one of the most common chemical denaturants is urea. In this work, we use molecular dynamics simulations to obtain a detailed picture of the solvation of the Burkholderia cepacia lipase (BCL) in the presence of the protecting osmolyte sorbitol and of the urea denaturant. We show that both sorbitol and urea compete with water for interactions with the protein surface. Overall, sorbitol promotes the organization of water in the first solvation shell and displaces water from the second solvation shell, while urea causes opposite effects. These effects are, however, highly heterogeneous among residue types. For instance, the depletion of water from the first protein solvation shell by urea can be traced down essentially to the side chain of negatively charged residues. The organization of water in the first solvation shell promoted by sorbitol occurs at polar (but not charged) residues, where the urea effect is minor. By contrast, sorbitol depletes water from the second solvation shell of polar residues, while urea promotes water organization at the same distances. The interactions of urea with negatively charged residues are insensitive to the presence of sorbitol. This osmolyte removes water and urea particularly from the second solvation shell of polar and non-polar residues. In summary, we provide a comprehensive description of the diversity of protein-solvent interactions, which can guide further investigations on the stability of proteins in non-conventional media, and assist solvent and protein design.

Salt formation improved the properties of a candidate drug during early formulation development.

PubMed

Sigfridsson, Kalle; Ahlqvist, Matti; Lindsjö, Martin; Paulsson, Stefan

2018-07-30

The purpose of this study was to investigate if AZD5329, a dual neurokinin NK1/2 receptor antagonist, is a suitable candidate for further development as an oral immediate release (IR) solid dosage form as a final product. The neutral form of AZD5329 has only been isolated as amorphous material. In order to search for a solid material with improved physical and chemical stability and more suitable solid-state properties, a salt screen was performed. Crystalline material of a maleic acid salt and a fumaric acid salt of AZD5329 were obtained. X-ray powder diffractiometry, thermogravimetric analysis, differential scanning calorimetry and dynamic vapor sorption were used to investigate the physicochemical characteristics of the two salts. The fumarate salt of AZD5329 is anhydrous, the crystallization is reproducible and the hygroscopicity is acceptable. Early polymorphism assessment work using slurry technique did not reveal any better crystal modification or crystallinity for the fumarate salt. For the maleate salt, the form isolated originally was found to be a solvate, but an anhydrous form was found in later experiments; by suspension in water or acetone, by drying of the solvate to 100-120 °C or by subjecting the solvate form to conditions of 40 °C/75%RH for 3 months. The dissolution behavior and the chemical stability (in aqueous solutions, formulations and solid-state) of both salts were also studied and found to be satisfactory. The compound displays sensitivity to low pH, and the salt of the maleic acid, which is the stronger acid, shows more degradation during stability studies, in line with this observation. The presented data indicate that the substance fulfils basic requirements for further development of an IR dosage form, based on the characterization on crystalline salts of AZD5329. Copyright © 2018 Elsevier B.V. All rights reserved.

CO2 Capture and Conversion on Rutile TiO2(110) in the Water Environment: Insight by First-Principles Calculations.

PubMed

Yin, Wen-Jin; Krack, Matthias; Wen, Bo; Ma, Shang-Yi; Liu, Li-Min

2015-07-02

The conversion of CO2 by the virtue of sunlight has the great potential to produce useful fuels or valuable chemicals while decreasing CO2 emission from the traditional fossil fuels. Here, we use the first-principles calculations combined with the periodic continuum solvation model (PCSM) to explore the adsorption and reactivity of CO2 on rutile TiO2(110) in the water environment. The results exhibit that both adsorption structures and reactivity of CO2 are greatly affected by water coadsorption on rutile TiO2(110). In particular, the solvation effect can change the most stable adsorption configuration of CO2 and H2O on rutile TiO2(110). In addition, the detailed conversion mechanism of CO2 reduction is further explored in the water environment. The results reveal that the solvation effect cannot only greatly decrease the energy barrier of CO2 reduction but also affect the selectivity of the reaction processes. These results presented here show the importance of the aqueous solution, which should be helpful to understand the detailed reaction processes of photocatalysts.

Cation solvation with quantum chemical effects modeled by a size-consistent multi-partitioning quantum mechanics/molecular mechanics method.

PubMed

Watanabe, Hiroshi C; Kubillus, Maximilian; Kubař, Tomáš; Stach, Robert; Mizaikoff, Boris; Ishikita, Hiroshi

2017-07-21

In the condensed phase, quantum chemical properties such as many-body effects and intermolecular charge fluctuations are critical determinants of the solvation structure and dynamics. Thus, a quantum mechanical (QM) molecular description is required for both solute and solvent to incorporate these properties. However, it is challenging to conduct molecular dynamics (MD) simulations for condensed systems of sufficient scale when adapting QM potentials. To overcome this problem, we recently developed the size-consistent multi-partitioning (SCMP) quantum mechanics/molecular mechanics (QM/MM) method and realized stable and accurate MD simulations, using the QM potential to a benchmark system. In the present study, as the first application of the SCMP method, we have investigated the structures and dynamics of Na + , K + , and Ca 2+ solutions based on nanosecond-scale sampling, a sampling 100-times longer than that of conventional QM-based samplings. Furthermore, we have evaluated two dynamic properties, the diffusion coefficient and difference spectra, with high statistical certainty. Furthermore the calculation of these properties has not previously been possible within the conventional QM/MM framework. Based on our analysis, we have quantitatively evaluated the quantum chemical solvation effects, which show distinct differences between the cations.

Molecular Dynamics Simulations of Hydration Effects on Solvation, Diffusivity, and Permeability in Chitosan/Chitin Films.

PubMed

McDonnell, Marshall T; Greeley, Duncan A; Kit, Kevin M; Keffer, David J

2016-09-01

The effects of hydration on the solvation, diffusivity, solubility, and permeability of oxygen molecules in sustainable, biodegradable chitosan/chitin food packaging films were studied via molecular dynamics and confined random walk simulations. With increasing hydration, the membrane has a more homogeneous water distribution with the polymer chains being fully solvated. The diffusivity increased by a factor of 4 for oxygen molecules and by an order of magnitude for water with increasing the humidity. To calculate the Henry's constant and solubility of oxygen in the membranes with changing hydration, the excess chemical potential was calculated via free energy perturbation, thermodynamic integration and direct particle deletion methods. The simulations predicted a higher solubility and permeability for the lower humidity, in contradiction to experimental results. All three methods for calculating the solubility were in good agreement. It was found that the Coulombic interactions in the potential caused the oxygen to bind too strongly to the protonated amine group. Insight from this work will help guide molecular modeling of chitosan/chitin membranes, specifically permeability measurements for small solute molecules. Efforts to chemically tailor chitosan/chitin membranes to favor discrete as opposed to continuous aqueous domains could reduce oxygen permeability.

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

Thin Metallic Films From Solvated Metal Atoms

NASA Astrophysics Data System (ADS)

Trivino, Galo C.; Klabunde, Kenneth J.; Dale, Brock

1988-02-01

Metals were evaporated under vacuum and the metal atoms solvated by excess organic solvents at low temperature. Upon warming stable colloidal metal particles were formed by controlled metal atom clustering. The particles were stabilized toward flocculation by solvation and electrostatic effects. Upon solvent removal the colloidal particles grew to form thin films that were metallic in appearance, but showed higher resistivities than pure metallic films. Gold, palladium, platinium, and especially indium are discussed.

Revisiting structure and dynamics of preferential solvation of K(I) ion in aqueous ammonia using QMCF-MD simulation

NASA Astrophysics Data System (ADS)

Hidayat, Yuniawan; Pranowo, Harno Dwi; Armunanto, Ria

2018-05-01

Structure and dynamics of preferential solvation of K(I) ion in aqueous ammonia have been reinvestigated using ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) simulation. The average coordination number of the first solvation consists of 2 ammonia and 4 waters. The mean residence time is less than 2 ps confirming the rapid mobility of ligands. The distance evolution data shows the frequent of ligand exchanges. The second solvation shell shows a more labile structure. The NBO analysis of the first shell structure emphasizes that interaction of K(I)-H2O is stronger than K(I)-NH3. The Wiberg bond confirms a weak electrostatic of ion-ligand interaction.

Decomposition of total solvation energy into core, side-chains and water contributions: Role of cross correlations and protein conformational fluctuations in dynamics of hydration layer

NASA Astrophysics Data System (ADS)

Mondal, Sayantan; Mukherjee, Saumyak; Bagchi, Biman

2017-09-01

Dynamical coupling between water and amino acid side-chain residues in solvation dynamics is investigated by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on protein surface. Such differently placed residues are found to exhibit different timescales of relaxation. The total solvation response measured by the probe is decomposed in terms of its interactions with (i) protein core, (ii) side-chain and (iii) water. Significant anti cross-correlation among these contributions are observed. When the motion of the protein side-chains is quenched, solvation either becomes faster or slower depending on the location of the probe.

Development and application of QM/MM methods to study the solvation effects and surfaces

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

Dibya, Pooja Arora

2010-01-01

Quantum mechanical (QM) calculations have the advantage of attaining high-level accuracy, however QM calculations become computationally inefficient as the size of the system grows. Solving complex molecular problems on large systems and ensembles by using quantum mechanics still poses a challenge in terms of the computational cost. Methods that are based on classical mechanics are an inexpensive alternative, but they lack accuracy. A good trade off between accuracy and efficiency is achieved by combining QM methods with molecular mechanics (MM) methods to use the robustness of the QM methods in terms of accuracy and the MM methods to minimize themore » computational cost. Two types of QM combined with MM (QM/MM) methods are the main focus of the present dissertation: the application and development of QM/MM methods for solvation studies and reactions on the Si(100) surface. The solvation studies were performed using a discreet solvation model that is largely based on first principles called the effective fragment potential method (EFP). The main idea of combining the EFP method with quantum mechanics is to accurately treat the solute-solvent and solvent-solvent interactions, such as electrostatic, polarization, dispersion and charge transfer, that are important in correctly calculating solvent effects on systems of interest. A second QM/MM method called SIMOMM (surface integrated molecular orbital molecular mechanics) is a hybrid QM/MM embedded cluster model that mimics the real surface.3 This method was employed to calculate the potential energy surfaces for reactions of atomic O on the Si(100) surface. The hybrid QM/MM method is a computationally inexpensive approach for studying reactions on larger surfaces in a reasonably accurate and efficient manner. This thesis is comprised of four chapters: Chapter 1 describes the general overview and motivation of the dissertation and gives a broad background of the computational methods that have been employed in this work. Chapter 2 illustrates the methodology of the interface of the EFP method with the configuration interaction with single excitations (CIS) method to study solvent effects in excited states. Chapter 3 discusses the study of the adiabatic electron affinity of the hydroxyl radical in aqueous solution and in micro-solvated clusters using a QM/EFP method. Chapter 4 describes the study of etching and diffusion of oxygen atom on a reconstructed Si(100)-2 x 1 surface using a hybrid QM/MM embedded cluster model (SIMOMM). Chapter 4 elucidates the application of the EFP method towards the understanding of the aqueous ionization potential of Na atom. Finally, a general conclusion of this dissertation work and prospective future direction are presented in Chapter 6.« less

Linear solvation energy relationship for the adsorption of synthetic organic compounds on single-walled carbon nanotubes in water.

PubMed

Ding, H; Chen, C; Zhang, X

2016-01-01

The linear solvation energy relationship (LSER) was applied to predict the adsorption coefficient (K) of synthetic organic compounds (SOCs) on single-walled carbon nanotubes (SWCNTs). A total of 40 log K values were used to develop and validate the LSER model. The adsorption data for 34 SOCs were collected from 13 published articles and the other six were obtained in our experiment. The optimal model composed of four descriptors was developed by a stepwise multiple linear regression (MLR) method. The adjusted r(2) (r(2)adj) and root mean square error (RMSE) were 0.84 and 0.49, respectively, indicating good fitness. The leave-one-out cross-validation Q(2) ([Formula: see text]) was 0.79, suggesting the robustness of the model was satisfactory. The external Q(2) ([Formula: see text]) and RMSE (RMSEext) were 0.72 and 0.50, respectively, showing the model's strong predictive ability. Hydrogen bond donating interaction (bB) and cavity formation and dispersion interactions (vV) stood out as the two most influential factors controlling the adsorption of SOCs onto SWCNTs. The equilibrium concentration would affect the fitness and predictive ability of the model, while the coefficients varied slightly.

Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent

NASA Astrophysics Data System (ADS)

Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu

2011-10-01

A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into "alpha helix" and "beta sheet" structures. The 5-residue polyalanine displays a substantial increase in the "beta strand" fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling.

Preferential solvation bromophenol blue in water-alcohol binary mixture.

PubMed

Dangui, Anayana Z; Santos, Vanessa M S; Gomes, Benhur S; de Castilho, Taiane S; Nicolini, Keller P; Nicolini, Jaqueline

2018-05-29

In this study, the perichromic behavior of bromophenol blue (BPB) in various binary solvent mixtures was investigated. The binary mixtures considered were comprised of water and methanol (MeOH), ethanol (EtOH), n-propanol (n-PrOH), isopropanol (iso-PrOH) or t-butanol (t-BuOH). The investigation of a preferential solvation model that considers the addition of small quantities of alcohol to water in the presence of bromophenol blue (BPB) is described in this paper. The data obtained were employed to study the preferential solvation (PS) of the probe. It was observed that with increases in the molar fraction of water the spontaneity of the system decreases. This can be explained by the high solubility of BPB in ethanol, with ∆G>0 at higher wavelengths (region rich in water with violet solution) and ∆G<0 at lower wavelengths (region rich in alcohol with yellow solution). The pK of the binary mixture changed in all solvents and for all ratios, and the higher the water ratio is the lower the pK In will be. In binary mixture, an increase in the hydrogen bond acceptor (HBA) nature of the solvents tested resulted in a bathochromic effect on the absorption band of BPB (Δλ=12nm). All of the data obtained showed a good nonlinear fit with the mathematical model (SD≤6.6×10 -3 ), suggesting that BPB has other potential applications besides its use as a pH indicator. Copyright © 2017. Published by Elsevier B.V.

First-principles prediction of the effects of temperature and solvent selection on the dimerization of benzoic acid.

PubMed

Pham, Hieu H; Taylor, Christopher D; Henson, Neil J

2013-01-24

We introduce a procedure of quantum chemical calculations (B3P86/6-31G**) to study carboxylic acid dimerization and its correlation with temperature and properties of the solvent. Benzoic acid is chosen as a model system for studying dimerization via hydrogen bonding. Organic solvents are simulated using the self-consistent reaction field (SCRF) method with the polarized continuum model (PCM). The cyclic dimer is the most stable structure both in gas phase and solution. Dimer mono- and dihydrates could be found in the gas phase if acid molecules are in contact with water vapor. However, the formation of these hydrated conformers is very limited and cyclic dimer is the principal conformer to coexist with monomer acid in solution. Solvation of the cyclic dimer is more favorable compared to other complexes, partially due to the diminishing of hydrogen bonding capability and annihilation of dipole moments. Solvents have a strong effect on inducing dimer dissociation and this dependence is more pronounced at low dielectric constants. By accounting for selected terms in the total free energy of solvation, the solvation entropy could be incorporated to predict the dimer behavior at elevated temperatures. The temperature dependence of benzoic acid dimerization obtained by this technique is in good agreement with available experimental measurements, in which a tendency of dimer to dissociate is observed with increased temperatures. In addition, dimer breakup is more sensitive to temperature in low dielectric environments rather than in solvents with a higher dielectric constant.

Modeling solubility of CO2/hydrocarbon gas in ionic liquid ([emim][FAP]) using Aspen Plus simulations.

PubMed

Bagchi, Bishwadeep; Sati, Sushmita; Shilapuram, Vidyasagar

2017-08-01

The Peng-Robinson equation of state with quadratic van der Waals (vdW) mixing rule model was chosen to perform the thermodynamic calculations in Flash3 column of Aspen Plus to predict the solubility of CO 2 or any one of the hydrocarbons (HCs) among methane, ethane, propane, and butane in an ionic liquid 1-ethyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate ([emim][FAP]). Bubble point pressure, solubility, bubble point temperature, fugacity, and partial molar volume at infinite dilution were obtained from the simulations, and enthalpy of absorption, Gibbs free energy of solvation, and entropy change of absorption were estimated by thermodynamic relations. Results show that carbon chain length has a significant effect on the bubble point pressure. Methane has the highest bubble point pressure among all the considered HCs and CO 2 . The bubble point pressure and fugacity variation with temperature is different for CO 2 as compared to HCs for mole fractions above 0.2. Two different profiles are noticed for enthalpy of absorption when plotted as a function of mole fraction of gas soluble in IL. Partial molar volume of CO 2 decreases with increase in temperature in [emim][FAP], while it is increased for HCs. Bubble point temperature decreases with increase in the mole fraction of the solute. Entropy of solvation increases with temperature till a particular value followed by a decrease with further increase in temperature. Gibbs free energy change of solvation showed that the process of solubility was spontaneous.

A simple model for solvation in mixed solvents. Applications to the stabilization and destabilization of macromolecular structures.

PubMed

Schellman, J A

1990-08-31

The properties of a simple model for solvation in mixed solvents are explored in this paper. The model is based on the supposition that solvent replacement is a simple one-for-one substitution reaction at macromolecular sites which are independent of one another. This leads to a new form for the binding polynomial in which all terms are associated with ligand interchange rather than ligand addition. The principal solvent acts as one of the ligands. Thermodynamic analysis then shows that thermodynamic binding (i.e., selective interaction) depends on the properties of K'-1, whereas stoichiometric binding (site occupation) depends on K'. K' is a 'practical' interchange equilibrium constant given by (f3/f1)K, where K is the true equilibrium constant for the interchange of components 3 and 1 on the site and f3 and f4 denote their respective activity coefficients on the mole fraction scale. Values of K' less than unity lead to negative selective interaction. It is selective interaction and not occupation number which determines the thermodynamic effects of solvation. When K' greater than 100 on the mole fraction scale or K' greater than 2 on the molality scale (in water), the differences between stoichiometric binding and selective interaction become less than 1%. The theory of this paper is therefore necessary only for very weak binding constants. When K'-1 is small, large concentrations of the added solvent component are required to produce a thermodynamic effect. Under these circumstances the isotherms for the selective interaction and for the excess (or transfer) free energy are strongly dependent on the behavior of the activity coefficients of both solvent components. Two classes of behavior are described depending on whether the components display positive or negative deviations from Raoult's law. Examples which are discussed are aqueous solutions of urea and guanidinium chloride for positive deviations and of sucrose and glucose for negative deviations. Examination of the few studies which have been reported in the literature shows that most of the qualitative features of the stabilization of proteins by sugars and their destabilization by urea and guanidinium chloride are faithfully represented with the model. This includes maxima in the free energy of stabilization and destabilization, decreased and zero selective interaction at high concentrations, etc. These phenomena had no prior explanation. Deficiencies in the model as a representation of solvation in aqueous solution are discussed in the appendix.

The road not taken: Applications of fluorescence spectroscopy and electronic structure theory to systems of materials and biological relevance

NASA Astrophysics Data System (ADS)

Carlson, Philip Joseph

Applications of Fluorescence Spectroscopy and Electronic Structure Theory to Systems of Materials and Biological Relevance. The photophysics of curcumin was studied in micelles and the solvation dynamics were probed. The high-energy ionic liquid HEATN was also studied using the fragment molecular orbital method. The solvation dynamics of the HEATN system were determined. This marks the first study of the solvation dynamics in a triazolium ionic liquid system.

Phase-Equilibria and Nanostructure Formation in Charged Rigid-Rod Polymers and Carbon Nanotubes

DTIC Science & Technology

2002-11-10

or liquid crystalline) and the crystalline polymer state. The form-I crystal solvate, identi- fied as a cocrystal of the protonated polymer and the...dissolution temperature, below 100 °C.12,13 The form-II crystal solvate, considered a polymer-solvent cocrystal in which the polymer is deprotonated,11,12...solvate that is a cocrystal of protonated PBZT and PPA anions. As previously mentioned, the fact that these two extreme cases result in similar

Understanding Lithium Solvation and Diffusion through Topological Analysis of First-Principles Molecular Dynamics

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

Bhatia, Harsh; Gyulassy, Attila; Ong, Mitchell

2016-09-27

The performance of lithium-ion batteries is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact, both, the solvation and diffusivity of Li ions. In this work, we present our application of the topological techniques to extract and predict such behavior in the data generated by the first-principles molecular dynamics simulation of Li ions in an important organic solvent -ethylene carbonate. More specifically, we use the scalar topology of the electron charge density field tomore » analyze the evolution of the solvation structures. This allows us to derive a parameter-free bond definition for lithium-oxygen bonds, to provide a quantitative measure for bond strength, and to understand the regions of influence of each atom in the simulation. This has provided new insights into how and under what conditions certain bonds may form and break. As a result, we can identify and, more importantly, predict, unstable configurations in solvation structures. This can be very useful in understanding when small changes to the atoms' movements can cause significantly different bond structures to evolve. Ultimately, this promises to allow scientists to explore lithium ion solvation and diffusion more systematically, with the aim of new insights and potentially accelerating the calculations themselves.« less

Accurate Theoretical Predictions of the Properties of Energetic Materials

DTIC Science & Technology

2008-09-18

decomposition, Monte Carlo, molecular dynamics, supercritical fluids, solvation and separation, quantum Monte Carlo, potential energy surfaces, RDX , TNAZ...labs, who are contributing to the theoretical efforts, providing data for testing of the models, or aiding in the transition of the methods, models...and results to DoD applications. The major goals of the project are: • Models that describe phase transitions and chemical reactions in

Theoretical and computational studies of renewable energy materials: Room temperature ionic liquids and proton exchange membranes

NASA Astrophysics Data System (ADS)

Feng, Shulu

2011-12-01

Two kinds of renewable energy materials, room temperature ionic liquids (RTILs) and proton exchange membranes (PEMs), especially Nafion, are studied by computational and theoretical approaches. The ultimate purpose of the present research is to design novel materials to meet the future energy demands. To elucidate the effect of alkyl side chain length and anion on the structure and dynamics of the mixtures, molecular dynamics (MD) simulations of three RTILs/water mixtures at various water mole fractions: 1-butyl-3-methylimidazolium (BMIM+)/BF4-, 1-octyl-3-methylimidazolium (OMIM+)/BF4-, and OMIM +/Cl- are performed. Replacing the BMIM + cation with OMIM+ results in stronger aggregation of the cations as well as a slower diffusion of the anions, and replacing the BF4- anion with Cl- alters the water distribution at low water mole fractions and slows diffusion of the mixtures. Potential experimental manifestations of these behaviors in both cases are provided. Proton solvation properties and transport mechanisms are studied in hydrated Nafion, by using the self-consistent multistate empirical valence bond (SCI-MS-EVB) method. It is found that by stabilizing a more Zundel-like (H5O 2+) structure in the first solvation shells, the solvation of excess protons, as well as the proton hydration structure are both influenced by the sulfonate groups. Hydrate proton-related hydrogen bond networks are observed to be more stable than those with water alone. In order to characterize the nature of the proton transport (PT), diffusive motion, Arrhenius activation energies, and transport pathways are calculated and analyzed. Analysis of diffusive motion suggests that (1) a proton-hopping mechanism dominates the proton transport for the studied water loading levels and (2) there is an obvious degree of anti-correlation between the proton hopping and the vehicular transport. The activation energy drops rapidly with an increasing water content when the water loading level is smaller than ˜ 10 H2O/SO 3-, which is consistent with experimental observations. The sulfonate groups are also found to have influence on the proton hopping directions. The temperature and water content effects on the PT pathways are also investigated. The morphological effects on proton solvation and transport in hydrated Nafion are investigated, by using the SCI-MS-EVB method. Two of the most significant morphological models of Nafion, the lamellar model and the cylinder model, are selected. The two models exhibit distinct PT patterns, which result in different proton diffusion rates. In both models, the interaction between protons and the sulfonate groups are proven to be the key to determining PT behavior. The proton solvation structure change as a function of the distance between protons and sulfonate groups has been analyzed. It is found that the increase of water cylinder radius or water layer height leads to the presence of more protons around the sulfonate groups. Furthermore, at a lower hydration level, the increased amount of protons around the sulfonate groups consists of more Zundel-like structures, which is influenced by the distinct morphological structures of Nafion.

Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

PubMed Central

Ricci, Clarisse Gravina; Li, Bo; Cheng, Li-Tien; Dzubiella, Joachim; McCammon, J. Andrew

2018-01-01

Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed) solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes. PMID:29484300

Influence of temperature and molecular structure on ionic liquid solvation layers.

PubMed

Wakeham, Deborah; Hayes, Robert; Warr, Gregory G; Atkin, Rob

2009-04-30

Atomic force microscopy (AFM) force profiling is used to investigate the structure of adsorbed and solvation layers formed on a mica surface by various room temperature ionic liquids (ILs) ethylammonium nitrate (EAN), ethanolammonium nitrate (EtAN), ethylammonium formate (EAF), propylammonium formate (PAF), ethylmethylammonium formate (EMAF), and dimethylethylammonium formate (DMEAF). At least seven layers are observed for EAN at 14 degrees C (melting point 13 degrees C), decreasing as the temperature is increased to 30 degrees C due to thermal energy disrupting solvophobic forces that lead to segregation of cation alkyl tails from the charged ammonium and nitrate moieties. The number and properties of the solvation layers can also be controlled by introducing an alcohol moiety to the cation's alkyl tail (EtAN), or by replacing the nitrate anion with formate (EAF and PAF), even leading to the detection of distinct cation and anion sublayers. Substitution of primary by secondary or tertiary ammonium cations reduces the number of solvation layers formed, and also weakens the cation layer adsorbed onto mica. The observed solvation and adsorbed layer structures are discussed in terms of the intermolecular cohesive forces within the ILs.

Computational analysis of the solvation of coffee ingredients in aqueous ionic liquid mixtures† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6ra24736a Click here for additional data file.

PubMed Central

Zeindlhofer, Veronika; Khlan, Diana; Bica, Katharina

2017-01-01

In this paper, we investigate the solvation of coffee ingredients including caffeine, gallic acid as representative for phenolic compounds and quercetin as representative for flavonoids in aqueous mixtures of the ionic liquid 1-ethyl-3-methylimidazolium acetate [C2mim][OAc] at various concentrations. Due to the anisotropy of the solutes we show that classical Kirkwood–Buff theory is not appropriate to study solvation effects with increasing ionic liquid content. However, excess coordination numbers as well as the mean residence time of solvent molecules at the surface of the solutes can be determined by Voronoi tessellation. Since the volume of the hydration shells is also available by this method, solvation free energies will be discussed as a function of the ionic liquid concentration to yield a physical meaningful picture of solvation for the anisotropic solutes. Hydrogen bonding capabilities of the solutes and their relevance for experimental extraction yields from spent coffee grounds are also discussed. PMID:28496974

Highly Stable Lithium Metal Batteries Enabled by Regulating the Solvation of Lithium Ions in Nonaqueous Electrolytes.

PubMed

Zhang, Xue-Qiang; Chen, Xiang; Cheng, Xin-Bing; Li, Bo-Quan; Shen, Xin; Yan, Chong; Huang, Jia-Qi; Zhang, Qiang

2018-05-04

Safe and rechargeable lithium metal batteries have been difficult to achieve because of the formation of lithium dendrites. Herein an emerging electrolyte based on a simple solvation strategy is proposed for highly stable lithium metal anodes in both coin and pouch cells. Fluoroethylene carbonate (FEC) and lithium nitrate (LiNO 3 ) were concurrently introduced into an electrolyte, thus altering the solvation sheath of lithium ions, and forming a uniform solid electrolyte interphase (SEI), with an abundance of LiF and LiN x O y on a working lithium metal anode with dendrite-free lithium deposition. Ultrahigh Coulombic efficiency (99.96 %) and long lifespans (1000 cycles) were achieved when the FEC/LiNO 3 electrolyte was applied in working batteries. The solvation chemistry of electrolyte was further explored by molecular dynamics simulations and first-principles calculations. This work provides insight into understanding the critical role of the solvation of lithium ions in forming the SEI and delivering an effective route to optimize electrolytes for safe lithium metal batteries. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Solvation of the fluorine containing anions and their lithium salts in propylene carbonate and dimethoxyethane.

PubMed

Chaban, Vitaly

2015-07-01

Electrolyte solutions based on the propylene carbonate (PC)-dimethoxyethane (DME) mixtures are of significant importance and urgency due to emergence of lithium-ion batteries. Solvation and coordination of the lithium cation in these systems have been recently attended in detail. However, analogous information concerning anions (tetrafluoroborate, hexafluorophosphate) is still missed. This work reports PM7-MD simulations (electronic-structure level of description) to include finite-temperature effects on the anion solvation regularities in the PC-DME mixture. The reported result evidences that the anions appear weakly solvated. This observation is linked to the absence of suitable coordination sites in the solvent molecules. In the concentrated electrolyte solutions, both BF4(-) and PF6(-) prefer to exist as neutral ion pairs (LiBF4, LiPF6).

Negative ion photoelectron spectroscopy of solvated electron cluster anions, (H2O){/n -} and (NH3){/n -}

NASA Astrophysics Data System (ADS)

Lee, G. H.; Arnold, S. T.; Eaton, J. G.; Sarkas, H. W.; Bowen, K. H.; Ludewigt, C.; Haberland, H.

1991-03-01

The photodetachment spectra of (H2O){/n =2-69/-} and (NH3){/n =41-1100/-} have been recorded, and vertical detachment energies (VDEs) were obtained from the spectra. For both systems, the cluster anion VDEs increase smoothly with increasing sizes and most species plot linearly with n -1/3, extrapolating to a VDE ( n=∞) value which is very close to the photoelectric threshold energy for the corresponding condensed phase solvated electron system. The linear extrapolation of this data to the analogous condensed phase property suggests that these cluster anions are gas phase counterparts to solvated electrons, i.e. they are embryonic forms of hydrated and ammoniated electrons which mature with increasing cluster size toward condensed phase solvated electrons.

Solvation of Cr 3+ cation in water-acetonitrile mixture studied by IR spectroscopy: molecular penetration into the solvation shells

NASA Astrophysics Data System (ADS)

Jamróz, Dorota; Wójcik, Marek; Lindgren, Jan

2000-09-01

Infrared spectra of mixtures of water and deuteroacetonitrile containing the Cr 3+ cation have been studied as a function of concentration, time and temperature. The CN stretching vibration of CD 3CN molecules has been used as a probe of the structural environments. The CN band in the spectra of the solutions is a superposition of four subbands, which may be attributed to CD 3CN bound in the first, second, and third solvation shells of the cation and to non-bound CD 3CN. The character of changes of the integral intensities of the subbands with time for various H 2O:Cr 3+ molar ratios are explained by suggesting mechanisms of molecular replacement within the solvation shells of Cr 3+.

Expedited Selection of NMR Chiral Solvating Agents for Determination of Enantiopurity

PubMed Central

2016-01-01

The use of NMR chiral solvating agents (CSAs) for the analysis of enantiopurity has been known for decades, but has been supplanted in recent years by chromatographic enantioseparation technology. While chromatographic methods for the analysis of enantiopurity are now commonplace and easy to implement, there are still individual compounds and entire classes of analytes where enantioseparation can prove extremely difficult, notably, compounds that are chiral by virtue of very subtle differences such as isotopic substitution or small differences in alkyl chain length. NMR analysis using CSAs can often be useful for such problems, but the traditional approach to selection of an appropriate CSA and the development of an NMR-based analysis method often involves a trial-and-error approach that can be relatively slow and tedious. In this study we describe a high-throughput experimentation approach to the selection of NMR CSAs that employs automation-enabled screening of prepared libraries of CSAs in a systematic fashion. This approach affords excellent results for a standard set of enantioenriched compounds, providing a valuable comparative data set for the effectiveness of CSAs for different classes of compounds. In addition, the technique has been successfully applied to challenging pharmaceutical development problems that are not amenable to chromatographic solutions. Overall, this methodology provides a rapid and powerful approach for investigating enantiopurity that compliments and augments conventional chromatographic approaches. PMID:27280168

The Denaturation Transition of DNA in Mixed Solvents

PubMed Central

Hammouda, Boualem; Worcester, David

2006-01-01

The helix-to-coil denaturation transition in DNA has been investigated in mixed solvents at high concentration using ultraviolet light absorption spectroscopy and small-angle neutron scattering. Two solvents have been used: water and ethylene glycol. The “melting” transition temperature was found to be 94°C for 4% mass fraction DNA/d-water and 38°C for 4% mass fraction DNA/d-ethylene glycol. The DNA melting transition temperature was found to vary linearly with the solvent fraction in the mixed solvents case. Deuterated solvents (d-water and d-ethylene glycol) were used to enhance the small-angle neutron scattering signal and 0.1M NaCl (or 0.0058 g/g mass fraction) salt concentration was added to screen charge interactions in all cases. DNA structural information was obtained by small-angle neutron scattering, including a correlation length characteristic of the inter-distance between the hydrogen-containing (desoxyribose sugar-amine base) groups. This correlation length was found to increase from 8.5 to 12.3 Å across the melting transition. Ethylene glycol and water mixed solvents were found to mix randomly in the solvation region in the helix phase, but nonideal solvent mixing was found in the melted coil phase. In the coil phase, solvent mixtures are more effective solvating agents than either of the individual solvents. Once melted, DNA coils behave like swollen water-soluble synthetic polymer chains. PMID:16815902

Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and their Complexes with Proteins

PubMed Central

Nguyen, Hai; Pérez, Alberto; Bermeo, Sherry; Simmerling, Carlos

2016-01-01

The Generalized Born (GB) implicit solvent model has undergone significant improvements in accuracy for modeling of proteins and small molecules. However, GB still remains a less widely explored option for nucleic acid simulations, in part because fast GB models are often unable to maintain stable nucleic acid structures, or they introduce structural bias in proteins, leading to difficulty in application of GB models in simulations of protein-nucleic acid complexes. Recently, GB-neck2 was developed to improve the behavior of protein simulations. In an effort to create a more accurate model for nucleic acids, a similar procedure to the development of GB-neck2 is described here for nucleic acids. The resulting parameter set significantly reduces absolute and relative energy error relative to Poisson Boltzmann for both nucleic acids and nucleic acid-protein complexes, when compared to its predecessor GB-neck model. This improvement in solvation energy calculation translates to increased structural stability for simulations of DNA and RNA duplexes, quadruplexes, and protein-nucleic acid complexes. The GB-neck2 model also enables successful folding of small DNA and RNA hairpins to near native structures as determined from comparison with experiment. The functional form and all required parameters are provided here and also implemented in the AMBER software. PMID:26574454

Coulomb repulsion in short polypeptides.

PubMed

Norouzy, Amir; Assaf, Khaleel I; Zhang, Shuai; Jacob, Maik H; Nau, Werner M

2015-01-08

Coulomb repulsion between like-charged side chains is presently viewed as a major force that impacts the biological activity of intrinsically disordered polypeptides (IDPs) by determining their spatial dimensions. We investigated short synthetic models of IDPs, purely composed of ionizable amino acid residues and therefore expected to display an extreme structural and dynamic response to pH variation. Two synergistic, custom-made, time-resolved fluorescence methods were applied in tandem to study the structure and dynamics of the acidic and basic hexapeptides Asp6, Glu6, Arg6, Lys6, and His6 between pH 1 and 12. (i) End-to-end distances were obtained from the short-distance Förster resonance energy transfer (sdFRET) from N-terminal 5-fluoro-l-tryptophan (FTrp) to C-terminal Dbo. (ii) End-to-end collision rates were obtained for the same peptides from the collision-induced fluorescence quenching (CIFQ) of Dbo by FTrp. Unexpectedly, the very high increase of charge density at elevated pH had no dynamical or conformational consequence in the anionic chains, neither in the absence nor in the presence of salt, in conflict with the common view and in partial conflict with accompanying molecular dynamics simulations. In contrast, the cationic peptides responded to ionization but with surprising patterns that mirrored the rich individual characteristics of each side chain type. The contrasting results had to be interpreted, by considering salt screening experiments, N-terminal acetylation, and simulations, in terms of an interplay of local dielectric constant and peptide-length dependent side chain charge-charge repulsion, side chain functional group solvation, N-terminal and side chain charge-charge repulsion, and side chain-side chain as well as side chain-backbone interactions. The common picture that emerged is that Coulomb repulsion between water-solvated side chains is efficiently quenched in short peptides as long as side chains are not in direct contact with each other or the main chain.

Prediction of pH-Dependent Hydrophobic Profiles of Small Molecules from Miertus-Scrocco-Tomasi Continuum Solvation Calculations.

PubMed

Zamora, William J; Curutchet, Carles; Campanera, Josep M; Luque, F Javier

2017-10-26

Hydrophobicity is a key physicochemical descriptor used to understand the biological profile of (bio)organic compounds as well as a broad variety of biochemical, pharmacological, and toxicological processes. This property is estimated from the partition coefficient between aqueous and nonaqueous environments for neutral compounds (P N ) and corrected for the pH-dependence of ionizable compounds as the distribution coefficient (D). Here, we have extended the parametrization of the Miertus-Scrocco-Tomasi continuum solvation model in n-octanol to nitrogen-containing heterocyclic compounds, as they are present in many biologically relevant molecules (e.g., purines and pyrimidines bases, amino acids, and drugs), to obtain accurate log P N values for these molecules. This refinement also includes solvation calculations for ionic species in n-octanol with the aim of reproducing the experimental partition of ionic compounds (P I ). Finally, the suitability of different formalisms to estimate the distribution coefficient for a wide range of pH values has been examined for a set of small acidic and basic compounds. The results indicate that in general the simple pH-dependence model of the ionizable compound in water suffices to predict the partitioning at or around physiological pH. However, at extreme pH values, where ionic species are predominant, more elaborate models provide a better prediction of the n-octanol/water distribution coefficient, especially for amino acid analogues. Finally, the results also show that these formalisms are better suited to reproduce the experimental pH-dependent distribution curves of log D for both acidic and basic compounds as well as for amino acid analogues.

Periodic density functional theory calculations of bulk and the (010) surface of goethite

PubMed Central

Kubicki, James D; Paul, Kristian W; Sparks, Donald L

2008-01-01

Background Goethite is a common and reactive mineral in the environment. The transport of contaminants and anaerobic respiration of microbes are significantly affected by adsorption and reduction reactions involving goethite. An understanding of the mineral-water interface of goethite is critical for determining the molecular-scale mechanisms of adsorption and reduction reactions. In this study, periodic density functional theory (DFT) calculations were performed on the mineral goethite and its (010) surface, using the Vienna Ab Initio Simulation Package (VASP). Results Calculations of the bulk mineral structure accurately reproduced the observed crystal structure and vibrational frequencies, suggesting that this computational methodology was suitable for modeling the goethite-water interface. Energy-minimized structures of bare, hydrated (one H2O layer) and solvated (three H2O layers) (010) surfaces were calculated for 1 × 1 and 3 × 3 unit cell slabs. A good correlation between the calculated and observed vibrational frequencies was found for the 1 × 1 solvated surface. However, differences between the 1 × 1 and 3 × 3 slab calculations indicated that larger models may be necessary to simulate the relaxation of water at the interface. Comparison of two hydrated surfaces with molecularly and dissociatively adsorbed H2O showed a significantly lower potential energy for the former. Conclusion Surface Fe-O and (Fe)O-H bond lengths are reported that may be useful in surface complexation models (SCM) of the goethite (010) surface. These bond lengths were found to change significantly as a function of solvation (i.e., addition of two extra H2O layers above the surface), indicating that this parameter should be carefully considered in future SCM studies of metal oxide-water interfaces. PMID:18477389

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

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

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

2016-06-28

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

Solvent Vapor Annealing of Amorphous Carbamazepine Films for Fast Polymorph Screening and Dissolution Alteration.

PubMed

Schrode, Benedikt; Bodak, Brigitta; Riegler, Hans; Zimmer, Andreas; Christian, Paul; Werzer, Oliver

2017-09-30

Solubility enhancement and thus higher bioavailability are of great importance and a constant challenge in pharmaceutical research whereby polymorph screening and selection is one of the most important tasks. A very promising approach for polymorph screening is solvent vapor annealing where a sample is exposed to an atmosphere saturated with molecules of a specific chemical/solvent. In this work, amorphous carbamazepine thin films were prepared by spin coating, and the transformation into crystalline forms under exposure to solvent vapors was investigated. Employing grazing incidence X-ray diffraction, four distinct carbamazepine polymorphs, a solvate, and hydrates could be identified, while optical microscopy showed mainly spherulitic morphologies. In vitro dissolution experiments revealed different carbamazepine release from the various thin-film samples containing distinct polymorphic compositions: heat treatment of amorphous samples at 80 °C results in an immediate release; samples exposed to EtOH vapors show a drug release about 5 times slower than this immediate one; and all the others had intermediate release profiles. Noteworthy, even the sample of slowest release has a manifold faster release compared to a standard powder sample demonstrating the capabilities of thin-film preparation for faster drug release in general. Despite the small number of samples in this screening experiment, the results clearly show how solvent vapor annealing can assist in identifying potential polymorphs and allows for estimating their impact on properties like bioavailability.

Computational prediction of the pKas of small peptides through Conceptual DFT descriptors

NASA Astrophysics Data System (ADS)

Frau, Juan; Hernández-Haro, Noemí; Glossman-Mitnik, Daniel

2017-03-01

The experimental pKa of a group of simple amines have been plotted against several Conceptual DFT descriptors calculated by means of different density functionals, basis sets and solvation schemes. It was found that the best fits are those that relate the pKa of the amines with the global hardness η through the MN12SX density functional in connection with the Def2TZVP basis set and the SMD solvation model, using water as a solvent. The parameterized equation resulting from the linear regression analysis has then been used for the prediction of the pKa of small peptides of interest in the study of diabetes and Alzheimer disease. The accuracy of the results is relatively good, with a MAD of 0.36 units of pKa.

Improved pKa Prediction of Substituted Alcohols, Phenols, and Hydroperoxides in Aqueous Medium Using Density Functional Theory and a Cluster-Continuum Solvation Model.

PubMed

Thapa, Bishnu; Schlegel, H Bernhard

2017-06-22

Acid dissociation constants (pK a 's) are key physicochemical properties that are needed to understand the structure and reactivity of molecules in solution. Theoretical pK a 's have been calculated for a set of 72 organic compounds with -OH and -OOH groups (48 with known experimental pK a 's). This test set includes 17 aliphatic alcohols, 25 substituted phenols, and 30 hydroperoxides. Calculations in aqueous medium have been carried out with SMD implicit solvation and three hybrid DFT functionals (B3LYP, ωB97XD, and M06-2X) with two basis sets (6-31+G(d,p) and 6-311++G(d,p)). The effect of explicit water molecules on calculated pK a 's was assessed by including up to three water molecules. pK a 's calculated with only SMD implicit solvation are found to have average errors greater than 6 pK a units. Including one explicit water reduces the error by about 3 pK a units, but the error is still far from chemical accuracy. With B3LYP/6-311++G(d,p) and three explicit water molecules in SMD solvation, the mean signed error and standard deviation are only -0.02 ± 0.55; a linear fit with zero intercept has a slope of 1.005 and R 2 = 0.97. Thus, this level of theory can be used to calculate pK a 's directly without the need for linear correlations or thermodynamic cycles. Estimated pK a values are reported for 24 hydroperoxides that have not yet been determined experimentally.

Physical driving force of actomyosin motility based on the hydration effect.

PubMed

Suzuki, Makoto; Mogami, George; Ohsugi, Hideyuki; Watanabe, Takahiro; Matubayasi, Nobuyuki

2017-12-01

We propose a driving force hypothesis based on previous thermodynamics, kinetics and structural data as well as additional experiments and calculations presented here on water-related phenomena in the actomyosin systems. Although Szent-Györgyi pointed out the importance of water in muscle contraction in 1951, few studies have focused on the water science of muscle because of the difficulty of analyzing hydration properties of the muscle proteins, actin, and myosin. The thermodynamics and energetics of muscle contraction are linked to the water-mediated regulation of protein-ligand and protein-protein interactions along with structural changes in protein molecules. In this study, we assume the following two points: (1) the periodic electric field distribution along an actin filament (F-actin) is unidirectionally modified upon binding of myosin subfragment 1 (M or myosin S1) with ADP and inorganic phosphate Pi (M.ADP.Pi complex) and (2) the solvation free energy of myosin S1 depends on the external electric field strength and the solvation free energy of myosin S1 in close proximity to F-actin can become the potential force to drive myosin S1 along F-actin. The first assumption is supported by integration of experimental reports. The second assumption is supported by model calculations utilizing molecular dynamics (MD) simulation to determine solvation free energies of a small organic molecule and two small proteins. MD simulations utilize the energy representation method (ER) and the roughly proportional relationship between the solvation free energy and the solvent-accessible surface area (SASA) of the protein. The estimated driving force acting on myosin S1 is as high as several piconewtons (pN), which is consistent with the experimentally observed force. © 2017 Wiley Periodicals, Inc.

Free energy functionals for polarization fluctuations: Pekar factor revisited

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

Dinpajooh, Mohammadhasan; Newton, Marshall D.; Matyushov, Dmitry V.

The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. Within dielectric continuum models, this separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom. The main qualitative prediction of Pekar’s perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation. The Pekar factor enters the solvent reorganization energy of electron transfer reactions and is a significant mechanistic parametermore » accounting for the solvent effect on electron transfer. Here, we study the separation of the fast and slow polarization modes in polar molecular liquids (polarizable dipolar liquids and polarizable water force fields) without relying on the continuum approximation. We derive the nonlocal free energy functional and use atomistic numerical simulations to obtain nonlocal, reciprocal space electronic and nuclear susceptibilities. A consistent transition to the continuum limit is introduced by extrapolating the results of finite-size numerical simulation to zero wavevector. The continuum nuclear susceptibility extracted from simulations is numerically close to the Pekar factor. However, we derive a new functionality involving the static and high-frequency dielectric constants. The main distinction of our approach from the traditional theories is found for the solvation free energy due to the nuclear polarization: the anticipated significant drop of its magnitude with increasing liquid polarizability does not occur. The reorganization energy of electron transfer is either nearly constant with increasing the solvent polarizability and the corresponding high-frequency dielectric constant (polarizable dipolar liquids) or actually noticeably increases (polarizable force fields of water).« less

Why are ionic liquid ions mainly associated in water? A Car-Parrinello study of 1-ethyl-3-methyl-imidazolium chloride water mixture

NASA Astrophysics Data System (ADS)

Spickermann, C.; Thar, J.; Lehmann, S. B. C.; Zahn, S.; Hunger, J.; Buchner, R.; Hunt, P. A.; Welton, T.; Kirchner, B.

2008-09-01

In this study we present the results of a first principles molecular dynamics simulation of a single 1-ethyl-3-methyl-imidazolium chloride [C2C1im][Cl] ion pair dissolved in 60 water molecules. We observe a preference of the in plane chloride coordination with respect to the cation ring plane as compared to the energetic slightly more demanding on top coordination. Evaluation of the different radial distribution functions demonstrates that the structure of the hydration shell around the ion pair differs significantly from bulk water and that no true ion pair dissociation in terms of completely autonomous solvation shells takes place on the timescale of the simulation. In addition, dipole moment distributions of the solvent in distinct solvation shells around different functional parts of the [C2C1im][Cl] ion pair are calculated from maximally localized Wannier functions. The analysis of these distributions gives evidence for a depolarization of water molecules close to the hydrophobic parts of the cation as well as close to the anion. Examination of the angular distribution of different OH(H2O )-X angles in turn shows a linear coordination of chloride accompanied by a tangential orientation of water molecules around the hydrophobic groups, being a typical feature of hydrophobic hydration. Based on these orientational aspects, a structural model for the obvious preference of ion pair association is developed, which justifies the associating behavior of solvated [C2C1im][Cl] ions in terms of an energetically favorable interface between the solvation shells of the anion and the hydrophobic parts of the cation.

Why are ionic liquid ions mainly associated in water? A Car-Parrinello study of 1-ethyl-3-methyl-imidazolium chloride water mixture.

PubMed

Spickermann, C; Thar, J; Lehmann, S B C; Zahn, S; Hunger, J; Buchner, R; Hunt, P A; Welton, T; Kirchner, B

2008-09-14

In this study we present the results of a first principles molecular dynamics simulation of a single 1-ethyl-3-methyl-imidazolium chloride [C(2)C(1)im][Cl] ion pair dissolved in 60 water molecules. We observe a preference of the in plane chloride coordination with respect to the cation ring plane as compared to the energetic slightly more demanding on top coordination. Evaluation of the different radial distribution functions demonstrates that the structure of the hydration shell around the ion pair differs significantly from bulk water and that no true ion pair dissociation in terms of completely autonomous solvation shells takes place on the timescale of the simulation. In addition, dipole moment distributions of the solvent in distinct solvation shells around different functional parts of the [C(2)C(1)im][Cl] ion pair are calculated from maximally localized Wannier functions. The analysis of these distributions gives evidence for a depolarization of water molecules close to the hydrophobic parts of the cation as well as close to the anion. Examination of the angular distribution of different OH(H(2)O)-X angles in turn shows a linear coordination of chloride accompanied by a tangential orientation of water molecules around the hydrophobic groups, being a typical feature of hydrophobic hydration. Based on these orientational aspects, a structural model for the obvious preference of ion pair association is developed, which justifies the associating behavior of solvated [C(2)C(1)im][Cl] ions in terms of an energetically favorable interface between the solvation shells of the anion and the hydrophobic parts of the cation.

Free energy functionals for polarization fluctuations: Pekar factor revisited

DOE PAGES

Dinpajooh, Mohammadhasan; Newton, Marshall D.; Matyushov, Dmitry V.

2017-02-13

The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. Within dielectric continuum models, this separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom. The main qualitative prediction of Pekar’s perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation. The Pekar factor enters the solvent reorganization energy of electron transfer reactions and is a significant mechanistic parametermore » accounting for the solvent effect on electron transfer. Here, we study the separation of the fast and slow polarization modes in polar molecular liquids (polarizable dipolar liquids and polarizable water force fields) without relying on the continuum approximation. We derive the nonlocal free energy functional and use atomistic numerical simulations to obtain nonlocal, reciprocal space electronic and nuclear susceptibilities. A consistent transition to the continuum limit is introduced by extrapolating the results of finite-size numerical simulation to zero wavevector. The continuum nuclear susceptibility extracted from simulations is numerically close to the Pekar factor. However, we derive a new functionality involving the static and high-frequency dielectric constants. The main distinction of our approach from the traditional theories is found for the solvation free energy due to the nuclear polarization: the anticipated significant drop of its magnitude with increasing liquid polarizability does not occur. The reorganization energy of electron transfer is either nearly constant with increasing the solvent polarizability and the corresponding high-frequency dielectric constant (polarizable dipolar liquids) or actually noticeably increases (polarizable force fields of water).« less

Free energy functionals for polarization fluctuations: Pekar factor revisited.

PubMed

Dinpajooh, Mohammadhasan; Newton, Marshall D; Matyushov, Dmitry V

2017-02-14

The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. Within dielectric continuum models, this separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom. The main qualitative prediction of Pekar's perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation. The Pekar factor enters the solvent reorganization energy of electron transfer reactions and is a significant mechanistic parameter accounting for the solvent effect on electron transfer. Here, we study the separation of the fast and slow polarization modes in polar molecular liquids (polarizable dipolar liquids and polarizable water force fields) without relying on the continuum approximation. We derive the nonlocal free energy functional and use atomistic numerical simulations to obtain nonlocal, reciprocal space electronic and nuclear susceptibilities. A consistent transition to the continuum limit is introduced by extrapolating the results of finite-size numerical simulation to zero wavevector. The continuum nuclear susceptibility extracted from the simulations is numerically close to the Pekar factor. However, we derive a new functionality involving the static and high-frequency dielectric constants. The main distinction of our approach from the traditional theories is found in the solvation free energy due to the nuclear polarization: the anticipated significant drop of its magnitude with increasing liquid polarizability does not occur. The reorganization energy of electron transfer is either nearly constant with increasing the solvent polarizability and the corresponding high-frequency dielectric constant (polarizable dipolar liquids) or actually noticeably increases (polarizable force fields of water).

Viscosity and Solvation

ERIC Educational Resources Information Center

Robertson, C. T.

1973-01-01

Discusses theories underlying the phenomena of solution viscosities, involving the Jones and Dole equation, B-coefficient determination, and flickering cluster model. Indicates that viscosity measurements provide a basis for the study of the structural effects of ions in aqueous solutions and are applicable in teaching high school chemistry. (CC)

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.

Thermodynamics of water structural reorganization due to geometric confinement

NASA Astrophysics Data System (ADS)

Stroberg, Wylie; Lichter, Seth

2015-03-01

Models of aqueous solvation have successfully quantified the behavior of water near convex bodies. However, many important processes occurring in aqueous solution involve interactions between solutes and surfaces with complicated non-convex geometries. Examples include the folding of proteins, hydrophobic association of solutes, ligand-receptor binding, and water confined within nanotubes and pores. For these geometries, models for solvation of convex bodies fail to account for the added interactions associated with structural confinement. Due to water's propensity to form networks of hydrogen bonds, small alterations to the confining geometry can induce large structural rearrangement within the water. We perform systematic Monte Carlo simulations of water confined to cylindrical cavities of varying aspect ratio to investigate how small geometric changes to the confining geometry may cause large changes to the structure and thermodynamic state of water. Using the Wang-Landau algorithm, we obtain free energies, enthalpies, entropies, and heat capacities across a broad range of temperatures, and show how these quantities are influenced by the structural rearrangement of water molecules due to geometric perturbations.

On the Dynamical Behavior of the Cysteine Dioxygenase-l-Cysteine Complex in the Presence of Free Dioxygen and l-Cysteine.

PubMed

Pietra, Francesco

2017-11-01

In this work, viable models of cysteine dioxygenase (CDO) and its complex with l-cysteine dianion were built for the first time, under strict adherence to the crystal structure from X-ray diffraction studies, for all atom molecular dynamics (MD). Based on the CHARMM36 FF, the active site, featuring an octahedral dummy Fe(II) model, allowed us observing water exchange, which would have escaped attention with the more popular bonded models. Free dioxygen (O 2 ) and l-cysteine, added at the active site, could be observed being expelled toward the solvating medium under Random Accelerated Molecular Dynamics (RAMD) along major and minor pathways. Correspondingly, free dioxygen (O 2 ), added to the solvating medium, could be observed to follow the same above pathways in getting to the active site under unbiased MD. For the bulky l-cysteine, 600 ns of trajectory were insufficient for protein penetration, and the molecule was stuck at the protein borders. These models pave the way to free energy studies of ligand associations, devised to better clarify how this cardinal enzyme behaves in human metabolism. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

Effect of the cation model on the equilibrium structure of poly-L-glutamate in aqueous sodium chloride solution

NASA Astrophysics Data System (ADS)

Marchand, Gabriel; Soetens, Jean-Christophe; Jacquemin, Denis; Bopp, Philippe A.

2015-12-01

We demonstrate that different sets of Lennard-Jones parameters proposed for the Na+ ion, in conjunction with the empirical combining rules routinely used in simulation packages, can lead to essentially different equilibrium structures for a deprotonated poly-L-glutamic acid molecule (poly-L-glutamate) dissolved in a 0.3M aqueous NaCl solution. It is, however, difficult to discriminate a priori between these model potentials; when investigating the structure of the Na+-solvation shell in bulk NaCl solution, all parameter sets lead to radial distribution functions and solvation numbers in broad agreement with the available experimental data. We do not find any such dependency of the equilibrium structure on the parameters associated with the Cl- ion. This work does not aim at recommending a particular set of parameters for any particular purpose. Instead, it stresses the model dependence of simulation results for complex systems such as biomolecules in solution and thus the difficulties if simulations are to be used for unbiased predictions, or to discriminate between contradictory experiments. However, this opens the possibility of validating a model specifically in view of analyzing experimental data believed to be reliable.

Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

NASA Astrophysics Data System (ADS)

Sanyal, Tanmoy; Shell, M. Scott

2016-07-01

Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one at which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.

Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding.

PubMed

Young, Tom; Abel, Robert; Kim, Byungchan; Berne, Bruce J; Friesner, Richard A

2007-01-16

The thermodynamic properties and phase behavior of water in confined regions can vary significantly from that observed in the bulk. This is particularly true for systems in which the confinement is on the molecular-length scale. In this study, we use molecular dynamics simulations and a powerful solvent analysis technique based on inhomogenous solvation theory to investigate the properties of water molecules that solvate the confined regions of protein active sites. Our simulations and analysis indicate that the solvation of protein active sites that are characterized by hydrophobic enclosure and correlated hydrogen bonds induce atypical entropic and enthalpic penalties of hydration. These penalties apparently stabilize the protein-ligand complex with respect to the independently solvated ligand and protein, which leads to enhanced binding affinities. Our analysis elucidates several challenging cases, including the super affinity of the streptavidin-biotin system.

Mapping the Free Energy of Lithium Solvation in the Protic Ionic Liquid Ethylammonuim Nitrate: A Metadynamics Study.

PubMed

Kachmar, Ali; Carignano, Marcelo; Laino, Teodoro; Iannuzzi, Marcella; Hutter, Jürg

2017-08-10

Understanding lithium solvation and transport in ionic liquids is important due to their possible application in electrochemical devices. Using first-principles simulations aided by a metadynamics approach we study the free-energy landscape for lithium ions at infinite dilution in ethylammonium nitrate, a protic ionic liquid. We analyze the local structure of the liquid around the lithium cation and obtain a quantitative picture in agreement with experimental findings. Our simulations show that the lowest two free energy minima correspond to conformations with the lithium ion being solvated either by three or four nitrate ions with a transition barrier between them of 0.2 eV. Other less probable conformations having different solvation pattern are also investigated. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of the composition of a solution on the enthalpies of solvation of piperidine in methanol-acetonitrile and dimethylsulfoxide-acetonitrile mixed solvents

NASA Astrophysics Data System (ADS)

Kuz'mina, I. A.; Volkova, M. A.; Sitnikova, K. A.; Sharnin, V. A.

2014-01-01

Heat effects of dissolution of piperidine (ppd) are measured by calorimetry at 298.15 K over the range of composition of acetonitrile-methanol (AN-MeOH) mixed solvents. Based on the Δsol H ○(ppd)AN-MeOH values obtained using the literature data on Δsol H ○ (ppd) in acetonitrile-dimethylsulfoxide (AN-DMSO) mixed solvents and the vaporization enthalpy of ppd, the enthalpies of solvation of amine in AN-MeOH and AN-DMSO binary mixtures are calculated. A rise in the exothermicity of solvation of piperidine is observed upon the transition from AN to DMSO and MeOH, due mainly to the enhanced solvation of the amino group of ppd as a result of changes in the acid-base properties of the mixed solvent.

Electrostatic Solvation Free Energy of Amino Acid Side Chain Analogs: Implications for the Validity of Electrostatic Linear Response in Water

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

Lin, Bin; Pettitt, Bernard M.

Electrostatic free energies of solvation for 15 neutral amino acid side chain analogs are computed. We compare three methods of varying computational complexity and accuracy for three force fields: free energy simulations, Poisson-Boltzmann (PB), and linear response approximation (LRA) using AMBER, CHARMM, and OPLSAA force fields. We find that deviations from simulation start at low charges for solutes. The approximate PB and LRA produce an overestimation of electrostatic solvation free energies for most of molecules studied here. These deviations are remarkably systematic. The variations among force fields are almost as large as the variations found among methods. Our study confirmsmore » that success of the approximate methods for electrostatic solvation free energies comes from their ability to evaluate free energy differences accurately.« less

Scaling Atomic Partial Charges of Carbonate Solvents for Lithium Ion Solvation and Diffusion

DOE PAGES

Chaudhari, Mangesh I.; Nair, Jijeesh R.; Pratt, Lawrence R.; ...

2016-10-21

Lithium-ion solvation and diffusion properties in ethylene carbonate (EC) and propylene carbonate (PC) were studied by molecular simulation, experiments, and electronic structure calculations. Studies carried out in water provide a reference for interpretation. Classical molecular dynamics simulation results are compared to ab initio molecular dynamics to assess nonpolarizable force field parameters for solvation structure of the carbonate solvents. Quasi-chemical theory (QCT) was adapted to take advantage of fourfold occupancy of the near-neighbor solvation structure observed in simulations and used to calculate solvation free energies. The computed free energy for transfer of Li + to PC from water, based on electronicmore » structure calculations with cluster-QCT, agrees with the experimental value. The simulation-based direct-QCT results with scaled partial charges agree with the electronic structure-based QCT values. The computed Li +/PF 6 - transference numbers of 0.35/0.65 (EC) and 0.31/0.69 (PC) agree well with NMR experimental values of 0.31/0.69 (EC) and 0.34/0.66 (PC) and similar values obtained here with impedance spectroscopy. These combined results demonstrate that solvent partial charges can be scaled in systems dominated by strong electrostatic interactions to achieve trends in ion solvation and transport properties that are comparable to ab initio and experimental results. Thus, the results support the use of scaled partial charges in simple, nonpolarizable force fields in future studies of these electrolyte solutions.« less

Picosecond solvation dynamics—A potential viewer of DMSO—Water binary mixtures

NASA Astrophysics Data System (ADS)

Banik, Debasis; Kundu, Niloy; Kuchlyan, Jagannath; Roy, Arpita; Banerjee, Chiranjib; Ghosh, Surajit; Sarkar, Nilmoni

2015-02-01

In this work, we have investigated the composition dependent anomalous behavior of dimethyl sulfoxide (DMSO)-water binary mixture by collecting the ultrafast solvent relaxation response around a well known solvation probe Coumarin 480 (C480) by using a femtosecond fluorescence up-conversion spectrometer. Recent molecular dynamics simulations have predicted two anomalous regions of DMSO-water binary mixture. Particularly, these studies encourage us to investigate the anomalies from experimental background. DMSO-water binary mixture has repeatedly given evidences of its dual anomalous nature in front of our systematic investigation through steady-state and time-resolved measurements. We have calculated average solvation times of C480 by two individual well-known methods, among them first one is spectral-reconstruction method and another one is single-wavelength measurement method. The results of both the methods roughly indicate that solvation time of C480 reaches maxima in the mole fraction of DMSO XD = 0.12-0.17 and XD = 0.27-0.35, respectively. Among them, the second region (XD = 0.27-0.35) is very common as most of the thermodynamic properties exhibit deviation in this range. Most probably, the anomalous solvation trend in this region is fully guided by the shear viscosity of the medium. However, the first region is the most interesting one. In this region due to formation of strongly hydrogen bonded 1DMSO:2H2O complexes, hydration around the probe C480 decreases, as a result of which solvation time increases.

Octanol-Water Partition Coefficient from 3D-RISM-KH Molecular Theory of Solvation with Partial Molar Volume Correction.

PubMed

Huang, WenJuan; Blinov, Nikolay; Kovalenko, Andriy

2015-04-30

The octanol-water partition coefficient is an important physical-chemical characteristic widely used to describe hydrophobic/hydrophilic properties of chemical compounds. The partition coefficient is related to the transfer free energy of a compound from water to octanol. Here, we introduce a new protocol for prediction of the partition coefficient based on the statistical-mechanical, 3D-RISM-KH molecular theory of solvation. It was shown recently that with the compound-solvent correlation functions obtained from the 3D-RISM-KH molecular theory of solvation, the free energy functional supplemented with the correction linearly related to the partial molar volume obtained from the Kirkwood-Buff/3D-RISM theory, also called the "universal correction" (UC), provides accurate prediction of the hydration free energy of small compounds, compared to explicit solvent molecular dynamics [ Palmer , D. S. ; J. Phys.: Condens. Matter 2010 , 22 , 492101 ]. Here we report that with the UC reparametrized accordingly this theory also provides an excellent agreement with the experimental data for the solvation free energy in nonpolar solvent (1-octanol) and so accurately predicts the octanol-water partition coefficient. The performance of the Kovalenko-Hirata (KH) and Gaussian fluctuation (GF) functionals of the solvation free energy, with and without UC, is tested on a large library of small compounds with diverse functional groups. The best agreement with the experimental data for octanol-water partition coefficients is obtained with the KH-UC solvation free energy functional.

Is there hope for multi-site complexation modeling?

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

Bickmore, Barry R.; Rosso, Kevin M.; Mitchell, S. C.

2006-06-06

It has been shown here that the standard formulation of the MUSIC model does not deliver the molecular-scale insight into oxide surface reactions that it promises. The model does not properly divide long-range electrostatic and short-range contributions to acid-base reaction energies, and it does not treat solvation in a physically realistic manner. However, even if the current MUSIC model does not succeed in its ambitions, its ambitions are still reasonable. It was a pioneering attempt in that Hiemstra and coworkers recognized that intrinsic equilibrium constants, where the effects of long-range electrostatic effects have been removed, must be theoretically constrained priormore » to model fitting if there is to be any hope of obtaining molecular-scale insights from SCMs. We have also shown, on the other hand, that it may be premature to dismiss all valence-based models of acidity. Not only can some such models accurately predict intrinsic acidity constants, but they can also now be linked to the results of molecular dynamics simulations of solvated systems. Significant challenges remain for those interested in creating SCMs that are accurate at the molecular scale. It will only be after all model parameters can be predicted from theory, and the models validated against titration data that we will be able to begin to have some confidence that we really are adequately describing the chemical systems in question.« less

Fluorescent probe studies of polarity and solvation within room temperature ionic liquids: a review.

PubMed

Pandey, Shubha; Baker, Sheila N; Pandey, Siddharth; Baker, Gary A

2012-09-01

Ionic liquids display an array of useful and sometimes unconventional, solvent features and have attracted considerable interest in the field of green chemistry for the potential they hold to significantly reduce environmental emissions. Some of these points have a bearing on the chemical reactivity of these systems and have also generated interest in the physical and theoretical aspects of solvation in ionic liquids. This review presents an introduction to the field of ionic liquids, followed by discussion of investigations into the solvation properties of neat ionic liquids or mixed systems including ionic liquids as a major or minor component. The ionic liquid based multicomponent systems discussed are composed of other solvents, other ionic liquids, carbon dioxide, surfactants or surfactant solutions. Although we clearly focus on fluorescence spectroscopy as a tool to illuminate ionic liquid systems, the issues discussed herein are of general relevance to discussions of polarity and solvent effects in ionic liquids. Transient solvation measurements carried out by means of time-resolved fluorescence measurements are particularly powerful for their ability to parameterize the kinetics of the solvation process in ionic liquids and are discussed as well.

Crystal structure and physicochemical characterization of ambazone monohydrate, anhydrous, and acetate salt solvate.

PubMed

Muresan-Pop, Marieta; Braga, Dario; Pop, Mihaela M; Borodi, Gheorghe; Kacso, Irina; Maini, Lucia

2014-11-01

The crystal structures of the monohydrate and anhydrous forms of ambazone were determined by single-crystal X-ray diffraction (SC-XRD). Ambazone monohydrate is characterized by an infinite three-dimensional network involving the water molecules, whereas anhydrous ambazone forms a two-dimensional network via hydrogen bonds. The reversible transformation between the monohydrate and anhydrous forms of ambazone was evidenced by thermal analysis, temperature-dependent X-ray powder diffraction and accelerated stability at elevated temperature, and relative humidity (RH). Additionally, a novel ambazone acetate salt solvate form was obtained and its nature was elucidated by SC-XRD. Powder dissolution measurements revealed a substantial solubility and dissolution rate improvement of acetate salt solvated form in water and physiological media compared with ambazone forms. Also, the acetate salt solvate displayed good thermal and solution stability but it transformed to the monohydrate on storage at elevated temperature and RH. Our study shows that despite the requirement for controlled storage conditions, the acetate salt solvated form could be an alternative to ambazone when solubility and bioavailability improvement is critical for the clinical efficacy of the drug product. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Spectroscopic and computational studies of ionic clusters as models of solvation and atmospheric reactions

NASA Astrophysics Data System (ADS)

Kuwata, Keith T.

Ionic clusters are useful as model systems for the study of fundamental processes in solution and in the atmosphere. Their structure and reactivity can be studied in detail using vibrational predissociation spectroscopy, in conjunction with high level ab initio calculations. This thesis presents the applications of infrared spectroscopy and computation to a variety of gas-phase cluster systems. A crucial component of the process of stratospheric ozone depletion is the action of polar stratospheric clouds (PSCs) to convert the reservoir species HCl and chlorine nitrate (ClONO2) to photochemically labile compounds. Quantum chemistry was used to explore one possible mechanism by which this activation is effected: Cl- + ClONO2 /to Cl2 + NO3- eqno(1)Correlated ab initio calculations predicted that the direct reaction of chloride ion with ClONO2 is facile, which was confirmed in an experimental kinetics study. In the reaction a weakly bound intermediate Cl2-NO3- is formed, with ~70% of the charge localized on the nitrate moiety. This enables the Cl2-NO3- cluster to be well solvated even in bulk solution, allowing (1) to be facile on PSCs. Quantum chemistry was also applied to the hydration of nitrosonium ion (NO+), an important process in the ionosphere. The calculations, in conjunction with an infrared spectroscopy experiment, revealed the structure of the gas-phase clusters NO+(H2O)n. The large degree of covalent interaction between NO+ and the lone pairs of the H2O ligands is contrasted with the weak electrostatic bonding between iodide ion and H2O. Finally, the competition between ion solvation and solvent self-association is explored for the gas-phase clusters Cl/-(H2O)n and Cl-(NH3)n. For the case of water, vibrational predissociation spectroscopy reveals less hydrogen bonding among H2O ligands than predicted by ab initio calculations. Nevertheless, for n /ge 5, cluster structure is dominated by water-water interactions, with Cl- only partially solvated by the water cluster. Preliminary infrared spectra and computations on Cl- (NH3)n indicate that NH3 preferentially binds to Cl- ion instead of forming inter-solvent networks.

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

PubMed

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

1998-09-01

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

Effect of solvation-related interaction on the low-temperature dynamics of proteins

NASA Astrophysics Data System (ADS)

Zuo, Guanghong; Wang, Jun; Qin, Meng; Xue, Bin; Wang, Wei

2010-03-01

The effect of solvation-related interaction on the low-temperature dynamics of proteins is studied by taking into account the desolvation barriers in the interactions of native contacts. It is found out that about the folding transition temperature, the protein folds in a cooperative manner, and the water molecules are expelled from the hydrophobic core at the final stage in the folding process. At low temperature, however, the protein would generally be trapped in many metastable conformations with some water molecules frozen inside the protein. The desolvation takes an important role in these processes. The number of frozen water molecules and that of frozen states of proteins are further analyzed with the methods based on principal component analysis (PCA) and the clustering of conformations. It is found out that both the numbers of frozen water molecules and the frozen states of the protein increase quickly below a certain temperature. Especially, the number of frozen states of the protein increases exponentially following the decrease in the temperature, which resembles the basic features of glassy dynamics. Interestingly, it is observed that the freezing of water molecules and that of protein conformations happen at almost the same temperature. This suggests that the solvation-related interaction performs an important role for the low-temperature dynamics of the model protein.

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

PubMed

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

2004-03-01

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

Photoionization and electron radical recombination dynamics in photoactive yellow protein investigated by ultrafast spectroscopy in the visible and near-infrared spectral region.

PubMed

Zhu, Jingyi; Paparelli, Laura; Hospes, Marijke; Arents, Jos; Kennis, John T M; van Stokkum, Ivo H M; Hellingwerf, Klaas J; Groot, Marie Louise

2013-09-26

Photoinduced ionization of the chromophore inside photoactive yellow protein (PYP) was investigated by ultrafast spectroscopy in the visible and near-infrared spectral regions. An absorption band that extended from around 550 to 850 nm was observed and ascribed to solvated electrons, ejected from the p-hydroxycinnamic acid anion chromophore upon the absorption of two 400 nm photons. Global kinetic analysis showed that the solvated electron absorption decayed in two stages: a shorter phase of around 10 ps and a longer phase of more than 3 ns. From a simulation based on a diffusion model we conclude that the diffusion rate of the electron is about 0.8 Å(2)/ps in wild type PYP, and that the electron is ejected to a short distance of only several angstroms away from the chromophore. The chromophore-protein pocket appears to provide a water-similar local environment for the electron. Because mutations at different places around the chromophore have different effect on the electron recombination dynamics, we suggest that solvated electrons could provide a new method to investigate the local dielectric environment inside PYP and thus help to understand the role of the protein in the photoisomerization process.

Papers from U.S. Department of Energy Science Undergraduate Laboratory Internship Program (SULI) 2010

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

Not Available

2011-06-22

The solvation sphere of halides in water has been investigated using a combination of extended x-ray absorption fine structure (EXAFS) and x-ray absorption near-edge structure (XANES) analysis techniques. The results have indicated that I{sup -} and Br{sup -} both have an asymmetric, 8 water molecule primary solvation spheres. These spheres are identical, with the Br{sup -} sphere about .3 {angstrom} smaller than the I{sup -} sphere. This study utilized near-edge analysis to supplement EXAFS analysis which suffers from signal dampening/broadening due to thermal noise. This paper has reported on the solvation first sphere of I{sup -} and Br{sup -} inmore » water. Using EXAFS and XANES analysis, strong models which describe the geometric configuration of water molecules coordinated to a central anion have been developed. The combination of these techniques has provided us with a more substantiated argument than relying solely on one or the other. An important finding of this study is that the size of the anion plays a smaller role than previously assumed in determining the number of coordinating water molecules. Further experimental and theoretical investigation is required to understand why the size of the anion plays a minor role in determining the number of water molecules bound.« less

Assessment of two theoretical methods to estimate potentiometrictitration curves of peptides: comparison with experiment

PubMed Central

Makowska, Joanna; Bagiñska, Katarzyna; Makowski, Mariusz; Jagielska, Anna; Liwo, Adam; Kasprzykowski, Franciszek; Chmurzyñski, Lech; Scheraga, Harold A.

2008-01-01

We compared the ability of two theoretical methods of pH-dependent conformational calculations to reproduce experimental potentiometric-titration curves of two models of peptides: Ac-K5-NHMe in 95% methanol (MeOH)/5% water mixture and Ac-XX(A)7OO-NH2 (XAO) (where X is diaminobutyric acid, A is alanine, and O is ornithine) in water, methanol (MeOH) and dimethylsulfoxide (DMSO), respectively. The titration curve of the former was taken from the literature, and the curve of the latter was determined in this work. The first theoretical method involves a conformational search using the Electrostatically Driven Monte Carlo (EDMC) method with a low-cost energy function (ECEPP/3 plus the SRFOPT surface-solvation model, assumming that all titratable groups are uncharged) and subsequent reevaluation of the free energy at a given pH with the Poisson-Boltzmann equation, considering variable protonation states. In the second procedure, MD simulations are run with the AMBER force field and the Generalized-Born model of electrostatic solvation, and the protonation states are sampled during constant-pH MD runs. In all three solvents, the first pKa of XAO is strongly downshifted compared to the value for the reference compounds (ethyl amine and propyl amine, respectively); the water and methanol curves have one, and the DMSO curve has two jumps characteristic of remarkable differences in the dissociation constants of acidic groups. The predicted titration curves of Ac-K5-NHMe are in good agreement with the experimental ones; better agreement is achieved with the MD-based method. The titration curves of XAO in methanol and DMSO, calculated using the MD-based approach, trace the shape of the experimental curves, reproducing the pH jump, while those calculated with the EDMC-based approach, and the titration curve in water calculated using the MD-based approach, have smooth shapes characteristic of the titration of weak multifunctional acids with small differences between the dissociation constants. Nevertheless, quantitative agreement between theoretically predicted and experimental titration curves is not achieved in all three solvents even with the MD-based approach which is manifested by a smaller pH range of the calculated titration curves with respect to the experimental curves. The poorer agreement obtained for water than for the non-aqueous solvents suggests a significant role of specific solvation in water, which cannot be accounted for by the mean-field solvation models. PMID:16509748

Assessment of two theoretical methods to estimate potentiometric titration curves of peptides: comparison with experiment.

PubMed

Makowska, Joanna; Bagiñska, Katarzyna; Makowski, Mariusz; Jagielska, Anna; Liwo, Adam; Kasprzykowski, Franciszek; Chmurzyñski, Lech; Scheraga, Harold A

2006-03-09

We compared the ability of two theoretical methods of pH-dependent conformational calculations to reproduce experimental potentiometric titration curves of two models of peptides: Ac-K5-NHMe in 95% methanol (MeOH)/5% water mixture and Ac-XX(A)7OO-NH2 (XAO) (where X is diaminobutyric acid, A is alanine, and O is ornithine) in water, methanol (MeOH), and dimethyl sulfoxide (DMSO), respectively. The titration curve of the former was taken from the literature, and the curve of the latter was determined in this work. The first theoretical method involves a conformational search using the electrostatically driven Monte Carlo (EDMC) method with a low-cost energy function (ECEPP/3 plus the SRFOPT surface-solvation model, assumming that all titratable groups are uncharged) and subsequent reevaluation of the free energy at a given pH with the Poisson-Boltzmann equation, considering variable protonation states. In the second procedure, molecular dynamics (MD) simulations are run with the AMBER force field and the generalized Born model of electrostatic solvation, and the protonation states are sampled during constant-pH MD runs. In all three solvents, the first pKa of XAO is strongly downshifted compared to the value for the reference compounds (ethylamine and propylamine, respectively); the water and methanol curves have one, and the DMSO curve has two jumps characteristic of remarkable differences in the dissociation constants of acidic groups. The predicted titration curves of Ac-K5-NHMe are in good agreement with the experimental ones; better agreement is achieved with the MD-based method. The titration curves of XAO in methanol and DMSO, calculated using the MD-based approach, trace the shape of the experimental curves, reproducing the pH jump, while those calculated with the EDMC-based approach and the titration curve in water calculated using the MD-based approach have smooth shapes characteristic of the titration of weak multifunctional acids with small differences between the dissociation constants. Nevertheless, quantitative agreement between theoretically predicted and experimental titration curves is not achieved in all three solvents even with the MD-based approach, which is manifested by a smaller pH range of the calculated titration curves with respect to the experimental curves. The poorer agreement obtained for water than for the nonaqueous solvents suggests a significant role of specific solvation in water, which cannot be accounted for by the mean-field solvation models.

Systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions

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

Cooks, Robert Graham; Li, Anyin; Luo, Qingjie

The invention generally relates to systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions. In certain aspects, the invention provides methods that involve providing a metal and a solvent. The methods additionally involve applying voltage to the solvated metal to thereby produce solvent droplets including ions of the metal containing compound, and directing the solvent droplets including the metal ions to a target. In certain embodiments, once at the target, the metal ions can react directly or catalyze reactions.

Preferential solvatation of human serum albumin in dimethylsulfoxide-H2O binary solution

NASA Astrophysics Data System (ADS)

Grigoryan, K. R.

2009-12-01

The preferential solvatation of human serum albumin (HSA) in dimethylsulfoxide (DMSO) aqueous solutions were studied using the densitometry method. It has been shown that at DMSO low concentrations HSA undergoes to preferential hydration, but at DMSO higher concentrations preferential binding of DMSO molecules to protein occurs. It has been estimated that DMSO exhibits stabilizing/destabilizing effect on HSA structure which is explained in terms of hydration/solvatation of protein, on the one hand, and the medium structure enhancement/disruption around the protein molecule, on the other hand.

Systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions

DOEpatents

Cooks, Robert Graham; Li, Anyin; Luo, Qingjie

2017-01-24

The invention generally relates to systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions. In certain aspects, the invention provides methods that involve providing a metal and a solvent. The methods additionally involve applying voltage to the solvated metal to thereby produce solvent droplets including ions of the metal containing compound, and directing the solvent droplets including the metal ions to a target. In certain embodiments, once at the target, the metal ions can react directly or catalyze reactions.

Electron Solvation in Two Dimensions

NASA Astrophysics Data System (ADS)

Miller, A. D.; Bezel, I.; Gaffney, K. J.; Garrett-Roe, S.; Liu, S. H.; Szymanski, P.; Harris, C. B.

2002-08-01

Ultrafast two-photon photoemission has been used to study electron solvation at two-dimensional metal/polar-adsorbate interfaces. The molecular motion that causes the excess electron solvation is manifested as a dynamic shift in the electronic energy. Although the initially excited electron is delocalized in the plane of the interface, interactions with the adsorbate can lead to its localization. A method for determining the spatial extent of the localized electron in the plane of the interface has been developed. This spatial extent was measured to be on the order of a single adsorbate molecule.

From Geometry Optimization to Time Dependent Molecular Structure Modeling: Method Developments, ab initio Theories and Applications

NASA Astrophysics Data System (ADS)

Liang, Wenkel

This dissertation consists of two general parts: (I) developments of optimization algorithms (both nuclear and electronic degrees of freedom) for time-independent molecules and (II) novel methods, first-principle theories and applications in time dependent molecular structure modeling. In the first part, we discuss in specific two new algorithms for static geometry optimization, the eigenspace update (ESU) method in nonredundant internal coordinate that exhibits an enhanced performace with up to a factor of 3 savings in computational cost for large-sized molecular systems; the Car-Parrinello density matrix search (CP-DMS) method that enables direct minimization of the SCF energy as an effective alternative to conventional diagonalization approach. For the second part, we consider the time dependence and first presents two nonadiabatic dynamic studies that model laser controlled molecular photo-dissociation for qualitative understandings of intense laser-molecule interaction, using ab initio direct Ehrenfest dynamics scheme implemented with real-time time-dependent density functional theory (RT-TDDFT) approach developed in our group. Furthermore, we place our special interest on the nonadiabatic electronic dynamics in the ultrafast time scale, and presents (1) a novel technique that can not only obtain energies but also the electron densities of doubly excited states within a single determinant framework, by combining methods of CP-DMS with RT-TDDFT; (2) a solvated first-principles electronic dynamics method by incorporating the polarizable continuum solvation model (PCM) to RT-TDDFT, which is found to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution. (3) applications of the PCM-RT-TDDFT method to study the intramolecular charge-transfer (CT) dynamics in a C60 derivative. Such work provides insights into the characteristics of ultrafast dynamics in photoexcited fullerene derivatives, and aids in the rational design for pre-dissociative exciton in the intramolecular CT process in organic solar cells.

Open-ended formulation of self-consistent field response theory with the polarizable continuum model for solvation.

PubMed

Di Remigio, Roberto; Beerepoot, Maarten T P; Cornaton, Yann; Ringholm, Magnus; Steindal, Arnfinn Hykkerud; Ruud, Kenneth; Frediani, Luca

2016-12-21

The study of high-order absorption properties of molecules is a field of growing importance. Quantum-chemical studies can help design chromophores with desirable characteristics. Given that most experiments are performed in solution, it is important to devise a cost-effective strategy to include solvation effects in quantum-chemical studies of these properties. We here present an open-ended formulation of self-consistent field (SCF) response theory for a molecular solute coupled to a polarizable continuum model (PCM) description of the solvent. Our formulation relies on the open-ended, density matrix-based quasienergy formulation of SCF response theory of Thorvaldsen, et al., [J. Chem. Phys., 2008, 129, 214108] and the variational formulation of the PCM, as presented by Lipparini et al., [J. Chem. Phys., 2010, 133, 014106]. Within the PCM approach to solvation, the mutual solute-solvent polarization is represented by means of an apparent surface charge (ASC) spread over the molecular cavity defining the solute-solvent boundary. In the variational formulation, the ASC is an independent, variational degree of freedom. This allows us to formulate response theory for molecular solutes in the fixed-cavity approximation up to arbitrary order and with arbitrary perturbation operators. For electric dipole perturbations, pole and residue analyses of the response functions naturally lead to the identification of excitation energies and transition moments. We document the implementation of this approach in the Dalton program package using a recently developed open-ended response code and the PCMSolver libraries and present results for one-, two-, three-, four- and five-photon absorption processes of three small molecules in solution.

Solvation Free Energies of Alanine Peptides: The Effect of Flexibility

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

Kokubo, Hironori; Harris, Robert C.; Asthagiri, Dilip

The electrostatic (?Gel), cavity-formation (?Gvdw), and total (?G) solvation free energies for 10 alanine peptides ranging in length (n) from 1 to 10 monomers were calculated. The free energies were computed both with xed, extended conformations of the peptides and again for some of the peptides without constraints. The solvation free energies, ?Gel, ?Gvdw, and ?G, were found to be linear in n, with the slopes of the best-fit lines being gamma_el, gamma_vdw, and gamma, respectively. Both gamma_el and gamma were negative for fixed and flexible peptides, and gamma_vdw was negative for fixed peptides. That gamma_vdw was negative was surprising,more » as experimental data on alkanes, theoretical models, and MD computations on small molecules and model systems generally suggest that gamma_vdw should be positive. A negative gamma_vdw seemingly contradicts the notion that ?Gvdw drives the initial collapse of the protein when it folds by favoring conformations with small surface areas, but when we computed ?Gvdw for the flexible peptides, thereby allowing the peptides to assume natural ensembles of more compact conformations, gamma-vdw was positive. Because most proteins do not assume extended conformations, a ?Gvdw that increases with increasing surface area may be typical for globular proteins. An alternative hypothesis is that the collapse is driven by intramolecular interactions. We show that the intramolecular van der Waal's interaction energy is more favorable for the flexible than for the extended peptides, seemingly favoring this hypothesis, but the large fluctuations in this energy may make attributing the collapse of the peptide to this intramolecular energy difficult.« less

Adapting Poisson-Boltzmann to the self-consistent mean field theory: Application to protein side-chain modeling

NASA Astrophysics Data System (ADS)

Koehl, Patrice; Orland, Henri; Delarue, Marc

2011-08-01

We present an extension of the self-consistent mean field theory for protein side-chain modeling in which solvation effects are included based on the Poisson-Boltzmann (PB) theory. In this approach, the protein is represented with multiple copies of its side chains. Each copy is assigned a weight that is refined iteratively based on the mean field energy generated by the rest of the protein, until self-consistency is reached. At each cycle, the variational free energy of the multi-copy system is computed; this free energy includes the internal energy of the protein that accounts for vdW and electrostatics interactions and a solvation free energy term that is computed using the PB equation. The method converges in only a few cycles and takes only minutes of central processing unit time on a commodity personal computer. The predicted conformation of each residue is then set to be its copy with the highest weight after convergence. We have tested this method on a database of hundred highly refined NMR structures to circumvent the problems of crystal packing inherent to x-ray structures. The use of the PB-derived solvation free energy significantly improves prediction accuracy for surface side chains. For example, the prediction accuracies for χ1 for surface cysteine, serine, and threonine residues improve from 68%, 35%, and 43% to 80%, 53%, and 57%, respectively. A comparison with other side-chain prediction algorithms demonstrates that our approach is consistently better in predicting the conformations of exposed side chains.

Level-Set Variational Implicit-Solvent Modeling of Biomolecules with the Coulomb-Field Approximation

PubMed Central

2011-01-01

Central in the variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett.2006, 96, 087802 and J. Chem. Phys.2006, 124, 084905] of molecular solvation is a mean-field free-energy functional of all possible solute–solvent interfaces or dielectric boundaries. Such a functional can be minimized numerically by a level-set method to determine stable equilibrium conformations and solvation free energies. Applications to nonpolar systems have shown that the level-set VISM is efficient and leads to qualitatively and often quantitatively correct results. In particular, it is capable of capturing capillary evaporation in hydrophobic confinement and corresponding multiple equilibrium states as found in molecular dynamics (MD) simulations. In this work, we introduce into the VISM the Coulomb-field approximation of the electrostatic free energy. Such an approximation is a volume integral over an arbitrary shaped solvent region, requiring no solutions to any partial differential equations. With this approximation, we obtain the effective boundary force and use it as the “normal velocity” in the level-set relaxation. We test the new approach by calculating solvation free energies and potentials of mean force for small and large molecules, including the two-domain protein BphC. Our results reveal the importance of coupling polar and nonpolar interactions in the underlying molecular systems. In particular, dehydration near the domain interface of BphC subunits is found to be highly sensitive to local electrostatic potentials as seen in previous MD simulations. This is a first step toward capturing the complex protein dehydration process by an implicit-solvent approach. PMID:22346739

Evaluating the Free Energies of Solvation and Electronic Structures of Lithium-Ion Battery Electrolytes.

PubMed

Shakourian-Fard, Mehdi; Kamath, Ganesh; Sankaranarayanan, Subramanian K R S

2016-09-19

Adaptive biasing force molecular dynamics simulations and density functional theory calculations were performed to understand the interaction of Li(+) with pure carbonates and ethylene carbonate (EC)-based binary mixtures. The most favorable Li carbonate cluster configurations obtained from molecular dynamics simulations were subjected to detailed structural and thermochemistry calculations on the basis of the M06-2X/6-311++G(d,p) level of theory. We report the ranking of these electrolytes on the basis of the free energies of Li-ion solvation in carbonates and EC-based mixtures. A strong local tetrahedral order involving four carbonates around the Li(+) was seen in the first solvation shell. Thermochemistry calculations revealed that the enthalpy of solvation and the Gibbs free energy of solvation of the Li(+) ion with carbonates are negative and suggested the ion-carbonate complexation process to be exothermic and spontaneous. Natural bond orbital analysis indicated that Li(+) interacts with the lone pairs of electrons on the carbonyl oxygen atom in the primary solvation sphere. These interactions lead to an increase in the carbonyl (C=O) bond lengths, as evidenced by a redshift in the vibrational frequencies [ν(C=O)] and a decrease in the electron density values at the C=O bond critical points in the primary solvation sphere. Quantum theory of atoms in molecules, localized molecular orbital energy decomposition analysis (LMO-EDA), and noncovalent interaction plots revealed the electrostatic nature of the Li(+) ion interactions with the carbonyl oxygen atoms in these complexes. On the basis of LMO-EDA, the strongest attractive interaction in these complexes was found to be the electrostatic interaction followed by polarization, dispersion, and exchange interactions. Overall, our calculations predicted EC and a binary mixture of EC/dimethyl carbonate to be appropriate electrolytes for Li-ion batteries, which complies with experiments and other theoretical results. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A shell-resolved analysis of preferential solvation of coffee ingredients in aqueous mixtures of the ionic liquid 1-ethyl-3-methylimidazolium acetate

NASA Astrophysics Data System (ADS)

Zeindlhofer, Veronika; Berger, Magdalena; Steinhauser, Othmar; Schröder, Christian

2018-05-01

Ionic liquids increase the solubility of various coffee ingredients in aqueous solution but little is known about the underlying mechanism. Kirkwood-Buff integrals as well as the potential of mean force indicate that the imidazolium cations are accumulated at the surface of the solutes, removing water molecules from the solute surface. Although hydrogen bonding of the anions to hydroxy groups of the solutes can be detected, their concentration at the surface is less enhanced compared to the cations. The decomposition into solvation shells by Voronoi tessellation reveals that structural features are only observed in the first solvation shell. Nevertheless, the depletion of water and the excess concentration of the ions and, in particular, of the cations are visible in the next solvation shells as well. Therefore, classical arguments of hydrotropic theory fail to explain this behavior.

Photo-illuminated diamond as a solid-state source of solvated electrons in water for nitrogen reduction.

PubMed

Zhu, Di; Zhang, Linghong; Ruther, Rose E; Hamers, Robert J

2013-09-01

The photocatalytic reduction of N₂ to NH₃ is typically hampered by poor binding of N₂ to catalytic materials and by the very high energy of the intermediates involved in this reaction. Solvated electrons directly introduced into the reactant solution can provide an alternative pathway to overcome such limitations. Here we demonstrate that illuminated hydrogen-terminated diamond yields facile electron emission into water, thus inducing reduction of N₂ to NH₃ at ambient temperature and pressure. Transient absorption measurements at 632 nm reveal the presence of solvated electrons adjacent to the diamond after photoexcitation. Experiments using inexpensive synthetic diamond samples and diamond powder show that photocatalytic activity is strongly dependent on the surface termination and correlates with the production of solvated electrons. The use of diamond to eject electrons into a reactant liquid represents a new paradigm for photocatalytic reduction, bringing electrons directly to reactants without requiring molecular adsorption to the surface.

Solvent effect on the self-assembly of salt solvates of an antihypertensive drug azilsartan and 2-methylimidazole

NASA Astrophysics Data System (ADS)

Zhang, Xian-Rui; Zhang, Lei

2017-06-01

Three salt solvates of azilsartan (AZ) with 2-methylimidazole (2MI) (namely AZ-2MI-H2O, AZ-2MI-ACE and AZ-2MI-THF) and one azilsartan solvate (AZ-DIO, ACE = acetone, THF = tetrahydrofuran, and DIO = 1,4-dioxane) were manufactured by solvent-controlled self-assembly in aqueous-organic solutions. The experimental result of AZ-DIO shows that AZ is high affinity to DIO molecule, which has a unique ability to prevent salt formation between AZ and 2MI. Thermal studies of three salt solvates exhibit poor thermodynamic stability in environmental conditions. Solubility experiments show that AZ-2MI-ACE and AZ-2MI-THF are unstable and convert to AZ-2MI-H2O in aqueous solution, and that AZ-2MI-H2O exhibits increased solubility and retention stability in an aqueous medium compared with the commercial AZ-A crystalline form.

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

Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies.

PubMed

Forouzesh, Negin; Izadi, Saeed; Onufriev, Alexey V

2017-10-23

Fast and accurate calculation of solvation free energies is central to many applications, such as rational drug design. In this study, we present a grid-based molecular surface implementation of "R6" flavor of the generalized Born (GB) implicit solvent model, named GBNSR6. The speed, accuracy relative to numerical Poisson-Boltzmann treatment, and sensitivity to grid surface parameters are tested on a set of 15 small protein-ligand complexes and a set of biomolecules in the range of 268 to 25099 atoms. Our results demonstrate that the proposed model provides a relatively successful compromise between the speed and accuracy of computing polar components of the solvation free energies (ΔG pol ) and binding free energies (ΔΔG pol ). The model tolerates a relatively coarse grid size h = 0.5 Å, where the grid artifact error in computing ΔΔG pol remains in the range of k B T ∼ 0.6 kcal/mol. The estimated ΔΔG pol s are well correlated (r 2 = 0.97) with the numerical Poisson-Boltzmann reference, while showing virtually no systematic bias and RMSE = 1.43 kcal/mol. The grid-based GBNSR6 model is available in Amber (AmberTools) package of molecular simulation programs.

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.

Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent

PubMed Central

Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu

2011-01-01

A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into “alpha helix” and “beta sheet” structures. The 5-residue polyalanine displays a substantial increase in the “beta strand” fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling. PMID:22029338

Docking ligands into flexible and solvated macromolecules. 7. Impact of protein flexibility and water molecules on docking-based virtual screening accuracy.

PubMed

Therrien, Eric; Weill, Nathanael; Tomberg, Anna; Corbeil, Christopher R; Lee, Devin; Moitessier, Nicolas

2014-11-24

The use of predictive computational methods in the drug discovery process is in a state of continual growth. Over the last two decades, an increasingly large number of docking tools have been developed to identify hits or optimize lead molecules through in-silico screening of chemical libraries to proteins. In recent years, the focus has been on implementing protein flexibility and water molecules. Our efforts led to the development of Fitted first reported in 2007 and further developed since then. In this study, we wished to evaluate the impact of protein flexibility and occurrence of water molecules on the accuracy of the Fitted docking program to discriminate active compounds from inactive compounds in virtual screening (VS) campaigns. For this purpose, a total of 171 proteins cocrystallized with small molecules representing 40 unique enzymes and receptors as well as sets of known ligands and decoys were selected from the Protein Data Bank (PDB) and the Directory of Useful Decoys (DUD), respectively. This study revealed that implementing displaceable crystallographic or computationally placed particle water molecules and protein flexibility can improve the enrichment in active compounds. In addition, an informed decision based on library diversity or research objectives (hit discovery vs lead optimization) on which implementation to use may lead to significant improvements.

PREDICTION OF THE SOLUBILITY, ACTIVITY COEFFICIENT AND LIQUID/LIQUID PARTITION COEFFICIENT OF ORGANIC COMPOUNDS

EPA Science Inventory

Solvation models, based on fundamental chemical structure theory, were developed in the SPARC mechanistic tool box to predict a large array of physical properties of organic compounds in water and in non-aqueous solvents strictly from molecular structure. The SPARC self-interact...

Comparison of molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics-three-dimensional reference interaction site model (MM-3D-RISM) method to calculate the binding free energy of protein-ligand complexes: Effect of metal ion and advance statistical test

NASA Astrophysics Data System (ADS)

Pandey, Preeti; Srivastava, Rakesh; Bandyopadhyay, Pradipta

2018-03-01

The relative performance of MM-PBSA and MM-3D-RISM methods to estimate the binding free energy of protein-ligand complexes is investigated by applying these to three proteins (Dihydrofolate Reductase, Catechol-O-methyltransferase, and Stromelysin-1) differing in the number of metal ions they contain. None of the computational methods could distinguish all the ligands based on their calculated binding free energies (as compared to experimental values). The difference between the two comes from both polar and non-polar part of solvation. For charged ligand case, MM-PBSA and MM-3D-RISM give a qualitatively different result for the polar part of solvation.

A structure-based virtual screening approach toward the discovery of histone deacetylase inhibitors: identification of promising zinc-chelating groups.

PubMed

Park, Hwangseo; Kim, Sukyoung; Kim, Yong Eun; Lim, Soo-Jeong

2010-04-06

The inhibitors of histone deacetylases (HDACs) have drawn a great deal of attention due to their promising potential as small-molecule therapeutics for the treatment of cancer. By means of virtual screening with docking simulations under consideration of the effects of ligand solvation, we were able to identify six novel HDAC inhibitors with IC(50) values ranging from 1 to 100 muM. These newly identified inhibitors are structurally diverse and have various chelating groups for the active site zinc ion, including N-[1,3,4]thiadiazol-2-yl sulfonamide, N-thiazol-2-yl sulfonamide, and hydroxamic acid moieties. The former two groups are included in many drugs in current clinical use and have not yet been reported as HDAC inhibitors. Therefore, they can be considered as new inhibitor scaffolds for the development of anticancer drugs by structure-activity relationship studies to improve the inhibitory activities against HDACs. Interactions with the HDAC1 active site residues responsible for stabilizing these new inhibitors are addressed in detail.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Phase Equilibria and Ionic Solvation in the Lithium Tetrafluoroborate-Dimethylsulfoxide System

NASA Astrophysics Data System (ADS)

Gafurov, M. M.; Kirillov, S. A.; Gorobets, M. I.; Rabadanov, K. Sh.; Ataev, M. B.; Tretyakov, D. O.; Aydemirov, K. M.

2015-01-01

The phase diagram and electrical conductivity isotherms for the lithium tetrafluoroborate (LiBF4)-dimethylsulfoxide (DMSO) system and Raman spectra of DMSO and the LiBF4-DMSO solution were studied. Spectroscopic signatures of a H-bond between DMSO and BF4 - ions were found. The bonds of Li+ ions to the solvent were stronger than the bonds in DMSO dimers because formation of the solvate destroyed dimeric DMSO molecules. The τω values for DMSO molecules in the Li+-ion solvate shell of the LiBF4-DMSO system were similar to those for associated solvent molecules.

Angle-Resolved Photoemission of Solvated Electrons in Sodium-Doped Clusters.

PubMed

West, Adam H C; Yoder, Bruce L; Luckhaus, David; Saak, Clara-Magdalena; Doppelbauer, Maximilian; Signorell, Ruth

2015-04-16

Angle-resolved photoelectron spectroscopy of the unpaired electron in sodium-doped water, methanol, ammonia, and dimethyl ether clusters is presented. The experimental observations and the complementary calculations are consistent with surface electrons for the cluster size range studied. Evidence against internally solvated electrons is provided by the photoelectron angular distribution. The trends in the ionization energies seem to be mainly determined by the degree of hydrogen bonding in the solvent and the solvation of the ion core. The onset ionization energies of water and methanol clusters do not level off at small cluster sizes but decrease slightly with increasing cluster size.

Predictions of the physicochemical properties of amino acid side chain analogs using molecular simulation.

PubMed

Ahmed, Alauddin; Sandler, Stanley I

2016-03-07

A candidate drug compound is released for clinical trails (in vivo activity) only if its physicochemical properties meet desirable bioavailability and partitioning criteria. Amino acid side chain analogs play vital role in the functionalities of protein and peptides and as such are important in drug discovery. We demonstrate here that the predictions of solvation free energies in water, in 1-octanol, and self-solvation free energies computed using force field-based expanded ensemble molecular dynamics simulation provide good accuracy compared to existing empirical and semi-empirical methods. These solvation free energies are then, as shown here, used for the prediction of a wide range of physicochemical properties important in the assessment of bioavailability and partitioning of compounds. In particular, we consider here the vapor pressure, the solubility in both water and 1-octanol, and the air-water, air-octanol, and octanol-water partition coefficients of amino acid side chain analogs computed from the solvation free energies. The calculated solvation free energies using different force fields are compared against each other and with available experimental data. The protocol here can also be used for a newly designed drug and other molecules where force field parameters and charges are obtained from density functional theory.

Computing pKa Values in Different Solvents by Electrostatic Transformation.

PubMed

Rossini, Emanuele; Netz, Roland R; Knapp, Ernst-Walter

2016-07-12

We introduce a method that requires only moderate computational effort to compute pKa values of small molecules in different solvents with an average accuracy of better than 0.7 pH units. With a known pKa value in one solvent, the electrostatic transform method computes the pKa value in any other solvent if the proton solvation energy is known in both considered solvents. To apply the electrostatic transform method to a molecule, the electrostatic solvation energies of the protonated and deprotonated molecular species are computed in the two considered solvents using a dielectric continuum to describe the solvent. This is demonstrated for 30 molecules belonging to 10 different molecular families by considering 77 measured pKa values in 4 different solvents: water, acetonitrile, dimethyl sulfoxide, and methanol. The electrostatic transform method can be applied to any other solvent if the proton solvation energy is known. It is exclusively based on physicochemical principles, not using any empirical fetch factors or explicit solvent molecules, to obtain agreement with measured pKa values and is therefore ready to be generalized to other solute molecules and solvents. From the computed pKa values, we obtained relative proton solvation energies, which agree very well with the proton solvation energies computed recently by ab initio methods, and used these energies in the present study.

Aqueous TMAO solutions as seen by theoretical THz spectroscopy: hydrophilic versus hydrophobic water.

PubMed

Imoto, Sho; Forbert, Harald; Marx, Dominik

2018-02-28

Solvation of trimethylamine-N-oxide (TMAO) by water is of great fundamental interest because this small molecule has both strongly hydrophilic and large hydrophobic groups at its opposite ends and, furthermore, stabilizes proteins against temperature and pressure denaturation. Since hydrophilic and hydrophobic groups affect the structural dynamics of the respective solvation water molecules in vastly different ways, we dissect their distinct influences on the THz spectrum of TMAO(aq) by using ab initio molecular dynamics simulations. In particular, we demonstrate that exclusively electronic polarization and charge transfer effects, being absent in the usual fixed-charge biomolecular force fields, are responsible for the significant enhancement of the effective molecular dipole moment of hydrophilic solvation water. This, in turn, leads to pronounced solute-solvent couplings and thus to specific THz modes that involve well-defined H-bond bending and stretching motion being characteristic to hydrophilic solvation. The THz response of individual H-bonded pairs of water molecules involving hydrophobic solvation water, in stark contrast, is nearly indistinguishable from such pairs in bulk water. Transcending the specific case, THz spectroscopy is suggested to be an ideal experimental approach to unravel the controversial piezolytic properties of TMAO including its counteracting effect on pressure-induced denaturation of proteins.

Distinctive Solvation Patterns Make Renal Osmolytes Diverse

PubMed Central

Jackson-Atogi, Ruby; Sinha, Prem Kumar; Rösgen, Jörg

2013-01-01

The kidney uses mixtures of five osmolytes to counter the stress induced by high urea and NaCl concentrations. The individual roles of most of the osmolytes are unclear, and three of the five have not yet been thermodynamically characterized. Here, we report partial molar volumes and activity coefficients of glycerophosphocholine (GPC), taurine, and myo-inositol. We derive their solvation behavior from the experimental data using Kirkwood-Buff theory. We also provide their solubility data, including solubility data for scyllo-inositol. It turns out that renal osmolytes fall into three distinct classes with respect to their solvation. Trimethyl-amines (GPC and glycine-betaine) are characterized by strong hard-sphere-like self-exclusion; urea, taurine, and myo-inositol have a tendency toward self-association; sorbitol and most other nonrenal osmolytes have a relatively constant, intermediate solvation that has components of both exclusion and association. The data presented here show that renal osmolytes are quite diverse with respect to their solvation patterns, and they can be further differentiated based on observations from experiments examining their effect on macromolecules. It is expected, based on the available surface groups, that each renal osmolyte has distinct effects on various classes of biomolecules. This likely allows the kidney to use specific combinations of osmolytes independently to fine-tune the chemical activities of several types of molecules. PMID:24209862

Aqueous solvation of polyalanine α-helices with specific water molecules and with the CPCM and SM5.2 aqueous continuum models using density functional theory.

PubMed

Marianski, Mateusz; Dannenberg, J J

2012-02-02

We present density functional theory (DFT) calculations at the X3LYP/D95(d,p) level on the solvation of polyalanine α-helices in water. The study includes the effects of discrete water molecules and the CPCM and AMSOL SM5.2 solvent continuum model both separately and in combination. We find that individual water molecules cooperatively hydrogen-bond to both the C- and N-termini of the helix, which results in increases in the dipole moment of the helix/water complex to more than the vector sum of their individual dipole moments. These waters are found to be more stable than in bulk solvent. On the other hand, individual water molecules that interact with the backbone lower the dipole moment of the helix/water complex to below that of the helix itself. Small clusters of waters at the termini increase the dipole moments of the helix/water aggregates, but the effect diminishes as more waters are added. We discuss the somewhat complex behavior of the helix with the discrete waters in the continuum models.

Aqueous Solvation of Polyalanine α-Helices with Specific Water Molecules and with the CPCM and SM5.2 Aqueous Continuum Models using Density Functional Theory

PubMed Central

Marianski, Mateusz

2012-01-01

We present density functional theory (DFT) calculations at the X3LYP/D95(d,p) level on the solvation of polyalanine α-helices in water. The study includes the effects of discrete water molecules and the CPCM and AMSOL SM5.2 solvent continuum model both separately and in combination. We find that individual water molecules cooperatively hydrogen-bond to both the C- and N-termini of the helix, which results in increases in the dipole moment of the helix/water complex to more than the vector sum of their individual dipole moments. These waters are found to be more stable than in bulk solvent. On the other hand, individual water that interact with the backbone lower the dipole moment of the helix/water complex to below that of the helix, itself. Small clusters of waters at the termini increase the dipole moments of the helix/water aggregates, but the effect diminishes as more waters are added. We discuss the somewhat complex behavior of the helix with the discrete waters in the continuum models. PMID:22201227

A Site Density Functional Theory for Water: Application to Solvation of Amino Acid Side Chains.

PubMed

Liu, Yu; Zhao, Shuangliang; Wu, Jianzhong

2013-04-09

We report a site density functional theory (SDFT) based on the conventional atomistic models of water and the universality ansatz of the bridge functional. The excess Helmholtz energy functional is formulated in terms of a quadratic expansion with respect to the local density deviation from that of a uniform system and a universal functional for all higher-order terms approximated by that of a reference hard-sphere system. With the atomistic pair direct correlation functions of the uniform system calculated from MD simulation and an analytical expression for the bridge functional from the modified fundamental measure theory, the SDFT can be used to predict the structure and thermodynamic properties of water under inhomogeneous conditions with a computational cost negligible in comparison to that of brute-force simulations. The numerical performance of the SDFT has been demonstrated with the predictions of the solvation free energies of 15 molecular analogs of amino acid side chains in water represented by SPC/E, SPC, and TIP3P models. For theTIP3P model, a comparison of the theoretical predictions with MD simulation and experimental data shows agreement within 0.64 and 1.09 kcal/mol on average, respectively.

Rapid-gradient HPLC method for measuring drug interactions with immobilized artificial membrane: comparison with other lipophilicity measures.

PubMed

Valko, K; Du, C M; Bevan, C D; Reynolds, D P; Abraham, M H

2000-08-01

A fast-gradient high-performance liquid chromatographic (HPLC) method has been suggested to characterize the interactions of drugs with an immobilized artificial membrane (IAM). With a set of standards, the gradient retention times can be converted to Chromatographic Hydrophobicity Index values referring to IAM chromatography (CHI(IAM)) that approximates an acetonitrile concentration with which the equal distribution of compound can be achieved between the mobile phase and IAM. The CHI(IAM) values are more suitable for interlaboratory comparison and for high throughput screening of new molecular entities than the log k(IAM) values (isocratic retention factor on IAM). The fast-gradient method has been validated against the isocratic log k(IAM) values using the linear free energy relationship solvation equations based on the data from 48 compounds. The compound set was selected to provide a wide range and the least cross-correlation between the molecular descriptors in the solvation equation: (2) where SP is a solute property (e.g., logarithm of partition coefficients, reversed-phase (RP)-HPLC retention parameters, such as log k, log k(w), etc.) and the explanatory variables are solute descriptors as follows: R(2) is an excess molar refraction that can be obtained from the measured refractive index of a compound, pi(2)(H) is the solute dipolarity/polarizability, summation operatoralpha(2)(H) and summation operatorbeta(2)(0) are the solute overall or effective hydrogen-bond acidity and basicity, respectively, and V(x) is the McGowan characteristic volume (in cm(3)/100 mol) that can be calculated for any solute simply from molecular structure using a table of atomic constants. It was found that the relative constants of the solvation equation were very similar for the CHI(IAM) and for the log k(IAM). The IAM lipophilicity scale was quite similar to the octanol/water lipophilicity scale for neutral compounds. The effect of charge on the interaction with IAM was studied by varying the mobile phase pH. Copyright 2000 Wiley-Liss, Inc.

Computational Insights into Materials and Interfaces for Capacitive Energy Storage

PubMed Central

Zhan, Cheng; Lian, Cheng; Zhang, Yu; Thompson, Matthew W.; Xie, Yu; Wu, Jianzhong; Kent, Paul R. C.; Cummings, Peter T.; Wesolowski, David J.

2017-01-01

Supercapacitors such as electric double‐layer capacitors (EDLCs) and pseudocapacitors are becoming increasingly important in the field of electrical energy storage. Theoretical study of energy storage in EDLCs focuses on solving for the electric double‐layer structure in different electrode geometries and electrolyte components, which can be achieved by molecular simulations such as classical molecular dynamics (MD), classical density functional theory (classical DFT), and Monte‐Carlo (MC) methods. In recent years, combining first‐principles and classical simulations to investigate the carbon‐based EDLCs has shed light on the importance of quantum capacitance in graphene‐like 2D systems. More recently, the development of joint density functional theory (JDFT) enables self‐consistent electronic‐structure calculation for an electrode being solvated by an electrolyte. In contrast with the large amount of theoretical and computational effort on EDLCs, theoretical understanding of pseudocapacitance is very limited. In this review, we first introduce popular modeling methods and then focus on several important aspects of EDLCs including nanoconfinement, quantum capacitance, dielectric screening, and novel 2D electrode design; we also briefly touch upon pseudocapactive mechanism in RuO2. We summarize and conclude with an outlook for the future of materials simulation and design for capacitive energy storage. PMID:28725531

Dielectric Screening Meets Optimally Tuned Density Functionals.

PubMed

Kronik, Leeor; Kümmel, Stephan

2018-04-17

A short overview of recent attempts at merging two independently developed methods is presented. These are the optimal tuning of a range-separated hybrid (OT-RSH) functional, developed to provide an accurate first-principles description of the electronic structure and optical properties of gas-phase molecules, and the polarizable continuum model (PCM), developed to provide an approximate but computationally tractable description of a solvent in terms of an effective dielectric medium. After a brief overview of the OT-RSH approach, its combination with the PCM as a potentially accurate yet low-cost approach to the study of molecular assemblies and solids, particularly in the context of photocatalysis and photovoltaics, is discussed. First, solvated molecules are considered, with an emphasis on the challenge of balancing eigenvalue and total energy trends. Then, it is shown that the same merging of methods can also be used to study the electronic and optical properties of molecular solids, with a similar discussion of the pros and cons. Tuning of the effective scalar dielectric constant as one recent approach that mitigates some of the difficulties in merging the two approaches is considered. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Long-ranged electrostatic repulsion and crystallization of emulsion droplets in an ultralow dielectric medium supercritical carbon dioxide.

PubMed

Ryoo, Won; Webber, Stephen E; Bonnecaze, Roger T; Johnston, Keith P

2006-01-31

Electrostatic repulsion stabilizes micrometer-sized water droplets with spacings greater than 10 microm in an ultralow dielectric medium, CO2 (epsilon = 1.5), at elevated pressures. The morphology of the water/CO2 emulsion is characterized by optical microscopy and laser diffraction as a function of height. The counterions, stabilized with a nonionic, highly branched, stubby hydrocarbon surfactant, form an extremely thick double layer with a Debye screening length of 8.9 microm. As a result of the balance between electrostatic repulsion and the downward force due to gravity, the droplets formed a hexagonal crystalline lattice at the bottom of the high-pressure cell with spacings of over 10 microm. The osmotic pressure, calculated by solving the Poisson-Boltzmann equation in the framework of the Wigner-Seitz cell model, is in good agreement with that determined from the sedimentation profile measured by laser diffraction. Thus, the long-ranged stabilization of the emulsion may be attributed to electrostatic stabilization. The ability to form new types of colloids in CO2 with electrostatic stabilization is beneficial because steric stabilization is often unsatisfactory because of poor solvation of the stabilizers.

The solvation structure of Mg ions in dichloro complex solutions from first-principles molecular dynamics and simulated X-ray absorption spectra.

PubMed

Wan, Liwen F; Prendergast, David

2014-10-15

The knowledge of Mg solvation structure in the electrolyte is requisite to understand the transport behavior of Mg ions and their dissolution/deposition mechanism at electrolyte/electrode interfaces. In the first established rechargeable Mg-ion battery system [D. Aurbach et al. Nature 2000, 407, 724], the electrolyte is of the dichloro complex (DCC) solution family, Mg(AlCl2BuEt)2/THF, resulting from the reaction of Bu2Mg and EtAlCl2 with a molar ratio of 1:2. There is disagreement in the literature regarding the exact solvation structure of Mg ions in such solutions, i.e., whether Mg(2+) is tetra- or hexacoordinated by a combination of Cl(-) and THF. In this work, theoretical insight into the solvation complexes present is provided based on first-principles molecular dynamics simulations (FPMD). Both Mg monomer and dimer structures are considered in both neutral and positively charged states. We found that, at room temperature, the Mg(2+) ion tends to be tetracoordinated in the THF solution phase instead of hexacoordinated, which is the predominant solid-phase coordination. Simulating the X-ray absorption spectra (XAS) at the Mg K-edge by sampling our FPMD trajectories, our predicted solvation structure can be readily compared with experimental measurements. It is found that when changing from tetra- to hexacoordination, the onset of X-ray absorption should exhibit at least a 1 eV blue shift. We propose that this energy shift can be used to monitor changes in the Mg solvation sphere as it migrates through the electrolyte to electrolyte/electrode interfaces and to elucidate the mechanism of Mg dissolution/deposition.

Solvation Thermodynamic Properties of Hydrogen Sulfide in [C4mim][PF6], [C4mim][BF4], and [C4mim][Cl] Ionic Liquids, Determined by Molecular Simulations.

PubMed

Sánchez-Badillo, Joel; Gallo, Marco; Alvarado, Sandra; Glossman-Mitnik, Daniel

2015-08-20

Removal of hydrogen sulfide (H2S) and acid gases from natural gas is accomplished by absorption processes using a solvent. The gas solubility in a liquid can be used to measure the degree of removal of the gas and is quantified by the Henry's constant, the free energy of solvation at infinite dilution, or the excess chemical potential. In this work, Henry's constants and thermodynamic properties of solvation of H2S were calculated in three ionic liquids: [C4mim][PF6], [C4mim][BF4], and [C4mim][Cl] ([C4mim], 1-butyl-3-methyl imidazolium). The first step in this work was the evaluation of the force fields for the gas and condensed phases in order to obtain accurate values for the excess chemical potential for H2S on each ionic liquid using free energy perturbation techniques. In the H2S-[C4mim][PF6] and H2S-[C4mim][BF4] systems, the results obtained by molecular simulation agree with the experimental values reported in the literature. However, the solvation free energy calculated for the H2S-[C4mim][Cl] system can be considered predictive because of the lack of experimental data at the simulated conditions. Based on these results, the best solvent for removing H2S is [C4mim][Cl] because it has the highest affinity for this species (lowest value of the Henry's constant). Also, solvation thermodynamic properties such as enthalpy and entropy were calculated in order to evaluate their contribution to the free energy of solvation.

Preferential solvation, ion pairing, and dynamics of concentrated aqueous solutions of divalent metal nitrate salts

NASA Astrophysics Data System (ADS)

Yadav, Sushma; Chandra, Amalendu

2017-12-01

We have investigated the characteristics of preferential solvation of ions, structure of solvation shells, ion pairing, and dynamics of aqueous solutions of divalent alkaline-earth metal nitrate salts at varying concentration by means of molecular dynamics simulations. Hydration shell structures and the extent of preferential solvation of the metal and nitrate ions in the solutions are investigated through calculations of radial distribution functions, tetrahedral ordering, and also spatial distribution functions. The Mg2+ ions are found to form solvent separated ion-pairs while the Ca2+ and Sr2+ ions form contact ion pairs with the nitrate ions. These findings are further corroborated by excess coordination numbers calculated through Kirkwood-Buff G factors for different ion-ion and ion-water pairs. The ion-pairing propensity is found to be in the order of Mg(NO3) 2 < C a (NO3) 2 < S r (NO3) 2, and it follows the trend given by experimental activity coefficients. It is found that proper modeling of these solutions requires the inclusion of electronic polarization of the ions which is achieved in the current study through electronic continuum correction force fields. A detailed analysis of the effects of ion-pairs on the structure and dynamics of water around the hydrated ions is done through classification of water into different subspecies based on their locations around the cations or anions only or bridged between them. We have looked at the diffusion coefficients, relaxation of orientational correlation functions, and also the residence times of different subspecies of water to explore the dynamics of water in different structural environments in the solutions. The current results show that the water molecules are incorporated into fairly well-structured hydration shells of the ions, thus decreasing the single-particle diffusivities and increasing the orientational relaxation times of water with an increase in salt concentration. The different structural motifs also lead to the presence of substantial dynamical heterogeneity in these solutions of strongly interacting ions. The current study helps us to understand the molecular details of hydration structure, ion pairing, and dynamics of water in the solvation shells and also of ion diffusion in aqueous solutions of divalent metal nitrate salts.

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

NASA Astrophysics Data System (ADS)

Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

2012-12-01

We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.

PubMed

Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

2012-12-07

We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

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

Sanyal, Tanmoy; Shell, M. Scott, E-mail: shell@engineering.ucsb.edu

Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one atmore » which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.« less

Cellulose Nanofibrils and Mechanism of their Mineralization in Biomimetic Synthesis of Hydroxyapatite/Native Bacterial Cellulose Nanocomposites: Molecular Dynamics Simulations.

PubMed

Lukasheva, N V; Tolmachev, D A

2016-01-12

Molecular dynamics (MD) simulation of a nanofibril of native bacterial cellulose (BC) in solutions of mineral ions is presented. The supersaturated calcium-phosphate (CP) solution with the ionic composition of hydroxyapatite and CaCl2 solutions with the concentrations below, equal to, and above the solubility limits are simulated. The influence of solvation models (TIP3P and TIP4P-ew water models) on structural characteristics of the simulated nanofibril and on the crystal nucleation process is assessed. The structural characteristics of cellulose nanofibrils (in particular, of the surface layer) are found to be nearly independent of the solvation models used in the simulation and on the presence of ions in the solutions. It is shown that ionic clusters are formed in the solution rather than on the fibril surface. The cluster sizes are slightly different for the two water models. The effect of the ion-ion interaction parameters on the results is discussed. The main conclusion is that the activity of hydroxyl groups on the BC fibril surface is not high enough to cause adsorption of Ca(2+) ions from the solution. Therefore, the nucleation of CP crystals takes place initially in solution, and then the crystallites formed can be adsorbed on BC nanofibril surfaces.

Electrostatic Solvation Energy for Two Oppositely Charged Ions in a Solvated Protein System: Salt Bridges Can Stabilize Proteins

PubMed Central

Gong, Haipeng; Freed, Karl F.

2010-01-01

Abstract Born-type electrostatic continuum methods have been an indispensable ingredient in a variety of implicit-solvent methods that reduce computational effort by orders of magnitude compared to explicit-solvent MD simulations and thus enable treatment using larger systems and/or longer times. An analysis of the limitations and failures of the Born approaches serves as a guide for fundamental improvements without diminishing the importance of prior works. One of the major limitations of the Born theory is the lack of a liquidlike description of the response of solvent dipoles to the electrostatic field of the solute and the changes therein, a feature contained in the continuum Langevin-Debye (LD) model applied here to investigate how Coulombic interactions depend on the location of charges relative to the protein/water boundary. This physically more realistic LD model is applied to study the stability of salt bridges. When compared head to head using the same (independently measurable) physical parameters (radii, dielectric constants, etc.), the LD model is in good agreement with observations, whereas the Born model is grossly in error. Our calculations also suggest that a salt bridge on the protein's surface can be stabilizing when the charge separation is ≤4 Å. PMID:20141761

Density functional theory study on carbon dioxide absorption into aqueous solutions of 2-amino-2-methyl-1-propanol using a continuum solvation model.

PubMed

Yamada, Hidetaka; Matsuzaki, Yoichi; Higashii, Takayuki; Kazama, Shingo

2011-04-14

We used density functional theory (DFT) calculations with the latest continuum solvation model (SMD/IEF-PCM) to determine the mechanism of CO(2) absorption into aqueous solutions of 2-amino-2-methyl-1-propanol (AMP). Possible absorption process reactions were investigated by transition-state optimization and intrinsic reaction coordinate (IRC) calculations in the aqueous solution at the SMD/IEF-PCM/B3LYP/6-31G(d) and SMD/IEF-PCM/B3LYP/6-311++G(d,p) levels of theory to determine the absorption pathways. We show that the carbamate anion forms by a two-step reaction via a zwitterion intermediate, and this occurs faster than the formation of the bicarbonate anion. However, we also predict that the carbamate readily decomposes by a reverse reaction rather than by hydrolysis. As a result, the final product is dominated by the thermodynamically stable bicarbonate anion that forms from AMP, H(2)O, and CO(2) in a single-step termolecular reaction.

Molecular Reactivity and Absorption Properties of Melanoidin Blue-G1 through Conceptual DFT.

PubMed

Frau, Juan; Glossman-Mitnik, Daniel

2018-03-02

This computational study presents the assessment of eleven density functionals that include CAM-B3LYP, LC-wPBE, M11, M11L, MN12L, MN12SX, N12, N12SX, wB97, wB97X and wB97XD related to the Def2TZVP basis sets together with the Solvation Model Density (SMD) solvation model in calculating the molecular properties and structure of the Blue-G1 intermediate melanoidin pigment. The chemical reactivity descriptors for the system are calculated via the conceptual Density Functional Theory (DFT). The choice of the active sites related to the nucleophilic, electrophilic, as well as radical attacks is made by linking them with the Fukui function indices, the electrophilic Parr functions and the condensed dual descriptor Δ f ( r ) . The prediction of the maximum absorption wavelength tends to be considerably accurate relative to its experimental value. The study found the MN12SX and N12SX density functionals to be the most appropriate density functionals in predicting the chemical reactivity of the studied molecule.

Synthesis and spectral properties of Methyl-Phenyl pyrazoloquinoxaline fluorescence emitters: Experiment and DFT/TDDFT calculations

NASA Astrophysics Data System (ADS)

Gąsiorski, P.; Matusiewicz, M.; Gondek, E.; Uchacz, T.; Wojtasik, K.; Danel, A.; Shchur, Ya.; Kityk, A. V.

2018-01-01

Paper reports the synthesis and spectroscopic studies of two novel 1-Methyl-3-phenyl-1H-pyrazolo[3,4-b]quinoxaline (PQX) derivatives with 6-substituted methyl (MeMPPQX) or methoxy (MeOMPPQX) side groups. The optical absorption and fluorescence emission spectra are recorded in solvents of different polarity. Steady state and time-resolved spectroscopy provide photophysical characterization of MeMPPQX and MeOMPPQX dyes as materials for potential luminescence or electroluminescence applications. Measured optical absorption and fluorescence emission spectra are compared with quantum-chemical DFT/TDDFT calculations using long-range corrected xc-functionals, LRC-BLYP and CAM-B3LYP in combination with self-consistent reaction field model based on linear response (LR), state specific (SS) or corrected linear response (CLR) solvations. Performances of relevant theoretical models and approaches are compared. The reparameterized LRC-BLYP functional (ω = 0.231 Bohr-1) in combination with CLR solvation provides most accurate prediction of both excitation and emission energies. The MeMPPQX and MeOMPPQX dyes represent efficient fluorescence emitters in blue-green region of the visible spectra.

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.

Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model.

PubMed

Diaz-Rodriguez, Sebastian; Bozada, Samantha M; Phifer, Jeremy R; Paluch, Andrew S

2016-11-01

We present blind predictions using the solubility parameter based method MOSCED submitted for the SAMPL5 challenge on calculating cyclohexane/water distribution coefficients at 298 K. Reference data to parameterize MOSCED was generated with knowledge only of chemical structure by performing solvation free energy calculations using electronic structure calculations in the SMD continuum solvent. To maintain simplicity and use only a single method, we approximate the distribution coefficient with the partition coefficient of the neutral species. Over the final SAMPL5 set of 53 compounds, we achieved an average unsigned error of [Formula: see text] log units (ranking 15 out of 62 entries), the correlation coefficient (R) was [Formula: see text] (ranking 35), and [Formula: see text] of the predictions had the correct sign (ranking 30). While used here to predict cyclohexane/water distribution coefficients at 298 K, MOSCED is broadly applicable, allowing one to predict temperature dependent infinite dilution activity coefficients in any solvent for which parameters exist, and provides a means by which an excess Gibbs free energy model may be parameterized to predict composition dependent phase-equilibrium.

Treecode-based generalized Born method

NASA Astrophysics Data System (ADS)

Xu, Zhenli; Cheng, Xiaolin; Yang, Haizhao

2011-02-01

We have developed a treecode-based O(Nlog N) algorithm for the generalized Born (GB) implicit solvation model. Our treecode-based GB (tGB) is based on the GBr6 [J. Phys. Chem. B 111, 3055 (2007)], an analytical GB method with a pairwise descreening approximation for the R6 volume integral expression. The algorithm is composed of a cutoff scheme for the effective Born radii calculation, and a treecode implementation of the GB charge-charge pair interactions. Test results demonstrate that the tGB algorithm can reproduce the vdW surface based Poisson solvation energy with an average relative error less than 0.6% while providing an almost linear-scaling calculation for a representative set of 25 proteins with different sizes (from 2815 atoms to 65456 atoms). For a typical system of 10k atoms, the tGB calculation is three times faster than the direct summation as implemented in the original GBr6 model. Thus, our tGB method provides an efficient way for performing implicit solvent GB simulations of larger biomolecular systems at longer time scales.

Preferential Solvation of an Asymmetric Redox Molecule

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

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

2016-12-15

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

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

Vijayakumar, M.; Nie, Zimin; Walter, Eric D.

Redox flow battery (RFB) is a promising candidate for energy storage component in designing resilient grid scale power supply due to the advantage of the separation of power and energy. However, poorly understood chemical and thermal stability issues of electrolytes currently limit the performance of RFB. Designing of high performance stable electrolytes requires comprehensive knowledge about the molecular level solvation structure and dynamics of their redox active species. The molecular level understanding of detrimental V2O5 precipitation process led to successful designing of mixed acid based electrolytes for vanadium redox flow batteries (VRFB). The higher stability of mixed acid based electrolytesmore » is attributed to the choice of hydrochloric acid as optimal co-solvent, which provides chloride anions for ligand exchange process in vanadium solvation structure. The role of chloride counter anion on solvation structure and dynamics of vanadium species were studied using combined magnetic resonance spectroscopy and DFT based theoretical methods. Finally, the solvation phenomenon of multiple vanadium species and their impact on VRFB electrolyte chemical stability were discussed.« less

Free Energy Wells and Barriers to Ion Transport Across Membranes

NASA Astrophysics Data System (ADS)

Rempe, Susan

2014-03-01

The flow of ions across cellular membranes is essential to many biological processes. Ion transport is also important in synthetic materials used as battery electrolytes. Transport often involves specific ions and fast conduction. To achieve those properties, ion conduction pathways must solvate specific ions by just the ``right amount.'' The right amount of solvation avoids ion traps due to deep free energy wells, and avoids ion block due to high free energy barriers. Ion channel proteins in cellular membranes demonstrate this subtle balance in solvation of specific ions. Using ab initio molecular simulations, we have interrogated the link between binding site structure and ion solvation free energies in biological ion binding sites. Our results emphasize the surprisingly important role of the environment that surrounds ion-binding sites for fast transport of specific ions. We acknowledge support from Sandia's LDRD program. Sandia National Labs is a multi-program laboratory operated by Sandia Corp., a wholly owned subsidiary of Lockheed Martin Corp., for the US DOE's NNSA under contract DE-AC04-94AL85000.

Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery

PubMed Central

Lee, Kyung-Koo; Park, Kwanghee; Lee, Hochan; Noh, Yohan; Kossowska, Dorota; Kwak, Kyungwon; Cho, Minhaeng

2017-01-01

Lithium cation is the charge carrier in lithium-ion battery. Electrolyte solution in lithium-ion battery is usually based on mixed solvents consisting of polar carbonates with different aliphatic chains. Despite various experimental evidences indicating that lithium ion forms a rigid and stable solvation sheath through electrostatic interactions with polar carbonates, both the lithium solvation structure and more importantly fluctuation dynamics and functional role of carbonate solvent molecules have not been fully elucidated yet with femtosecond vibrational spectroscopic methods. Here we investigate the ultrafast carbonate solvent exchange dynamics around lithium ions in electrolyte solutions with coherent two-dimensional infrared spectroscopy and find that the time constants of the formation and dissociation of lithium-ion···carbonate complex in solvation sheaths are on a picosecond timescale. We anticipate that such ultrafast microscopic fluxional processes in lithium-solvent complexes could provide an important clue to understanding macroscopic mobility of lithium cation in lithium-ion battery on a molecular level. PMID:28272396

Quantitative measurement of solvation shells using frequency modulated atomic force microscopy

NASA Astrophysics Data System (ADS)

Uchihashi, T.; Higgins, M.; Nakayama, Y.; Sader, J. E.; Jarvis, S. P.

2005-03-01

The nanoscale specificity of interaction measurements and additional imaging capability of the atomic force microscope make it an ideal technique for measuring solvation shells in a variety of liquids next to a range of materials. Unfortunately, the widespread use of atomic force microscopy for the measurement of solvation shells has been limited by uncertainties over the dimensions, composition and durability of the tip during the measurements, and problems associated with quantitative force calibration of the most sensitive dynamic measurement techniques. We address both these issues by the combined use of carbon nanotube high aspect ratio probes and quantifying the highly sensitive frequency modulation (FM) detection technique using a recently developed analytical method. Due to the excellent reproducibility of the measurement technique, additional information regarding solvation shell size as a function of proximity to the surface has been obtained for two very different liquids. Further, it has been possible to identify differences between chemical and geometrical effects in the chosen systems.

Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery

NASA Astrophysics Data System (ADS)

Lee, Kyung-Koo; Park, Kwanghee; Lee, Hochan; Noh, Yohan; Kossowska, Dorota; Kwak, Kyungwon; Cho, Minhaeng

2017-03-01

Lithium cation is the charge carrier in lithium-ion battery. Electrolyte solution in lithium-ion battery is usually based on mixed solvents consisting of polar carbonates with different aliphatic chains. Despite various experimental evidences indicating that lithium ion forms a rigid and stable solvation sheath through electrostatic interactions with polar carbonates, both the lithium solvation structure and more importantly fluctuation dynamics and functional role of carbonate solvent molecules have not been fully elucidated yet with femtosecond vibrational spectroscopic methods. Here we investigate the ultrafast carbonate solvent exchange dynamics around lithium ions in electrolyte solutions with coherent two-dimensional infrared spectroscopy and find that the time constants of the formation and dissociation of lithium-ion...carbonate complex in solvation sheaths are on a picosecond timescale. We anticipate that such ultrafast microscopic fluxional processes in lithium-solvent complexes could provide an important clue to understanding macroscopic mobility of lithium cation in lithium-ion battery on a molecular level.

Significance of solvated electrons (e(aq)-) as promoters of life on earth.

PubMed

Getoff, Nikola

2014-01-01

Based on the present state of knowledge a new hypothesis concerning the origin of life on Earth is presented, and emphasizes the particular significance of solvated electrons (e(aq)(-)). Solvated electrons are produced in seawater, mainly by (40)K radiation and in atmospheric moisture by VUV light, electrical discharges and cosmic ray. Solvated electrons are involved in primary chemical processes and in biological processes. The conversion of aqueous CO2 and CO into simple organic substances, the generation of ammonia from N2 and water, the formation of amines, amino acids and simple proteins under the action of e(aq)(-) has been experimentally proven. Furthermore, it is supposed that the generation of the primitive cell and equilibria of primitive enzymes are also realized due to the strong reducing property of e(aq)(-). The presented hypothesis is mainly founded on recently obtained experimental results. The involvement of e(aq)(-) in such mechanisms, as well as their action as an initiator of life is also briefly discussed.

Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery.

PubMed

Lee, Kyung-Koo; Park, Kwanghee; Lee, Hochan; Noh, Yohan; Kossowska, Dorota; Kwak, Kyungwon; Cho, Minhaeng

2017-03-08

Lithium cation is the charge carrier in lithium-ion battery. Electrolyte solution in lithium-ion battery is usually based on mixed solvents consisting of polar carbonates with different aliphatic chains. Despite various experimental evidences indicating that lithium ion forms a rigid and stable solvation sheath through electrostatic interactions with polar carbonates, both the lithium solvation structure and more importantly fluctuation dynamics and functional role of carbonate solvent molecules have not been fully elucidated yet with femtosecond vibrational spectroscopic methods. Here we investigate the ultrafast carbonate solvent exchange dynamics around lithium ions in electrolyte solutions with coherent two-dimensional infrared spectroscopy and find that the time constants of the formation and dissociation of lithium-ion···carbonate complex in solvation sheaths are on a picosecond timescale. We anticipate that such ultrafast microscopic fluxional processes in lithium-solvent complexes could provide an important clue to understanding macroscopic mobility of lithium cation in lithium-ion battery on a molecular level.

Exit channel dynamics in a micro-hydrated SN2 reaction of the hydroxyl anion.

PubMed

Otto, R; Brox, J; Trippel, S; Stei, M; Best, T; Wester, R

2013-08-29

We report on the reaction dynamics of the monosolvated SN2 reaction of cold OH(-)(H2O) with CH3I that have been studied using crossed beam ion imaging. Two SN2 reaction channels are possible for this reaction: Formation of unsolvated I(-) and of solvated I(-)(H2O) products. We find a strong preference for the formation of unsolvated I(-) reaction products with respect to the energetically favored reaction toward solvated I(-)(H2O). Angle differential cross section measurements reveal similar velocity and angular distributions for all solvated and parts of the unsolvated reaction products. We furthermore find that the contribution of these two products to the total product flux can be described by the same collision energy dependence. We interpret our findings in terms of a joint reaction mechanism in which a CH3OH(H2O)···I(-) complex is formed that decays into either solvated or unsolvated products. Quantum chemical calculation are used to support this assumption.

Molecular dynamics study of thermodynamic stability and dynamics of [Li(glyme)]+ complex in lithium-glyme solvate ionic liquids

NASA Astrophysics Data System (ADS)

Shinoda, Wataru; Hatanaka, Yuta; Hirakawa, Masashi; Okazaki, Susumu; Tsuzuki, Seiji; Ueno, Kazuhide; Watanabe, Masayoshi

2018-05-01

Equimolar mixtures of glymes and organic lithium salts are known to produce solvate ionic liquids, in which the stability of the [Li(glyme)]+ complex plays an important role in determining the ionic dynamics. Since these mixtures have attractive physicochemical properties for application as electrolytes, it is important to understand the dependence of the stability of the [Li(glyme)]+ complex on the ion dynamics. A series of microsecond molecular dynamics simulations has been conducted to investigate the dynamic properties of these solvate ionic liquids. Successful solvate ionic liquids with high stability of the [Li(glyme)]+ complex have been shown to have enhanced ion dynamics. Li-glyme pair exchange rarely occurs: its characteristic time is longer than that of ion diffusion by one or two orders of magnitude. Li-glyme pair exchange most likely occurs through cluster formation involving multiple [Li(glyme)]+ pairs. In this process, multiple exchanges likely take place in a concerted manner without the production of energetically unfavorable free glyme or free Li+ ions.

Molecular density functional theory of water describing hydrophobicity at short and long length scales

NASA Astrophysics Data System (ADS)

Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel

2013-10-01

We present an extension of our recently introduced molecular density functional theory of water [G. Jeanmairet et al., J. Phys. Chem. Lett. 4, 619 (2013)] to the solvation of hydrophobic solutes of various sizes, going from angstroms to nanometers. The theory is based on the quadratic expansion of the excess free energy in terms of two classical density fields: the particle density and the multipolar polarization density. Its implementation requires as input a molecular model of water and three measurable bulk properties, namely, the structure factor and the k-dependent longitudinal and transverse dielectric susceptibilities. The fine three-dimensional water structure around small hydrophobic molecules is found to be well reproduced. In contrast, the computed solvation free-energies appear overestimated and do not exhibit the correct qualitative behavior when the hydrophobic solute is grown in size. These shortcomings are corrected, in the spirit of the Lum-Chandler-Weeks theory, by complementing the functional with a truncated hard-sphere functional acting beyond quadratic order in density, and making the resulting functional compatible with the Van-der-Waals theory of liquid-vapor coexistence at long range. Compared to available molecular simulations, the approach yields reasonable solvation structure and free energy of hard or soft spheres of increasing size, with a correct qualitative transition from a volume-driven to a surface-driven regime at the nanometer scale.

Rate theory of solvent exchange and kinetics of Li(+) - BF4 (-)/PF6 (-) ion pairs in acetonitrile.

PubMed

Dang, Liem X; Chang, Tsun-Mei

2016-09-07

In this paper, we describe our efforts to apply rate theories in studies of solvent exchange around Li(+) and the kinetics of ion pairings in lithium-ion batteries (LIBs). We report one of the first computer simulations of the exchange dynamics around solvated Li(+) in acetonitrile (ACN), which is a common solvent used in LIBs. We also provide details of the ion-pairing kinetics of Li(+)-[BF4] and Li(+)-[PF6] in ACN. Using our polarizable force-field models and employing classical rate theories of chemical reactions, we examine the ACN exchange process between the first and second solvation shells around Li(+). We calculate exchange rates using transition state theory and weighted them with the transmission coefficients determined by the reactive flux, Impey, Madden, and McDonald approaches, and Grote-Hynes theory. We found the relaxation times changed from 180 ps to 4600 ps and from 30 ps to 280 ps for Li(+)-[BF4] and Li(+)-[PF6] ion pairs, respectively. These results confirm that the solvent response to the kinetics of ion pairing is significant. Our results also show that, in addition to affecting the free energy of solvation into ACN, the anion type also should significantly influence the kinetics of ion pairing. These results will increase our understanding of the thermodynamic and kinetic properties of LIB systems.

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

Dang, Liem X.; Chang, Tsun-Mei

In this paper, we describe our efforts to apply rate theories in studies of solvent exchange around Li{sup +} and the kinetics of ion pairings in lithium-ion batteries (LIBs). We report one of the first computer simulations of the exchange dynamics around solvated Li{sup +} in acetonitrile (ACN), which is a common solvent used in LIBs. We also provide details of the ion-pairing kinetics of Li{sup +}-[BF{sub 4}] and Li{sup +}-[PF{sub 6}] in ACN. Using our polarizable force-field models and employing classical rate theories of chemical reactions, we examine the ACN exchange process between the first and second solvation shellsmore » around Li{sup +}. We calculate exchange rates using transition state theory and weighted them with the transmission coefficients determined by the reactive flux, Impey, Madden, and McDonald approaches, and Grote-Hynes theory. We found the relaxation times changed from 180 ps to 4600 ps and from 30 ps to 280 ps for Li{sup +}-[BF{sub 4}] and Li{sup +}-[PF{sub 6}] ion pairs, respectively. These results confirm that the solvent response to the kinetics of ion pairing is significant. Our results also show that, in addition to affecting the free energy of solvation into ACN, the anion type also should significantly influence the kinetics of ion pairing. These results will increase our understanding of the thermodynamic and kinetic properties of LIB systems.« less

Rate theory of solvent exchange and kinetics of Li+ - BF4-/PF6- ion pairs in acetonitrile

NASA Astrophysics Data System (ADS)

Dang, Liem X.; Chang, Tsun-Mei

2016-09-01

In this paper, we describe our efforts to apply rate theories in studies of solvent exchange around Li+ and the kinetics of ion pairings in lithium-ion batteries (LIBs). We report one of the first computer simulations of the exchange dynamics around solvated Li+ in acetonitrile (ACN), which is a common solvent used in LIBs. We also provide details of the ion-pairing kinetics of Li+-[BF4] and Li+-[PF6] in ACN. Using our polarizable force-field models and employing classical rate theories of chemical reactions, we examine the ACN exchange process between the first and second solvation shells around Li+. We calculate exchange rates using transition state theory and weighted them with the transmission coefficients determined by the reactive flux, Impey, Madden, and McDonald approaches, and Grote-Hynes theory. We found the relaxation times changed from 180 ps to 4600 ps and from 30 ps to 280 ps for Li+-[BF4] and Li+-[PF6] ion pairs, respectively. These results confirm that the solvent response to the kinetics of ion pairing is significant. Our results also show that, in addition to affecting the free energy of solvation into ACN, the anion type also should significantly influence the kinetics of ion pairing. These results will increase our understanding of the thermodynamic and kinetic properties of LIB systems.

Anion photoelectron spectroscopy of acid-base systems, solvated molecules and MALDI matrix molecules

NASA Astrophysics Data System (ADS)

Eustis, Soren Newman

Gas phase, mass-selected, anion photoelectron spectroscopic studies were performed on a variety of molecular systems. These studies can be grouped into three main themes: acid-base interactions, solvation, and ions of analytical interest. Acid-base interactions represent some of the most fundamental processes in chemistry. The study of these processes elucidates elementary principles such as inner and outer sphere complexes, hard and soft ions, and salt formation---to name a few. Apart from their appeal from a pedagogical standpoint, the ubiquity of chemical reactions which involve acids, bases or the resulting salts makes the study of their fundamental interactions both necessary and fruitful. With this in mind, the neutral and anionic series (NH3···HX) (X= F, Cl, Br, I) were examined experimentally and theoretically. The relatively small size of these systems, combined with the advances in computational methods, allowed our experimental results to be compared with very high level ab initio theoretical results. The synergy between theory and experiment yielded an understanding of the nature of the complexes that could not be achieved with either method in isolation. The second theme present in this body or work is molecular solvation. Solvation is a phenomenon which is present in biology, chemistry and physics. Many biological molecules do not become 'active' until they are solvated by water. Thus, the study of biologically relevant species solvated by water is one step in a bottom up approach to studying the biochemical interactions in living organisms. Furthermore, the hydration of acidic molecules in the atmosphere is what drives the formation of 'free' protons or hydronium ions which are the key players in acid driven chemistry. Here are presented two unique solvation studies, Adenine(H2O)-n and C6F6(H2O)-n, these systems are very distinct, but show somewhat similar responses to hydration. The last theme presented in this work is the electronic properties of molecules relevant to analytical chemistry, or more specifically, Matrix Assisted Laser Desorption Interaction (MALDI) chemistry. For the first time electron affinities are presented for many of the common MALDI matrix compounds.

Investigation of efflorescence of inorganic aerosols using fluorescence spectroscopy.

PubMed

Choi, Man Yee; Chan, Chak K

2005-02-17

The phase transition is one of the most fundamental phenomena affecting the physical and chemical properties of atmospheric aerosols. Efflorescence, in particular, is not well understood, partly because the molecular interactions between the solute and water molecules of saturated or supersaturated solution droplets have not been well characterized. Recently, we developed a technique that combines the use of an electrodynamic balance and a fluorescence dye, 8-hydroxyl-1,3,6-pyrenetrisulfonate (pyranine), to study the distributions of solvated and free water in aqueous droplets (Choi, M. Y.; Chan, C. K.; Zhang, Y. H. J. Phys. Chem. A 2004, 108, 1133). We found that the equality of the amounts of solvated and free water is a necessary but not sufficient condition for efflorescence. For efflorescing compounds such as Na2SO4, (NH4)2SO4, and a mixture of NaCl and Na2SO4, the amount of free water decreases, while that of solvated water is roughly constant in bulk measurements and decreases less dramatically than that of free water in single-particle measurements as the relative humidity (RH) decreases. Efflorescence of the supersaturated droplets of these solutions occurs when the amounts of free and solvated water are equal, which is consistent with our previous observation for NaCl. For nonefflorescing compounds in single-particle levitation experiments such as MgSO4 and Mg(NO3)2, the amounts of free and solvated water are equal at a water-to-solute molar ratio of about 6, at which spectral changes due to the formation of contact ion pairs between magnesium and the anions occur as shown by Raman spectroscopy. Fluorescence imaging shows that the droplets of diluted Mg(NO3)2 (at 80% RH) and MgSO4 are homogeneous but those of NaCl, Na2SO4, (NH4)2SO4, and supersaturated Mg(NO3)2 (at 10% RH) are heterogeneous in terms of the solvated-to-free water distribution. The solvated-to-free water ratios in NaCl, Na2SO4, and (NH4)2SO4 droplets are higher in the outer regions by about half a radius deep than at the center of the droplets.

Excited state intramolecular proton transfer reaction of 4'-N,N-diethylamino-3-hydroxyflavone and solvation dynamics in room temperature ionic liquids studied by optical Kerr gate fluorescence measurement.

PubMed

Kimura, Yoshifumi; Fukuda, Masanori; Suda, Kayo; Terazima, Masahide

2010-09-16

Fluorescence dynamics of 4'-N,N-diethylamino-3-hydroxyflavone (DEAHF) and its methoxy derivative (DEAMF) in various room temperature ionic liquids (RTILs) have been studied mainly by an optical Kerr gate method. DEAMF showed a single band fluorescence whose peak shifted with time by the solvation dynamics. The averaged solvation time determined by the fluorescence peak shift was proportional to the viscosity of the solvent except for tetradecyltrihexylphosphonium bis(trifluoromethanesulfonyl)amide. The solvation times were consistent with reported values determined with different probe molecules. DEAHF showed dual fluorescence due to the normal and tautomer forms produced by the excited state intramolecular proton transfer (ESIPT), and the relative intensities were dependent on the time and the solvent cation or anion species. By using the information of the fluorescence spectrum of DEAMF, the fluorescence spectrum of DEAHF at each delay time after the photoexcitation was decomposed into the normal and the tautomer fluorescence components, respectively. The normal component showed a very fast decay simulated by a biexponential function (2-3 and 20-30 ps) with an additional slower decay component. The tautomer component showed a rise with the time constants corresponding to the faster decay of the normal form with an additional instantaneous rise. The faster dynamics of the normal and tautomer population changes were assigned to the ESIPT process, while the slower decay of the fluorescence was attributed to the population decay from the excited state through the radiative and nonradiative processes. The average ESIPT time was much faster than the averaged solvation time of RTILs. Basically, the ESIPT kinetics in RTILs is similar to those in conventional liquid solvents like acetonitrile (Chou et al. J. Phys. Chem. A 2005, 109, 3777). The faster ESIPT is interpreted in terms of the activation barrierless process from the Franck-Condon state before the solvation of the normal state in the electronic excited state. With the advance of the solvation in the excited state, the normal form becomes relatively more stable than the tautomer form, which makes the ESIPT become an activation process.

Structure prediction and molecular simulation of gases diffusion pathways in hydrogenase.

PubMed

Sundaram, Shanthy; Tripathi, Ashutosh; Gupta, Vipul

2010-10-06

Although hydrogen is considered to be one of the most promising future energy sources and the technical aspects involved in using it have advanced considerably, the future supply of hydrogen from renewable sources is still unsolved. The [Fe]- hydrogenase enzymes are highly efficient H(2) catalysts found in ecologically and phylogenetically diverse microorganisms, including the photosynthetic green alga, Chlamydomonas reinhardtii. While these enzymes can occur in several forms, H(2) catalysis takes place at a unique [FeS] prosthetic group or H-cluster, located at the active site. 3D structure of the protein hydA1 hydrogenase from Chlamydomonas reinhardtti was predicted using the MODELER 8v2 software. Conserved region was depicted from the NCBI CDD Search. Template selection was done on the basis NCBI BLAST results. For single template 1FEH was used and for multiple templates 1FEH and 1HFE were used. The result of the Homology modeling was verified by uploading the file to SAVS server. On the basis of the SAVS result 3D structure predicted using single template was chosen for performing molecular simulation. For performing molecular simulation three strategies were used. First the molecular simulation of the protein was performed in solvated box containing bulk water. Then 100 H(2) molecules were randomly inserted in the solvated box and two simulations of 50 and 100 ps were performed. Similarly 100 O(2) molecules were randomly placed in the solvated box and again 50 and 100 ps simulation were performed. Energy minimization was performed before each simulation was performed. Conformations were saved after each simulation. Analysis of the gas diffusion was done on the basis of RMSD, Radius of Gyration and no. of gas molecule/ps plot.

Polarization and charge transfer in the hydration of chloride ions

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

Zhao Zhen; Rogers, David M.; Beck, Thomas L.

2010-01-07

A theoretical study of the structural and electronic properties of the chloride ion and water molecules in the first hydration shell is presented. The calculations are performed on an ensemble of configurations obtained from molecular dynamics simulations of a single chloride ion in bulk water. The simulations utilize the polarizable AMOEBA force field for trajectory generation and MP2-level calculations are performed to examine the electronic structure properties of the ions and surrounding waters in the external field of more distant waters. The ChelpG method is employed to explore the effective charges and dipoles on the chloride ions and first-shell waters.more » The quantum theory of atoms in molecules (QTAIM) is further utilized to examine charge transfer from the anion to surrounding water molecules. The clusters extracted from the AMOEBA simulations exhibit high probabilities of anisotropic solvation for chloride ions in bulk water. From the QTAIM analysis, 0.2 elementary charges are transferred from the ion to the first-shell water molecules. The default AMOEBA model overestimates the average dipole moment magnitude of the ion compared to the quantum mechanical value. The average magnitude of the dipole moment of the water molecules in the first shell treated at the MP2-level, with the more distant waters handled with an AMOEBA effective charge model, is 2.67 D. This value is close to the AMOEBA result for first-shell waters (2.72 D) and is slightly reduced from the bulk AMOEBA value (2.78 D). The magnitude of the dipole moment of the water molecules in the first solvation shell is most strongly affected by the local water-water interactions and hydrogen bonds with the second solvation shell, rather than by interactions with the ion.« less

Advances in free-energy-based simulations of protein folding and ligand binding.

PubMed

Perez, Alberto; Morrone, Joseph A; Simmerling, Carlos; Dill, Ken A

2016-02-01

Free-energy-based simulations are increasingly providing the narratives about the structures, dynamics and biological mechanisms that constitute the fabric of protein science. Here, we review two recent successes. It is becoming practical: first, to fold small proteins with free-energy methods without knowing substructures and second, to compute ligand-protein binding affinities, not just their binding poses. Over the past 40 years, the timescales that can be simulated by atomistic MD are doubling every 1.3 years--which is faster than Moore's law. Thus, these advances are not simply due to the availability of faster computers. Force fields, solvation models and simulation methodology have kept pace with computing advancements, and are now quite good. At the tip of the spear recently are GPU-based computing, improved fast-solvation methods, continued advances in force fields, and conformational sampling methods that harness external information. Copyright © 2015 Elsevier Ltd. All rights reserved.

Hydroxide diffuses slower than hydronium in water because its solvated structure inhibits correlated proton transfer

NASA Astrophysics Data System (ADS)

Chen, Mohan; Zheng, Lixin; Santra, Biswajit; Ko, Hsin-Yu; DiStasio, Robert A., Jr.; Klein, Michael L.; Car, Roberto; Wu, Xifan

2018-03-01

Proton transfer via hydronium and hydroxide ions in water is ubiquitous. It underlies acid-base chemistry, certain enzyme reactions, and even infection by the flu. Despite two centuries of investigation, the mechanism underlying why hydroxide diffuses slower than hydronium in water is still not well understood. Herein, we employ state-of-the-art density-functional-theory-based molecular dynamics—with corrections for non-local van der Waals interactions, and self-interaction in the electronic ground state—to model water and hydrated water ions. At this level of theory, we show that structural diffusion of hydronium preserves the previously recognized concerted behaviour. However, by contrast, proton transfer via hydroxide is less temporally correlated, due to a stabilized hypercoordination solvation structure that discourages proton transfer. Specifically, the latter exhibits non-planar geometry, which agrees with neutron-scattering results. Asymmetry in the temporal correlation of proton transfer leads to hydroxide diffusing slower than hydronium.

Preferential solvation of lysozyme in dimethyl sulfoxide/water binary mixture probed by terahertz spectroscopy.

PubMed

Das, Dipak Kumar; Patra, Animesh; Mitra, Rajib Kumar

2016-09-01

We report the changes in the hydration dynamics around a model protein hen egg white lysozyme (HEWL) in water-dimethyl sulfoxide (DMSO) binary mixture using THz time domain spectroscopy (TTDS) technique. DMSO molecules get preferentially solvated at the protein surface, as indicated by circular dichroism (CD) and Fourier transform infrared (FTIR) study in the mid-infrared region, resulting in a conformational change in the protein, which consequently modifies the associated hydration dynamics. As a control we also study the collective hydration dynamics of water-DMSO binary mixture and it is found that it follows a non-ideal behavior owing to the formation of DMSO-water clusters. It is observed that the cooperative dynamics of water at the protein surface does follow the DMSO-mediated conformational modulation of the protein. Copyright © 2016 Elsevier B.V. All rights reserved.

Coordination chemistry in magnesium battery electrolytes: how ligands affect their performance.

PubMed

Shao, Yuyan; Liu, Tianbiao; Li, Guosheng; Gu, Meng; Nie, Zimin; Engelhard, Mark; Xiao, Jie; Lv, Dongping; Wang, Chongmin; Zhang, Ji-Guang; Liu, Jun

2013-11-04

Magnesium battery is potentially a safe, cost-effective, and high energy density technology for large scale energy storage. However, the development of magnesium battery has been hindered by the limited performance and the lack of fundamental understandings of electrolytes. Here, we present a study in understanding coordination chemistry of Mg(BH₄)₂ in ethereal solvents. The O donor denticity, i.e. ligand strength of the ethereal solvents which act as ligands to form solvated Mg complexes, plays a significant role in enhancing coulombic efficiency of the corresponding solvated Mg complex electrolytes. A new electrolyte is developed based on Mg(BH₄)₂, diglyme and LiBH₄. The preliminary electrochemical test results show that the new electrolyte demonstrates a close to 100% coulombic efficiency, no dendrite formation, and stable cycling performance for Mg plating/stripping and Mg insertion/de-insertion in a model cathode material Mo₆S₈ Chevrel phase.

Comparison of volume and surface area nonpolar solvation free energy terms for implicit solvent simulations.

PubMed

Lee, Michael S; Olson, Mark A

2013-07-28

Implicit solvent models for molecular dynamics simulations are often composed of polar and nonpolar terms. Typically, the nonpolar solvation free energy is approximated by the solvent-accessible-surface area times a constant factor. More sophisticated approaches incorporate an estimate of the attractive dispersion forces of the solvent and∕or a solvent-accessible volume cavitation term. In this work, we confirm that a single volume-based nonpolar term most closely fits the dispersion and cavitation forces obtained from benchmark explicit solvent simulations of fixed protein conformations. Next, we incorporated the volume term into molecular dynamics simulations and find the term is not universally suitable for folding up small proteins. We surmise that while mean-field cavitation terms such as volume and SASA often tilt the energy landscape towards native-like folds, they also may sporadically introduce bottlenecks into the folding pathway that hinder the progression towards the native state.

Phenol-quinone tautomerism in (arylazo)naphthols and the analogous Schiff bases: benchmark calculations.

PubMed

Ali, S Tahir; Antonov, Liudmil; Fabian, Walter M F

2014-01-30

Tautomerization energies of a series of isomeric [(4-R-phenyl)azo]naphthols and the analogous Schiff bases (R = N(CH3)2, OCH3, H, CN, NO2) are calculated by LPNO-CEPA/1-CBS using the def2-TZVPP and def2-QZVPP basis sets for extrapolation. The performance of various density functionals (B3LYP, M06-2X, PW6B95, B2PLYP, mPW2PLYP, PWPB95) as well as MP2 and SCS-MP2 is evaluated against these results. M06-2X and SCS-MP2 yield results close to the LPNO-CEPA/1-CBS values. Solvent effects (CCl4, CHCl3, CH3CN, and CH3OH) are treated by a variety of bulk solvation models (SM8, IEFPCM, COSMO, PBF, and SMD) as well as explicit solvation (Monte Carlo free energy perturbation using the OPLSAA force field).

Comparison of volume and surface area nonpolar solvation free energy terms for implicit solvent simulations

NASA Astrophysics Data System (ADS)

Lee, Michael S.; Olson, Mark A.

2013-07-01

Implicit solvent models for molecular dynamics simulations are often composed of polar and nonpolar terms. Typically, the nonpolar solvation free energy is approximated by the solvent-accessible-surface area times a constant factor. More sophisticated approaches incorporate an estimate of the attractive dispersion forces of the solvent and/or a solvent-accessible volume cavitation term. In this work, we confirm that a single volume-based nonpolar term most closely fits the dispersion and cavitation forces obtained from benchmark explicit solvent simulations of fixed protein conformations. Next, we incorporated the volume term into molecular dynamics simulations and find the term is not universally suitable for folding up small proteins. We surmise that while mean-field cavitation terms such as volume and SASA often tilt the energy landscape towards native-like folds, they also may sporadically introduce bottlenecks into the folding pathway that hinder the progression towards the native state.