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Sample records for abraham solvation equations

  1. Estimation of Abraham solvation equation coefficients for hydrogen bond formation from Abraham solvation parameters for solute acidity and basicity.

    PubMed

    van Noort, Paul

    2013-01-01

    Abraham solvation equations find widespread use in environmental chemistry and pharmaco-chemistry. The coefficients in these equations, which are solvent (system) descriptors, are usually determined by fitting experimental data. To simplify the determination of these coefficients in Abraham solvation equations, this study derives equations, based on Abraham solvation parameters for hydrogen acidity and basicity of the solvents involved, to estimate the value of the coefficients for hydrogen bond formation. These equations were applied to calculate Abraham solvation parameters for hydrogen acidity and basicity for polyoxymethylene, polyacrylate, sodium dodecylsulfate, some ionic liquids, alkanoyl phosphatidyl cholines, and lipids for which fitted values for Abraham coefficients for hydrogen bond formation were available. PMID:22892357

  2. Lorentz Abraham Force and Power Equations

    NASA Astrophysics Data System (ADS)

    Yaghjian, Arthur D.

    Toward the end of the nineteenth century Lorentz modeled the electron (“vibrating charged particle,” as he called it) by a spherical shell of uniform surface charge density and set about the difficult task of deriving the equation of motion of this electron model by determining, from Maxwell's equations and the Lorentz force law, the retarded self electromagnetic force that the fields of the accelerating charge distribution exert upon the charge itself [1]. (This initial work of Lorentz in 1892 on a moving charged sphere appeared five years before J.J. Thomson's “discovery” of the electron. It is summarized in English by J.Z. Buchwald [2, app. 7].) With the help of Abraham,1 a highly successful theory of the moving electron model was completed by the early 1900's [3, 4]. Before Einstein's papers [5, 6] on special relativity appeared in 1905, they had derived the following force equation of motion

  3. Energy conservation equation for a radiating pointlike charge in the context of the Abraham-Lorentz versus the Abraham-Becker radiation-reaction force

    NASA Astrophysics Data System (ADS)

    Bellotti, U.; Bornatici, M.

    1997-12-01

    With reference to a radiating pointlike charge, the energy conservation equation comprising the effect of the Abraham-Lorentz radiation-reaction force is contrasted with the incorrect energy conservation equation obtained by Hartemann and Luhmann [Phys. Rev. Lett. 74, 1107 (1995)] on considering instead the Abraham-Becker force that accounts only for a part of the instantaneous radiation-reaction force.

  4. Basic Equations and Constitutive Equations of Micropolar Magnetic Fluids with E-BAnalogy and the Abraham Expression of Electromagnetic Momentum

    NASA Astrophysics Data System (ADS)

    Ido, Yasushi

    A complete set of basic equations for magnetic fluids with internal rotation is proposed in this paper. The basic equations are derived from the conservation laws of mass, linear momentum, angular momentum and energy, while the constitutive equations are obtained by the thermodynamical method that is based on the free energy and the dissipation function. The concrete expression of constitutive equations are determined by the principle of material frame indifference and the principle of maximal dissipation rate. The Abraham expression of the electromagnetic momentum and E-Banalogy are adopted in this theory. It is shown that the difference in the basic equations in case of adopting the Abraham expression and the Minkowski expression, respectively. The constitutive equation of magnetization which includes the Shliomis relaxation equation (1972) is proposed.

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

    SciTech Connect

    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.

  6. Solvation!

    SciTech Connect

    Ivana Adamovic

    2004-12-19

    This dissertation consists of two closely related parts: theory development and coding of correlation effects in a model potential for solvation, and study of solvent effects on chemical reactions and processes. The effective fragment potential (EFP) method has been re-parameterized, using density functional theory (DFT), more specifically, the B3LYP functional. The DFT based EFP method includes short-range correlation effects; hence it is a first step in incorporating the treatment of correlation in the EFP solvation model. In addition, the gradient of the charge penetration term in the EFP model was derived and coded. The new method has been implemented in the electronic structure code GAMESS and is in use. Formulas for the dynamic dipole polarizability, C{sub 6} dispersion coefficient and dispersion energy were derived and coded as a part of a treatment of the dispersion interactions in the general solvation model, EFP2. Preliminary results are in good agreement with experimental and other theoretical data. The DFT based EFP (EFP1/DFT) method was used in the study of microsolvation effects on the S{sub N}2 substitution reaction, between chloride and methyl bromide. Changes in the central barrier, for several lowest lying isomers of the systems with one, two, three and four waters, were studied using second order perturbation theory (MP2), DFT and mixed quantum mechanics (QM)/(EFP1/DFT) methods. EFP1/DFT is found to reproduce QM results with high accuracy, at just a fraction of the cost. Molecular structures and potential energy surfaces for IHI{sup -} {center_dot} Ar{sub n} (n=1-7) were studied using the MP2 method. Experimentally observed trends in the structural arrangement of the Ar atoms were explained through the analysis of the geometrical parameters and three-dimensional MP2 molecular electrostatic potentials.

  7. Incorporation of solvation effects into the fragment molecular orbital calculations with the Poisson-Boltzmann equation

    NASA Astrophysics Data System (ADS)

    Watanabe, Hirofumi; Okiyama, Yoshio; Nakano, Tatsuya; Tanaka, Shigenori

    2010-11-01

    We developed FMO-PB method, which incorporates solvation effects into the Fragment Molecular Orbital calculation with the Poisson-Boltzmann equation. This method retains good accuracy in energy calculations with reduced computational time. We calculated the solvation free energies for polyalanines, Alpha-1 peptide, tryptophan cage, and complex of estrogen receptor and 17 β-estradiol to show the applicability of this method for practical systems. From the calculated results, it has been confirmed that the FMO-PB method is useful for large biomolecules in solution. We also discussed the electric charges which are used in solving the Poisson-Boltzmann equation.

  8. Efficient quantum mechanical calculation of solvation free energies based on density functional theory, numerical atomic orbitals and Poisson Boltzmann equation

    NASA Astrophysics Data System (ADS)

    Wang, Mingliang; Wong, Chung F.; Liu, Jianhong; Zhang, Peixin

    2007-07-01

    We have successfully coupled the Kohn-Sham with Poisson-Boltzmann equations to predict the solvation free energy, where the Kohn-Sham equations were solved by implementing the flexible pseudo atomic orbitals as in S IESTA package. It was found that the calculated solvation free energy is in good agreement with experimental results for small neutral molecules, and its standard error is 1.33 kcal/mol, the correlation coefficient is 0.97. Due to its high efficiency and accuracy, the proposed model can be a promising tool for computing solvation free energies in computer aided drug design in future.

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

    NASA Astrophysics Data System (ADS)

    Yang, Pei-Kun

    2016-06-01

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

  10. Charge Central Interpretation of the Full Nonlinear PB Equation: Implications for Accurate and Scalable Modeling of Solvation Interactions.

    PubMed

    Xiao, Li; Wang, Changhao; Ye, Xiang; Luo, Ray

    2016-08-25

    Continuum solvation modeling based upon the Poisson-Boltzmann equation (PBE) is widely used in structural and functional analysis of biomolecules. In this work, we propose a charge-central interpretation of the full nonlinear PBE electrostatic interactions. The validity of the charge-central view or simply charge view, as formulated as a vacuum Poisson equation with effective charges, was first demonstrated by reproducing both electrostatic potentials and energies from the original solvated full nonlinear PBE. There are at least two benefits when the charge-central framework is applied. First the convergence analyses show that the use of polarization charges allows a much faster converging numerical procedure for electrostatic energy and forces calculation for the full nonlinear PBE. Second, the formulation of the solvated electrostatic interactions as effective charges in vacuum allows scalable algorithms to be deployed for large biomolecular systems. Here, we exploited the charge-view interpretation and developed a particle-particle particle-mesh (P3M) strategy for the full nonlinear PBE systems. We also studied the accuracy and convergence of solvation forces with the charge-view and the P3M methods. It is interesting to note that the convergence of both the charge-view and the P3M methods is more rapid than the original full nonlinear PBE method. Given the developments and validations documented here, we are working to adapt the P3M treatment of the full nonlinear PBE model to molecular dynamics simulations. PMID:27146097

  11. Abraham Lincoln's Gettysburg illness.

    PubMed

    Goldman, Armond S; Schmalstieg, Frank C

    2007-05-01

    When Abraham Lincoln delivered the Gettysburg Address, he was weak and dizzy; his face had a ghastly colour. That evening on the train to Washington, DC, he was febrile and weak, and suffered severe headaches. The symptoms continued; back pains developed. On the fourth day of the illness, a widespread scarlet rash appeared that soon became vesicular. By the tenth day, the lesions itched and peeled. The illness lasted three weeks. The final diagnosis, a touch of varioloid, was an old name for smallpox that was later used in the 20th century to denote mild smallpox in a partially immune individual. It was unclear whether Lincoln had been immunized against smallpox. Indeed, this review suggests that Lincoln had unmodified smallpox and that Lincoln's physicians tried to reassure the public that Lincoln was not seriously ill. Indeed, the successful conclusion of the Civil War and reunification of the country were dependent upon Lincoln's presidency. PMID:17551612

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

    NASA Astrophysics Data System (ADS)

    Qiao, Yu; Tu, Bin; Lu, Benzhuo

    2014-05-01

    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

  13. 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

    2014-05-01

    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

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

    PubMed

    Frach, Roland; Kast, Stefan M

    2014-12-11

    The accurate computational prediction of nuclear magnetic resonance (NMR) parameters like chemical shifts represents a challenge if the species studied is immersed in strongly polarizing environments such as water. Common approaches to treating a solvent in the form of, e.g., the polarizable continuum model (PCM) ignore strong directional interactions such as H-bonds to the solvent which can have substantial impact on magnetic shieldings. We here present a computational methodology that accounts for atomic-level solvent effects on NMR parameters by extending the embedded cluster reference interaction site model (EC-RISM) integral equation theory to the prediction of chemical shifts of N-methylacetamide (NMA) in aqueous solution. We examine the influence of various so-called closure approximations of the underlying three-dimensional RISM theory as well as the impact of basis set size and different treatment of electrostatic solute-solvent interactions. We find considerable and systematic improvement over reference PCM and gas phase calculations. A smaller basis set in combination with a simple point charge model already yields good performance which can be further improved by employing exact electrostatic quantum-mechanical solute-solvent interaction energies. A larger basis set benefits more significantly from exact over point charge electrostatics, which can be related to differences of the solvent's charge distribution. PMID:25377116

  15. Abraham Maslow's Legacy for Counseling.

    ERIC Educational Resources Information Center

    Hoffman, Edward

    1990-01-01

    Reviews the life of Abraham Maslow, a key founder of the humanistic approach to counseling, and his contributions to the counseling field. Maintains that Maslow's innovative work was often misinterpreted by both his admirers and his critics, yet remains highly relevant to current concerns in counseling. (Author/PVV)

  16. Olanzapine solvates.

    PubMed

    Cavallari, Cristina; Santos, Beatriz Pérez-Artacho; Fini, Adamo

    2013-11-01

    Olanzapine was crystallized from 12 organic solvents alone or in mixture, by cooling in the freezer, by slow evaporation of the solvent, or by suspending olanzapine powder for some time in the solvent. All the samples thus obtained were examined by thermal analysis (differential scanning calorimetry-DSC and thermogravimetry-TG) to certify the formation of a solvate, the presence of polymorph (form 1 or 2) in the desolvated olanzapine, comparing the different profile of the thermograms, and to calculate the stoichiometry of the possible solvate. According to the DSC thermogram, the solvents can be divided into four classes: those that do not form solvates and leave olanzapine form 1 (ethyl acetate, toluene, diethyl ether, and acetone); those that form solvate and leave form 1 of olanzapine after desolvation (methanol, 1- and 2-propanol); those that after desolvation of the solvate show a polymorph transition in the thermogram indicating the presence of form 2 of olanzapine (ethanol); other solvents (tetrahydrofuran, chloroform, acetonitrile) give solvate thermograms, where this last thermal trace is only poorly evident. With few exceptions, each solvent forms solvate both when pure and in mixture (10%, v/v, in ethyl acetate). Methanol monosolvate displays complex thermogram and thermogravimetric desolvation profiles, depending on the crystallization experimental conditions, used to prepare the solvates. Dichloromethane solvate was found by X-ray diffraction analysis to be amorphous and, on heating during DSC analysis, allowed the crystallization of both form 1 and 2, with different weight ratio, according to the experimental conditions of the solvate preparation. PMID:23963777

  17. Experimental evidence for Abraham pressure of light

    NASA Astrophysics Data System (ADS)

    Zhang, Li; She, Weilong; Peng, Nan; Leonhardt, Ulf

    2015-05-01

    The question of how much momentum light carries in media has been debated for over a century. Two rivalling theories, one from 1908 by Hermann Minkowski and the other from 1909 by Max Abraham, predict the exact opposite when light enters an optical material: a pulling force in Minkowski's case and a pushing force in Abraham's. Most experimental tests have agreed with Minkowski's theory, but here we report the first quantitative experimental evidence for Abraham's pushing pressure of light. Our results matter in optofluidics and optomechanics, and wherever light exerts mechanical pressure.

  18. Abraham Maslow: On the Potential of Women

    ERIC Educational Resources Information Center

    Podeschi, Ronald L.; Podeschi, Phyllis J.

    1973-01-01

    Authors presented some principal perspectives by the psychologist, Abraham Maslow, who died in 1970, and who was writing about the potential of women long before it became popular to do so. (Author/RK)

  19. Abraham Flexner and medical education.

    PubMed

    Ludmerer, Kenneth M

    2011-01-01

    The Flexner Report had its roots in the recognition in the mid-19th century that medical knowledge is not something fixed but something that grows and evolves. This new view of medical knowledge led to a recasting of the goal of medical education as that of instilling the proper techniques of acquiring and evaluating information rather than merely inculcating facts through rote memorization. Abraham Flexner, a brilliant educator, had the background to understand and popularize the meaning of this new view of education, and he took the unprecedented step of relating the developments in medical education to the ideas of John Dewey and the progressive education movement. Although the Flexner Report is typically viewed as a historical document--due to an understandable tendency to refer only to the second half of the report, where Flexner provides his famous critiques of the medical schools that existed at the time--this article argues that the Flexner Report is actually a living educational document of as much significance to medical educators today as in Flexner's time. The article analyzes Flexner's discussion of medical education and shows that his message--the importance of academic excellence, professional leadership, proper financial support, and service and altruism--is timeless, as applicable to the proper education of physicians today and tomorrow as in the past. PMID:21399378

  20. Anion solvation in alcohols

    SciTech Connect

    Jonah, C.D.; Xujia, Zhang; Lin, Yi

    1996-03-01

    Anion solvation is measured in alcohols using pump-probe pulse radiolysis and the activation energy of solvation is determined. Solvation of an anion appears to be different than excited state solvation. The continuum dielectric model does not appear to explain the results.

  1. Famous Americans: George Washington & Abraham Lincoln.

    ERIC Educational Resources Information Center

    Fleming, Maria

    Introducing students in grade 1-3 to George Washington and Abraham Lincoln, this book presents thematic units that present biographical information, and literature links such as poems, songs, stories, cross-curricular activities, and hands-on reproducibles. Chapters in the book are: (1) Getting to Know George; (2) The Father and His Country; (3)…

  2. Famous Americans: George Washington and Abraham Lincoln.

    ERIC Educational Resources Information Center

    Fleming, Maria

    This book provides background information and ideas for teaching about George Washington and Abraham Lincoln at the primary grade level. Cross-curricular activities include work in music, writing, art, research, plays, and games. A pull-out poster with a poem on "President's Day" is stapled in the center of the book. Chapters in the book are: (1)…

  3. Abraham Lincoln: American Lawyer-President

    ERIC Educational Resources Information Center

    Dirck, Brian

    2009-01-01

    Abraham Lincoln was the most experienced trial lawyer Americans have ever placed in the White House. While more than half of the United State's presidents have been attorneys, none possessed Lincoln's extensive courtroom experience: approximately 3,800 known cases, litigated during a quarter century at the Illinois bar. However, the law's…

  4. Variational approach for nonpolar solvation analysis

    PubMed Central

    Chen, Zhan; Zhao, Shan; Chun, Jaehun; Thomas, Dennis G.; Baker, Nathan A.; Bates, Peter W.; Wei, G. W.

    2012-01-01

    Solvation analysis is one of the most important tasks in chemical and biological modeling. Implicit solvent models are some of the most popular approaches. However, commonly used implicit solvent models rely on unphysical definitions of solvent-solute boundaries. Based on differential geometry, the present work defines the solvent-solute boundary via the variation of the nonpolar solvation free energy. The solvation free energy functional of the system is constructed based on a continuum description of the solvent and the discrete description of the solute, which are dynamically coupled by the solvent-solute boundaries via van der Waals interactions. The first variation of the energy functional gives rise to the governing Laplace-Beltrami equation. The present model predictions of the nonpolar solvation energies are in an excellent agreement with experimental data, which supports the validity of the proposed nonpolar solvation model. PMID:22938212

  5. Production of solvated electrons

    NASA Technical Reports Server (NTRS)

    Thomas, J. K.

    1969-01-01

    Current research, both theoretical and experimental, relating to the production and kinetics of interactions of solvated electrons is reviewed. Particular attention is focused on solvated electrons generated by ionizing radiation in water, alcohols, and organic systems.

  6. Proton solvation in protic and aprotic solvents.

    PubMed

    Rossini, Emanuele; Knapp, Ernst-Walter

    2016-05-01

    Protonation pattern strongly affects the properties of molecular systems. To determine protonation equilibria, proton solvation free energy, which is a central quantity in solution chemistry, needs to be known. In this study, proton affinities (PAs), electrostatic energies of solvation, and pKA values were computed in protic and aprotic solvents. The proton solvation energy in acetonitrile (MeCN), methanol (MeOH), water, and dimethyl sulfoxide (DMSO) was determined from computed and measured pKA values for a specially selected set of organic compounds. pKA values were computed with high accuracy using a combination of quantum chemical and electrostatic approaches. Quantum chemical density functional theory computations were performed evaluating PA in the gas-phase. The electrostatic contributions of solvation were computed solving the Poisson equation. The computations yield proton solvation free energies with high accuracy, which are in MeCN, MeOH, water, and DMSO -255.1, -265.9, -266.3, and -266.4 kcal/mol, respectively, where the value for water is close to the consensus value of -265.9 kcal/mol. The pKA values of MeCN, MeOH, and DMSO in water correlates well with the corresponding proton solvation energies in these liquids, indicating that the solvated proton was attached to a single solvent molecule. © 2016 Wiley Periodicals, Inc. PMID:26786747

  7. View southwest, buildings of the Abraham Cyrus Farmstead. (Left to ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    View southwest, buildings of the Abraham Cyrus Farmstead. (Left to right in photograph: hen house, chicken shed, equipment shed, large tree at center foreground, barn, evergreen in yard, wash house, farmhouse - Abraham Cyrus Farmstead, 3271 Cyrus Road (County Road 1/6), Cyrus, Wayne County, WV

  8. Parameter optimization in differential geometry based solvation models.

    PubMed

    Wang, Bao; Wei, G W

    2015-10-01

    Differential geometry (DG) based solvation models are a new class of variational implicit solvent approaches that are able to avoid unphysical solvent-solute boundary definitions and associated geometric singularities, and dynamically couple polar and non-polar interactions in a self-consistent framework. Our earlier study indicates that DG based non-polar solvation model outperforms other methods in non-polar solvation energy predictions. However, the DG based full solvation model has not shown its superiority in solvation analysis, due to its difficulty in parametrization, which must ensure the stability of the solution of strongly coupled nonlinear Laplace-Beltrami and Poisson-Boltzmann equations. In this work, we introduce new parameter learning algorithms based on perturbation and convex optimization theories to stabilize the numerical solution and thus achieve an optimal parametrization of the DG based solvation models. An interesting feature of the present DG based solvation model is that it provides accurate solvation free energy predictions for both polar and non-polar molecules in a unified formulation. Extensive numerical experiment demonstrates that the present DG based solvation model delivers some of the most accurate predictions of the solvation free energies for a large number of molecules. PMID:26450304

  9. 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…

  10. Abraham Lincoln and the insanity plea.

    PubMed

    Spiegel, A D

    1994-06-01

    A confederate civilian physician shot and killed a white Union officer who was drilling Negro troops in Norfolk, Virginia. With no question as to guilt, President Abraham Lincoln decided to have a medical expert conduct a professional sanity/insanity examination. Documentation indicates that legal and political factors may have influenced Lincoln's decision. As a lawyer, Lincoln prosecuted a case where the insanity plea was used as a defense. Two influential Cabinet members, William H. Seward and Edwin M. Stanton, also had legal experience involving the insanity plea. Politically, Lincoln faced serious issues such as the draft riots, the military necessity to recruit slaves into the army, the impact of Union Negro soldiers upon the border states, the morale and discipline of the army and the upcoming presidential election. Upon Seward's recommendation, Lincoln chose a physician who had a reputation for finding the accused sane and who did so in this case. As the southern physician was hanged, Lincoln's means achieved the desired legal and political ends. PMID:8089270

  11. Redefining solubility parameters: the partial solvation parameters.

    PubMed

    Panayiotou, Costas

    2012-03-21

    The present work reconsiders a classical and universally accepted concept of physical chemistry, the solubility parameter. Based on the insight derived from modern quantum chemical calculations, a new definition of solubility parameter is proposed, which overcomes some of the inherent restrictions of the original definition and expands its range of applications. The original single solubility parameter is replaced by four partial solvation parameters reflecting the dispersion, the polar, the acidic and the basic character of the chemical compounds as expressed either in their pure state or in mixtures. Simple rules are adopted for the definition and calculation of these four parameters and their values are tabulated for a variety of common substances. In contrast, however, to the well known Hansen solubility parameters, their design and evaluation does not rely exclusively on the basic rule of "similarity matching" for solubility but it makes also use of the other basic rule of compatibility, namely, the rule of "complementarity matching". This complementarity matching becomes particularly operational with the sound definition of the acidic and basic components of the solvation parameter based on the third σ-moments of the screening charge distributions of the quantum mechanics-based COSMO-RS theory. The new definitions are made in a simple and straightforward manner, thus, preserving the strength and appeal of solubility parameter stemming from its simplicity. The new predictive method has been applied to a variety of solubility data for systems of pharmaceuticals and polymers. The results from quantum mechanics calculations are critically compared with the results from Abraham's acid/base descriptors. PMID:22327537

  12. DFT solvation studies of carbohydrates: implicit and explicit solvation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Solvents play a role in carbohydrate structure. Therefore, it is important to include solvation effects in calculations to allow a more realistic comparison with experimental data. A possible way to include solvation effects is to use implicit solvation models such as COSMO and PCM. Another avenu...

  13. Abraham Lincoln and the global economy.

    PubMed

    Hormats, Robert D

    2003-08-01

    Abraham Lincoln would have well understood the challenges facing many modern emerging nations. In Lincoln's America, as in many developing nations today, sweeping economic change threatened older industries, traditional ways of living, and social and national cohesion by exposing economies and societies to new and powerful competitive forces. Yet even in the midst of the brutal and expensive American Civil war--and in part because of it--Lincoln and the Republican Congress enacted bold legislation that helped create a huge national market, a strong and unified economy governed by national institutions, and a rising middle class of businessmen and property owners. Figuring out how to maximize the benefits of globalization while minimizing its disruptions is a formidable challenge for policy makers. How do you expand opportunities for the talented and the lucky while making sure the rest of society doesn't fall behind? It may be helpful to look at the principles that informed the policies that Lincoln and the Republican Congress instituted after they came to power in 1861: Facilitate the upward mobility of low- and middle-income groups to give them a significant stake in the country. Emphasize the good of the national economy over regional interests. Affirm the need for sound government institutions to temper the dynamics of the free enterprise system. Tailor policies to the national situation. Realize that a period of turmoil may present a unique opportunity for reform. These principles drove the reforms that helped Americans cope with and benefit from rapid technological advances and the fast integration of the American economy in the nineteenth century. They may be instructive to today's policy makers who are struggling to help their own citizens integrate into the fast-changing global economy of the twenty-first century. PMID:12884668

  14. Polar solvation and electron transfer

    SciTech Connect

    Not Available

    1993-04-13

    The report is divided into the following sections: completion of previous studies on solvation dynamics, dipole lattice studies, inertial components of solvation response, simple models of solvation dynamics, rotational dynamics and dielectric friction, intramolecular electron transfer reactions, and intermolecular donor-acceptor complexes.

  15. 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

  16. The Enigmatic Savior of the Union: Abraham Lincoln.

    ERIC Educational Resources Information Center

    Diamond, Ronald L.; Diamond, Linda W.

    Abraham Lincoln rose from the depths of obscurity to guide the United States successfully through the turbulent and menacing years of the Civil War. Laborer, businessman, postmaster, politician, and lawyer were some of the vocations, not all successful, that Lincoln tried during the years leading to his ascent to the Presidency. This review of the…

  17. "Happy Birthday, Mr. President!" New Books for Abraham Lincoln's Bicentennial

    ERIC Educational Resources Information Center

    Young, Terrell A.; Ward, Barbara A.; Day, Deanna

    2009-01-01

    Stories about Abraham Lincoln have captivated children for generations. The Lincoln story has taken on almost mythic proportions, making it difficult to separate fact from fiction or exaggeration. Young readers never tire of talking about Lincoln's early days--from his birth in a log cabin in Hardin County, Kentucky to his childhood in…

  18. Quantifying solvated electrons' delocalization.

    PubMed

    Janesko, Benjamin G; Scalmani, Giovanni; Frisch, Michael J

    2015-07-28

    Delocalized, solvated electrons are a topic of much recent interest. We apply the electron delocalization range EDR(r;u) (J. Chem. Phys., 2014, 141, 144104) to quantify the extent to which a solvated electron at point r in a calculated wavefunction delocalizes over distance u. Calculations on electrons in one-dimensional model cavities illustrate fundamental properties of the EDR. Mean-field calculations on hydrated electrons (H2O)n(-) show that the density-matrix-based EDR reproduces existing molecular-orbital-based measures of delocalization. Correlated calculations on hydrated electrons and electrons in lithium-ammonia clusters illustrates how electron correlation tends to move surface- and cavity-bound electrons onto the cluster or cavity surface. Applications to multiple solvated electrons in lithium-ammonia clusters provide a novel perspective on the interplay of delocalization and strong correlation central to lithium-ammonia solutions' concentration-dependent insulator-to-metal transition. The results motivate continued application of the EDR to simulations of delocalized electrons. PMID:25994586

  19. Interfacial solvation thermodynamics.

    PubMed

    Ben-Amotz, Dor

    2016-10-19

    Previous studies have reached conflicting conclusions regarding the interplay of cavity formation, polarizability, desolvation, and surface capillary waves in driving the interfacial adsorptions of ions and molecules at air-water interfaces. Here we revisit these questions by combining exact potential distribution results with linear response theory and other physically motivated approximations. The results highlight both exact and approximate compensation relations pertaining to direct (solute-solvent) and indirect (solvent-solvent) contributions to adsorption thermodynamics, of relevance to solvation at air-water interfaces, as well as a broader class of processes linked to the mean force potential between ions, molecules, nanoparticles, proteins, and biological assemblies. PMID:27545849

  20. 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.

  1. A closure relation to molecular theory of solvation for macromolecules.

    PubMed

    Kobryn, Alexander E; Gusarov, Sergey; Kovalenko, Andriy

    2016-10-12

    We propose a closure to the integral equations of molecular theory of solvation, particularly suitable for polar and charged macromolecules in electrolyte solution. This includes such systems as oligomeric polyelectrolytes at a finite concentration in aqueous and various non-aqueous solutions, as well as drug-like compounds in solution. The new closure by Kobryn, Gusarov, and Kovalenko (KGK closure) imposes the mean spherical approximation (MSA) almost everywhere in the solvation shell but levels out the density distribution function to zero (with the continuity at joint boundaries) inside the repulsive core and in the spatial regions of strong density depletion emerging due to molecular associative interactions. Similarly to MSA, the KGK closure reduces the problem to a linear equation for the direct correlation function which is predefined analytically on most of the solvation shells and has to be determined numerically on a relatively small (three-dimensional) domain of strong depletion, typically within the repulsive core. The KGK closure leads to the solvation free energy in the form of the Gaussian fluctuation (GF) functional. We first test the performance of the KGK closure coupled to the reference interaction site model (RISM) integral equations on the examples of Lennard-Jones liquids, polar and nonpolar molecular solvents, including water, and aqueous solutions of simple ions. The solvation structure, solvation chemical potential, and compressibility obtained from RISM with the KGK closure favorably compare to the results of the hypernetted chain (HNC) and Kovalenko-Hirata (KH) closures, including their combination with the GF solvation free energy. We then use the KGK closure coupled to RISM to obtain the solvation structure and thermodynamics of oligomeric polyelectrolytes and drug-like compounds at a finite concentration in electrolyte solution, for which no convergence is obtained with other closures. For comparison, we calculate their solvation

  2. Abraham Lincoln, psychotherapist to the nation: the use of metaphors.

    PubMed

    Leetz, K L

    1997-01-01

    Metaphors are widely utilized in psychotherapy to effect change in patients. Psychotherapeutic metaphors, in their various versions, may offer new choices and ways of viewing oneself to the patient which are more palatable than straight discussions or sterile insights. By addressing resistances indirectly, metaphors can be an effective tool for the therapist to use, regardless of theoretical orientation. Abraham Lincoln, a master of metaphor, utilized this tool effectively in dealing with crises and the ultimate fragmentation, disunion of the national identity. The author argues that Lincoln was able to address complex issues (such as slavery, liberty, nationhood, union, and conduct of the war) with metaphors, much as a skilled psychotherapist addresses complex issues within his or her purview. Abraham Lincoln effectively disarmed his critics, established a means of communication with the people, and sought to make his points in an understandable nonconfrontational fashion. These are skills highly valued by psychotherapists. One might say that Abraham Lincoln conducted psychotherapy on a national scale. Without formal training, he was ultimately able to create a new and more stable sense of national self using a metaphorical approach. PMID:9139547

  3. Anion Solvation in Carbonate Electrolytes

    SciTech Connect

    Zhang, Zhengcheng

    2015-11-16

    With 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. As of 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. As a mirror effort to prior Li+ solvation studies, this work focuses on the interactions between carbonate-based solvents and two anions (hexafluorophosphate, PF6–, and tetrafluoroborate, BF4–) 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.

  4. Solvation forces between rough surfaces

    SciTech Connect

    Frink, L.J.; van Swol, F.

    1998-04-01

    We investigate the role of surface roughness on solvation forces and solvation free energies. Roughness is introduced by dividing a surface into an array of square tiles that are then randomly displaced in the direction perpendicular to the wall. The integrated wall strength of these tiled surfaces is independent of the surface roughness and hence this class of rough walls is ideally suited for isolating roughness effects. We use grand canonical Monte Carlo simulations of a Lennard-Jones fluid confined in a slit pore with rough walls to generate the solvation interactions as a function of roughness, tile size, and surface area. The simulation data are compared to a simple superposition approximation of smooth wall solvation interactions (obtained from simulation or density functional theory), based on a distribution of wall separations. We find that this approximation provides a surprisingly accurate route to the solvation interaction of rough surfaces. In general, increased roughness leads to a reduction of oscillations in the solvation forces and surface free energies. However, nonmonotonic behavior of the oscillation amplitude with roughness can be observed for finite surfaces. The washing out of the oscillations found for large surface roughness produces a solvation force that exhibits a broad repulsive peak with separation. The broad repulsion is a consequence of the resistance to squeezing out fluid from the smallest gaps between two opposing rough surfaces. It is as much a reflection of packing effects as are the solvation oscillations for perfectly smooth pores. In addition, we present results for patterned and undulating surfaces produced by an analogous modification of the one-body external field for smooth walls. Finally, we discuss the implications of our results for a number of experimental systems including self-assembled monolayers, microporous materials, protein solutions, and DNA crystals. {copyright} {ital 1998 American Institute of Physics.}

  5. Unilateral coronal craniosynostosis in Abraham Lincoln and his family.

    PubMed

    Fishman, Ronald S

    2010-09-01

    Premature closure of one coronal skull suture produces a characteristic arching or relative elevation of the superior orbital rim on the involved side. This sign is associated with facial asymmetry, and both signs are usually the most conspicuous features in patients with mild unilateral coronal craniosynostosis. Photographs suggest that at least 9 individuals over 5 generations of the Abraham Lincoln family had premature closure of 1 coronal suture. In 8 males, there was involvement of the left side; in 1 female, there was involvement of the right side. PMID:20856045

  6. Abraham Flexner and the black medical schools. 1992.

    PubMed Central

    Savitt, Todd

    2006-01-01

    "Abraham Flexner and the Black Medical Schools" first appeared in Beyond Flexner: Medical Education in the Twentieth Century, Barbara Barzansky and Norman Gevitz, eds. Copyright 1992 by Barbara Barzansky and Norman Gevitz. Reproduced with permission of Greenwood Publishing Group Inc., Westport, CT. The article will be reprinted in a collection of the author's writings on African-American medical history called Race and Medicine in Nineteenth- and Early-Twentieth-Century America, to be published in December 2006 by Kent State University Press and published here with permission of the Kent State University Press. PMID:17019906

  7. Solvation in supercritical water

    SciTech Connect

    Cochran, H.D. ); Cummings, P.T.; Karaborni, S. . Dept. of Chemical Engineering)

    1991-01-01

    The aim of this work is to determine the solvation structure in supercritical water composed with that in ambient water and in simple supercritical solvents. Molecular dynamics studies have been undertaken of systems that model ionic sodium and chloride, atomic argon, and molecular methanol in supercritical aqueous solutions using the simple point charge model of Berendsen for water. Because of the strong interactions between water and ions, ionic solutes are strongly attractive in supercritical water, forming large clusters of water molecules around each ion. Methanol is found to be a weakly-attractive solute in supercritical water. The cluster of excess water molecules surrounding a dissolved ion or polar molecule in supercritical aqueous solutions is comparable to the solvent clusters surrounding attractive solutes in simple supercritical fluids. Likewise, the deficit of water molecules surrounding a dissolved argon atom in supercritical aqueous solutions is comparable to that surrounding repulsive solutes in simple supercritical fluids. The number of hydrogen bonds per water molecule in supercritical water was found to be about one third the number in ambient water. The number of hydrogen bonds per water molecule surrounding a central particle in supercritical water was only mildly affected by the identify of the central particle--atom, molecule, or ion. These results should be helpful in developing a qualitative understanding of important processes that occur in supercritical water. 29 refs., 6 figs.

  8. Li(+) solvation in glyme-Li salt solvate ionic liquids.

    PubMed

    Ueno, Kazuhide; Tatara, Ryoichi; Tsuzuki, Seiji; Saito, Soshi; Doi, Hiroyuki; Yoshida, Kazuki; Mandai, Toshihiko; Matsugami, Masaru; Umebayashi, Yasuhiro; Dokko, Kaoru; Watanabe, Masayoshi

    2015-03-28

    Certain molten complexes of Li salts and solvents can be regarded as ionic liquids. In this study, the local structure of Li(+) ions in equimolar mixtures ([Li(glyme)]X) of glymes (G3: triglyme and G4: tetraglyme) and Li salts (LiX: lithium bis(trifluoromethanesulfonyl)amide (Li[TFSA]), lithium bis(pentafluoroethanesulfonyl)amide (Li[BETI]), lithium trifluoromethanesulfonate (Li[OTf]), LiBF4, LiClO4, LiNO3, and lithium trifluoroacetate (Li[TFA])) was investigated to discriminate between solvate ionic liquids and concentrated solutions. Raman spectra and ab initio molecular orbital calculations have shown that the glyme molecules adopt a crown-ether like conformation to form a monomeric [Li(glyme)](+) in the molten state. Further, Raman spectroscopic analysis allowed us to estimate the fraction of the free glyme in [Li(glyme)]X. The amount of free glyme was estimated to be a few percent in [Li(glyme)]X with perfluorosulfonylamide type anions, and thereby could be regarded as solvate ionic liquids. Other equimolar mixtures of [Li(glyme)]X were found to contain a considerable amount of free glyme, and they were categorized as traditional concentrated solutions. The activity of Li(+) in the glyme-Li salt mixtures was also evaluated by measuring the electrode potential of Li/Li(+) as a function of concentration, by using concentration cells against a reference electrode. At a higher concentration of Li salt, the amount of free glyme diminishes and affects the electrode reaction, leading to a drastic increase in the electrode potential. Unlike conventional electrolytes (dilute and concentrated solutions), the significantly high electrode potential found in the solvate ILs indicates that the solvation of Li(+) by the glyme forms stable and discrete solvate ions ([Li(glyme)](+)) in the molten state. This anomalous Li(+) solvation may have a great impact on the electrode reactions in Li batteries. PMID:25733406

  9. Multiple time step molecular dynamics in the optimized isokinetic ensemble steered with the molecular theory of solvation: Accelerating with advanced extrapolation of effective solvation forces

    SciTech Connect

    Omelyan, Igor E-mail: omelyan@icmp.lviv.ua; Kovalenko, Andriy

    2013-12-28

    We develop efficient handling of solvation forces in the multiscale method of multiple time step molecular dynamics (MTS-MD) of a biomolecule steered by the solvation free energy (effective solvation forces) obtained from the 3D-RISM-KH molecular theory of solvation (three-dimensional reference interaction site model complemented with the Kovalenko-Hirata closure approximation). To reduce the computational expenses, we calculate the effective solvation forces acting on the biomolecule by using advanced solvation force extrapolation (ASFE) at inner time steps while converging the 3D-RISM-KH integral equations only at large outer time steps. The idea of ASFE consists in developing a discrete non-Eckart rotational transformation of atomic coordinates that minimizes the distances between the atomic positions of the biomolecule at different time moments. The effective solvation forces for the biomolecule in a current conformation at an inner time step are then extrapolated in the transformed subspace of those at outer time steps by using a modified least square fit approach applied to a relatively small number of the best force-coordinate pairs. The latter are selected from an extended set collecting the effective solvation forces obtained from 3D-RISM-KH at outer time steps over a broad time interval. The MTS-MD integration with effective solvation forces obtained by converging 3D-RISM-KH at outer time steps and applying ASFE at inner time steps is stabilized by employing the optimized isokinetic Nosé-Hoover chain (OIN) ensemble. Compared to the previous extrapolation schemes used in combination with the Langevin thermostat, the ASFE approach substantially improves the accuracy of evaluation of effective solvation forces and in combination with the OIN thermostat enables a dramatic increase of outer time steps. We demonstrate on a fully flexible model of alanine dipeptide in aqueous solution that the MTS-MD/OIN/ASFE/3D-RISM-KH multiscale method of molecular dynamics

  10. 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

  11. 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

  12. 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.

  13. The chemical interpretation and practice of linear solvation energy relationships in chromatography.

    PubMed

    Vitha, Mark; Carr, Peter W

    2006-09-01

    This review focuses on the use of linear solvation energy relationships (LSERs) to understand the types and relative strength of the chemical interactions that control retention and selectivity in the various modes of chromatography ranging from gas chromatography to reversed phase and micellar electrokinetic capillary chromatography. The most recent, widely accepted symbolic representation of the LSER model, as proposed by Abraham, is given by the equation: SP=c + eE + sS + aA + bB + vV, in which, SP can be any free energy related property. In chromatography, SP is most often taken as logk' where k' is the retention factor. The letters E, S, A, B, and V denote solute dependent input parameters that come from scales related to a solute's polarizability, dipolarity (with some contribution from polarizability), hydrogen bond donating ability, hydrogen bond accepting ability, and molecular size, respectively. The e-, s-, a-, b-, and v-coefficients and the constant, c, are determined via multiparameter linear least squares regression analysis of a data set comprised of solutes with known E, S, A, B, and V values and which span a reasonably wide range in interaction abilities. Thus, LSERs are designed to probe the type and relative importance of the interactions that govern solute retention. In this review, we include a synopsis of the various solvent and solute scales in common use in chromatography. More importantly, we emphasize the development and physico-chemical basis of - and thus meaning of - the solute parameters. After establishing the meaning of the parameters, we discuss their use in LSERs as applied to understanding the intermolecular interactions governing various gas-liquid and liquid-liquid phase equilibria. The gas-liquid partition process is modeled as the sum of an endoergic cavity formation/solvent reorganization process and exoergic solute-solvent attractive forces, whereas the partitioning of a solute between two solvents is thermodynamically

  14. Abraham Lincoln did not have type 5 spinocerebellar ataxia.

    PubMed

    Sotos, John G

    2009-10-20

    An autosomal dominant genetic disorder, type 5 spinocerebellar ataxia (SCA5), occurs in multiple descendants of one paternal uncle and one paternal aunt of President Abraham Lincoln. It has been suggested that Lincoln himself had the disease and that his DNA should be tested for an SCA5-conferring gene. Herein, I review the pertinent phenotypes of Lincoln, his father, and his paternal grandmother, and conclude that 1) Lincoln's father did not have SCA5, and, therefore, that Lincoln was not at special risk of the disease; 2) Lincoln had neither subclinical nor visible manifestations of SCA5; 3) little evidence suggests SCA5 is a "Lincolnian" disorder; and 4) without additional evidence, Lincoln's DNA should not be tested for SCA5. PMID:19841386

  15. 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)

  16. Radiolytic yields of solvated electrons in ionic liquid and its solvation dynamics at low temperature

    NASA Astrophysics Data System (ADS)

    Musat, Raluca M.; Kondoh, Takafumi; Gohdo, Masao; Yoshida, Yoichi; Takahashi, Kenji

    2016-07-01

    We present an investigation of the solvated electron in the ionic liquid 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide (P14NTf2) using pulse radiolytic techniques. Temperature-dependent studies reveal that the yield of the solvated electron decreases with decreasing temperature. The lower initial yield measured indicates that we have a loss of some electrons before they become fully solvated. There may be a high probability that the excess dry electrons (pre-solvated electron) react before the electron solvation is completed because the solvation dynamics is slowing down with decreasing temperature.

  17. Detection of the Abraham force with a succession of short optical pulses

    NASA Astrophysics Data System (ADS)

    Brevik, Iver; Ellingsen, Simen Å.

    2012-08-01

    For over a century, two rival descriptions of electromagnetic field momentum in matter have coexisted, due to Abraham and Minkowski, respectively. We propose a setup for measuring the difference between Abraham's and Minkowski's predictions in optics. To wit, a setup is proposed in which the transient “Abraham force,” a consequence of the Abraham energy-momentum tensor of 1909, may be measured directly. We show that when a train of short laser pulses is sent through a fiber wound up on a cylindrical drum, the Abraham theory predicts a torque, which, by inserting realistic parameters, is found to be detectable. Indeed, the same torque when calculated with the Minkowski tensor takes the opposite sign. Numerical estimates show that with a typical torsion pendulum setup and standard laser parameters, the angular deflection is in the order of 10-3 rad, which is easily measurable and even visible to the naked eye. Although its prediction is a century old, the Abraham force has proven experimentally elusive, and to our knowledge no macroscopic experimental demonstration of the difference between the predictions of the two mentioned energy-momentum tensors exists at optical frequencies.

  18. Physical Modeling of Aqueous Solvation

    PubMed Central

    Fennell, Christopher J.

    2014-01-01

    We consider the free energies of solvating molecules in water. Computational modeling usually involves either detailed explicit-solvent simulations, or faster computations, which are based on implicit continuum approximations or additivity assumptions. These simpler approaches often miss microscopic physical details and non-additivities present in experimental data. We review explicit-solvent modeling that identifies the physical bases for the errors in the simpler approaches. One problem is that water molecules that are shared between two substituent groups often behave differently than waters around each substituent individually. One manifestation of non-additivities is that solvation free energies in water can depend not only on surface area or volume, but on other properties, such as the surface curvature. We also describe a new computational approach, called Semi-Explicit Assembly, that aims to repair these flaws and capture more of the physics of explicit water models, but with computational efficiencies approaching those of implicit-solvent models. PMID:25143658

  19. Legends about Legends: Abraham Eleazar's Adaptation of Nicolas Flamel.

    PubMed

    Priesner, Claus

    2016-02-01

    This paper explores the relationship between three illustrated alchemical treatises, all of which are associated with Jewish adepts: the famous Le Livre des figures hieroglyphiques attributed to Nicolas Flamel, and two treatises published in 1735 in Erfurt-the Uraltes Chymisches Werckh and the Donum Dei. The Werckh is supposedly written by Rabbi Abraham Eleazar, while the Donum Dei is attributed to an ancient alchemist-cabalist, Rabbi Samuel Baruch. I argue that these authors are fictitious, and that both works were in fact written in the early eighteenth century by their supposed editor, the probably pseudonymous Julius Gervasius. Gervasius connects the Werckh with the legend of Nicolas Flamel by suggesting that it is based on the original, Jewish manuscript which helped Flamel to find the Stone of the Sages. Gervasius used various strategies to confer a sense of Jewish "authenticity" on these works, borrowing from contemporary (non-Jewish) perceptions of Jewish ritual, Hebrew language, and Christian Cabala. The Werckh also borrows and adapts a sequence of allegorical illustrations from those in pseudo-Flamel's Livre, and I compare the two sets of figures and, where possible, interpret them. I conclude that the later works in fact teach us far more about the state of alchemy in the seventeenth and eighteenth centuries than they do about either medieval alchemy or Judaism. PMID:27376176

  20. Picosecond dynamics of benzophenone anion solvation

    SciTech Connect

    Lin, Y.; Jonah, C.D. )

    1993-01-14

    The dynamics of benzophenone anion solvation in alcohols are studied by pulse-radiolysis techniques. The solvation process is characterized by the blue shift of the transient absorption spectrum of the anion and is faster for the smaller alcohols. The anion is solvated more slowly than the electron in the same solvent, but the solvation times of both are similar to [tau][sub 2], the solvent dielectric relaxation time. The familiar phenomenological two-state model of solvation was found to be inappropriate for describing the anion solvation process. A multistate process appears to be a more appropriate description. The authors modeled the kinetics of the spectral relaxation. In most cases, nearly quantitative agreement between the calculated and observed spectra is achieved. The characteristic relaxation times for the alcohol solvents around the anions were also reproduced. 50 refs., 8 figs., 3 tabs.

  1. Solvation and Cavity Occupation in Biomolecules

    PubMed Central

    Perkyns, John S.; Nguyen, Bao Linh; Pettitt, B. Montgomery

    2014-01-01

    Background Solvation density locations are important for protein dynamics and structure. Knowledge of the preferred hydration sites at biomolecular interfaces and those in the interior of cavities can enhance understanding of structure and function. While advanced X-ray diffraction methods can provide accurate atomic structures for proteins, that technique is challenged when it comes to providing accurate hydration structures, especially for interfacial and cavity bound solvent molecules. Methods Advances in integral equation theories which include more accurate methods for calculating the long-ranged Coulomb interaction contributions to the three-dimensional distribution functions make it possible to calculate angle dependent average solvent structure, accurately, around and inside irregular molecular conformations. The proximal Radial Distribution method provides another approximate method to determine average solvent structures for biomolecular systems based on a proximal or near neighbor solvent distribution that can be constructed from previously collected solvent distributions. These two approximate methods, along with all-atom molecular dynamics simulations are used to determine the solvent density inside the myoglobin heme cavity. Discussion and Results Myoglobin is a good test system for these methods because the cavities are many and one is large, tens of Å, but is shown to have only four hydration sites. These sites are not near neighbors which implies that the large cavity must have more than one way in and out. Conclusions Our results show that main solvation sites are well reproduced by all three methods. The techniques also produce a clearly identifiable solvent pathway into the interior of the protein. General Significance The agreement between Molecular Dynamics and less computationally demanding approximate methods is encouraging. PMID:25261777

  2. Solvates of Dasatinib: Diversity and Isostructurality.

    PubMed

    Sarceviča, Inese; Grante, Ilze; Belyakov, Sergey; Rekis, Toms; Bērziņš, Kārlis; Actiņš, Andris; Orola, Liāna

    2016-04-01

    A series of dasatinib crystalline forms were obtained, and a hierarchical cluster analysis of their powder X-ray diffraction patterns was performed. The resulting dendrogram implies 3 structural groups. The crystal structures of several solvates representing 2 of these groups were determined. The crystal structure analysis confirms the isostructurality of solvates within structural group I and suggests a correlation between solvent molecule size and trends in crystal structures within this group. In addition, the formation relationships in 2-solvent media between different dasatinib solvate groups were determined. The formation preference of solvates was found to follow the ranking group I > group III > group II. PMID:27019962

  3. DFT Solvation Studies of Carbohydrates: Solvation effects in alpha-linked carbohydrates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the current paper we address the effect of solvation on the landscape of alpha-linked glucose residues. The solvent is introduced via the implicit solvation models COSMO and PCM. Geometry optimizations, at the B3LYP/6-311++G** level of theory with and without implicit solvation were carried out...

  4. Symmetric energy-momentum tensor: The Abraham form and the explicitly covariant formula

    NASA Astrophysics Data System (ADS)

    Nesterenko, V. V.; Nesterenko, A. V.

    2016-03-01

    We compare the known in literature, explicitly covariant 4-dimensional formula for the symmetric energy-momentum tensor of electromagnetic field in a medium and the energy-momentum tensor derived by Abraham in the 3-dimensional vector form. It is shown that these two objects coincide only on the physical configuration space Γ ¯ , formed by the field vectors and the velocity of the medium, which satisfy the Minkowski constitutive relations. It should be emphasized that the 3-dimensional vector formulae for the components of the energy-momentum tensor were obtained by Abraham only on Γ ¯ , and the task of their extension to the whole unconditional configuration space Γ was not posed. In order to accomplish the comparison noted above, we derive the covariant formula a new by another method, namely, by generalizing the Abraham reasoning. The comparison conducted enables one to treat the explicitly covariant formula as a unique consistent extension of the Abraham formulae to the whole configuration space Γ. Thus the question concerning the relativistic covariance of the original 3-dimensional Abraham formulae defined on Γ ¯ is solved positively. We discuss in detail the relativistic covariance of the 3-dimensional vector formulae for individual components of the 4-dimensional tensors in electrodynamics which is manifested in the form-invariance of these formulae under Lorentz transformations.

  5. 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…

  6. Solvated Electrons on Metal Oxide Surfaces

    SciTech Connect

    Zhao, Jin; Li, Bin; Onda, Ken; Feng, Min; Petek, Hrvoje

    2006-09-13

    An electron added to a solvent polarizes its surrounding medium to minimize the free energy. Such an electron with its polarization cloud, which we refer to as the solvated electron, is one of the most fundamental chemical reagents of significant experimental and theoretical interest. The structure and dynamics of solvated electrons in protic solvents have been explored ever since the discovery of intense blue coloration in solutions of alkali metals in ammonia.1-3 Because solvated electrons are the most fundamental chemical reagents as well as carriers of negative charge, substantial experimental and theoretical efforts have focused on elucidating their equilibrium structure and solvation dynamics in a variety of neat liquids.4,5 One of the most important but least explored environments for solvated electrons, namely, the two-dimensional liquid/solid and liquid/vacuum interfaces, is the subject of this review.

  7. Studies of ion solvation using pulse radiolysis

    SciTech Connect

    Jonah, C.D.; Lin, Yi.

    1991-01-01

    In this paper we describe our measurements of ion solvation in a series of alcohols. Benzophenone is dissolved in an alcohol at a sufficiently high concentration so that the electrons formed by radiation will react with the benzophenone molecule to form the anion. The spectrum of the anion is then observed as a function of time. As the benzophenone anion solvates, the spectrum shifts to the blue. The results of our measurements clearly show that both the size of the solvent molecules and their shapes are important in the solvation process. Different spectral relaxation processes are observed for ions than are observed for electron solvation, the simple'' ion system that has been most heavily studied. In addition, these results suggest that the rate of solvation may be different for ions in solution than for dipoles in solution. 26 refs., 3 figs.

  8. 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

  9. Non-polynomial extensions of solvable potentials à la Abraham-Moses

    NASA Astrophysics Data System (ADS)

    Odake, Satoru; Sasaki, Ryu

    2013-10-01

    Abraham-Moses transformations, besides Darboux transformations, are well-known procedures to generate extensions of solvable potentials in one-dimensional quantum mechanics. Here we present the explicit forms of infinitely many seed solutions for adding eigenstates at arbitrary real energy through the Abraham-Moses transformations for typical solvable potentials, e.g., the radial oscillator, the Darboux-Pöschl-Teller, and some others. These seed solutions are simple generalisations of the virtual state wavefunctions, which are obtained from the eigenfunctions by discrete symmetries of the potentials. The virtual state wavefunctions have been an essential ingredient for constructing multi-indexed Laguerre and Jacobi polynomials through multiple Darboux-Crum transformations. In contrast to the Darboux transformations, the virtual state wavefunctions generate non-polynomial extensions of solvable potentials through the Abraham-Moses transformations.

  10. Karl Abraham's revolution of 1916: from sensual sucking to the oral-aggressive wish of destruction.

    PubMed

    May, Ulrike

    2012-01-01

    The author argues that "The First Pregenital Stage of the Libido" (Abraham 1916-1917) expounds a new conception of orality, i.e., of purposeful oral aggression directed against an object during the first stage of psychic development. This conception is shown to be contrary to Freud's view of orality as elaborated in Three Essays on the Theory of Sexuality (1905), as well as in other writings of late 1914 and 1915. Abraham's conception ignores fundamental dimensions of Freud's thinking during these years, namely, the difference between autoerotism/narcissism and object love, on the one hand, and also between the leading role of sexuality and the secondary role of aggression, on the other. Thus, Abraham's thinking represents a basic theoretical change that had far-reaching consequences for psychoanalytic practice. PMID:22423435

  11. U.S. Medical Education Reformers Abraham Flexner (1866-1959) and Simon Flexner (1863-1946).

    ERIC Educational Resources Information Center

    Parker, Franklin; Parker, Betty J.

    This paper (in the form of a dialogue) tells the stories of two members of a remarkable family of nine children, the Flexners of Louisville, Kentucky. The paper focuses on Abraham and Simon, who were reformers in the field of medical education in the United States. The dialogue takes Abraham Flexner through his undergraduate education at Johns…

  12. 3 CFR 8636 - Proclamation 8636 of March 4, 2011. 150th Anniversary of the Inauguration of Abraham Lincoln

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 3 The President 1 2012-01-01 2012-01-01 false Proclamation 8636 of March 4, 2011. 150th Anniversary of the Inauguration of Abraham Lincoln 8636 Proclamation 8636 Presidential Documents Proclamations Proclamation 8636 of March 4, 2011 Proc. 8636 150th Anniversary of the Inauguration of Abraham LincolnBy the President of the United States...

  13. Solvation of fullerene and fulleride ion in liquid ammonia: structure and dynamics of the solvation shells.

    PubMed

    Rana, Malay Kumar; Chandra, Amalendu

    2012-10-01

    Molecular dynamics simulations have been performed to investigate the solvation characteristics of neutral fullerene (C(60)) and charged fulleride anion (C(60)(5-)) in liquid ammonia. Potassium ions are present as counterions in the system containing fulleride ion. In addition to solvation characteristics, dynamical properties of solvation shells are also found out for both the neutral and anionic solutes. Our results reveal the presence of a rather large solvation shell of ammonia molecules around the C(60)(5-) ion. It is found that the ammonia molecules are more closely packed in the first solvation shell of C(60)(5-) than that of C(60). The distributions of ammonia molecules in the solvation shells of C(60) and C(60)(5-) solutes together with hydrogen bonding characteristics of the solvent in different solvation shells are investigated. It is found that the solvation of the small counterions (K(+)) in liquid ammonia is affected very little by the presence of the large C(60)(5-) anion. Regarding the dynamics of ammonia in solvation shells, it is found that the residence, translational and rotational dynamics of ammonia molecules differ significantly between the solvation shells of the neutral and charged fullerene solutes, especially in the first solvation shells. The average lifetimes of ammonia-ammonia hydrogen bonds are calculated from both continuous and intermittent hydrogen bond correlation functions. The calculations of binding energies reveal that the hydrogen bonds are weaker, hence short lived in the solvation shell of C(60)(5-) compared to those in the solvation shell of neutral C(60) and also in bulk liquid ammonia. PMID:23039601

  14. Solvation of fullerene and fulleride ion in liquid ammonia: Structure and dynamics of the solvation shells

    NASA Astrophysics Data System (ADS)

    Rana, Malay Kumar; Chandra, Amalendu

    2012-10-01

    Molecular dynamics simulations have been performed to investigate the solvation characteristics of neutral fullerene (C_{60}) and charged fulleride anion (C_{60}^{5-}) in liquid ammonia. Potassium ions are present as counterions in the system containing fulleride ion. In addition to solvation characteristics, dynamical properties of solvation shells are also found out for both the neutral and anionic solutes. Our results reveal the presence of a rather large solvation shell of ammonia molecules around the C_{60}^{5-} ion. It is found that the ammonia molecules are more closely packed in the first solvation shell of C_{60}^{5-} than that of C_{60}. The distributions of ammonia molecules in the solvation shells of C_{60} and C_{60}^{5-} solutes together with hydrogen bonding characteristics of the solvent in different solvation shells are investigated. It is found that the solvation of the small counterions (K+) in liquid ammonia is affected very little by the presence of the large C_{60}^{5-} anion. Regarding the dynamics of ammonia in solvation shells, it is found that the residence, translational and rotational dynamics of ammonia molecules differ significantly between the solvation shells of the neutral and charged fullerene solutes, especially in the first solvation shells. The average lifetimes of ammonia-ammonia hydrogen bonds are calculated from both continuous and intermittent hydrogen bond correlation functions. The calculations of binding energies reveal that the hydrogen bonds are weaker, hence short lived in the solvation shell of C_{60}^{5-} compared to those in the solvation shell of neutral C60 and also in bulk liquid ammonia.

  15. 3DRISM Multigrid Algorithm for Fast Solvation Free Energy Calculations.

    PubMed

    Sergiievskyi, Volodymyr P; Fedorov, Maxim V

    2012-06-12

    In this paper we present a fast and accurate method for modeling solvation properties of organic molecules in water with a main focus on predicting solvation (hydration) free energies of small organic compounds. The method is based on a combination of (i) a molecular theory, three-dimensional reference interaction sites model (3DRISM); (ii) a fast multigrid algorithm for solving the high-dimensional 3DRISM integral equations; and (iii) a recently introduced universal correction (UC) for the 3DRISM solvation free energies by properly scaled molecular partial volume (3DRISM-UC, Palmer et al., J. Phys.: Condens. Matter2010, 22, 492101). A fast multigrid algorithm is the core of the method because it helps to reduce the high computational costs associated with solving the 3DRISM equations. To facilitate future applications of the method, we performed benchmarking of the algorithm on a set of several model solutes in order to find optimal grid parameters and to test the performance and accuracy of the algorithm. We have shown that the proposed new multigrid algorithm is on average 24 times faster than the simple Picard method and at least 3.5 times faster than the MDIIS method which is currently actively used by the 3DRISM community (e.g., the MDIIS method has been recently implemented in a new 3DRISM implicit solvent routine in the recent release of the AmberTools 1.4 molecular modeling package (Luchko et al. J. Chem. Theory Comput. 2010, 6, 607-624). Then we have benchmarked the multigrid algorithm with chosen optimal parameters on a set of 99 organic compounds. We show that average computational time required for one 3DRISM calculation is 3.5 min per a small organic molecule (10-20 atoms) on a standard personal computer. We also benchmarked predicted solvation free energy values for all of the compounds in the set against the corresponding experimental data. We show that by using the proposed multigrid algorithm and the 3DRISM-UC model, it is possible to obtain good

  16. Multigrid-Based Methodology for Implicit Solvation Models in Periodic DFT.

    PubMed

    Garcia-Ratés, Miquel; López, Núria

    2016-03-01

    Continuum solvation models have become a widespread approach for the study of environmental effects in Density Functional Theory (DFT) methods. Adding solvation contributions mainly relies on the solution of the Generalized Poisson Equation (GPE) governing the behavior of the electrostatic potential of a system. Although multigrid methods are especially appropriate for the solution of partial differential equations, up to now, their use is not much extended in DFT-based codes because of their high memory requirements. In this Article, we report the implementation of an accelerated multigrid solver-based approach for the treatment of solvation effects in the Vienna ab initio Simulation Package (VASP). The stated implicit solvation model, named VASP-MGCM (VASP-Multigrid Continuum Model), uses an efficient and transferable algorithm for the product of sparse matrices that highly outperforms serial multigrid solvers. The calculated solvation free energies for a set of molecules, including neutral and ionic species, as well as adsorbed molecules on metallic surfaces, agree with experimental data and with simulation results obtained with other continuum models. PMID:26771105

  17. Differential geometry based solvation model I: Eulerian formulation.

    PubMed

    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 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

  18. Polymorphs and Versatile Solvates of 7-Hydroxyisoflavone.

    PubMed

    Gong, Ningbo; Zhang, Guoshun; Jin, Guimin; Du, Guanhua; Lu, Yang

    2016-04-01

    7-hydroxyisoflavone has been crystallized, identified, and characterized as 2 solvent-free conformational polymorphs and 5 solvates, which differ from each other in the mode of packing and in molecular conformation. All the 7 crystal structures were previously unreported. The conformational polymorphs and solvates were compared by Hirshfeld surface and fingerprint plot analysis and were spectroscopically characterized by powder X-ray diffraction, differential scanning calorimetry, and thermal gravimetric analysis. Hydrogen bond played an important role in the formation of polymorphs. From this study, we can predict that more solvates could be cultivated in other polarity solvents such as isopropanol or 2-butanol at appropriate conditions. PMID:26935882

  19. Solvation dynamics in a protein surfactant complex

    NASA Astrophysics Data System (ADS)

    Dutta, Partha; Sen, Pratik; Halder, Arnab; Mukherjee, Saptarshi; Sen, Sobhan; Bhattacharyya, Kankan

    2003-08-01

    Solvation dynamics in the denatured state of a protein, lysozyme (denatured by sodium dodecyl sulfate, SDS) is markedly slower than that in the native state. For coumarin 153 bound to lysozyme, the average solvation time, < τs> is 330 ps. In the lysozyme-SDS complex, the solvation dynamics is markedly slower with < τs>=7250 ps. On addition of dithiothreitol (DTT) to the lysozyme-SDS complex, when the di-sulfide bonds are destroyed, < τs> is found to be 1140 ps. The slow dynamics in the denatured protein is attributed to the polymer chain dynamics and the exchange of bound and free water molecules.

  20. Segue between Favorable and Unfavorable Solvation

    SciTech Connect

    Maibaum, Lutz; Chandler, David

    2007-03-21

    Solvation of small and large clusters are studied by simulation, considering a range of solvent-solute attractive energy strengths. Over a wide range of conditions, both for solvation in the Lennard-Jones liquid and in the SPC model of water, it is shown that the mean solvent density varies linearly with changes in solvent-solute adhesion or attractive energy strength. This behavior is understood from the perspective of Weeks theory of solvation [Ann. Rev. Phys. Chem. 2002, 53, 533] and supports theories based upon that perspective.

  1. Incorporating excluded solvent volume and physical dipoles for computing solvation free energy.

    PubMed

    Yang, Pei-Kun

    2015-07-01

    The solvation free energy described using the Born equation depends on the solute charge, solute radius, and solvent dielectric constant. However, the dielectric polarization derived from Gauss's law used in the Born equation differs from that obtained from molecular dynamics simulations. Therefore, the adjustment of Born radii is insufficient for fitting the solvation free energy to various solute conformations. In order to mimic the dielectric polarization surrounding a solute in molecular dynamics simulations, the water molecule in the first coordination shell is modeled as a physical dipole in a van der Waals sphere, and the intermediate water is treated as a bulk solvent. The electric dipole of the first-shell water is modeled as positive and negative surface charge layers with fixed charge magnitudes, but with variable separation distance as derived from the distributions of hydrogen and oxygen atoms of water dictated by their orientational distribution functions. An equation that describes the solvation free energy of ions using this solvent scheme with a TIP3P water model is derived, and the values of the solvation free energies of ions estimated from this derived equation are found to be similar to those obtained from the experimental data. PMID:26113115

  2. Abraham Lincoln and Harry Potter: Children's Differentiation between Historical and Fantasy Characters

    ERIC Educational Resources Information Center

    Corriveau, Kathleen H.; Kim, Angie L.; Schwalen, Courtney E.; Harris, Paul L.

    2009-01-01

    Based on the testimony of others, children learn about a variety of figures that they never meet. We ask when and how they are able to differentiate between the historical figures that they learn about (e.g., Abraham Lincoln) and fantasy characters (e.g., Harry Potter). Experiment 1 showed that both younger (3- and 4-year-olds) and older children…

  3. Abraham Lincoln--His Words and His World: a Unit Plan.

    ERIC Educational Resources Information Center

    Diamond, Ronald L.; Diamond, Linda W.

    Planned for an eighth-grade classroom, this unit plan, consisting of 19 lesson plans on the topic of Abraham Lincoln, is based upon the fulfillment of 17 unit objectives. Each daily lesson plan specifies the following: lesson theme, learner objective, needed prerequisites, new vocabulary or terms, learning set/motivation, presentation of new…

  4. Anatomy of a Masterpiece: A Close Textual Analysis of Abraham Lincoln's Second Inaugural Address.

    ERIC Educational Resources Information Center

    Slagell, Amy R.

    1991-01-01

    States that Abraham Lincoln's second inaugural address is a recognized rhetorical masterpiece. Accounts for this recognition by examining the text microscopically. Uses the method of close textual analysis that explores the inner workings of the text to discover the complexity of Lincoln's masterwork. (PRA)

  5. Hereditary premature closure of a coronal suture in the Abraham Lincoln family.

    PubMed

    Fishman, Ronald S

    2013-10-01

    The most easily recognized facial features of unilateral premature closure of a coronal suture in the skull are an upward arching of the superior orbital rim and a smaller face on the involved side. Photographs indicate that at least 9 individuals over 5 generations of the Abraham Lincoln family showed this anomaly. PMID:23856133

  6. Abraham Baldwin: Soldier-Statesmen of the Constitution. A Bicentennial Series, No. 12.

    ERIC Educational Resources Information Center

    Army Center of Military History, Washington, DC.

    Although his father was an illiterate blacksmith, Abraham Baldwin demonstrated how academic achievement opened opportunities in colonial society, and he later became a fervent missionary of public education. This booklet on Baldwin is one in a series on Revolutionary War soldiers who signed the U.S. Constitution. The booklet reviews his education,…

  7. An Interview with Abraham J. Tannenbaum: Innovative Programs for the Gifted and Talented.

    ERIC Educational Resources Information Center

    Kay, Sandra I.

    2002-01-01

    In this interview, Dr. Abraham Tannenbaum, an author and leader of numerous research projects concerning gifted and talented students, discusses homeschooling, the impact of charter schools, magnet schools, and school choice on gifted education, the Ganiech psychosocial definition of giftedness, and the development of gifted programs. (Contains 7…

  8. Technology Staff-Development and Support Programs: Applying Abraham Maslow's Hierarchy of Needs.

    ERIC Educational Resources Information Center

    Bailey, Gerald D.; Pownell, David

    1998-01-01

    Presents Abraham Maslow's hierarchy of needs (physiological, safety, belonging, esteem, self-actualization) as a model for developing technology training and support for teachers, identifies basic technology-related needs that must be met before higher levels of technology integration can be achieved, and offers seven implications to help…

  9. Electromagnetic Momentum in Magnetic Media and the Abraham-Minkowski Controversy

    ERIC Educational Resources Information Center

    Jimenez, J. L.; Campos, I.; Lopez-Marino, M. A.

    2011-01-01

    We explore the consequences of a force density, [image omitted], studied by some authors, for the device designed by Lai (1980 "Am. J. Phys. 48" 658) to analyse which definition of electromagnetic momentum density, either Minkowski's or Abraham's, is consistent with mechanical torques that arise from the change in time of a magnetic field, which…

  10. The solvation structure of alprazolam.

    PubMed

    Sridhar, Akshay; Johnston, Andrew J; Varathan, Luxmmi; McLain, Sylvia E; Biggin, Philip C

    2016-08-10

    Alprazolam is a benzodiazepine that is commonly prescribed for the treatment of anxiety and other related disorders. Like other benzodiazepines, it is thought to exert its effect through interaction with GABAA receptors. However, it has also been described as a potent and selective protein interaction inhibitor of bromodomain and extra-terminal (BET) proteins. Indeed, the only crystal structure of alprazolam bound to a protein is a complex between alprazolam and the BRD4 bromodomain. The structure shows that the complex also involves many water interactions that mediate contacts between the drug and the protein, a scenario that exists in many drug-protein complexes. How such waters relate to solvation patterns of small molecules may improve our understanding of what dictates their appearance or absence in bridging positions within complexes and thus will be important in terms of future rational drug-design. Here, we use neutron diffraction in conjunction with molecular dynamics simulations to provide a detailed analysis of how water molecules interact with alprazolam in methanol/water mixtures. The agreement between the neutron diffraction and the molecular dynamics is extremely good. We discuss the results in the context of drug design. PMID:27465367

  11. Femtosecond resolved solvation dynamics in polar solvents

    NASA Astrophysics Data System (ADS)

    Kahlow, Michael A.; Jarzeba, Włodzimierz; Kang, Tai Jong; Barbara, Paul F.

    1989-01-01

    The transient solvation of a polar fluorescent probe has been studied by the time resolved Stokes shift technique with roughly five times shorter time resolution than previously reported. New shorter time components in the solvation relaxation function C(t) have been discovered for methanol, propionitrile, and propylene carbonate; the C(t) function for acetonitrile is singly exponential within the limitations of the instrument. The observed C(t) has been compared to theoretical calculations using the dielectric continuum (DC) model for each solvent, with non-Debye expressions for the solvent dielectric response. For methanol the DC model predictions agree closely with experiment. For the polar aprotic solvents propylene carbonate and propionitrile, the shape of the experimental decay is different from the DC predictions, but the average decay times <τs> are closer to the DC predictions than previously reported. The comparison of theory and experiment is clearly limited by the inconsistencies and limited frequency range of the dielectric relaxation data found in the literature. The dynamic solvation measurements have also been compared to predictions of the mean spherical approximation as applied to solvation dynamics, which appear to give slower solvation rates than are observed experimentally.

  12. 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

  13. Excess Electron Localization in Solvated DNA Bases

    SciTech Connect

    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.

  14. Quantum Chemistry for Solvated Molecules on Graphical Processing Units Using Polarizable Continuum Models.

    PubMed

    Liu, Fang; Luehr, Nathan; Kulik, Heather J; Martínez, Todd J

    2015-07-14

    The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale biomolecular systems can be limited by computational expense of both the gas phase electronic structure and the solvation interaction. We have previously used graphical processing units (GPUs) to accelerate the first of these steps. Here, we extend the use of GPUs to accelerate electronic structure calculations including C-PCM solvation. Implementation on the GPU leads to significant acceleration of the generation of the required integrals for C-PCM. We further propose two strategies to improve the solution of the required linear equations: a dynamic convergence threshold and a randomized block-Jacobi preconditioner. These strategies are not specific to GPUs and are expected to be beneficial for both CPU and GPU implementations. We benchmark the performance of the new implementation using over 20 small proteins in solvent environment. Using a single GPU, our method evaluates the C-PCM related integrals and their derivatives more than 10× faster than that with a conventional CPU-based implementation. Our improvements to the linear solver provide a further 3× acceleration. The overall calculations including C-PCM solvation require, typically, 20-40% more effort than that for their gas phase counterparts for a moderate basis set and molecule surface discretization level. The relative cost of the C-PCM solvation correction decreases as the basis sets and/or cavity radii increase. Therefore, description of solvation with this model should be routine. We also discuss applications to the study of the conformational landscape of an amyloid fibril. PMID:26575750

  15. Tuning structure and mobility of solvation shells surrounding tracer additives

    SciTech Connect

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

    2015-03-28

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

  16. Tuning structure and mobility of solvation shells surrounding tracer additives.

    PubMed

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

    2015-03-28

    Molecular dynamics simulations and a stochastic Fokker-Planck equation based approach are used to illuminate how position-dependent solvent mobility near one or more tracer particle(s) is affected when tracer-solvent interactions are rationally modified to affect corresponding solvation structure. For tracers in a dense hard-sphere fluid, we compare two types of tracer-solvent interactions: (1) a hard-sphere-like interaction, and (2) a soft repulsion extending beyond the hard core designed via statistical mechanical theory to enhance tracer mobility at infinite dilution by suppressing coordination-shell structure [Carmer et al., Soft Matter 8, 4083-4089 (2012)]. For the latter case, we show that the mobility of surrounding solvent particles is also increased by addition of the soft repulsive interaction, which helps to rationalize the mechanism underlying the tracer's enhanced diffusivity. However, if multiple tracer surfaces are in closer proximity (as at higher tracer concentrations), similar interactions that disrupt local solvation structure instead suppress the position-dependent solvent dynamics. PMID:25833590

  17. Experimental and computational studies of polar solvation

    SciTech Connect

    Not Available

    1991-01-01

    Many articles and papers were published; a few are still in preparation or will be published. The solvation dynamics studies will be extended to ionic solutions. Computer simulations were also performed. A new line of research was begun on excited-state proton-transfer reactions catalyzed by alcohol solvents. (DLC)

  18. Reactions of Solvated Ions Final Report

    DOE R&D Accomplishments Database

    Taube, H.

    1962-09-24

    Brief summaries are presented on isotopic dilution studies on salts dissolved in CH{sub 3}OH, studies on metal and metal salts in solvents of the amine type, and studies on phosphato complexes of the pentammine Co(III) series. A list of papers published on reactions of solvated ions is included. (N.W.R.)

  19. Solvation and Reaction in Ionic Liquids

    SciTech Connect

    Maroncelli, Mark

    2015-01-15

    The long-range goal of our DOE-sponsored research is to obtain a fundamental understanding of solvation effects on photo-induced charge transfer and related processes. Much of the focus during the past funding period has been on studies of ionic liquids and on characterizing various reactions with which to probe the nature of this interesting new solvent medium.

  20. FAST MOLECULAR SOLVATION ENERGETICS AND FORCE COMPUTATION.

    PubMed

    Bajaj, Chandrajit; Zhao, Wenqi

    2010-01-20

    The total free energy of a molecule includes the classical molecular mechanical energy (which is understood as the free energy in vacuum) and the solvation energy which is caused by the change of the environment of the molecule (solute) from vacuum to solvent. The solvation energy is important to the study of the inter-molecular interactions. In this paper we develop a fast surface-based generalized Born method to compute the electrostatic solvation energy along with the energy derivatives for the solvation forces. The most time-consuming computation is the evaluation of the surface integrals over an algebraic spline molecular surface (ASMS) and the fast computation is achieved by the use of the nonequispaced fast Fourier transform (NFFT) algorithm. The main results of this paper involve (a) an efficient sampling of quadrature points over the molecular surface by using nonlinear patches, (b) fast linear time estimation of energy and inter-molecular forces, (c) error analysis, and (d) efficient implementation combining fast pairwise summation and the continuum integration using nonlinear patches. PMID:20200598

  1. Inertial solvation in femtosecond 2D spectra

    NASA Astrophysics Data System (ADS)

    Hybl, John; Albrecht Ferro, Allison; Farrow, Darcie; Jonas, David

    2001-03-01

    We have used 2D Fourier transform spectroscopy to investigate polar solvation. 2D spectroscopy can reveal molecular lineshapes beneath ensemble averaged spectra and freeze molecular motions to give an undistorted picture of the microscopic dynamics of polar solvation. The transition from "inhomogeneous" to "homogeneous" 2D spectra is governed by both vibrational relaxation and solvent motion. Therefore, the time dependence of the 2D spectrum directly reflects the total response of the solvent-solute system. IR144, a cyanine dye with a dipole moment change upon electronic excitation, was used to probe inertial solvation in methanol and propylene carbonate. Since the static Stokes' shift of IR144 in each of these solvents is similar, differences in the 2D spectra result from solvation dynamics. Initial results indicate that the larger propylene carbonate responds more slowly than methanol, but appear to be inconsistent with rotational estimates of the inertial response. To disentangle intra-molecular vibrations from solvent motion, the 2D spectra of IR144 will be compared to the time-dependent 2D spectra of the structurally related nonpolar cyanine dye HDITCP.

  2. Solvation free energies in [bmim]-based ionic liquids: Anion effect toward solvation of amino acid side chain analogues

    NASA Astrophysics Data System (ADS)

    Latif, Muhammad Alif Mohammad; Micaêlo, Nuno; Abdul Rahman, Mohd Basyaruddin

    2014-11-01

    Stochastic molecular dynamics simulations were performed to investigate the solvation free energy of 15 neutral amino acid side chain analogues in aqueous and five, 1-butyl-3-methylimidazolium ([BMIM])-based ionic liquids. The results in aqueous were found highly correlated with previous experimental and simulation data. Meanwhile, [BMIM]-based RTILs showed better solvation thermodynamics than water to an extent that they were capable of solvating molecules immiscible in water. Non-polar analogues showed stronger solvation in hydrophobic RTIL anions such as [PF6]- and [Tf2N]- while polar analogues showed stronger solvation in the more hydrophilic RTIL anions such as [Cl]-, [TfO]- and [BF4]-.

  3. LS-VISM: A Software Package for Analysis of Biomolecular Solvation

    PubMed Central

    Zhou, Shenggao; Cheng, Li-Tien; Sun, Hui; Che, Jianwei; Dzubiella, Joachim; Li, Bo; McCammon, J. Andrew

    2015-01-01

    We introduce a software package for the analysis of biomolecular solvation. The package collects computer codes that implement numerical methods for a variational implicit-solvent model (VISM). The input of the package includes the atomic data of biomolecules under consideration and the macroscopic parameters such as solute-solvent surface tension, bulk solvent density and ionic concentrations, and the dielectric coefficients. The output includes estimated solvation free energies and optimal macroscopic solute-solvent interfaces that are obtained by minimizing the VISM solvation free-energy functional among all possible solute-solvent interfaces enclosing the solute atoms. We review the VISM with various descriptions of electrostatics. We also review our numerical methods that consist mainly of the level-set method for relaxing the VISM free-energy functional and a compact coupling interface method for the dielectric Poisson–Boltzmann equation. Such numerical methods and algorithms constitute the central modules of the software package. We detail the structure of the package, format of input and output files, work flow of the codes, and the post-processing of output data. Our demo application to a host-guest system illustrates how to use the package to perform solvation analysis for biomolecules, including ligand-receptor binding systems. The package is simple and flexible with respect to minimum adjustable parameters and a wide range of applications. Future extensions of the package use can include the efficient identification of ligand binding pockets on protein surfaces. PMID:25766844

  4. LS-VISM: A software package for analysis of biomolecular solvation.

    PubMed

    Zhou, Shenggao; Cheng, Li-Tien; Sun, Hui; Che, Jianwei; Dzubiella, Joachim; Li, Bo; McCammon, J Andrew

    2015-05-30

    We introduce a software package for the analysis of biomolecular solvation. The package collects computer codes that implement numerical methods for a variational implicit-solvent model (VISM). The input of the package includes the atomic data of biomolecules under consideration and the macroscopic parameters such as solute-solvent surface tension, bulk solvent density and ionic concentrations, and the dielectric coefficients. The output includes estimated solvation free energies and optimal macroscopic solute-solvent interfaces that are obtained by minimizing the VISM solvation free-energy functional among all possible solute-solvent interfaces enclosing the solute atoms. We review the VISM with various descriptions of electrostatics. We also review our numerical methods that consist mainly of the level-set method for relaxing the VISM free-energy functional and a compact coupling interface method for the dielectric Poisson-Boltzmann equation. Such numerical methods and algorithms constitute the central modules of the software package. We detail the structure of the package, format of input and output files, workflow of the codes, and the postprocessing of output data. Our demo application to a host-guest system illustrates how to use the package to perform solvation analysis for biomolecules, including ligand-receptor binding systems. The package is simple and flexible with respect to minimum adjustable parameters and a wide range of applications. Future extensions of the package use can include the efficient identification of ligand binding pockets on protein surfaces. PMID:25766844

  5. A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules

    NASA Astrophysics Data System (ADS)

    Geng, Weihua; Krasny, Robert

    2013-08-01

    We present a treecode-accelerated boundary integral (TABI) solver for electrostatics of solvated biomolecules described by the linear Poisson-Boltzmann equation. The method employs a well-conditioned boundary integral formulation for the electrostatic potential and its normal derivative on the molecular surface. The surface is triangulated and the integral equations are discretized by centroid collocation. The linear system is solved by GMRES iteration and the matrix-vector product is carried out by a Cartesian treecode which reduces the cost from O(N2) to O(NlogN), where N is the number of faces in the triangulation. The TABI solver is applied to compute the electrostatic solvation energy in two cases, the Kirkwood sphere and a solvated protein. We present the error, CPU time, and memory usage, and compare results for the Poisson-Boltzmann and Poisson equations. We show that the treecode approximation error can be made smaller than the discretization error, and we compare two versions of the treecode, one with uniform clusters and one with non-uniform clusters adapted to the molecular surface. For the protein test case, we compare TABI results with those obtained using the grid-based APBS code, and we also present parallel TABI simulations using up to eight processors. We find that the TABI solver exhibits good serial and parallel performance combined with relatively simple implementation, efficient memory usage, and geometric adaptability.

  6. The role of Abraham Lincoln in securing a charter for a homeopathic medical college.

    PubMed

    Spiegel, Allen D; Kavaler, Florence

    2002-10-01

    In 1854, Abraham Lincoln was retained to prepare a state legislative proposal to charter a homeopathic medical college in Chicago. This was a complex task in view of the deep-seated animosity between allopathic or orthodox medical practitioners and irregular healers. Homeopathy was regarded as a cult by the nascent American Medical Association. In addition, the poor reputation of medical education in the United States in general, further complicated the project. Lincoln and influential individuals in Illinois lobbied legislators and succeeded in securing the charter. Subsequently, the Hahnemann Homeopathic Medical College accepted its first class in 1860 and with its successors remained in existence for almost sixty-five years. PMID:12238734

  7. Cells containing solvated electron lithium negative electrodes

    NASA Astrophysics Data System (ADS)

    Uribe, Francisco A.; Semkow, Krystyna W.; Sammells, Anthony F.

    1989-12-01

    This paper presents results obtained on cells based on solvated electron lithium negative electrodes, which may have application in high-energy-density secondary or reserve battery systems. The approach uses Li initially dissolved in liquid ammonia to give a solvated electron lithium/ammonia solution. This liquid negative active material is protected from direct contact with the liquid nonaqueous electrolyte in the positive electrode compartment by a lithium-intercalated electronically conducting ceramic membrane possessing Li(x)WoO2 composition with x values between 0.1 and 1.0. Depending upon initial lithium activity in the negative electrode compartments, the experimental cell was found to possess an initial open-circuit potential between 2.1 and 2.5 V.

  8. Single-Molecule Solvation-Shell Sensing

    NASA Astrophysics Data System (ADS)

    Leary, E.; Höbenreich, H.; Higgins, S. J.; van Zalinge, H.; Haiss, W.; Nichols, R. J.; Finch, C. M.; Grace, I.; Lambert, C. J.; McGrath, R.; Smerdon, J.

    2009-02-01

    We present a new route to single-molecule sensing via solvation shells surrounding a current-carrying backbone molecule. As an example, we show that the presence of a water solvation shell “gates” the conductance of a family of oligothiophene-containing molecular wires, and that the longer the oligothiophene, the larger is the effect. For the longest example studied, the molecular conductance is over 2 orders of magnitude larger in the presence of a shell comprising just 10 water molecules. A first principles theoretical investigation of electron transport through the molecules, using the nonequilibrium Green’s function method, shows that water molecules interact directly with the thiophene rings, significantly shifting transport resonances and greatly increasing the conductance. This reversible effect is confirmed experimentally through conductance measurements performed in the presence of moist air and dry argon.

  9. Preferential solvation: dividing surface vs excess numbers.

    PubMed

    Shimizu, Seishi; Matubayasi, Nobuyuki

    2014-04-10

    How do osmolytes affect the conformation and configuration of supramolecular assembly, such as ion channel opening and actin polymerization? The key to the answer lies in the excess solvation numbers of water and osmolyte molecules; these numbers are determinable solely from experimental data, as guaranteed by the phase rule, as we show through the exact solution theory of Kirkwood and Buff (KB). The osmotic stress technique (OST), in contrast, purposes to yield alternative hydration numbers through the use of the dividing surface borrowed from the adsorption theory. However, we show (i) OST is equivalent, when it becomes exact, to the crowding effect in which the osmolyte exclusion dominates over hydration; (ii) crowding is not the universal driving force of the osmolyte effect (e.g., actin polymerization); (iii) the dividing surface for solvation is useful only for crowding, unlike in the adsorption theory which necessitates its use due to the phase rule. KB thus clarifies the true meaning and limitations of the older perspectives on preferential solvation (such as solvent binding models, crowding, and OST), and enables excess number determination without any further assumptions. PMID:24689966

  10. Simulated solvation of organic ions: protonated methylamines in water nanodroplets. Convergence toward bulk properties and the absolute proton solvation enthalpy.

    PubMed

    Houriez, Céline; Meot-Ner Mautner, Michael; Masella, Michel

    2014-06-12

    We applied an alternative, purely theoretical route to estimate thermodynamical properties of organic ions in bulk solution. The method performs a large ensemble of simulations of ions solvated in water nanodroplets of different sizes, using a polarizable molecular dynamics approach. We consider protonated ammonia and methylamines, and K(+) for comparison, solvated in droplets of 50-1000 water molecules. The parameters of the model are assigned from high level quantum computations of small clusters. All the bulk phase results extrapolated from droplet simulations match, and confirm independently, the relative and absolute experiment-based ion solvation energies. Without using experiment-based parameters or assumptions, the results confirm independently the solvation enthalpy of the proton, as -270.3 ± 1.1 kcal mol(-1). The calculated relative solvation enthalpies of these ions are constant from small water clusters, where only the ionic headgroups are solvated, up to bulk solution. This agrees with experimental thermochemistry, that the relative solvation energies of alkylammonium ions by only four H2O molecules reproduce the relative bulk solvation energies, although the small clusters lack major bulk solvation factors. The droplet results also show a slow convergence of ion solvation properties toward their bulk limit, and predict that the stepwise solvation enthalpies of ion/water droplets are very close to those of pure neutral water droplets already after 50 water molecules. Both the ionic and neutral clusters approach the bulk condensation energy very gradually up to 10,000 water molecules, consistent with the macroscopic liquid drop model for pure water droplets. Compared to standard computational methods based on infinite periodic systems, our protocol represents a new purely theoretical approach to investigate the solvation properties of ions. It is applicable to the solvation of organic ions, which are pivotal in environmental, industrial, and

  11. Molecular correlations and solvation in simple fluids

    NASA Astrophysics Data System (ADS)

    Barbosa, Marco A. A.; Widom, B.

    2010-06-01

    We study the molecular correlations in a lattice model of a solution of a low-solubility solute, with emphasis on how the thermodynamics is reflected in the correlation functions. The model is treated in the Bethe-Guggenheim approximation, which is exact on a Bethe lattice (Cayley tree). The solution properties are obtained in the limit of infinite dilution of the solute. With h11(r), h12(r), and h22(r) the three pair correlation functions as functions of the separation r (subscripts 1 and 2 referring to solvent and solute, respectively), we find for r ≥2 lattice steps that h22(r)/h12(r)≡h12(r)/h11(r). This illustrates a general theorem that holds in the asymptotic limit of infinite r. The three correlation functions share a common exponential decay length (correlation length), but when the solubility of the solute is low the amplitude of the decay of h22(r) is much greater than that of h12(r), which in turn is much greater than that of h11(r). As a consequence the amplitude of the decay of h22(r) is enormously greater than that of h11(r). The effective solute-solute attraction then remains discernible at distances at which the solvent molecules are essentially no longer correlated, as found in similar circumstances in an earlier model. The second osmotic virial coefficient is large and negative, as expected. We find that the solvent-mediated part W(r ) of the potential of mean force between solutes, evaluated at contact, r =1, is related in this model to the Gibbs free energy of solvation at fixed pressure, ΔGp∗, by (Z /2)W(1)+ΔGp∗≡pv0, where Z is the coordination number of the lattice, p is the pressure, and v0 is the volume of the cell associated with each lattice site. A large, positive ΔGp∗ associated with the low solubility is thus reflected in a strong attraction (large negative W at contact), which is the major contributor to the second osmotic virial coefficient. In this model, the low solubility (large positive ΔGp∗) is due partly to an

  12. Molecular correlations and solvation in simple fluids.

    PubMed

    Barbosa, Marco A A; Widom, B

    2010-06-01

    We study the molecular correlations in a lattice model of a solution of a low-solubility solute, with emphasis on how the thermodynamics is reflected in the correlation functions. The model is treated in the Bethe-Guggenheim approximation, which is exact on a Bethe lattice (Cayley tree). The solution properties are obtained in the limit of infinite dilution of the solute. With h(11)(r), h(12)(r), and h(22)(r) the three pair correlation functions as functions of the separation r (subscripts 1 and 2 referring to solvent and solute, respectively), we find for r > or = 2 lattice steps that h(22)(r)/h(12)(r) is identical with h(12)(r)/h(11)(r). This illustrates a general theorem that holds in the asymptotic limit of infinite r. The three correlation functions share a common exponential decay length (correlation length), but when the solubility of the solute is low the amplitude of the decay of h(22)(r) is much greater than that of h(12)(r), which in turn is much greater than that of h(11)(r). As a consequence the amplitude of the decay of h(22)(r) is enormously greater than that of h(11)(r). The effective solute-solute attraction then remains discernible at distances at which the solvent molecules are essentially no longer correlated, as found in similar circumstances in an earlier model. The second osmotic virial coefficient is large and negative, as expected. We find that the solvent-mediated part W(r) of the potential of mean force between solutes, evaluated at contact, r = 1, is related in this model to the Gibbs free energy of solvation at fixed pressure, DeltaG(p)(*), by (Z/2)W(1) + DeltaG(p)(*) is identical with pv(0), where Z is the coordination number of the lattice, p is the pressure, and v(0) is the volume of the cell associated with each lattice site. A large, positive DeltaG(p)(*) associated with the low solubility is thus reflected in a strong attraction (large negative W at contact), which is the major contributor to the second osmotic virial coefficient

  13. 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.

  14. 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

  15. A Brief Analysis of Abraham Maslow's Original Writing of "Self-Actualizing People: A Study of Psychological Health"

    ERIC Educational Resources Information Center

    Francis, Nedra H.; Kritsonis, William Allan

    2006-01-01

    This article analyzes Abraham Maslow's original writing of "Self-Actualizing People: A Study of Psychological Health." The review of literature in this article reveals that Maslow's hierarchy of needs have had profound effects in the area of psychology. In addition, the authors present information regarding self-actualized people, theorists of…

  16. In Favour of a Multi-Method Approach to Differentiation-Polarization Theory-Building: A Response to Abraham

    ERIC Educational Resources Information Center

    Van Houtte, Mieke

    2007-01-01

    This response to the comment of Abraham on Van Houtte's study within the differentiation-polarization tradition discusses the difference between her quantitative study and the ethnographic tradition. The quantification of the polarization part of the theory--the anti-school culture--makes it possible to merge the differentiation-polarization…

  17. Experimental determination of solvent-water partition coefficients and Abraham parameters for munition constituents.

    PubMed

    Liang, Yuzhen; Kuo, Dave T F; Allen, Herbert E; Di Toro, Dominic M

    2016-10-01

    There is concern about the environmental fate and effects of munition constituents (MCs). Polyparameter linear free energy relationships (pp-LFERs) that employ Abraham solute parameters can aid in evaluating the risk of MCs to the environment. However, poor predictions using pp-LFERs and ABSOLV estimated Abraham solute parameters are found for some key physico-chemical properties. In this work, the Abraham solute parameters are determined using experimental partition coefficients in various solvent-water systems. The compounds investigated include hexahydro-1,3,5-trinitro-1,3,5-triazacyclohexane (RDX), octahydro-1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX), hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine (MNX), hexahydro-1,3,5-trinitroso-1,3,5-triazine (TNX), hexahydro-1,3-dinitroso-5- nitro-1,3,5-triazine (DNX), 2,4,6-trinitrotoluene (TNT), 1,3,5-trinitrobenzene (TNB), and 4-nitroanisole. The solvents in the solvent-water systems are hexane, dichloromethane, trichloromethane, octanol, and toluene. The only available reported solvent-water partition coefficients are for octanol-water for some of the investigated compounds and they are in good agreement with the experimental measurements from this study. Solvent-water partition coefficients fitted using experimentally derived solute parameters from this study have significantly smaller root mean square errors (RMSE = 0.38) than predictions using ABSOLV estimated solute parameters (RMSE = 3.56) for the investigated compounds. Additionally, the predictions for various physico-chemical properties using the experimentally derived solute parameters agree with available literature reported values with prediction errors within 0.79 log units except for water solubility of RDX and HMX with errors of 1.48 and 2.16 log units respectively. However, predictions using ABSOLV estimated solute parameters have larger prediction errors of up to 7.68 log units. This large discrepancy is probably due to the missing R2NNO2

  18. Creating a Project on Difference Equations with Primary Sources: Challenges and Opportunities

    ERIC Educational Resources Information Center

    Ruch, David

    2014-01-01

    This article discusses the creation of a student project about linear difference equations using primary sources. Early 18th-century developments in the area are outlined, focusing on efforts by Abraham De Moivre (1667-1754) and Daniel Bernoulli (1700-1782). It is explained how primary sources from these authors can be used to cover material…

  19. Preferential Solvation of Lithium Cations and Impacts on Oxygen Reduction in Lithium-Air Batteries.

    PubMed

    Zheng, Dong; Qu, Deyu; Yang, Xiao-Qing; Lee, Hung-Sui; Qu, Deyang

    2015-09-16

    The solvation of Li+ with 11 nonaqueous solvents commonly used as electrolytes for lithium batteries was 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 redox reaction was also investigated. PMID:26301499

  20. Solvation of chromone using combined Discrete/SCRF models

    NASA Astrophysics Data System (ADS)

    Alemán, Carlos; Galembeck, Sergio E.

    1998-06-01

    The solvation of chromone has been investigated using three different combined Discrete/SCRF models. Four chromone-H 2O complexes and one chromone-4H 2O complex were obtained from geometry optimizations at the HF/6-31G(d) level. Three SCRF methods (PCM/6-31G(d), PCM/AM1 and SM2/AM1) were applied to such complexes in order to: (1) evaluate the reliability of the combined Discrete/SCRF models; (2) investigate the effects of the explicit water molecules on the free energy of solvation; and (3) analyze the characteristics of the different solvation sites of chromone. The results show that explicit solvent molecules exert a large influence on the free energy of solvation of a given molecular system providing some information about the solvation sites. Thus, the interaction of the carbonyl oxygen of chromone with the explicit water molecules is stronger than interaction provided by the ether oxygen, providing the complexes with the former interaction a more hydrophobic free energy of solvation than those with the latter. On the other hand, the comparison of the free energies of solvation for solutes with explicit water molecules in the first hydration shell and the free energies of solvation of the molecular system computed in an all-continuum approach reveals that the combined Discrete/SCRF models constitute a very reasonable strategy.

  1. Abraham Lincoln's marfanoid mother: the earliest known case of multiple endocrine neoplasia type 2B?

    PubMed

    Sotos, John G

    2012-07-01

    The nature and cause of President Abraham Lincoln's unusual physical features have long been debated, with the greatest attention directed at two monogenic disorders of the transforming growth factor β system: Marfan syndrome and multiple endocrine neoplasia type 2B. The present report examines newly discovered phenotypic information about Lincoln's biological mother, Nancy Hanks Lincoln, and concludes that (a) Lincoln's mother was skeletally marfanoid, (b) the President and his mother were highly concordant for the presence of numerous facial features found in various transforming growth factor β disorders, and (c) Lincoln's mother, like her son, had hypotonic skeletal muscles, resulting in myopathic facies and 'pseudodepression'. These conclusions establish that mother and son had the same monogenic autosomal dominant marfanoid disorder. A description of Nancy Hanks Lincoln as coarse-featured, and a little-known statement that a wasting disease contributed to her death at age 34, lends support to the multiple endocrine neoplasia type 2B hypothesis. PMID:22504423

  2. Abraham Lincoln's blue pills. Did our 16th president suffer from mercury poisoning?

    PubMed

    Hirschhorn, N; Feldman, R G; Greaves, I A

    2001-01-01

    It is well known that Abraham Lincoln took a medicine called "blue mass" or "blue pill," commonly prescribed in the 19th century. What is now hardly known is that the main ingredient of blue mass was finely dispersed elemental mercury. As his friends understood, mercury was often prescribed for melancholy or "hypochondriasis," a condition Lincoln famously endured. Mercury in the form of the blue pill is a potential neurotoxin, which we have demonstrated by recreating and testing the recipe. We present the testimony of many of Lincoln's contemporaries to suggest that Lincoln suffered the neurobehavioural consequences of mercury intoxication but, perhaps crucial to history, before the main years of his presidency; he was astute enough to recognize the effects and stop the medication soon after his inauguration. PMID:11482002

  3. Abraham Flexner and the Development of the Yale School of Medicine

    PubMed Central

    Prutkin, Jordan M.

    2010-01-01

    Abraham Flexner first toured the Yale University School of Medicine in preparation for his report of 1910, but it was just the beginning of his relationship with the school. While his review of Yale in his report was generally favorable, he mentioned several shortfalls that needed to be improved to make the school acceptable. Throughout the next twenty-five years, Flexner worked with Deans George Blumer and Milton C. Winternitz to improve the school’s finances, infrastructure, and quality of education through his work with the Carnegie Foundation and General Education Board. Flexner has been given great accolades for his work on medical education for the country, but little mention is made of him at Yale, even though he was one of the most influential figures in the development of Yale in the last century. PMID:20885903

  4. Religion, Sexuality, and Internalized Homonegativity: Confronting Cognitive Dissonance in the Abrahamic Religions.

    PubMed

    Meladze, Pikria; Brown, Jac

    2015-10-01

    This research was aimed at investigating how religious beliefs and internalized shame predicted homonegativity. An online survey, which consisted of a self-report questionnaire assessing religious orientation, internalized shame, and internalized homonegativity, was completed by 133 Caucasian and Asian gay men. The respondents also were asked to write a short answer in which they had to explain how they integrated their religion and sexual practices. The quantitative analyses of data demonstrated no significant difference in internalized homonegativity among the two cultural groups. Internalized homonegativity was predicted by the main Abrahamic faiths (i.e. Christianity, Islam, and Judaism) and internalized shame. Qualitative analysis showed that gay men who adhere to a monotheistic religious faith follow a different path to reconciling their religion and homosexuality compared to gay men who adhere to Philosophical/New Age religions or to gay men who have no religious faith. The implications of these findings as well as directions for future research studies were discussed. PMID:25772199

  5. Lithium pinacolone enolate solvated by hexamethylphosphoramide.

    PubMed

    Guang, Jie; Liu, Qiyong Peter; Hopson, Russell; Williard, Paul G

    2015-06-17

    We report the crystal structure of a substoichiometric, HMPA-trisolvated lithium pinacolone enolate tetramer (LiOPin)4·HMPA3 abbreviated as T3. In this tetramer one HMPA binds to lithium more strongly than the other two causing a reduction in spatial symmetry with corresponding loss of C3 symmetry. A variety of NMR experiments, including HMPA titration, diffusion coefficient-formula weight (D-FW) analysis, and other multinuclear one- and two-dimensional NMR techniques reveal that T3 is the major species in hydrocarbon solution when more than 0.6 equiv of HMPA is present. Due to a small amount of moisture from HMPA or air leaking into the solution, a minor complex was identified and confirmed by X-ray diffraction analysis as a mixed aggregate containing enolate, lithium hydroxide, and HMPA in a 4:2:4 ratio, [(LiOPin)4·(LiOH)2·HMPA4], that we refer to as pseudo-T4. A tetra-HMPA-solvated lithium cyclopentanone enolate tetramer was also prepared and characterized by X-ray diffraction, leading to the conclusion that steric effects dominate the formation and solvation of the pinacolone aggregates. An unusual mixed aggregate consisting of pinacolone enolate, lithium diisopropyl amide, lithium oxide, and HMPA in the ratio 5:1:1:2 is also described. PMID:25933508

  6. Partial solvation parameters and mixture thermodynamics.

    PubMed

    Panayiotou, Costas

    2012-06-21

    The recently introduced partial solvation parameters (PSPs) are molecular descriptors that combine elements from quantum mechanics with the QSPR/LSER/solvatochromic and solubility parameter approaches. Basic regularities and universalities exhibited by PSPs are examined in this work and the concepts of homosolvation, heterosolvation and solvation energy density are quantified. A simple consistent thermodynamic framework is developed, through which the validity of the PSP approach is tested. The predictions are compared with experimental phase equilibrium data that span the full composition range from the pure fluid state to infinite dilution. They include vapor-liquid equilibria of fluids interacting with strong specific forces, dissolution of solids/liquids in various solvents and probe/oligomer or probe/polymer interactions as typically determined by inverse gas-chromatography. These applications show the potential of the PSP approach not only to reasonably predict a variety of properties of classes of complex systems but, also, to shed light to challenging aspects of intermolecular interactions. The perspectives of this unified approach to solution thermodynamics are discussed. PMID:22642662

  7. A simple McGowan specific volume correction for branching in hydrocarbons and its consequences for some other solvation parameter values.

    PubMed

    van Noort, Paul C M; Haftka, Joris J H; Parsons, John R

    2011-08-01

    Differences in molecular properties between linear and branched alkanes as well as between compounds with branched alkyl groups is of relevance due to the large number of branched isomers of environmentally relevant compounds (e.g. fuels, fuel additives, surfactants). For branched alkane vapor pressures, the McGowan specific volume is a poor predictor. Therefore, in this study a correction on the McGowan specific volume is derived in terms of the number of branches and the number of pairs of vicinal branches to improve the prediction of branched alkane vapor pressures. This branching correction also brought branched/alkane solvent accessible volumes, octanol/water partition coefficients, air/hexadecane partition coefficients, and aqueous solubilities as well as alkyl-branched substituted aliphatic hydrocarbon air/hexadecane partition coefficients more in line with corresponding linear hydrocarbon properties when compared on a McGowan specific volume basis. Even for air-hexadecane partition coefficients of substituted aliphatic hydrocarbons with substituents at non-terminal carbons, application of the branching correction to the carbon bearing the substituent caused these partition coefficients to be more in line with those for linear compounds. Values for the Abraham A and B solvation parameters for nonlinear aliphatic ethers, amines, and alcohols, recalculated using branching corrected McGowan specific volumes, turned out to be closer to chemical expectations based on linear aliphatic ether, amine and alcohol values compared to previously reported experimental values obtained using uncorrected McGowan specific volumes. A comparison of alkylbenzene and alkene partition coefficient estimates from two different linear solvation energy relations, one containing a McGowan specific volume term and one without such a term, suggests that no branching correction is needed for alkyl groups at sp2 carbons. The main advantage of using branching corrected McGowan specific

  8. Solvation effect on kinetic rate constant of reactions in supercritical solvents

    SciTech Connect

    Chialvo, A.A.; Cummings, P.T. |; Kalyuzhnyi, Yu.V.

    1998-03-01

    A statistical mechanical analysis of the solvation effects on the kinetic rate constants of reactions in near and supercritical solvents is presented to understand the experimental findings regarding the thermodynamic pressure effects. This is an extension of the solvation formalism of Chialvo and Cummings to the analysis of the microscopic basis for the macroscopic pressure and temperature effects on the kinetic rate constants of reactions conducted in the compressible region of the solvent phase diagram. This analysis is illustrated with integral equations calculations involving Lennard-Jones infinitely dilute quaternary systems to describe the species in solution during the reaction of triplet benzophenone ({sup 3}BP) with a cosolvent (either O{sub 2} or 1,4-cyclohexadiene) in supercritical CO{sub 2} along the supercritical isotherms T{sub r} = 1.01 and 1.06. The role of the species molecular asymmetries and consequently their solvation behavior in determining the thermodynamic pressure and temperature effects on the kinetic rate constant of reactions at near-critical conditions are discussed.

  9. Solvation free energies from a coupled reference interaction site model/simulation approach

    NASA Astrophysics Data System (ADS)

    Freedman, Holly

    2005-12-01

    Accounting for solvation in thermodynamic studies is one issue requiring further work so that computational models may be more advantageously applied to studies of systems in solution, especially studies of large systems such as aqueous biosystems. In the area of applied molecular biology, this capability is very significant, since computational thermodynamic studies can supply valuable information to assist in the design of molecules with specific desired binding or conformational properties, such as inhibitors. This dissertation addresses the issue by suggesting a new approach for the calculation of solvation free energies using a modified reference interaction site model (RISM) integral equation approach in which molecular simulations are used to provide the solvent structure around a solute at infinite dilution in the form of radial distribution functions. The intent is to compensate for insufficiencies arising in the standard RISM approach, and in this way to establish an alternative to the very time consuming free energy simulations, which are usually depended upon for high accuracy and have seen some recent applications, although falling somewhat short as far as practicality. Chapter 2 of this dissertation investigates how it is possible to implement such a scheme, with consideration given to the inherent errors associated with such an approach. In Chapter 3, the resulting coupled RISM simulation methodology is first tested by its application to determine absolute solvation free energies of some small molecules. Applications of relative solvation free energy determination by the coupled RISM/simulation methodology to the conformational analysis of the alanine dipeptide, and to the tautomeric equilibria of the DNA base cytosine and one of its analogues, are then described in Chapters 4 and 5, respectively. Chapter 6 is concerned with the determination of a potential of mean force profile for a simple atom transfer reaction in aqueous solution. By means of

  10. Revised self-consistent continuum solvation in electronic-structure calculations.

    PubMed

    Andreussi, Oliviero; Dabo, Ismaila; Marzari, Nicola

    2012-02-14

    The solvation model proposed by Fattebert and Gygi [J. Comput. Chem. 23, 662 (2002)] and Scherlis et al. [J. Chem. Phys. 124, 074103 (2006)] is reformulated, overcoming some of the numerical limitations encountered and extending its range of applicability. We first recast the problem in terms of induced polarization charges that act as a direct mapping of the self-consistent continuum dielectric; this allows to define a functional form for the dielectric that is well behaved both in the high-density region of the nuclear charges and in the low-density region where the electronic wavefunctions decay into the solvent. Second, we outline an iterative procedure to solve the Poisson equation for the quantum fragment embedded in the solvent that does not require multigrid algorithms, is trivially parallel, and can be applied to any Bravais crystallographic system. Last, we capture some of the non-electrostatic or cavitation terms via a combined use of the quantum volume and quantum surface [M. Cococcioni, F. Mauri, G. Ceder, and N. Marzari, Phys. Rev. Lett. 94, 145501 (2005)] of the solute. The resulting self-consistent continuum solvation model provides a very effective and compact fit of computational and experimental data, whereby the static dielectric constant of the solvent and one parameter allow to fit the electrostatic energy provided by the polarizable continuum model with a mean absolute error of 0.3 kcal/mol on a set of 240 neutral solutes. Two parameters allow to fit experimental solvation energies on the same set with a mean absolute error of 1.3 kcal/mol. A detailed analysis of these results, broken down along different classes of chemical compounds, shows that several classes of organic compounds display very high accuracy, with solvation energies in error of 0.3-0.4 kcal/mol, whereby larger discrepancies are mostly limited to self-dissociating species and strong hydrogen-bond-forming compounds. PMID:22360164

  11. Theoretical Characterization of Oxoanion, XOmn-, Solvation

    SciTech Connect

    Camaioni, Donald M.; Dupuis, Michel; Bentley, John ..

    2003-07-31

    We propose an empirically-derived cavity definition scheme that permits the prediction of accurate solvation energies of oxoanions using a COSMO dielectric continuum model of solvation. Assuming a cavity made up of interlocked atomic spheres, the radii are given by simple, empirically-derived, expressions involving effective atomic charges of the solute atoms that fit the solute molecular electrostatic potential (from DFT calculations), and a bond length-dependent factor to account for atomic size and hybridization. We illustrate the new scheme for the case of oxoanions. The expression for the atomic radii of the terminal oxygen atoms is based on a training set that included only O-, O2-, and O2. The expression for the radius of the central atom is based on a limited training set made of O3-, NO2-, HCO2-, NO3-, ClO2-, O3, NO2, CO2, ClO2, and SO2. The scheme is applied to several oxoanions outside the training sets, such as CO2-, CO3-, CO32-, NO32-, SO2-, ClO3-, and ClO4-. The predicted solvation energies and half-reaction potentials are in close agreement with experiment. The new cavity scheme shows substantial qualitative differences from other previously proposed schemes. For example in contrast to the widely used UAHF scheme that assigns small radii to the central atoms of these oxoanions, our new scheme assigns large radii. This difference is put on a firm theoretical basis in the case of nitrate NO3- through an analysis of the molecular electrostatic potential of the nitrate ion and an analysis of its interaction with a `solvent? water molecule. In spite of a large positive partial charge assigned to nitrogen in nitrate ion, the water `solvent? molecule remains acting as an H-bond donor in the region of the central N-atom as a result of the electrostatic potential of the anion, although the water-nitrate interaction in that region is weaker than near the terminal O atoms. From these results we surmise that the solvent molecules remain further away from the

  12. Extension of the FACTS Implicit Solvation Model to Membranes.

    PubMed

    Carballo-Pacheco, Martín; Vancea, Ioan; Strodel, Birgit

    2014-08-12

    The generalized Born (GB) formalism can be used to model water as a dielectric continuum. Among the different implicit solvent models using the GB formalism, FACTS is one of the fastest. Here, we extend FACTS so that it can represent a membrane environment. This extension is accomplished by considering a position dependent dielectric constant and empirical surface tension parameter. For the calculation of the effective Born radii in different dielectric environments we present a parameter-free approximation to Kirkwood's equation, which uses the Born radii obtained with FACTS for the water environment as input. This approximation is tested for the calculation of self-free energies, pairwise interaction energies in solution and solvation free energies of complete protein conformations. The results compare well to those from the finite difference Poisson method. The new implicit membrane model is applied to estimate free energy insertion profiles of amino acid analogues and in molecular dynamics simulations of melittin, WALP23 and KALP23, glycophorin A, bacteriorhodopsin, and a Clc channel dimer. In all cases, the results agree qualitatively with experiments and explicit solvent simulations. Moreover, the implicit membrane model is only six times slower than a vacuum simulation. PMID:26588287

  13. Variational Implicit Solvation with Poisson–Boltzmann Theory

    PubMed Central

    2015-01-01

    We incorporate the Poisson–Boltzmann (PB) theory of electrostatics into our variational implicit-solvent model (VISM) for the solvation of charged molecules in an aqueous solvent. In order to numerically relax the VISM free-energy functional by our level-set method, we develop highly accurate methods for solving the dielectric PB equation and for computing the dielectric boundary force. We also apply our VISM-PB theory to analyze the solvent potentials of mean force and the effect of charges on the hydrophobic hydration for some selected molecular systems. These include some single ions, two charged particles, two charged plates, and the host–guest system Cucurbit[7]uril and Bicyclo[2.2.2]octane. Our computational results show that VISM with PB theory can capture well the sensitive response of capillary evaporation to the charge in hydrophobic confinement and the polymodal hydration behavior and can provide accurate estimates of binding affinity of the host–guest system. We finally discuss several issues for further improvement of VISM. PMID:24803864

  14. The AGBNP2 Implicit Solvation Model

    PubMed Central

    Gallicchio, Emilio; Paris, Kristina; Levy, Ronald M.

    2009-01-01

    The AGBNP2 implicit solvent model, an evolution of the Analytical Generalized Born plus Non-Polar (AGBNP) model we have previously reported, is presented with the aim of modeling hydration effects beyond those described by conventional continuum dielectric representations. A new empirical hydration free energy component based on a procedure to locate and score hydration sites on the solute surface is introduced to model first solvation shell effects, such as hydrogen bonding, which are poorly described by continuum dielectric models. This new component is added to the Generalized Born and non-polar AGBNP terms. Also newly introduced is an analytical Solvent Excluded Volume (SEV) model which improves the solute volume description by reducing the effect of spurious high-dielectric interstitial spaces present in conventional van der Waals representations. The AGBNP2 model is parametrized and tested with respect to experimental hydration free energies of small molecules and the results of explicit solvent simulations. Modeling the granularity of water is one of the main design principles employed for the the first shell solvation function and the SEV model, by requiring that water locations have a minimum available volume based on the size of a water molecule. It is shown that the new volumetric model produces Born radii and surface areas in good agreement with accurate numerical evaluations of these quantities. The results of molecular dynamics simulations of a series of mini-proteins show that the new model produces conformational ensembles in substantially better agreement with reference explicit solvent ensembles than the original AGBNP model with respect to both structural and energetics measures. PMID:20419084

  15. Solvation Effects on Structure and Charge Distribution in Anionic Clusters

    NASA Astrophysics Data System (ADS)

    Weber, J. Mathias

    2015-03-01

    The interaction of ions with solvent molecules modifies the properties of both solvent and solute. Solvation generally stabilizes compact charge distributions compared to more diffuse ones. In the most extreme cases, solvation will alter the very composition of the ion itself. We use infrared photodissociation spectroscopy of mass-selected ions to probe how solvation affects the structures and charge distributions of metal-CO2 cluster anions. We gratefully acknowledge the National Science Foundation for funding through Grant CHE-0845618 (for graduate student support) and for instrumentation funding through Grant PHY-1125844.

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

    PubMed

    You, Zhi-Qiang; Mewes, Jan-Michael; Dreuw, Andreas; Herbert, John M

    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 fails 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. PMID:26627947

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

    SciTech Connect

    You, Zhi-Qiang; Herbert, John M.; Mewes, Jan-Michael; Dreuw, Andreas

    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 fails 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.

  18. Extended solvent-contact model for protein solvation: test cases for dipeptides.

    PubMed

    Choi, Hwanho; Kang, Hongsuk; Park, Hwangseo

    2013-05-01

    Solvation effects are critically important in the structural stabilization and functional optimization of proteins. Here, we propose a new solvation free energy function for proteins, and test its applicability in predicting the solvation free energies of dipeptides. The present solvation model involves the improvement of the previous solvent-contact model assuming that the molecular solvation free energy could be given by the sum over the individual atomic contributions. In addition to the existing solvent-contact term, the modified solvation free energy function includes the self-solvation term that reflects the effects of intramolecular interactions in the solute molecule on solute-solvent interactions. Four kinds of atomic parameters should be determined in this solvation model: atomic fragmental volume, maximum atomic occupancy, atomic solvation, and atomic self-solvation parameters. All of these parameters for 16 atom types are optimized with a standard genetic algorithm in such a way to minimize the difference between the solvation free energies of dipeptides obtained from high-level quantum chemical calculations and those predicted by the solvation free energy function. The solvation free energies of dipeptides estimated from the new solvation model are in good agreement with the quantum chemical results. Therefore, the optimized solvation free energy function is expected to be useful for examining the structural and energetic features of proteins in aqueous solution. PMID:23548585

  19. Potentials of Mean Force Between Rigid Solvated Polymers

    SciTech Connect

    FRINK, LAURA J.D.; SALINGER, ANDREW G.

    1999-09-29

    In this letter we discusses the first application of 3-dimensional nonlocal density functional calculations to the interactions of solvated rigid polymers. The three cases considered are cylindrical polymers, bead-chain polymers, and periodic polymers. We calculate potentials of mean force, and show that polymer surface structure plays a critical role in determining the solvation energy landscape which in turn controls routes to assembly of the macromolecules.

  20. Abraham Lincoln loses a medical malpractice case, debates Stephen A. Douglas, and secures two murder acquittals.

    PubMed

    Spiegel, Allen D; Kavaler, Florence

    2004-02-01

    An improperly healed fracture was the most common reason for the medical malpractice crisis between the 1830s and 1860s in the United States. As a practicing lawyer in Illinois, Abraham Lincoln defended physicians in medical malpractice law suits. One of these was Dr. Powers Ritchey, who was sued for malpractice in 1855. Lincoln agreed to represent Dr. Ritchey in 1858 as the case was appealed to the supreme court of Illinois. In the interim, Lincoln defended two indicted murderers and won acquittals for both. Between the two murder trials, Lincoln debated Stephen A. Douglas while running for U.S. Senator from Illinois. Lincoln believed that Ritchey's case was poorly represented in the lower court. Ritchey's prior attorneys did not file a bill of exceptions to the testimony of the plaintiff's expert medical witnesses. Lincoln attempted to rebut the allegation of a lack of reasonable medical care and diligence by Ritchey, and he sought to secure a new trial for his client. In its decision, the supreme court of Illinois did not find any error and affirmed the lower court's judgment. PMID:14768936

  1. Abraham Lincoln and Harry Potter: children's differentiation between historical and fantasy characters.

    PubMed

    Corriveau, Kathleen H; Kim, Angie L; Schwalen, Courtney E; Harris, Paul L

    2009-11-01

    Based on the testimony of others, children learn about a variety of figures that they never meet. We ask when and how they are able to differentiate between the historical figures that they learn about (e.g., Abraham Lincoln) and fantasy characters (e.g., Harry Potter). Experiment 1 showed that both younger (3- and 4-year-olds) and older children (5-, 6-, and 7-year-olds) understand the status of familiar figures, correctly judging historical figures to be real and fictional figures to be pretend. However, when presented with information about novel figures embedded in either a realistic narrative or a narrative with obvious fantasy elements, only older children used the narrative to make an appropriate assessment of the status of the protagonist. In Experiment 2, 3-, and 4-year-olds were prompted to judge whether the story events were really possible or not. Those who did so accurately were able to deploy that judgment to correctly assess the status of the protagonist. PMID:19766203

  2. Sulfapyridine (polymorph III), sulfapyridine dioxane solvate, sulfapyridine tetrahydrofuran solvate and sulfapyridine piperidine solvate, all at 173 K.

    PubMed

    Pratt, Jamal; Hutchinson, Janna; Stevens, Cheryl L Klein

    2011-12-01

    The X-ray crystal structures of solvates of sulfapyridine have been determined to be conformational polymorphs. 4-Amino-N-(1,2-dihydropyridin-2-ylidene)benzenesulfonamide (polymorph III), C(11)H(11)N(3)O(2)S, (1), 4-amino-N-(1,2-dihydropyridin-2-ylidene)benzenesulfonamide 1,3-dioxane monosolvate, C(11)H(11)N(3)O(2)S·C(4)H(8)O(2), (2), and 4-amino-N-(1,2-dihydropyridin-2-ylidene)benzenesulfonamide tetrahydrofuran monosolvate, C(11)H(11)N(3)O(2)S·C(4)H(8)O, (3), crystallized as the imide form, while piperidin-1-ium 4-amino-N-(pyridin-2-yl)benzenesulfonamidate, C(5)H(12)N(+)·C(11)H(10)N(3)O(2)S(-), (4), crystallized as the piperidinium salt. The tetrahydrofuran and dioxane solvent molecules in their respective structures were disordered and were refined using a disorder model. Three-dimensional hydrogen-bonding networks exist in all structures between at least one sulfone O atom and the aniline N atom. PMID:22138921

  3. Modeling aqueous solvation with semi-explicit assembly

    PubMed Central

    Fennell, Christopher J.; Kehoe, Charles W.; Dill, Ken A.

    2011-01-01

    We describe a computational solvation model called semi-explicit assembly (SEA). SEA water captures much of the physics of explicit-solvent models but with computational speeds approaching those of implicit-solvent models. We use an explicit-water model to precompute properties of water solvation shells around simple spheres, then assemble a solute’s solvation shell by combining the shells of these spheres. SEA improves upon implicit-solvent models of solvation free energies by accounting for local solute curvature, accounting for near-neighbor nonadditivities, and treating water’s dipole as being asymmetrical with respect to positive or negative solute charges. SEA does not involve parameter fitting, because parameters come from the given underlying explicit-solvation model. SEA is about as accurate as explicit simulations as shown by comparisons against four different homologous alkyl series, a set of 504 varied solutes, solutes taken retrospectively from two solvation-prediction events, and a hypothetical polar-solute series, and SEA is about 100-fold faster than Poisson–Boltzmann calculations. PMID:21300905

  4. Water-enhanced solvation of organics

    SciTech Connect

    Lee, J.H.

    1993-07-01

    Water-enhanced solvation (WES) was explored for Lewis acid solutes in Lewis base organic solvents, to develop cheap extract regeneration processes. WES for solid solutes was determined from ratios of solubilities of solutes in water-sat. and low-water solvent; both were determined from solid-liquid equilibrium. Vapor-headspace analysis was used to determine solute activity coefficients as function of organic phase water concentration. WES magnitudes of volatile solutes were normalized, set equal to slope of log {gamma}{sub s} vs x{sub w}/x{sub s} curve. From graph shape {Delta}(log {gamma}{sub s}) represents relative change in solute activity coefficient. Solutes investigated by vapor-headspace analysis were acetic acid, propionic acid, ethanol, 1,2-propylene glycol, 2,3-butylene glycol. Monocarboxylic acids had largest decrease in activity coefficient with water addition followed by glycols and alcohols. Propionic acid in cyclohexanone showed greatest water-enhancement {Delta} (log {gamma}{sub acid})/{Delta}(x{sub w}/x{sub acid}) = {minus}0.25. In methylcyclohexanone, the decrease of the activity coefficient of propionic acid was {minus}0.19. Activity coefficient of propionic acid in methylcyclohexanone stopped decreasing once the water reached a 2:1 water to acid mole ratio, implying a stoichiometric relation between water, ketone, and acid. Except for 2,3-butanediol, activity coefficients of the solutes studied decreased monotonically with water content. Activity coefficient curves of ethanol, 1,2-propanediol and 2,3-butanediol did not level off at large water/solute mole ratio. Solutes investigated by solid-liquid equilibrium were citric acid, gallic acid, phenol, xylenols, 2-naphthol. Saturation concentration of citric acid in anhydrous butyl acetate increased from 0.0009 to 0.087 mol/L after 1.3 % (g/g) water co-dissolved into organic phase. Effect of water-enhanced solvation for citric acid is very large but very small for phenol and its derivatives.

  5. Temperature and length scale dependence of solvophobic solvation in a single-site water-like liquid

    NASA Astrophysics Data System (ADS)

    Dowdle, John R.; Buldyrev, Sergey V.; Stanley, H. Eugene; Debenedetti, Pablo G.; Rossky, Peter J.

    2013-02-01

    The temperature and length scale dependence of solvation properties of spherical hard solvophobic solutes is investigated in the Jagla liquid, a simple liquid that consists of particles interacting via a spherically symmetric potential combining a hard core repulsion and a longer ranged soft core interaction, yet exhibits water-like anomalies. The results are compared with equivalent calculations for a model of a typical atomic liquid, the Lennard-Jones potential, and with predictions for hydrophobic solvation in water using the cavity equation of state and the extended simple point charge model. We find that the Jagla liquid captures the qualitative thermodynamic behavior of hydrophobic hydration as a function of temperature for both small and large length scale solutes. In particular, for both the Jagla liquid and water, we observe temperature-dependent enthalpy and entropy of solvation for all solute sizes as well as a negative solvation entropy for sufficiently small solutes at low temperature. This feature of water-like solvation is distinct from the strictly positive and temperature independent enthalpy and entropy of cavity solvation observed in the Lennard-Jones fluid. The results suggest that, compared to a simple liquid, it is the presence of a second thermally accessible repulsive energy scale, acting to increasingly favor larger separations for decreasing temperature, that is the essential characteristic of a liquid that favors low-density, open structures, and models hydrophobic hydration, and that it is the presence of this second energy scale that leads to the similarity in the behavior of water and the Jagla liquid. In addition, the Jagla liquid dewets surfaces of large radii of curvature less readily than the Lennard-Jones liquid, reflecting a greater flexibility or elasticity in the Jagla liquid structure than that of a typical liquid, a behavior also similar to that of water's hydrogen bonding network. The implications of the temperature and

  6. Theoretical estimation of solvation parameters and interfacial tension of clusters of potassium halides in aqueous solutions

    NASA Astrophysics Data System (ADS)

    Polak, W.; Sangwal, K.

    1996-03-01

    Using the model of the formation of ionic clusters, an analytical equation valid for the equilibrium concentration of solute in the solution is derived. Employing Boltzmann statistics in conjunction with the experimental values of the equilibrium concentration of KF, KCl, KBr and KI electrolytes in aqueous solution at 25°C, the above analytical equation is used to compute the best values of the dielectric permittivity of the solvation shell for the K + ion and four anions separately. These values of the dielectric permittivity of the solvation shells are then used to compute adsorption energy of water molecules on the {100} surface of regular clusters and their surface tension in the solution as functions of type of the salt, its concentration and cluster size. It is found that both the average adsorption energy and the interfacial tension of regular clusters composed of i ions can be approximated by a linear function of i - {1}/{2} for different concentrations of all the investigated potassium halides, and that, depending on the concentration of the solutions, the surface tension of regular clusters in solutions can increase or decrease with their size.

  7. Solvatochromism and the solvation structure of benzophenone

    NASA Astrophysics Data System (ADS)

    Elenewski, Justin E.; C Hackett, John

    2013-06-01

    Many complex molecular phenomena, including macromolecular association, protein folding, and chemical reactivity, are determined by the nuances of their electrostatic landscapes. The measurement of such electrostatic effects is nonetheless difficult, and is typically accomplished by exploiting a spectroscopic probe within the system of interest, such as through the vibrational Stark effect. Raman spectroscopy and solvatochromism afford an alternative to this method, circumventing the limitations of infrared spectroscopy, providing a lower detection limit, and permitting measurement in a native chemical environment. To explore this possibility, the solvatochromism of the C=O and aromatic C-H stretching modes of benzophenone are investigated using Raman spectroscopy. In conjunction with density functional theory calculations, these observations are sufficient to determine the probe electrostatic environment as well as contributions from halogen and hydrogen bonding. Further analysis using a detailed Kubo-Anderson lineshape model permits the detailed assignment of distinct hydrogen bonding configurations for water in the benzophenone solvation shell. These observations reinforce the use of benzophenone as an effective electrostatic probe for complex chemical systems.

  8. Solvatochromism and the solvation structure of benzophenone.

    PubMed

    Elenewski, Justin E; Hackett, John C

    2013-06-14

    Many complex molecular phenomena, including macromolecular association, protein folding, and chemical reactivity, are determined by the nuances of their electrostatic landscapes. The measurement of such electrostatic effects is nonetheless difficult, and is typically accomplished by exploiting a spectroscopic probe within the system of interest, such as through the vibrational Stark effect. Raman spectroscopy and solvatochromism afford an alternative to this method, circumventing the limitations of infrared spectroscopy, providing a lower detection limit, and permitting measurement in a native chemical environment. To explore this possibility, the solvatochromism of the C=O and aromatic C-H stretching modes of benzophenone are investigated using Raman spectroscopy. In conjunction with density functional theory calculations, these observations are sufficient to determine the probe electrostatic environment as well as contributions from halogen and hydrogen bonding. Further analysis using a detailed Kubo-Anderson lineshape model permits the detailed assignment of distinct hydrogen bonding configurations for water in the benzophenone solvation shell. These observations reinforce the use of benzophenone as an effective electrostatic probe for complex chemical systems. PMID:23781796

  9. Tuned range separated hybrid functionals for solvated low bandgap oligomers

    SciTech Connect

    Queiroz, Thiago B. 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 to 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.

  10. Solvation of polymers as mutual association. I. General theory

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

    A Flory-Huggins (FH) type lattice theory of self-assembly is generalized to describe the equilibrium solvation of long polymer chains B by small solvent molecules A. Solvation is modeled as a thermally reversible mutual association between the polymer and a relatively low molar mass solvent. The FH Helmholtz free energy F is derived for a mixture composed of the A and B species and the various possible mutual association complexes AiB, and F is then used to generate expressions for basic thermodynamic properties of solvated polymer solutions, including the size distribution of the solvated clusters, the fraction of solvent molecules contained in solvated states (an order parameter for solvation), the specific heat (which exhibits a maximum at the solvation transition), the second and the third osmotic virial coefficients, and the boundaries for phase stability of the mixture. Special attention is devoted to the analysis of the "entropic" contribution χs to the FH interaction parameter χ of polymer solutions, both with and without associative interactions. The entropic χs parameter arises from correlations associated with polymer chain connectivity and disparities in molecular structure between the components of the mixture. Our analysis provides the first explanation of the longstanding enigma of why χs for polymer solutions significantly exceeds χs for binary polymer blends. Our calculations also reveal that χs becomes temperature dependent when interactions are strong, in sharp contrast to models currently being used for fitting thermodynamic data of associating polymer-solvent mixtures, where χs is simply assumed to be an adjustable constant based on experience with solutions of homopolymers in nonassociating solvents.

  11. Order and correlation contributions to the entropy of hydrophobic solvation

    NASA Astrophysics Data System (ADS)

    Liu, Maoyuan; Besford, Quinn Alexander; Mulvaney, Thomas; Gray-Weale, Angus

    2015-03-01

    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 models 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

  12. Order and correlation contributions to the entropy of hydrophobic solvation

    SciTech Connect

    Liu, Maoyuan; Besford, Quinn Alexander; Mulvaney, Thomas; Gray-Weale, Angus

    2015-03-21

    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 models 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

  13. Order and correlation contributions to the entropy of hydrophobic solvation.

    PubMed

    Liu, Maoyuan; Besford, Quinn Alexander; Mulvaney, Thomas; Gray-Weale, Angus

    2015-03-21

    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 models 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

  14. The solvation of electrons by an atmospheric-pressure plasma

    PubMed Central

    Rumbach, Paul; Bartels, David M.; Sankaran, R. Mohan; Go, David B.

    2015-01-01

    Solvated electrons are typically generated by radiolysis or photoionization of solutes. While plasmas containing free electrons have been brought into contact with liquids in studies dating back centuries, there has been little evidence that electrons are solvated by this approach. Here we report direct measurements of solvated electrons generated by an atmospheric-pressure plasma in contact with the surface of an aqueous solution. The electrons are measured by their optical absorbance using a total internal reflection geometry. The measured absorption spectrum is unexpectedly blue shifted, which is potentially due to the intense electric field in the interfacial Debye layer. We estimate an average penetration depth of 2.5±1.0 nm, indicating that the electrons fully solvate before reacting through second-order recombination. Reactions with various electron scavengers including H+, NO2−, NO3− and H2O2 show that the kinetics are similar, but not identical, to those for solvated electrons formed in bulk water by radiolysis. PMID:26088017

  15. Lithium solvation in dimethyl sulfoxide-acetonitrile mixtures.

    PubMed

    Semino, Rocío; Zaldívar, Gervasio; Calvo, Ernesto J; Laria, Daniel

    2014-12-01

    We present molecular dynamics simulation results pertaining to the solvation of Li(+) in dimethyl sulfoxide-acetonitrile binary mixtures. The results are potentially relevant in the design of Li-air batteries that rely on aprotic mixtures as solvent media. To analyze effects derived from differences in ionic size and charge sign, the solvation of Li(+) is compared to the ones observed for infinitely diluted K(+) and Cl(-) species, in similar solutions. At all compositions, the cations are preferentially solvated by dimethyl sulfoxide. Contrasting, the first solvation shell of Cl(-) shows a gradual modification in its composition, which varies linearly with the global concentrations of the two solvents in the mixtures. Moreover, the energetics of the solvation, described in terms of the corresponding solute-solvent coupling, presents a clear non-ideal concentration dependence. Similar nonlinear trends were found for the stabilization of different ionic species in solution, compared to the ones exhibited by their electrically neutral counterparts. These tendencies account for the characteristics of the free energy associated to the stabilization of Li(+)Cl(-), contact-ion-pairs in these solutions. Ionic transport is also analyzed. Dynamical results show concentration trends similar to those recently obtained from direct experimental measurements. PMID:25481154

  16. Lithium solvation in dimethyl sulfoxide-acetonitrile mixtures

    SciTech Connect

    Semino, Rocío; Zaldívar, Gervasio; Calvo, Ernesto J.; Laria, Daniel

    2014-12-07

    We present molecular dynamics simulation results pertaining to the solvation of Li{sup +} in dimethyl sulfoxide-acetonitrile binary mixtures. The results are potentially relevant in the design of Li-air batteries that rely on aprotic mixtures as solvent media. To analyze effects derived from differences in ionic size and charge sign, the solvation of Li{sup +} is compared to the ones observed for infinitely diluted K{sup +} and Cl{sup −} species, in similar solutions. At all compositions, the cations are preferentially solvated by dimethyl sulfoxide. Contrasting, the first solvation shell of Cl{sup −} shows a gradual modification in its composition, which varies linearly with the global concentrations of the two solvents in the mixtures. Moreover, the energetics of the solvation, described in terms of the corresponding solute-solvent coupling, presents a clear non-ideal concentration dependence. Similar nonlinear trends were found for the stabilization of different ionic species in solution, compared to the ones exhibited by their electrically neutral counterparts. These tendencies account for the characteristics of the free energy associated to the stabilization of Li{sup +}Cl{sup −}, contact-ion-pairs in these solutions. Ionic transport is also analyzed. Dynamical results show concentration trends similar to those recently obtained from direct experimental measurements.

  17. Lithium solvation in dimethyl sulfoxide-acetonitrile mixtures

    NASA Astrophysics Data System (ADS)

    Semino, Rocío; Zaldívar, Gervasio; Calvo, Ernesto J.; Laria, Daniel

    2014-12-01

    We present molecular dynamics simulation results pertaining to the solvation of Li+ in dimethyl sulfoxide-acetonitrile binary mixtures. The results are potentially relevant in the design of Li-air batteries that rely on aprotic mixtures as solvent media. To analyze effects derived from differences in ionic size and charge sign, the solvation of Li+ is compared to the ones observed for infinitely diluted K+ and Cl- species, in similar solutions. At all compositions, the cations are preferentially solvated by dimethyl sulfoxide. Contrasting, the first solvation shell of Cl- shows a gradual modification in its composition, which varies linearly with the global concentrations of the two solvents in the mixtures. Moreover, the energetics of the solvation, described in terms of the corresponding solute-solvent coupling, presents a clear non-ideal concentration dependence. Similar nonlinear trends were found for the stabilization of different ionic species in solution, compared to the ones exhibited by their electrically neutral counterparts. These tendencies account for the characteristics of the free energy associated to the stabilization of Li+Cl-, contact-ion-pairs in these solutions. Ionic transport is also analyzed. Dynamical results show concentration trends similar to those recently obtained from direct experimental measurements.

  18. Structure of salts solution in polar dielectric liquids and electrically induced separation of solvated ions

    NASA Astrophysics Data System (ADS)

    Shamanin, Igor V.; Kazaryan, Mishik A.; Sachkov, Victor I.

    2015-12-01

    The aim of study is to demonstrate that separation of solvated ions in solution of mix of salts under the action of external periodic electric field happens because of around ions there are formed clusters consisting of molecules of solvent and the sizes of such clusters have dimensions ~ 0.1 μm. In investigations the sizes of clusters theoretically were defined and experimentally value of frequency of external electric field which action excites the effect of separation of the solvated ions was defined. Experiments were done in the Technical Physics Chair of the National Research Tomsk Polytechnic University. At theoretical determination of the dimensions of clusters Poisson's equation was solved and was considered that polar molecules of solvent are oriented under the action of electric field of an ion. The chemical composition of samples of solutions was determined by means of the spectrophotometry and he X-ray excited fluorescent radiation analysis method. Theoretical estimates and results of experiments confirmed the assumption that clusters which are formed around ions in solutions have the dimensions ~ 0.1 μm. Results of investigation testify that placing of volume distributed electric charge of ion in dielectric liquid is accompanied by formation of the supramolecular particles, which we called "clusters", linear sizes of which is significantly more than first and second radiuses of solvation (~ 1 Angstrom) and reach size ~ 0.1 μm. At such sizes inertial properties of clusters and their natural frequencies give the chance to operate their movement by means of action of external electric field on solution.

  19. 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. PMID:24058213

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

    PubMed Central

    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. PMID:24058213

  1. Dependence of the benzophenone anion solvation on solvent structure

    SciTech Connect

    Lin, Y.; Jonah, C.D. )

    1992-12-10

    The solvation of the benzophenone anion has been studied at room temperature using the pulse radiolytic pump-probe technique. The time-dependent benzophenone anion absorption spectra have been monitored in several different solvents ranging from linear alcohols to branched alcohols to acetonitrile. The maximum of the steady-state spectrum shifts to the red as the solvent is changed from linear alcohols to branched alcohols to acetonitrile. Computer Monte Carlo simulations indicate that the observed spectral shift can be assigned to the position and the orientation of the dipole functional group. The experimental dynamics of the anion solvation were also studied. By fitting the time-dependent absorption data to a multistate evolution kinetic model, the solvation time for these systems is obtained. 26 refs., 8 figs., 1 tab.

  2. The Oil-Water Interface: Mapping the Solvation Potential

    SciTech Connect

    Bell, Richard C.; Wu, Kai; Iedema, Martin J.; Schenter, Gregory K.; Cowin, James P.

    2009-01-06

    Ions moving across the oil water interface are strongly impacted by the continuous changes in solvation. The solvation potential for Cs+ is directly measured as they approach the oil-water interface (“oil” = 3-methylpentane), from 0.4 to 4 nm away. The oil-water interfaces are created at 40K using molecular beam epitaxy and a softlanding ion beam, with pre-placed ions. The solvation potential slope was determined at each distance by balancing it against an increasing electrostatic potential made by increasing the number of imbedded ions at that distance, and monitoring the resulting ion motion. The potential approaches the Born model for greater than z>0.4nm, and shows the predicted reduction of the polarizability at z<0.4nm.

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

    SciTech Connect

    Zheng, Dong; Qu, Deyu; Yang, Xiao -Qing; Lee, Hung -Sui; Qu, Deyang

    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 redox reaction was also investigated.

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

    DOE PAGESBeta

    Zheng, Dong; Qu, Deyu; Yang, Xiao -Qing; Lee, Hung -Sui; Qu, Deyang

    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

  5. Fast estimation of solvation free energies for diverse chemical species.

    PubMed

    Boyer, Robert D; Bryan, Richard L

    2012-03-29

    The free energy of solvation can play an important or even dominant role in the accurate prediction of binding affinities and various other molecular-scale interaction phenomena critical to the study of biochemical processes. Many research applications for solvation modeling, such as fragment-based drug design, require algorithms that are both accurate and computationally inexpensive. We have developed a calculation of solvation free energy which runs fast enough for interactive applications, functions for a wide range of chemical species relevant to simulating molecules for biological and pharmaceutical applications, and is readily extended when data for new species becomes available. We have also demonstrated that the incorporation of ab initio data provides necessary access to sufficient reference data for a broad range of chemical features. Our empirical model, including an electrostatic term and a different set of atom types, demonstrates improvements over a previous, solvent-accessible surface area-only model by Wang et al. when fit to identical training sets (mean absolute error of 0.513 kcal/mol versus the 0.538 kcal/mol reported by Wang). The incorporation of ab initio solvation free energies provides a significant increase in the breadth of chemical features for which the model can be applied by introducing classes of compounds for which little or no experimental data is available. The increased breadth and the speed of this solvation model allow for conformational minimization, conformational search, and ligand binding free energy calculations that economically account for the complex interplay of bonded, nonbonded, and solvation free energies as conformations with varying solvent-accessible surfaces are sampled. PMID:22339050

  6. SISGR: Linking Ion Solvation and Lithium Battery Electrolyte Properties

    SciTech Connect

    Trulove, Paul C.; Foley, Matthew P.

    2012-09-30

    The solvation and phase behavior of the model battery electrolyte salt lithium trifluoromethanesulfonate (LiCF3SO3) 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 could 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.

  7. Difference of solvation site between halide ions and electrons in an alkylammonium ionic liquid

    NASA Astrophysics Data System (ADS)

    Katoh, Ryuzi

    2009-11-01

    The difference of solvation site between halide ions and electrons in an alkylammonium ionic liquid is discussed on the basis of spectroscopic data. The data indicate that the halide ions replaced the anions of the ionic liquid and were fully solvated by the ammonium cations. In contrast, the solvated electrons were less solvated, suggesting that they were located near the region of the alkyl chain of the cations.

  8. Solvated electrons formed in methanol cluster in ethane

    SciTech Connect

    Takahashi, K.; Bartels, D. M.; Jonah, C. D.; Dimitrijevic, N. A.

    2000-03-09

    The authors have studied the spectral shift of the solvated electron in MeOH/C{sub 2}H{sub 6} mixture using pulse radiolysis. The solvated electrons were formed by ionizing the solution. The spectral shift can be explained in terms of MeOH cluster size formed in the solution. With increasing temperature at constant mole fraction of MeOH, the spectral maximum shifts toward low energy. The width at red side increased with increasing temperature, however, there is no significant changes in the blue side of the spectra with temperature.

  9. Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril.

    PubMed

    Nguyen, Crystal N; Young, Tom Kurtzman; Gilson, Michael K

    2012-07-28

    The displacement of perturbed water upon binding is believed to play a critical role in the thermodynamics of biomolecular recognition, but it is nontrivial to unambiguously define and answer questions about this process. We address this issue by introducing grid inhomogeneous solvation theory (GIST), which discretizes the equations of inhomogeneous solvation theory (IST) onto a three-dimensional grid situated in the region of interest around a solute molecule or complex. Snapshots from explicit solvent simulations are used to estimate localized solvation entropies, energies, and free energies associated with the grid boxes, or voxels, and properly summing these thermodynamic quantities over voxels yields information about hydration thermodynamics. GIST thus provides a smoothly varying representation of water properties as a function of position, rather than focusing on hydration sites where solvent is present at high density. It therefore accounts for full or partial displacement of water from sites that are highly occupied by water, as well as for partly occupied and water-depleted regions around the solute. GIST can also provide a well-defined estimate of the solvation free energy and therefore enables a rigorous end-states analysis of binding. For example, one may not only use a first GIST calculation to project the thermodynamic consequences of displacing water from the surface of a receptor by a ligand, but also account, in a second GIST calculation, for the thermodynamics of subsequent solvent reorganization around the bound complex. In the present study, a first GIST analysis of the molecular host cucurbit[7]uril is found to yield a rich picture of hydration structure and thermodynamics in and around this miniature receptor. One of the most striking results is the observation of a toroidal region of high water density at the center of the host's nonpolar cavity. Despite its high density, the water in this toroidal region is disfavored energetically and

  10. Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril

    NASA Astrophysics Data System (ADS)

    Nguyen, Crystal N.; Kurtzman Young, Tom; Gilson, Michael K.

    2012-07-01

    The displacement of perturbed water upon binding is believed to play a critical role in the thermodynamics of biomolecular recognition, but it is nontrivial to unambiguously define and answer questions about this process. We address this issue by introducing grid inhomogeneous solvation theory (GIST), which discretizes the equations of inhomogeneous solvation theory (IST) onto a three-dimensional grid situated in the region of interest around a solute molecule or complex. Snapshots from explicit solvent simulations are used to estimate localized solvation entropies, energies, and free energies associated with the grid boxes, or voxels, and properly summing these thermodynamic quantities over voxels yields information about hydration thermodynamics. GIST thus provides a smoothly varying representation of water properties as a function of position, rather than focusing on hydration sites where solvent is present at high density. It therefore accounts for full or partial displacement of water from sites that are highly occupied by water, as well as for partly occupied and water-depleted regions around the solute. GIST can also provide a well-defined estimate of the solvation free energy and therefore enables a rigorous end-states analysis of binding. For example, one may not only use a first GIST calculation to project the thermodynamic consequences of displacing water from the surface of a receptor by a ligand, but also account, in a second GIST calculation, for the thermodynamics of subsequent solvent reorganization around the bound complex. In the present study, a first GIST analysis of the molecular host cucurbit[7]uril is found to yield a rich picture of hydration structure and thermodynamics in and around this miniature receptor. One of the most striking results is the observation of a toroidal region of high water density at the center of the host's nonpolar cavity. Despite its high density, the water in this toroidal region is disfavored energetically and

  11. DFT SOLVATION STUDIES OF CARBOHYDRATES: DETERMINATION OF ACCURATE ALPHA/BETA-ANOMERIC RATIOS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Solvents play an important role in carbohydrate structure. Therefore, it is important to include solvation effects in calculations to allow a better comparison with experimental data. One way to include solvation effects is via the use of continuum solvation models such as COSMO. Another possibil...

  12. Polar solvation and electron transfer. Annual progress report, July 1, 1992--June 30, 1993

    SciTech Connect

    Not Available

    1993-04-13

    The report is divided into the following sections: completion of previous studies on solvation dynamics, dipole lattice studies, inertial components of solvation response, simple models of solvation dynamics, rotational dynamics and dielectric friction, intramolecular electron transfer reactions, and intermolecular donor-acceptor complexes.

  13. Modeling self-potential data in the Abraham and Meadow-Hatton geothermal systems: The search for upflow zones

    SciTech Connect

    Schima, S.; Wilt, M.; Ross, H.

    1995-12-31

    Self-potential (SP) measurements may be used to locate up-flow zones in geothermal systems. As geothermal waters move beneath the surface, the resulting pressure and heat variations are seen as anomalies in the electrical currents that are measured within or at the surface. Beginning in 1991, Ross et al. collected SP data at Abraham and Meadow-Hatton Hot Springs, two of the largest thermal spring systems in Utah. In this paper, these data were modeled to determine upflow zones and source characteristics using a numerical modeling code. The code calculates the forward solution for fluid or heat flow models and the resulting self-potential anomalies. These results were matched to field data by iterative forward modeling; that is, we adjusted the model until field and numerical data agreed. At Abraham Hot Springs, a 3 km, north-south trending, dipolar anomaly was measured, centered on a suspected fault zone. The anomaly was not coincident with the hot springs themselves. Modeling indicates that the upflow originates from about 200 m depth, ascends up the fault zone to a shallow aquifer, where it then migrates eastward to outflow at the hot springs. At Meadow-Hatton Hot Springs, two closely spaced negative anomalies, also about 3 km long trending north-south, were modeled to show two upflow sources at about 200 m depth. The flow likely ascends up fractured zones until it reaches a shallow travertine layer and disperses laterally, with very little outflow at the hot springs at present.

  14. Towards Accurate Microscopic Calculation of Solvation Entropies: Extending the Restraint Release Approach to Studies of Solvation Effects

    PubMed Central

    Singh, Nidhi; Warshel, Arieh

    2009-01-01

    The evaluation of the solvation entropies is a major conceptual and practical challenge. On the one hand, it is interesting to quantify the factors that are responsible for the solvation entropies in solutions, while on the other, it is essential to be able to assess the contributions of the solvation entropies to the binding free energies and related properties. In fact, the solvation entropies are neglected in almost all the studies of the binding entropies. The main problem is that widely used approaches, such as the quasiharmonic (QH) approximation do not provide reliable results particularly, in cases of shallow potential and multidimensional surfaces while brute force evaluations of the entropic effects by simulating temperature dependence of the free energy converges very slowly. This paper addresses the above issue by starting with an analysis of the factors that are responsible for the negative solvation entropy of ions, showing that it is not due to the change in the solvent vibration modes or to the solvent force constant but to the changes in the solvent configurational space upon change in the solute charges. We begin by clarifying that when one deals with aqueous solutions, it is easy to evaluate the corresponding entropic effect by the Langevin dipole(LD) treatment. However, in this work we are interested in developing a general microscopic tool that can be used to study similar effects in the proteins. To this end, we explore the ability of our restraint release (RR) approach to evaluate the solvation entropy. We start this analysis by reviewing the foundation of this approach and in particular, the requirements of minimizing the enthalpy contribution to the RR free energy. We then establish that our approach is not a specialized harmonic treatment but a rather powerful approach. Moving to the main topic of this work, we demonstrate that the RR approach provides quantitative results for the solvation entropies of monovalent and divalent ions and

  15. Surface solvation for an ion in a water cluster.

    PubMed

    Herce, David H; Perera, Lalith; Darden, Thomas A; Sagui, Celeste

    2005-01-01

    We have used molecular dynamics simulations to study the structural, dynamical, and thermodynamical properties of ions in water clusters. 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 iodinelike ion in a polarizable water cluster, but not in a nonpolarizable water cluster. PMID:15638604

  16. Electron solvation in aqueous reverse micelles: Equilibrium properties

    NASA Astrophysics Data System (ADS)

    Laria, Daniel; Kapral, Raymond

    2002-10-01

    Microscopic aspects of electron solvation in aqueous reverse micelles are investigated using molecular dynamics simulation techniques. Two micelle sizes, with water/surfactant ratios of 3 and 7.5, are examined. The electron is treated quantum mechanically using Feynman path integral methods while the water, surfactant head groups, and counter ions are treated classically. Through computations of the free energy as a function of the radial distance, the electron is found to be preferentially solvated in the interior of the micelle in the "bulk" water pool. For small micelles, the presence of the electron leads to a depletion of water in the central region of the micelle and thus strongly disrupts the water equilibrium structure. Contact and solvent-separated ion pairs between the electron and Na+ counter ions are found to play an important role in the equilibrium structure. For the two micelle sizes investigated, the most stable solvation structures correspond to contact ion pairs. The localization of the electronic charge distribution is found to increase with micelle size, signaling more efficient solvation in larger micelles.

  17. Maleic acid solvation in mixed water-ethanol solvents

    NASA Astrophysics Data System (ADS)

    Usacheva, T. R.; Kuz'mina, I. A.; Sharnin, V. A.; Tukumova, I. R.

    2012-04-01

    Heat effects of maleic acid dissolution in mixed water-ethanol solvents at 298.15 K are determined by means of calorimetry. A rise in exothermicity of maleic acid solvation is observed upon changes in the solvent copmosition in the direction of H2O → EtOH, the minimum being at ˜0.2 mol fraction of EtOH.

  18. Continuum estimates of rotational dielectric friction and polar solvation

    SciTech Connect

    Maroncelli, M.

    1997-01-01

    Dynamical solvation data recently obtained with the probe solute coumarin 153 are used to test the reliability of dielectric continuum models for estimating dielectric friction effects. In particular, the predictions of the Nee{endash}Zwanzig theory of rotational dielectric friction are examined in some detail. The analysis undertaken here uncovers an error made in virtually all previous applications of the Nee{endash}Zwanzig formalism. The error involves neglect of the solvent{close_quote}s electronic polarizability when calculating dielectric friction constants. In highly polar solvents the effect of this neglect is shown to be minor, so that the results of past studies should not be appreciably altered. However, in weakly polar and especially in nondipolar solvents, the proper inclusion of electronic polarizability terms is essential. The equivalence between the Nee{endash}Zwanzig theory of dielectric friction and more general continuum treatments of polar solvation dynamics is also demonstrated. This equivalence enables the use of solvation data to test the reliability of the Nee{endash}Zwanzig description of electrical interactions between a solute and solvent that form the core of this and related continuum theories of dielectric friction. Comparisons to experimental data show that, with the important exception of nondipolar solvents, such continuum treatments provide reasonably accurate ({plus_minus}40{percent}) predictors of time-dependent solvation and/or dielectric friction. {copyright} {ital 1997 American Institute of Physics.}

  19. Extrapolating Single Organic Ion Solvation Thermochemistry from Simulated Water Nanodroplets.

    PubMed

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

    2016-09-01

    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. PMID:27420562

  20. A continuum solvent model of the multipolar dispersion solvation energy.

    PubMed

    Duignan, Timothy T; Parsons, Drew F; Ninham, Barry W

    2013-08-15

    The dispersion energy is an important contribution to the total solvation energies of ions and neutral molecules. Here, we present a new continuum model calculation of these energies, based on macroscopic quantum electrodynamics. The model uses the frequency dependent multipole polarizabilities of molecules in order to accurately calculate the dispersion interaction of a solute particle with surrounding water molecules. It includes the dipole, quadrupole, and octupole moment contributions. The water is modeled via a bulk dielectric susceptibility with a spherical cavity occupied by the solute. The model invokes damping functions to account for solute-solvent wave function overlap. The assumptions made are very similar to those used in the Born model. This provides consistency and additivity of electrostatic and dispersion (quantum mechanical) interactions. The energy increases in magnitude with cation size, but decreases slightly with size for the highly polarizable anions. The higher order multipole moments are essential, making up more than 50% of the dispersion solvation energy of the fluoride ion. This method provides an accurate and simple way of calculating the notoriously problematic dispersion contribution to the solvation energy. The result establishes the importance of using accurate calculations of the dispersion energy for the modeling of solvation. PMID:23837890

  1. Structural Interactions within Lithium Salt Solvates. Acyclic Carbonates and Esters

    SciTech Connect

    Afroz, Taliman; Seo, D. M.; Han, Sang D.; Boyle, Paul D.; Henderson, Wesley A.

    2015-03-06

    Solvate crystal structures serve as useful models for the molecular-level interactions within the diverse solvates present in liquid electrolytes. Although acyclic carbonate solvents are widely used for Li-ion battery electrolytes, only three solvate crystal structures with lithium salts are known for these and related solvents. The present work, therefore, reports six lithium salt solvate structures with dimethyl and diethyl carbonate: (DMC)2:LiPF6, (DMC)1:LiCF3SO3, (DMC)1/4:LiBF4, (DEC)2:LiClO4, (DEC)1:LiClO4 and (DEC)1:LiCF3SO3 and four with the structurally related methyl and ethyl acetate: (MA)2:LiClO4, (MA)1:LiBF4, (EA)1:LiClO4 and (EA)1:LiBF4.

  2. Ionic Liquids: Radiation Chemistry, Solvation Dynamics and Reactivity Patterns

    SciTech Connect

    Wishart, J.F.

    2011-06-12

    Ionic liquids (ILs) are a rapidly expanding family of condensed-phase media with important applications in energy production, nuclear fuel and waste processing, improving the efficiency and safety of industrial chemical processes, and pollution prevention. ILs generally have low volatilities and are combustion-resistant, highly conductive, recyclable and capable of dissolving a wide variety of materials. They are finding new uses in chemical synthesis, catalysis, separations chemistry, electrochemistry and other areas. Ionic liquids have dramatically different properties compared to conventional molecular solvents, and they provide a new and unusual environment to test our theoretical understanding of primary radiation chemistry, charge transfer and other reactions. We are interested in how IL properties influence physical and dynamical processes that determine the stability and lifetimes of reactive intermediates and thereby affect the courses of reactions and product distributions. We study these issues by characterization of primary radiolysis products and measurements of their yields and reactivity, quantification of electron solvation dynamics and scavenging of electrons in different states of solvation. From this knowledge we wish to learn how to predict radiolytic mechanisms and control them or mitigate their effects on the properties of materials used in nuclear fuel processing, for example, and to apply IL radiation chemistry to answer questions about general chemical reactivity in ionic liquids that will aid in the development of applications listed above. Very early in our radiolysis studies it became evident that the slow solvation dynamics of the excess electron in ILs (which vary over a wide viscosity range) increase the importance of pre-solvated electron reactivity and consequently alter product distributions and subsequent chemistry. This difference from conventional solvents has profound effects on predicting and controlling radiolytic yields

  3. Lithium ion solvation by ethylene carbonates in lithium-ion battery electrolytes, revisited by density functional theory with the hybrid solvation model and free energy correction in solution.

    PubMed

    Cui, Wei; Lansac, Yves; Lee, Hochun; Hong, Seung-Tae; Jang, Yun Hee

    2016-09-14

    Complex formation between lithium (Li(+)) ions and electrolyte molecules would affect the ionic conductivity through the electrolyte in lithium-ion batteries (LIBs). We hence revisit the solvation number of Li(+) in the most commonly used ethylene carbonate (EC) electrolyte. The solvation number n of Li(+)(EC)n in the first solvation shell of Li(+) is estimated on the basis of the free energy calculated by the density functional theory combined with a hybrid solvation model where the explicit solvation shell of Li(+) is immersed in a free volume of an implicit bulk solvent. This new hybrid solvation (implicit and explicit) model predicts the most probable solvation number (n = 4) and solvation free energy (-91.3 kcal mol(-1)) of Li(+) in a good agreement with those predicted by calculations employing simpler solvation models (either implicit or explicit). The desolvation (n = 2) of Li(0)(EC)n upon reduction near anodes is also well described with this new hybrid model. PMID:27506245

  4. Adamantane derivatives of sulfonamides: sublimation, solubility, solvation and transfer processes in biologically relevant solvents.

    PubMed

    Perlovich, G L; Volkova, T V; Sharapova, A V; Kazachenko, V P; Strakhova, N N; Proshin, A N

    2016-04-01

    Eight adamantane derivatives of sulfonamides were synthesized and characterized. Temperature dependencies of saturation vapor pressure were obtained using the transpiration method and thermodynamic functions of the sublimation processes were calculated. Solubility values of the selected compounds in buffer (pH 7.4), 1-octanol and 1-hexane were determined at different temperatures using the isothermal saturation method. Thermophysical characteristics of fusion processes (melting points and fusion enthalpies) of the substances were studied using the DSC method. Transfer processes from buffer to 1-octanol, from buffer to 1-hexane and 1-hexane to 1-octanol were analyzed. The impact of the molecules' structural modification on sublimation, solubility and solvation/hydration processes in the solvents was studied. Correlation equations connecting the thermodynamic functions with physicochemical descriptors were obtained. PMID:26976747

  5. Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories

    NASA Astrophysics Data System (ADS)

    Perkyns, John S.; Lynch, Gillian C.; Howard, Jesse J.; Pettitt, B. Montgomery

    2010-02-01

    Solvation forces dominate protein structure and dynamics. Integral equation theories allow a rapid and accurate evaluation of the effect of solvent around a complex solute, without the sampling issues associated with simulations of explicit solvent molecules. Advances in integral equation theories make it possible to calculate the angle dependent average solvent structure around an irregular molecular solution. We consider two methodological problems here: the treatment of long-ranged forces without the use of artificial periodicity or truncations and the effect of closures. We derive a method for calculating the long-ranged Coulomb interaction contributions to three-dimensional distribution functions involving only a rewriting of the system of integral equations and introducing no new formal approximations. We show the comparison of the exact forms with those implied by the supercell method. The supercell method is shown to be a good approximation for neutral solutes whereas the new method does not exhibit the known problems of the supercell method for charged solutes. Our method appears more numerically stable with respect to thermodynamic starting state. We also compare closures including the Kovalenko-Hirata closure, the hypernetted-chain (HNC) and an approximate three-dimensional bridge function combined with the HNC closure. Comparisons to molecular dynamics results are made for water as well as for the protein solute bovine pancreatic trypsin inhibitor. The proposed equations have less severe approximations and often provide results which compare favorably to molecular dynamics simulation where other methods fail.

  6. Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories

    PubMed Central

    Perkyns, John S.; Lynch, Gillian C.; Howard, Jesse J.; Pettitt, B. Montgomery

    2010-01-01

    Solvation forces dominate protein structure and dynamics. Integral equation theories allow a rapid and accurate evaluation of the effect of solvent around a complex solute, without the sampling issues associated with simulations of explicit solvent molecules. Advances in integral equation theories make it possible to calculate the angle dependent average solvent structure around an irregular molecular solution. We consider two methodological problems here: the treatment of long-ranged forces without the use of artificial periodicity or truncations and the effect of closures. We derive a method for calculating the long-ranged Coulomb interaction contributions to three-dimensional distribution functions involving only a rewriting of the system of integral equations and introducing no new formal approximations. We show the comparison of the exact forms with those implied by the supercell method. The supercell method is shown to be a good approximation for neutral solutes whereas the new method does not exhibit the known problems of the supercell method for charged solutes. Our method appears more numerically stable with respect to thermodynamic starting state. We also compare closures including the Kovalenko–Hirata closure, the hypernetted-chain (HNC) and an approximate three-dimensional bridge function combined with the HNC closure. Comparisons to molecular dynamics results are made for water as well as for the protein solute bovine pancreatic trypsin inhibitor. The proposed equations have less severe approximations and often provide results which compare favorably to molecular dynamics simulation where other methods fail. PMID:20151732

  7. Protein Solvation from Theory and Simulation: Exact Treatment of Coulomb Interactions in Three-Dimensional Theories

    SciTech Connect

    Perkyns, John S.; Lynch, Gillian C.; Howard, Jesse J.; Pettitt, Bernard M.

    2010-02-14

    Solvation forces dominate protein structure and dynamics. Integral equation theories allow a rapid and accurate evaluation of the effect of solvent around a complex solute, without the sampling issues associated with simulations of explicit solvent molecules. Advances in integral equation theories make it possible to calculate the angle dependent average solvent structure around an irregular molecular solution. We consider two methodological problems here: the treatment of long-ranged forces without the use of artificial periodicity or truncations and the effect of closures. We derive a method for calculating the long-ranged Coulomb interaction contributions to three-dimensional distribution functions involving only a rewriting of the system of integral equations and introducing no new formal approximations. We show the comparison of the exact forms with those implied by the supercell method. The supercell method is shown to be a good approximation for neutral solutes whereas the new method does not exhibit the known problems of the supercell method for charged solutes. Our method appears more numerically stable with respect to thermodynamic starting state. We also compare closures including the Kovalenko–Hirata closure, the hypernetted-chain _HNC_ and an approximate three-dimensional bridge fu nction combined with the HNC closure. Comparisons to molecular dynamics results are made for water as well as for the protein solute bovine pancreatic trypsin inhibitor. The proposed equations have less severe approximations and often provide results which compare favorably to molecular dynamics simulation where other methods fail.

  8. Improving the performance of the coupled reference interaction site model-hyper-netted chain (RISM-HNC)/simulation method for free energy of solvation.

    PubMed

    Freedman, Holly; Le, Ly; Tuszynski, Jack A; Truong, Thanh N

    2008-02-28

    The coupled reference interaction site model-hyper-netted chain (RISM-HNC)/ simulation methodology determines solvation free energies as a function of the set of all radial distribution functions of solvent atoms about atomic solute sites. These functions are determined from molecular dynamics (MD) or Monte Carlo (MC) simulations rather than from solving the RISM and HNC equations iteratively. Previous applications of the method showed that it can predict relative free energies of solvation for small solutes accurately. However, the errors scale with the system size. In this study, we propose the use of the hard-sphere free energy as the reference and a linear response approximation to improve the performance, i.e., accuracy and robustness, of the method, particularly removing the size dependency of the error. The details of the new formalism are presented. To validate the proposed formalism, solvation free energies of N-methylacetamide and methylamine are computed using the new RISM-HNC-based expressions in addition to a linear response expression, which are compared to previous thermodynamic integration and thermodynamic perturbation results performed with the same force field. Additionally, free energies of solvation for cyclohexane, pyridine, benzene and derivatives, and other small organic molecules are calculated and compared to experimental values. PMID:18251537

  9. It Is My Desire to Be Free: Annie Davis's Letter to Abraham Lincoln and Winslow Homer's Painting "A Visit from the Old Mistress"

    ERIC Educational Resources Information Center

    Hussey, Michael; Eder, Elizabeth K.

    2010-01-01

    "Mr. President, It is my Desire to be free," wrote Annie Davis to Abraham Lincoln, 20 months after he issued the Emancipation Proclamation. The Emancipation Proclamation affected only those parts of the country that were in rebellion against the United States on the date it was issued, January 1, 1863. The slaveholding border states of Delaware,…

  10. The Lincoln Legal Papers Curriculum: Understanding Illinois Social History through Documents from the Law Practice of Abraham Lincoln, 1836-1861.

    ERIC Educational Resources Information Center

    McBride, Lawrence W., Ed.; Drake, Frederick D., Ed.

    This curriculum considers the social history of Illinois during the years of 1836-1861 by studying Abraham Lincoln's legal papers from his time as a lawyer. Nearly 100,000 documents have been discovered in the archives of local, county, state, federal courts, libraries, and other repositories. The documents include detailed information about the…

  11. Effect of ionic size on solvate stability of glyme-based solvate ionic liquids.

    PubMed

    Mandai, Toshihiko; Yoshida, Kazuki; Tsuzuki, Seiji; Nozawa, Risa; Masu, Hyuma; Ueno, Kazuhide; Dokko, Kaoru; Watanabe, Masayoshi

    2015-01-29

    A series of binary mixtures composed of glymes (triglyme, G3; tetraglyme, G4; pentaglyme, G5) and alkali-metal bis(trifluoromethanesulfonyl)amide salts (M[TFSA]; M = Li, Na, and K) were prepared, and the correlation between the composition and solvate stability was systematically investigated. Their phase diagrams and Raman spectra suggested complexation of the glymes with M[TFSA] in 1:1 and/or 2:1 molar ratio(s). From isothermal stability measurements, it was found that the formation of structurally stable complexes in the solid state did not necessarily ensure their thermal stability in the liquid state, especially in the case of 2:1 complexes, where uncoordinating or highly exchangeable glyme ligands existed in the molten complexes. The phase-state-dependent Raman spectra also supported the presence of free glymes in certain liquid complexes. The effect of the electric field induced by the alkali-metal cations on the oxidative stability of certain glyme complexes was examined by linear sweep voltammetry and quantum chemical calculations. Although the actual oxidative stability of complexes did not necessarily reflect the calculated HOMO energy levels of the glymes, the strong electric field induced by the smaller M(+) cations and proper coordination structures impart high stability to the glyme complexes. The results of thermogravimetry of complexes with different M(+) cations revealed that a balance of competitive interactions of the M(+) ions with the glymes and [TFSA](-) anions predominates the thermal stability. PMID:25530321

  12. Solvation in pure liquids: what can be learned from the use of pairs of indicators?

    PubMed

    Silva, Priscilla L; Pires, Paulo A R; Trassi, Marco A S; El Seoud, Omar A

    2008-11-27

    The solvation of six solvatochromic probes in a large number of solvents (33-68) was examined at 25 degrees C. The probes employed were the following: 2,6-diphenyl-4-(2,4,6-triphenylpyridinium-1-yl) phenolate (RB); 4-[(E)2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePM; 1-methylquinolinium-8-olate, QB; 2-bromo-4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePMBr, 2,6-dichloro-4-(2,4,6-triphenyl pyridinium-1-yl) phenolate (WB); and 2,6-dibromo-4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePMBr(2), respectively. Of these, MePMBr is a novel compound. They can be grouped in three pairs, each with similar pK(a) in water but with different molecular properties, for example, lipophilicity and dipole moment. These pairs are formed by RB and MePM; QB and MePMBr; WB and MePMBr(2), respectively. Theoretical calculations were carried out in order to calculate their physicochemical properties including bond lengths, dihedral angles, dipole moments, and wavelength of absorption of the intramolecular charge-transfer band in four solvents, water, methanol, acetone, and DMSO, respectively. The data calculated were in excellent agreement with available experimental data, for example, bond length and dihedral angles. This gives credence to the use of the calculated properties in explaining the solvatochromic behaviors observed. The dependence of an empirical solvent polarity scale E(T)(probe) in kcal/mol on the physicochemical properties of the solvent (acidity, basicity, and dipolarity/polarizability) and those of the probes (pK(a), and dipole moment) was analyzed by using known multiparameter solvation equations. For each pair of probes, values of E(T)(probe) (for example, E(T)(MePM) versus E(T)(RB)) were found to be linearly correlated with correlation coefficients, r, between 0.9548 and 0.9860. For the mercyanine series, the values of E(T)(probe) also correlated linearly, with (r) of 0.9772 (MePMBr versus MePM) and 0.9919 (MePMBr(2) versus MePM). The response

  13. Modeling self-potential data in the Abraham and Meadow-Hatton geothermal systems: The search for upflow zones

    SciTech Connect

    Schima, S.; Wilt, M.; Ross, H.

    1995-07-01

    Computer code SPXCL is a finite difference modeling algorithm that calculates the response of embedded point sources within a rectangular, two-dimensional medium. The code calculates the electrical potential anywhere in the medium from thermal or pressure sources. This code is useful in calculating self-potential measurements that may be used to locate upflow zones in geothermal systems. Beginning in 1991 data on self-potential was collected at Abraham and Meadow-Hatton Hot Springs, two of the largest thermal spring systems in Utah. In this paper, these data were modeled to determine upflow zones and source characteristics using the SPXCL code. The forward solution for fluid and heat flow models and the resulting self-potential anomalies were calculated.

  14. Probe Dependent Solvation Dynamics Study in a Microscopically Immiscible Dimethyl Sulfoxide-Glycerol Binary Solvent.

    PubMed

    Kaur, Harveen; Koley, Somnath; Ghosh, Subhadip

    2014-06-26

    Excited state dipole solvation of three coumarin dyes with different hydrophobicities was studied in DMSO-glycerol binary solvent. The solvation times obtained from the three dyes are remarkably different. The highly hydrophilic dye coumarin 343 (C343) exhibits the slowest solvation time (>12 ns) among all the dyes we used. This is in contrast to the most hydrophobic dye coumarin 153 (C153), where the solvated state is reached just within ∼104 ps. However, the moderately hydrophobic dye coumarin 480 (C480) demonstrates an intermediate (∼396 ps) solvation time. Unprecedented slowdown of solvation time of C343 is probably due to the slow diffusion of solvent molecules in the glycerol-rich first solvation shell followed by hydrogen bond rearrangements around the solute dipole. On the other hand, fast solvation of hydrophobic dye C153 is most likely caused by the fast reorganization dynamics of hydrophobic -CH3 groups of DMSO or the carbon backbone of the glycerol molecule around the solute dipole. Interestingly, a remarkable probe dependency in solvation dynamics was not observed in the case of DMSO-water binary solvent or in a neat solvent isopropanol. Probe dependent solvation in a DMSO-glycerol mixture is attributed to the microscopic phase segregation and different locations of coumarin dyes within this binary solvent. PMID:24942350

  15. Composition fluctuations, correlated response, and protein solvation in membranes

    NASA Astrophysics Data System (ADS)

    McConnell, Harden

    2010-05-01

    Membrane composition fluctuations are deduced from the deuterium NMR relaxation data of S. L. Veatch et al. [Proc. Natl. Acad. Sci. U.S.A. 104, 17650 (2007)]. A theoretical model for these fluctuations is used to determine the parameters of a correlation function. A fluctuation-response relation is then derived to infer the response of a lipid bilayer membrane to perturbations, such as the presence of a protein. The energy of the correlated response is shown to decrease as a bilayer miscibility critical point is approached from higher temperatures. Near the critical temperature the low energy of the composition response facilitates the lipid solvation of membrane proteins and minimizes lipid-mediated nonspecific protein-protein interactions. This facilitated lipid solvation of membrane proteins may be the basis of reports that at the growth temperature, the lipids of animal cell membranes have compositions such that they are within ˜10° of a miscibility critical point.

  16. 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

  17. IONIC LIQUIDS: RADIATION CHEMISTRY, SOLVATION DYNAMICS AND REACTIVITY PATTERNS.

    SciTech Connect

    WISHART,J.F.

    2007-10-01

    energy production, nuclear fuel and waste processing, improving the efficiency and safety of industrial chemical processes, and pollution prevention. ILs are generally nonvolatile, noncombustible, highly conductive, recyclable and capable of dissolving a wide variety of materials. They are finding new uses in chemical synthesis, catalysis, separations chemistry, electrochemistry and other areas. Ionic liquids have dramatically different properties compared to conventional molecular solvents, and they provide a new and unusual environment to test our theoretical understanding of charge transfer and other reactions. We are interested in how IL properties influence physical and dynamical processes that determine the stability and lifetimes of reactive intermediates and thereby affect the courses of chemical reactions and product distributions. Successful use of ionic liquids in radiation-filled environments, where their safety advantages could be significant, requires an understanding of ionic liquid radiation chemistry. For example, characterizing the primary steps of IL radiolysis will reveal radiolytic degradation pathways and suggest ways to prevent them or mitigate their effects on the properties of the material. An understanding of ionic liquid radiation chemistry will also facilitate pulse radiolysis studies of general chemical reactivity in ILs, which will aid in the development of applications listed above. Very early in our radiolysis studies it became evident that slow solvation dynamics of the excess electron in ILs (which vary over a wide viscosity range) increases the importance of pre-solvated electron reactivity and consequently alters product distributions. Parallel studies of IL solvation phenomena using coumarin-153 dynamic Stokes shifts and polarization anisotropy decay rates are done to compare with electron solvation studies and to evaluate the influence of ILs on charge transport processes. Methods. Picosecond pulse radiolysis studies at BNL

  18. Ionic Liquids: Radiation Chemistry, Solvation Dynamics and Reactivity Patterns

    SciTech Connect

    Wishart,J.F.

    2008-09-29

    Ionic liquids (ILs) are a rapidly expanding family of condensed-phase media with important applications in energy production, nuclear fuel and waste processing, improving the efficiency and safety of industrial chemical processes, and pollution prevention. ILs are generally nonvolatile, noncombustible, highly conductive, recyclable and capable of dissolving a wide variety of materials. They are finding new uses in chemical synthesis, catalysis, separations chemistry, electrochemistry and other areas. Ionic liquids have dramatically different properties compared to conventional molecular solvents, and they provide a new and unusual environment to test our theoretical understanding of charge transfer and other reactions. We are interested in how IL properties influence physical and dynamical processes that determine the stability and lifetimes of reactive intermediates and thereby affect the courses of chemical reactions and product distributions. Successful use of ionic liquids in radiation-filled environments, where their safety advantages could be significant, requires an understanding of ionic liquid radiation chemistry. For example, characterizing the primary steps of IL radiolysis will reveal radiolytic degradation pathways and suggest ways to prevent them or mitigate their effects on the properties of the material. An understanding of ionic liquid radiation chemistry will also facilitate pulse radiolysis studies of general chemical reactivity in ILs, which will aid in the development of applications listed above. Very early in our radiolysis studies it became evident that slow solvation dynamics of the excess electron in ILs (which vary over a wide viscosity range) increases the importance of pre-solvated electron reactivity and consequently alters product distributions. Parallel studies of IL solvation phenomena using coumarin-153 dynamic Stokes shifts and polarization anisotropy decay rates are done to compare with electron solvation studies and to evaluate

  19. How does the solvation unveil AtO+ reactivity?

    PubMed

    Ayed, Tahra; Seydou, Mahamadou; Réal, Florent; Montavon, Gilles; Galland, Nicolas

    2013-05-01

    The AtO(+) molecular ion, a potential precursor for the synthesis of radiotherapeutic agents in nuclear medicine, readily reacts in aqueous solution with organic and inorganic compounds, but at first glance, these reactions must be hindered by spin restriction quantum rules. Using relativistic quantum calculations, coupled to implicit solvation models, on the most stable AtO(+)(H2O)6 clusters, we demonstrate that specific interactions with water molecules of the first solvation shell induce a spin change for the AtO(+) ground state, from a spin state of triplet character in the gas phase to a Kramers-restricted closed-shell configuration in solution. This peculiarity allows rationalization of the AtO(+) reactivity with closed-shell species in aqueous solution and may explain the differences in astatine reactivity observed in (211)At production protocols based on "wet" and "dry" processes. PMID:23537101

  20. Benzonitrile: Electron affinity, excited states, and anion solvation

    NASA Astrophysics Data System (ADS)

    Dixon, Andrew R.; Khuseynov, Dmitry; Sanov, Andrei

    2015-10-01

    We report a negative-ion photoelectron imaging study of benzonitrile and several of its hydrated, oxygenated, and homo-molecularly solvated cluster anions. The photodetachment from the unsolvated benzonitrile anion to the X ˜ 1 A 1 state of the neutral peaks at 58 ± 5 meV. This value is assigned as the vertical detachment energy (VDE) of the valence anion and the upper bound of adiabatic electron affinity (EA) of benzonitrile. The EA of the lowest excited electronic state of benzonitrile, a ˜ 3 A 1 , is determined as 3.41 ± 0.01 eV, corresponding to a 3.35 eV lower bound for the singlet-triplet splitting. The next excited state, the open-shell singlet A ˜ 1 A 1 , is found about an electron-volt above the triplet, with a VDE of 4.45 ± 0.01 eV. These results are in good agreement with ab initio calculations for neutral benzonitrile and its valence anion but do not preclude the existence of a dipole-bound state of similar energy and geometry. The step-wise and cumulative solvation energies of benzonitrile anions by several types of species were determined, including homo-molecular solvation by benzonitrile, hydration by 1-3 waters, oxygenation by 1-3 oxygen molecules, and mixed solvation by various combinations of O2, H2O, and benzonitrile. The plausible structures of the dimer anion of benzonitrile were examined using density functional theory and compared to the experimental observations. It is predicted that the dimer anion favors a stacked geometry capitalizing on the π-π interactions between the two partially charged benzonitrile moieties.

  1. A thermodynamic study of selective solvation in solvent mixtures.

    PubMed

    Cabot, Rafel; Hunter, Christopher A

    2010-04-21

    Changes in the (31)P NMR chemical shift of tri-n-butylphosphine oxide have been measured as function of solvent composition in a number of binary solvent mixtures. The data were analysed using a model that separates the contributions of specific H-bond interactions with the first solvation shell and the non-specific effects of the bulk solvent on the chemical shift. This allowed measurement of equilibrium constants between differently solvated states of the probe and hence thermodynamic quantification of preferential solvation in the binary mixtures. The results are analysed in the context of the electrostatic solvent competition model, which assumes that solvent effects on intermolecular interactions can be interpreted based on the exchange of specific functional group contacts, with minimal involvement of the bulk solvent. The thermodynamic measurements of preferential solvation were used to determine the H-bond donor parameter alpha for cyclohexane, n-octane, n-dodecane, benzene, 1,4-dioxane, carbon tetrachloride, acetone, dichloromethane, dimethyl sulfoxide and chloroform. For solvents where the H-bond donor parameters have been measured as solutes in carbon tetrachloride solution, the H-bond donor parameters measured here for the same compounds as solvents are practically identical, i.e. solute and solvent H-bond parameters are directly interchangable. For alkanes, the experimental H-bond donor parameter is significantly larger than expected based on calculated molecular electrostatic potential surfaces. This might suggest an increase in the relative importance of van der Waals interactions when electrostatic effects are weak. PMID:20449502

  2. 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. PMID:26716727

  3. Solvation Sphere of I- and Br- in Water

    SciTech Connect

    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- and Br- 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 -} in 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.

  4. Structural chemistry of new lithium bis(oxalato)borate solvates.

    PubMed

    Zavalij, Peter Y; Yang, Shoufeng; Whittingham, M Stanley

    2004-12-01

    Recently lithium bis(oxalato)borate, LiB(C2O4)2, has been proposed as an alternative lithium salt for the electrolyte in rechargeable batteries that do not contain explosive perchlorate, reactive fluoride or toxic arsenic. This lithium salt crystallizes in the form of solvates from such solvents as water, acetonitrile, acetone, dimethoxyethane, 1,3-dioxolane and ethylene carbonate. Their crystal structures were determined in order to explore the crystal chemistry of this lithium salt. It was found that most of the solvents consist of a lithium bis(oxalato)borate dimer in which the ligand acts as both a chelating and a bridging agent. Lithium has octahedral coordination that typically includes one or, less commonly, two solvent molecules. An exception to this rule is the ethylene carbonate solvate where the lithium is tetrahedrally surrounded exclusively by the solvent and bis(oxalato)borate plays the role of counter-ion only. The ethylene carbonate solvates were also studied for LiPF6 and LiAsF6 salts and they have similar structures to the bis(oxalato)borate tetrahedral complexes. PMID:15534382

  5. 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. PMID:26395146

  6. Solvation structure of the halides from x-ray absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Antalek, Matthew; Pace, Elisabetta; Hedman, Britt; Hodgson, Keith O.; Chillemi, Giovanni; Benfatto, Maurizio; Sarangi, Ritimukta; Frank, Patrick

    2016-07-01

    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, and 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.

  7. Solvation structure of the halides from x-ray absorption spectroscopy.

    PubMed

    Antalek, Matthew; Pace, Elisabetta; Hedman, Britt; Hodgson, Keith O; Chillemi, Giovanni; Benfatto, Maurizio; Sarangi, Ritimukta; Frank, Patrick

    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, and 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. PMID:27475372

  8. Ab initio joint density-functional theory of solvated electrodes, with model and explicit solvation

    NASA Astrophysics Data System (ADS)

    Arias, Tomas

    2015-03-01

    the electrochemical context and how it is needed for realistic description of solvated electrode systems [], and how simple ``implicit'' polarized continuum methods fail radically in this context. Finally, we shall present a series of results relevant to battery, supercapacitor, and solar-fuel systems, one of which has led to a recent invention disclosure for improving battery cycle lifetimes. Supported as a part of the Energy Materials Center at Cornell, an Energy Frontier Research Center funded by DOE/BES (award de-sc0001086) and by the New York State Division of Science, Technology and Innovation (NYSTAR, award 60923).

  9. Free energy calculations on the relative solvation free energies of benzene, anisole, and 1,2,3-trimethoxygenzene: Theoretical and experimental analysis of aromatic methoxy solvation

    SciTech Connect

    Kuyper, L.F.; Hunter, R.N. ); Ashton, D. ); Merz, K.M. Jr.; Kollman, P.A. )

    1991-08-22

    The authors have carried out experimental determinations of the free energy of solvation of anisole, 1,2-dimethoxybenzene (DMB), and 1,2,3-trimethoxybenzene (TMB) in water and perturbation free energy calculations on the relative aqueous solvation free energies of benzene, anisole, and TMB. The measured differences between the relative experimental free energies of solvation of benzene, anisole, DMB, and TMB support the concept of near additivity of aromatic methoxy group contributions to such gas phase to water transfer free energies. Calculated differences in solvation free energies were shown to be sensitive to the choice of electrostatic charge distribution model. Quantum mechanical electrostatic potential fit charge models from STO-3G, 4-31G, and 6-31G* basis sets were compared for their ability to reproduce the relative free energies of solvation found experimentally. The 6-31G* basis sets were compared for their ability to reproduce the relative free energies of solvation found experimentally. The 6-31G* charge model was the best in this regard and the STO-3G model was next in quality, but the 4-31G model significantly overestimated the effect of O-CH{sub 3} substitution on solvation free energies. Models based on scaled 4-31G charges also produced reasonable results.

  10. A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule

    NASA Astrophysics Data System (ADS)

    Ying, Jinyong; Xie, Dexuan

    2015-10-01

    The Poisson-Boltzmann equation (PBE) is one widely-used implicit solvent continuum model for calculating electrostatics of ionic solvated biomolecule. In this paper, a new finite element and finite difference hybrid method is presented to solve PBE efficiently based on a special seven-overlapped box partition with one central box containing the solute region and surrounded by six neighboring boxes. In particular, an efficient finite element solver is applied to the central box while a fast preconditioned conjugate gradient method using a multigrid V-cycle preconditioning is constructed for solving a system of finite difference equations defined on a uniform mesh of each neighboring box. Moreover, the PBE domain, the box partition, and an interface fitted tetrahedral mesh of the central box can be generated adaptively for a given PQR file of a biomolecule. This new hybrid PBE solver is programmed in C, Fortran, and Python as a software tool for predicting electrostatics of a biomolecule in a symmetric 1:1 ionic solvent. Numerical results on two test models with analytical solutions and 12 proteins validate this new software tool, and demonstrate its high performance in terms of CPU time and memory usage.

  11. Electron Solvation in Liquid Ammonia: Lithium, Sodium, Magnesium, and Calcium as Electron Sources.

    PubMed

    Chaban, Vitaly V; Prezhdo, Oleg V

    2016-03-10

    A free electron in solution, known as a solvated electron, is the smallest possible anion. Alkali and alkaline earth atoms serve as electron donors in solvents that mediate outer-sphere electron transfer. We report herein ab initio molecular dynamics simulations of lithium, sodium, magnesium, and calcium in liquid ammonia at 250 K. By analyzing the electronic properties and the ionic and solvation structures and dynamics, we systematically characterize these metals as electron donors and ammonia molecules as electron acceptors. We show that the solvated metal strongly modifies the properties of its solvation shells and that the observed effect is metal-specific. Specifically, the radius and charge exhibit major impacts. The single solvated electron present in the alkali metal systems is distributed more uniformly among the solvent molecules of each metal's two solvation shells. In contrast, alkaline earth metals favor a less uniform distribution of the electron density. Alkali and alkaline earth atoms are coordinated by four and six NH3 molecules, respectively. The smaller atoms, Li and Mg, are stronger electron donors than Na and Ca. This result is surprising, as smaller atoms in a column of the periodic table have higher ionization potentials. However, it can be explained by stronger electron donor-acceptor interactions between the smaller atoms and the solvent molecules. The structure of the first solvation shell is sharpest for Mg, which has a large charge and a small radius. Solvation is weakest for Na, which has a small charge and a large radius. Weak solvation leads to rapid dynamics, as reflected in the diffusion coefficients of NH3 molecules of the first two solvation shells and the Na atom. The properties of the solvated electrons established in the present study are important for radiation chemistry, synthetic chemistry, condensed-matter charge transfer, and energy sources. PMID:26886153

  12. Multibody correlations in the hydrophobic solvation of glycine peptides

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    Protein collapse during folding is often assumed to be driven by a hydrophobic solvation energy (ΔGvdw) that scales linearly with solvent-accessible surface area (A). In a previous study, we argued that ΔGvdw, as well as its attractive (ΔGatt) and repulsive (ΔGrep) components, was not simply a linear function of A. We found that the surface tensions, γrep, γatt, and γvdw, gotten from ΔGrep, ΔGatt, and ΔGvdw against A for four configurations of deca-alanine differed from those obtained for a set of alkanes. In the present study, we extend our analysis to fifty decaglycine structures and atomic decompositions. We find that different configurations of decaglycine generate different estimates of γrep. Additionally, we considered the reconstruction of the solvation free energy from scaling the free energy of solvation of each atom type, free in solution. The free energy of the isolated atoms, scaled by the inverse surface area the atom would expose in the molecule does not reproduce the γrep for the intact decaglycines. Finally, γatt for the decaglycine conformations is much larger in magnitude than those for deca-alanine or the alkanes, leading to large negative values of γvdw (-74 and -56 cal/mol/Å2 for CHARMM27 and AMBER ff12sb force fields, respectively). These findings imply that ΔGvdw favors extended rather than compact structures for decaglycine. We find that ΔGrep and ΔGvdw have complicated dependencies on multibody correlations between solute atoms, on the geometry of the molecular surface, and on the chemical identities of the atoms.

  13. Multibody correlations in the hydrophobic solvation of glycine peptides

    PubMed Central

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

    2014-01-01

    Protein collapse during folding is often assumed to be driven by a hydrophobic solvation energy (ΔGvdw) that scales linearly with solvent-accessible surface area (A). In a previous study, we argued that ΔGvdw, as well as its attractive (ΔGatt) and repulsive (ΔGrep) components, was not simply a linear function of A. We found that the surface tensions, γrep, γatt, and γvdw, gotten from ΔGrep, ΔGatt, and ΔGvdw against A for four configurations of deca-alanine differed from those obtained for a set of alkanes. In the present study, we extend our analysis to fifty decaglycine structures and atomic decompositions. We find that different configurations of decaglycine generate different estimates of γrep. Additionally, we considered the reconstruction of the solvation free energy from scaling the free energy of solvation of each atom type, free in solution. The free energy of the isolated atoms, scaled by the inverse surface area the atom would expose in the molecule does not reproduce the γrep for the intact decaglycines. Finally, γatt for the decaglycine conformations is much larger in magnitude than those for deca-alanine or the alkanes, leading to large negative values of γvdw (−74 and −56 cal/mol/Å2 for CHARMM27 and AMBER ff12sb force fields, respectively). These findings imply that ΔGvdw favors extended rather than compact structures for decaglycine. We find that ΔGrep and ΔGvdw have complicated dependencies on multibody correlations between solute atoms, on the geometry of the molecular surface, and on the chemical identities of the atoms. PMID:25494796

  14. Multibody correlations in the hydrophobic solvation of glycine peptides.

    PubMed

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

    2014-12-14

    Protein collapse during folding is often assumed to be driven by a hydrophobic solvation energy (ΔGvdw) that scales linearly with solvent-accessible surface area (A). In a previous study, we argued that ΔGvdw, as well as its attractive (ΔGatt) and repulsive (ΔGrep) components, was not simply a linear function of A. We found that the surface tensions, γrep, γatt, and γvdw, gotten from ΔGrep, ΔGatt, and ΔGvdw against A for four configurations of deca-alanine differed from those obtained for a set of alkanes. In the present study, we extend our analysis to fifty decaglycine structures and atomic decompositions. We find that different configurations of decaglycine generate different estimates of γrep. Additionally, we considered the reconstruction of the solvation free energy from scaling the free energy of solvation of each atom type, free in solution. The free energy of the isolated atoms, scaled by the inverse surface area the atom would expose in the molecule does not reproduce the γrep for the intact decaglycines. Finally, γatt for the decaglycine conformations is much larger in magnitude than those for deca-alanine or the alkanes, leading to large negative values of γvdw (-74 and -56 cal/mol/Å(2) for CHARMM27 and AMBER ff12sb force fields, respectively). These findings imply that ΔGvdw favors extended rather than compact structures for decaglycine. We find that ΔGrep and ΔGvdw have complicated dependencies on multibody correlations between solute atoms, on the geometry of the molecular surface, and on the chemical identities of the atoms. PMID:25494796

  15. Multibody correlations in the hydrophobic solvation of glycine peptides

    SciTech Connect

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

    2014-12-14

    Protein collapse during folding is often assumed to be driven by a hydrophobic solvation energy (ΔG{sub vdw}) that scales linearly with solvent-accessible surface area (A). In a previous study, we argued that ΔG{sub vdw}, as well as its attractive (ΔG{sub att}) and repulsive (ΔG{sub rep}) components, was not simply a linear function of A. We found that the surface tensions, γ{sub rep}, γ{sub att}, and γ{sub vdw}, gotten from ΔG{sub rep}, ΔG{sub att}, and ΔG{sub vdw} against A for four configurations of deca-alanine differed from those obtained for a set of alkanes. In the present study, we extend our analysis to fifty decaglycine structures and atomic decompositions. We find that different configurations of decaglycine generate different estimates of γ{sub rep}. Additionally, we considered the reconstruction of the solvation free energy from scaling the free energy of solvation of each atom type, free in solution. The free energy of the isolated atoms, scaled by the inverse surface area the atom would expose in the molecule does not reproduce the γ{sub rep} for the intact decaglycines. Finally, γ{sub att} for the decaglycine conformations is much larger in magnitude than those for deca-alanine or the alkanes, leading to large negative values of γ{sub vdw} (−74 and −56 cal/mol/Å{sup 2} for CHARMM27 and AMBER ff12sb force fields, respectively). These findings imply that ΔG{sub vdw} favors extended rather than compact structures for decaglycine. We find that ΔG{sub rep} and ΔG{sub vdw} have complicated dependencies on multibody correlations between solute atoms, on the geometry of the molecular surface, and on the chemical identities of the atoms.

  16. Equation of motion with radiation reaction in ultrarelativistic laser-electron interactions

    SciTech Connect

    Seto, Keita; Nagatomo, Hideo; Mima, Kunioki; Koga, James

    2011-12-15

    The intensity of the ultra-short pulse lasers has reached 10{sup 22} W/cm{sup 2} owing to the advancements of laser technology. When the motion of an electron becomes relativistic, bremsstrahlung accompanies it. The energy from this bremsstrahlung corresponds to the energy loss of the electron; therefore, the motion of the electron deviates from the case without radiation. The radiation behaves something like resistance. This effect called ''radiation reaction'' or ''radiation damping'' and the force converted from the radiation is named the ''radiation reaction force'' or the ''damping force''. The equation of motion with the reaction force is known as the Lorentz-Abraham-Dirac (LAD) equation, but the solution of this equation is not physical due to the fact that it has a ''run-away'' solution. As one solution of this problem, we have derived a new equation which takes the place of the Lorentz-Abraham-Dirac equation. We will show the validity of this equation with a simple theoretical analysis.

  17. Numerical solution of boundary-integral equations for molecular electrostatics.

    PubMed

    Bardhan, Jaydeep P

    2009-03-01

    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. PMID:19275391

  18. Polar confinement modulates solvation behavior of methane molecules

    NASA Astrophysics Data System (ADS)

    Xu, Weixin; Mu, Yuguang

    2008-06-01

    Polar confinement induces an amorphous solidlike state of water characterized by an orientational correlation time longer than hundreds of picoseconds and significant structural disorder. Solvation behavior of methane molecules is dramatically modulated under polar confinement. Moreover our simulations indicate that the charges equivalent to those borne by atoms of amino acids could generate an electric field which is strong enough to stimulate the phase transition of water. In our results, polar confinement is found to be more capable of aggregating hydrophobic molecules. This study raises an interesting mechanism by which the cagelike structure of the Escherichia coli chaperonin GroEL and the cochaperonin GroES complex helps protein folding.

  19. Kinetic investigation of the solvation of lithium salts in siloxanes.

    SciTech Connect

    Chen, Z.; Wang, H. H.; Vissers, D. R.; Zhang, L.; West, R.; Lyons, L. J.; Amine, K.; Chemical Sciences and Engineering Division; Univ. of Wisconsin; Grinnell Coll.

    2008-02-14

    The solvation of lithium salts in siloxanes was investigated with the aim to understand the key barriers that limit the ionic conductivity of siloxane-based electrolytes. The conductivity and kinetic data were measured for electrolytes with different salts, different salt concentrations, and solvents. The results show that both the conductivity and the kinetics of ionic transportation were greatly impacted by the specific interactions between ions and the solvent molecules. The high content of ion pairs in the electrolytes can be one of the main reasons for the low ionic conductivity observed in the siloxane-based electrolytes.

  20. Editorial of the PCCP themed issue on "Solvation Science".

    PubMed

    Morgenstern, Karina; Marx, Dominik; Havenith, Martina; Muhler, Martin

    2015-04-01

    The present special issue presents exciting experimental and theoretical results in the topic of "Solvation Science", a topic that emerges from physical, theoretical, and industrial chemistry, and is also of interest to a multitude of neighboring fields, such as inorganic and organic chemistry, biochemistry, physics and engineering. We hope that the articles will be highly useful for researchers who would like to enter this newly emerging area, and that it is a valuable source for the nucleation of new ideas and collaborations to better understand the active role of the solvent in reactions. PMID:25660560

  1. Ion solvation in aqueous and non-aqueous solvents

    NASA Astrophysics Data System (ADS)

    Arslanargin, Ayse

    The thermodynamics of ion solvation is studied in both water and some organic solvents using computational and theoretical techniques. Free energy partitioning analysis is employed to explore the driving forces for ions interacting with the water liquid/vapor interface using optimized point charge models for the Na+ and I- ions and the extended simple point charge water model. The absolute hydration free energy is partitioned into cavity formation, attractive van der Waals, local electrostatic, and far-field electrostatic contributions. The bulk hydration free energy of the ions is computed first, followed by the free energy to insert the ions at the center of a water slab. Shifts of the ion free energies occur in the slab geometry are consistent with the extended simple point charge water model surface potential of the water liquid/vapor interface. Then the free energy profiles are examined for ion passage from the slab center to the dividing surface. The profiles show that, for the large chaotropic I- ion, the relatively flat total free energy profile results from the near cancellation of several large contributions. On the other hand, the small Na+ ion is repelled from the liquid/vapor interface mainly by the far field electrostatic term. The far-field electrostatic part of the free energy, largely due to the water liquid/vapor interface potential, has an important effect on ion distributions near the surface in the classical model. However, that the individual forms of the local and far-field electrostatic contributions are expected to be model dependent when comparing classical and quantum results. Non-aqueous solvents such as ethylene carbonate, and propylene carbonate are widely used as liquid electrolytes in electrochemical energy storage systems. The electrolyte structure affects the efficiency of the ion transport, and understanding the solvent structure is essential for battery performance enhancements. Free energy and enthalpy of solvation calculations

  2. Preparing medical students for the continual improvement of health and health care: Abraham Flexner and the new "public interest".

    PubMed

    Berwick, Donald M; Finkelstein, Jonathan A

    2010-09-01

    In 1910, in his recommendations for reforming medical education, Abraham Flexner responded to what he deemed to be the "public interest." Now, 100 years later, to respond to the current needs of society, the education of physicians must once again change. In addition to understanding the biological basis of health and disease, and mastering technical skills for treating individual patients, physicians will need to learn to navigate in and continually improve complex systems in order to improve the health of the patients and communities they serve. Physicians should not be mere participants in, much less victims of, such systems. Instead, they ought to be prepared to help lead those systems toward ever-higher-quality care for all. A number of innovative programs already exist for students and residents to help integrate improvement skills into professional preparation, and that goal is enjoying increasing support from major professional organizations and accrediting bodies. These experiences have shown that medical schools and residency programs will need to both teach the scientific foundations of system performance and provide opportunities for trainees to participate in team-based improvement of the real-world health systems in which they work. This significant curricular change, to meet the social need of the 21st century, will require educators and learners to embrace new core values, in addition to those held by the profession for generations. These include patient-centeredness, transparency, and stewardship of limited societal resources for health care. PMID:20736631

  3. Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect.

    PubMed

    Yan, Zhiqiang; Wang, Jin

    2015-09-01

    Solvation effect is an important factor for protein-ligand binding in aqueous water. Previous scoring function of protein-ligand interactions rarely incorporates the solvation model into the quantification of protein-ligand interactions, mainly due to the immense computational cost, especially in the structure-based virtual screening, and nontransferable application of independently optimized atomic solvation parameters. In order to overcome these barriers, we effectively combine knowledge-based atom-pair potentials and the atomic solvation energy of charge-independent implicit solvent model in the optimization of binding affinity and specificity. The resulting scoring functions with optimized atomic solvation parameters is named as specificity and affinity with solvation effect (SPA-SE). The performance of SPA-SE is evaluated and compared to 20 other scoring functions, as well as SPA. The comparative results show that SPA-SE outperforms all other scoring functions in binding affinity prediction and "native" pose identification. Our optimization validates that solvation effect is an important regulator to the stability and specificity of protein-ligand binding. The development strategy of SPA-SE sets an example for other scoring function to account for the solvation effect in biomolecular recognitions. PMID:26111900

  4. Moving solvated electrons with light: Nonadiabatic mixed quantum/classical molecular dynamics simulations of the relocalization of photoexcited solvated electrons in tetrahydrofuran (THF)

    SciTech Connect

    Bedard-Hearn, Michael J.; Larsen, Ross E.; Schwartz, Benjamin J.

    2006-11-21

    Motivated by recent ultrafast spectroscopic experiments [Martini et al., Science 293, 462 (2001)], which suggest that photoexcited solvated electrons in tetrahydrofuran (THF) can relocalize (that is, return to equilibrium in solvent cavities far from where they started), we performed a series of nonequilibrium, nonadiabatic, mixed quantum/classical molecular dynamics simulations that mimic one-photon excitation of the THF-solvated electron. We find that as photoexcited THF-solvated electrons relax to their ground states either by continuous mixing from the excited state or via nonadiabatic transitions, {approx}30% of them relocalize into cavities that can be over 1 nm away from where they originated, in close agreement with the experiments. A detailed investigation shows that the ability of excited THF-solvated electrons to undergo photoinduced relocalization stems from the existence of preexisting cavity traps that are an intrinsic part of the structure of liquid THF. This explains why solvated electrons can undergo photoinduced relocalization in solvents like THF but not in solvents like water, which lack the preexisting traps necessary to stabilize the excited electron in other places in the fluid. We also find that even when they do not ultimately relocalize, photoexcited solvated electrons in THF temporarily visit other sites in the fluid, explaining why the photoexcitation of THF-solvated electrons is so efficient at promoting recombination with nearby scavengers. Overall, our study shows that the defining characteristic of a liquid that permits the photoassisted relocalization of solvated electrons is the existence of nascent cavities that are attractive to an excess electron; we propose that other such liquids can be found from classical computer simulations or neutron diffraction experiments.

  5. Long-ranged solvation forces in a fluid with short-ranged interactions

    NASA Astrophysics Data System (ADS)

    Pertsin, Alexander J.; Grunze, Michael

    2003-05-01

    The grand canonical Monte Carlo technique is used to calculate the solvation force and interfacial tension in a simple Lennard-Jones fluid confined between two solid walls. Emphasis is placed on large wall-to-wall separations, where the oscillations of density and solvation force due to layering effects have decayed. Despite the short range of the fluid-fluid and fluid-wall interaction potentials used, the solvation force shows an unsuspectedly long-ranged behavior, remaining quite perceptible up to a separation of 100 molecular diameters. It is also found that the sign of the solvation force at large separations is not uniquely determined by the sign of the interfacial tension: The walls that are "philic" with respect to the constrained fluid may well exhibit both repulsive and attractive solvation forces.

  6. The effect of air on solvated electron chemistry at a plasma/liquid interface

    NASA Astrophysics Data System (ADS)

    Rumbach, Paul; Bartels, David M.; Mohan Sankaran, R.; Go, David B.

    2015-10-01

    Plasmas in contact with liquids initiate complex chemistry that leads to the generation of a wide range of reactive species. For example, in an electrolytic configuration with a cathodic plasma electrode, electrons from the plasma are injected into the solution, leading to solvation and ensuing reactions. If the gas contains oxygen, electronegative oxygen molecules may react with the plasma electrons via attachment to reduce the electron flux to the solution reducing the production of solvated electrons or produce reactive oxygen species that quickly scavenge solvated electrons in solution. Here, we applied a total internal reflection absorption spectroscopy technique to compare the concentration of solvated electrons produced in solution by an argon plasma containing various amounts of oxygen, nitrogen, and air. Our measurements indicate that in oxygen or air ambients, electron attachment in the plasma phase greatly attenuates the electron flux incident on the liquid surface. The remaining electrons then solvate but are quickly scavenged by reactive oxygen species in the liquid phase.

  7. 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

  8. Injector for scattering measurements on fully solvated biospecies

    NASA Astrophysics Data System (ADS)

    Weierstall, U.; Spence, J. C. H.; Doak, R. B.

    2012-03-01

    We describe a liquid jet injector system developed to deliver fully solvated microscopic target species into a probe beam under either vacuum or ambient conditions. The injector was designed specifically for x-ray scattering studies of biological nanospecies using x-ray free electron lasers and third generation synchrotrons, but is of interest to any application in which microscopic samples must be delivered in a fully solvated state and with microscopic precision. By utilizing a gas dynamic virtual nozzle (GDVN) to generate a sample-containing liquid jet of diameter ranging from 300 nm to 20 μm, the injector avoids the clogging problems associated in this size range with conventional Rayleigh jets. A differential pumping system incorporated into the injector shields the experimental chamber from the gas load of the GDVN, making the injector compatible with high vacuum systems. The injector houses a fiber-optically coupled pump laser to illuminate the jet for pump-probe experiments and a hermetically sealed microscope to observe the liquid jet for diagnostics and alignment during operation. This injector system has now been used during several experimental runs at the Linac Coherent Light Source. Recent refinements in GDVN design are also presented.

  9. A Protein Solvation Model Based on Residue Burial.

    PubMed

    Ceres, Nicoletta; Pasi, Marco; Lavery, Richard

    2012-06-12

    The influence of solvent on the individual amino acids of a protein depends not simply on their surface exposure but rather on the degree of their burial within the structure. This property can be related to a simple geometrical measure termed circular variance. Circular variance depends on the spatial distribution of neighboring residues and varies from zero to one as a residue becomes buried. Its only adjustable parameter is a cutoff distance for selecting neighbors. Here, we show that circular variance can be used to build a fast and effective model of protein solvation energies. For this, we combine a coarse-grain protein representation with statistical potentials derived by Boltzmann inversion of circular variance probability distributions for different classes of pseudoatom within a large protein structure database. The method is shown to work well for distinguishing native protein structures from decoy structures generated in a variety of ways. It can also be used to detect specific residues in unfavorable solvent environments. Compared to surface accessibility, circular variance calculations are faster, less sensitive to small conformational changes, and able to account for the longer-range interactions that characterize the electrostatic component of solvent effects. The resulting solvation energies can be used alone or as part of a more general coarse-grain protein model. PMID:26593844

  10. Solvation dynamics of biomolecules: modeling and terahertz experiments.

    PubMed

    Leitner, David M; Gruebele, Martin; Havenith, Martina

    2008-12-01

    The role of water in biomolecule dynamics has attracted much interest over the past decade, due in part to new probes of biomolecule-water interactions and developments in molecular simulations. Terahertz (THz) spectroscopy, among the most recent experimental methods brought to bear on this problem, is able to detect even small solute induced changes of the collective water network dynamics at the biomolecule-water interface. THz measurements reveal that proteins influence up to 1000 water molecules in their surroundings, and that even small saccharides influence the dynamics of hundreds of surrounding water molecules. The THz spectrum of a protein is sensitive to mutation and depends on the surface charge and flexibility of the protein. Influence on the solvation shell appears most pronounced for native wildtype proteins and decreases upon partial unfolding or mutation. THz spectra of solvated saccharides reveal that the number of water molecules coupled dynamically to a saccharide, forming a dynamical hydration shell around it, is related to the number of exposed oxygen atoms on the solute. The thickness of this layer appears correlated with the bioprotection efficiency of the saccharide. All findings support the thesis of a long-range dynamic coupling between biomolecule and solvent. PMID:19436490

  11. Solvation dynamics of biomolecules: modeling and terahertz experiments

    PubMed Central

    Leitner, David M; Gruebele, Martin; Havenith, Martina

    2008-01-01

    The role of water in biomolecule dynamics has attracted much interest over the past decade, due in part to new probes of biomolecule-water interactions and developments in molecular simulations. Terahertz (THz) spectroscopy, among the most recent experimental methods brought to bear on this problem, is able to detect even small solute induced changes of the collective water network dynamics at the biomolecule-water interface. THz measurements reveal that proteins influence up to 1000 water molecules in their surroundings, and that even small saccharides influence the dynamics of hundreds of surrounding water molecules. The THz spectrum of a protein is sensitive to mutation and depends on the surface charge and flexibility of the protein. Influence on the solvation shell appears most pronounced for native wildtype proteins and decreases upon partial unfolding or mutation. THz spectra of solvated saccharides reveal that the number of water molecules coupled dynamically to a saccharide, forming a dynamical hydration shell around it, is related to the number of exposed oxygen atoms on the solute. The thickness of this layer appears correlated with the bioprotection efficiency of the saccharide. All findings support the thesis of a long-range dynamic coupling between biomolecule and solvent. PMID:19436490

  12. Structural Interactions within Lithium Salt Solvates: Cyclic Carbonates and Esters

    SciTech Connect

    Seo, D. M.; Afroz, Taliman; Allen, Joshua L.; Boyle, Paul D.; Trulove, Paul C.; De Long, Hugh C.; Henderson, Wesley A.

    2014-11-13

    Only limited information is available regarding the manner in which cyclic carbonate and ester solvents coordinate Li+ cations in electrolyte solutions for lithium batteries. One approach to gleaning significant insight into these interactions is to examine crystalline solvate structures. To this end, eight new solvate structures are reported with ethylene carbonate, γ-butyrolactone and γ-valerolactone: (EC)3:LiClO4, (EC)2:LiClO4, (EC)2:LiBF4, (GBL)4:LiPF6, (GBL)1:LiClO4, (GVL)1:LiClO4, (GBL)1:LiBF4 and (GBL)1:LiCF3SO3. The crystal structure of (EC)1:LiCF3SO3 is also re-reported for comparison. These structures enable the factors which govern the manner in which the ions are coordinated and the ion/solvent packing—in the solid-state—to be scrutinized in detail.

  13. Molecular modeling of nucleic Acid structure: electrostatics and solvation.

    PubMed

    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 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. PMID:25631536

  14. Computer simulations of solvation dynamics in lithium clay materials

    SciTech Connect

    Greathouse, J.A.

    1997-12-31

    Monte Carlo and molecular dynamics computer simulations were performed concurrently for the first time on lithium-smectites (montmorillonite, beidellite, and hectorite) at very low water content (about 0.5 monolayer). These simulation conditions were selected to provide a comparison with existing NMR, IR, neutron scattering, and X-ray diffraction data which have been interpreted in terms of inner-sphere (IS) Li surface complexes solvated by three water molecules exhibiting hindered rotational degrees of freedom. Our simulations predicted layer spacings (c-axis direction) ranging from 10.32 {angstrom} (Hectorite) to 11.93 {angstrom} (beidellite). Both IS and outer-sphere (OS) Li surface complexes formed in the interlayers of montmorillonite, whereas only one type of surface complex formed in the interlayers of beidellite (IS) and hectorite (OS). Lithium ions were solvated by 2, 3, or 4 water molecules. Some evidence of Li-hydrate rotation was seen for beidellite, but the other smectites showed no Li-hydrate rotational motion. However water molecules were observed to rotate about their C{sub 2} axes of symmetry in montmorillonite. Additional spectroscopic data are needed to resolve the differences between the simulation predictions and current experimental interpretations.

  15. Electrostatics of solvated systems in periodic boundary conditions

    NASA Astrophysics Data System (ADS)

    Andreussi, Oliviero; Marzari, Nicola

    2014-12-01

    Continuum solvation methods can provide an accurate and inexpensive embedding of quantum simulations in liquid or complex dielectric environments. Notwithstanding a long history and manifold applications to isolated systems in open boundary conditions, their extension to materials simulations, typically entailing periodic boundary conditions, is very recent, and special care is needed to address correctly the electrostatic terms. We discuss here how periodic boundary corrections developed for systems in vacuum should be modified to take into account solvent effects, using as a general framework the self-consistent continuum solvation model developed within plane-wave density-functional theory [O. Andreussi et al., J. Chem. Phys. 136, 064102 (2012), 10.1063/1.3676407]. A comprehensive discussion of real- and reciprocal-space corrective approaches is presented, together with an assessment of their ability to remove electrostatic interactions between periodic replicas. Numerical results for zero- and two-dimensional charged systems highlight the effectiveness of the different suggestions, and underline the importance of a proper treatment of electrostatic interactions in first-principles studies of charged systems in solution.

  16. Calculating Free Energy Changes in Continuum Solvation Models.

    PubMed

    Ho, Junming; Ertem, Mehmed Z

    2016-02-25

    We recently showed for a large data set of pKas 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 calculating general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMD-M062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems. This includes cluster-continuum schemes for pKa calculations as well as various neutral, radical, and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and 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 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. PMID:26878566

  17. Backbone additivity in the transfer model of protein solvation

    PubMed Central

    Hu, Char Y; Kokubo, Hironori; Lynch, Gillian C; Bolen, D Wayne; Pettitt, B Montgomery

    2010-01-01

    The transfer model implying additivity of the peptide backbone free energy of transfer is computationally tested. Molecular dynamics simulations are used to determine the extent of change in transfer free energy (ΔGtr) with increase in chain length of oligoglycine with capped end groups. Solvation free energies of oligoglycine models of varying lengths in pure water and in the osmolyte solutions, 2M urea and 2M trimethylamine N-oxide (TMAO), were calculated from simulations of all atom models, and ΔGtr values for peptide backbone transfer from water to the osmolyte solutions were determined. The results show that the transfer free energies change linearly with increasing chain length, demonstrating the principle of additivity, and provide values in reasonable agreement with experiment. The peptide backbone transfer free energy contributions arise from van der Waals interactions in the case of transfer to urea, but from electrostatics on transfer to TMAO solution. The simulations used here allow for the calculation of the solvation and transfer free energy of longer oligoglycine models to be evaluated than is currently possible through experiment. The peptide backbone unit computed transfer free energy of −54 cal/mol/M compares quite favorably with −43 cal/mol/M determined experimentally. PMID:20306490

  18. Backbone Additivity in the Transfer Model of Protein Solvation

    SciTech Connect

    Hu, Char Y.; Kokubo, Hironori; Lynch, Gillian C.; Bolen, D Wayne; Pettitt, Bernard M.

    2010-05-01

    The transfer model implying additivity of the peptide backbone free energy of transfer is computationally tested. Molecular dynamics simulations are used to determine the extent of change in transfer free energy (ΔGtr) with increase in chain length of oligoglycine with capped end groups. Solvation free energies of oligoglycine models of varying lengths in pure water and in the osmolyte solutions, 2M urea and 2M trimethylamine N-oxide (TMAO), were calculated from simulations of all atom models, and ΔGtr values for peptide backbone transfer from water to the osmolyte solutions were determined. The results show that the transfer free energies change linearly with increasing chain length, demonstrating the principle of additivity, and provide values in reasonable agreement with experiment. The peptide backbone transfer free energy contributions arise from van der Waals interactions in the case of transfer to urea, but from electrostatics on transfer to TMAO solution. The simulations used here allow for the calculation of the solvation and transfer free energy of longer oligoglycine models to be evaluated than is currently possible through experiment. The peptide backbone unit computed transfer free energy of –54 cal/mol/Mcompares quite favorably with –43 cal/mol/M determined experimentally.

  19. Injector for scattering measurements on fully solvated biospecies.

    PubMed

    Weierstall, U; Spence, J C H; Doak, R B

    2012-03-01

    We describe a liquid jet injector system developed to deliver fully solvated microscopic target species into a probe beam under either vacuum or ambient conditions. The injector was designed specifically for x-ray scattering studies of biological nanospecies using x-ray free electron lasers and third generation synchrotrons, but is of interest to any application in which microscopic samples must be delivered in a fully solvated state and with microscopic precision. By utilizing a gas dynamic virtual nozzle (GDVN) to generate a sample-containing liquid jet of diameter ranging from 300 nm to 20 μm, the injector avoids the clogging problems associated in this size range with conventional Rayleigh jets. A differential pumping system incorporated into the injector shields the experimental chamber from the gas load of the GDVN, making the injector compatible with high vacuum systems. The injector houses a fiber-optically coupled pump laser to illuminate the jet for pump-probe experiments and a hermetically sealed microscope to observe the liquid jet for diagnostics and alignment during operation. This injector system has now been used during several experimental runs at the Linac Coherent Light Source. Recent refinements in GDVN design are also presented. PMID:22462961

  20. Injector for scattering measurements on fully solvated biospecies

    SciTech Connect

    Weierstall, U.; Spence, J. C. H.; Doak, R. B.

    2012-03-15

    We describe a liquid jet injector system developed to deliver fully solvated microscopic target species into a probe beam under either vacuum or ambient conditions. The injector was designed specifically for x-ray scattering studies of biological nanospecies using x-ray free electron lasers and third generation synchrotrons, but is of interest to any application in which microscopic samples must be delivered in a fully solvated state and with microscopic precision. By utilizing a gas dynamic virtual nozzle (GDVN) to generate a sample-containing liquid jet of diameter ranging from 300 nm to 20 {mu}m, the injector avoids the clogging problems associated in this size range with conventional Rayleigh jets. A differential pumping system incorporated into the injector shields the experimental chamber from the gas load of the GDVN, making the injector compatible with high vacuum systems. The injector houses a fiber-optically coupled pump laser to illuminate the jet for pump-probe experiments and a hermetically sealed microscope to observe the liquid jet for diagnostics and alignment during operation. This injector system has now been used during several experimental runs at the Linac Coherent Light Source. Recent refinements in GDVN design are also presented.

  1. Minimalist explicit solvation models for surface loops in proteins.

    PubMed

    White, Ronald P; Meirovitch, Hagai

    2006-01-01

    We have performed molecular dynamics simulations of protein surface loops solvated by explicit water, where a prime focus of the study is the small numbers (e.g., ~100) of explicit water molecules employed. The models include only part of the protein (typically 500 - 1000 atoms), and the water molecules are restricted to a region surrounding the loop. In this study, the number of water molecules (N(w)) is systematically varied, and convergence with large N(w) is monitored to reveal N(w)(min), the minimum number required for the loop to exhibit realistic (fully hydrated) behavior. We have also studied protein surface coverage, as well as diffusion and residence times for water molecules as a function of N(w). A number of other modeling parameters are also tested. These include the number of environmental protein atoms explicitly considered in the model, as well as two ways to constrain the water molecules to the vicinity of the loop (where we find one of these methods to perform better when N(w) is small). The results (for RMSD and its fluctuations for four loops) are further compared to much larger, fully solvated systems (using ~10,000 water molecules under periodic boundary conditions and Ewald electrostatics), and to results for the GBSA implicit solvation model. We find that the loop backbone can stabilize with a surprisingly small number of water molecules (as low as 5 molecules per amino acid residue). The side chains of the loop require somewhat larger N(w), where the atomic fluctuations become too small if N(w) is further reduced. Thus, in general, we find adequate hydration to occur at roughly 12 water molecules per residue. This is an important result, because at this hydration level, computational times are comparable to those required for GBSA. Therefore these "minimalist explicit models" can provide a viable and potentially more accurate alternative. The importance of protein loop modeling is discussed in the context of these, and other, loop models

  2. Solvation of electrolytes and nonelectrolytes in aqueous solutions.

    PubMed

    Afanas'ev, V N

    2011-05-26

    A new theory of electrolyte and nonelectrolyte solutions has been developed which, unlike the Debye-Hückel method applicable for small concentrations only, makes it possible to estimate thermodynamic properties of a solution in a wide range of state parameters. One of the main novelties of the proposed theory is that it takes into account the dependence of solvation numbers upon the concentration of solution, and all changes occurring in the solution are connected with solvation of the stoichiometric mixture of electrolyte ions or molecules. The present paper proposes a rigorous thermodynamic analysis of hydration parameters of solutions. Ultrasound and densimetric measurements in combination with data on isobaric heat capacity have been used to study aqueous solutions of electrolytes NaNO3, KI, NaCl, KCl, MgCl2, and MgSO4 and of nonelectrolytes urea, urotropine, and acetonitrile. Structural characteristics of hydration complexes have been analyzed: hydration numbers h, the proper volume of the stoichiometric mixture of ions without hydration shells V(2h), compressibility β(1h), and the molar volume of water in hydration shells V(1h), their dependencies on concentration and temperature. It has been shown that for aqueous solutions the electric field of ions and molecules of nonelectrolytes has a greater influence on the temperature dependence of the molar volume of solution in hydration shells than a simple change of pressure. The cause of this effect may be due to the change in the dielectric permeability of water in the immediate vicinity of hydrated ions or molecules. The most studied compounds (NaCl, KCl, KI, MgCl2) have been studied in a wider range of solute concentrations of up to 4-5 mol/kg. Up to the complete solvation limit (CSL), the functions V(1h) = f(T) and β(1h) = f(T) are linear with a high correlation factor, and the dependence Y(K,S) = f(β1V1*) at all investigated concentrations of electrolytes and nonelectrolytes up to the CSL enables h and

  3. A solvation-free-energy functional: a reference-modified density functional formulation.

    PubMed

    Sumi, Tomonari; Mitsutake, Ayori; Maruyama, Yutaka

    2015-07-01

    The three-dimensional reference interaction site model (3D-RISM) theory, which is one of the most applicable integral equation theories for molecular liquids, overestimates the absolute values of solvation-free-energy (SFE) for large solute molecules in water. To improve the free-energy density functional for the SFE of solute molecules, we propose a reference-modified density functional theory (RMDFT) that is a general theoretical approach to construct the free-energy density functional systematically. In the RMDFT formulation, hard-sphere (HS) fluids are introduced as the reference system instead of an ideal polyatomic molecular gas, which has been regarded as the appropriate reference system of the interaction-site-model density functional theory for polyatomic molecular fluids. We show that using RMDFT with a reference HS system can significantly improve the absolute values of the SFE for a set of neutral amino acid side-chain analogues as well as for 504 small organic molecules. PMID:26032201

  4. Solvation phenomena in dilute multicomponent solutions I. Formal results and molecular outlook.

    PubMed

    Chialvo, Ariel A; Chialvo, Sebastian; Simonson, J Michael; Kalyuzhnyi, Yu V

    2008-06-01

    We derive second-order thermodynamically consistent truncated composition expansions for the species residual partial molar properties--including volume, enthalpy, entropy, and Gibbs free energy--of dilute ternary systems aimed at the molecular account of solvation phenomena in compressible media. Then, we provide explicit microscopic interpretation of the expansion coefficients in terms of direct and total correlation function integrals over the microstructure of the corresponding infinite dilution reference system, as well as their pressure and temperature derivatives, allowing for the direct prediction of the species partial molar properties from the knowledge of the effective intermolecular interactions. Finally, we apply these formal results (a) to derive consistent expressions for the corresponding properties of the binary system counterparts, (b) to illustrate how the formal expressions converge, at the zero density limit, to those for multicomponent mixtures of imperfect gases obeying the virial equation of state Z = 1 + BPkT, and (c) to discuss, and highlight with examples from the literature, the thermodynamic inconsistencies encountered in the currently available first-order truncated expansions, by pinpointing the mathematical origin and physical meaning of the inconsistencies that render the first-order truncated expansions invalid. PMID:18537438

  5. Mixed direct-iterative methods for boundary integral formulations of continuum dielectric solvation models

    SciTech Connect

    Corcelli, S.A.; Kress, J.D.; Pratt, L.R.

    1995-08-07

    This paper develops and characterizes mixed direct-iterative methods for boundary integral formulations of continuum dielectric solvation models. We give an example, the Ca{sup ++}{hor_ellipsis}Cl{sup {minus}} pair potential of mean force in aqueous solution, for which a direct solution at thermal accuracy is difficult and, thus for which mixed direct-iterative methods seem necessary to obtain the required high resolution. For the simplest such formulations, Gauss-Seidel iteration diverges in rare cases. This difficulty is analyzed by obtaining the eigenvalues and the spectral radius of the non-symmetric iteration matrix. This establishes that those divergences are due to inaccuracies of the asymptotic approximations used in evaluation of the matrix elements corresponding to accidental close encounters of boundary elements on different atomic spheres. The spectral radii are then greater than one for those diverging cases. This problem is cured by checking for boundary element pairs closer than the typical spatial extent of the boundary elements and for those cases performing an ``in-line`` Monte Carlo integration to evaluate the required matrix elements. These difficulties are not expected and have not been observed for the thoroughly coarsened equations obtained when only a direct solution is sought. Finally, we give an example application of hybrid quantum-classical methods to deprotonation of orthosilicic acid in water.

  6. Adsorption and solvation of ethanol at the water liquid-vapor interface: a molecular dynamics study

    NASA Technical Reports Server (NTRS)

    Wilson, M. A.; Pohorille, A.

    1997-01-01

    The free energy profiles of methanol and ethanol at the water liquid-vapor interface at 310K were calculated using molecular dynamics computer simulations. Both alcohols exhibit a pronounced free energy minimum at the interface and, therefore, have positive adsorption at this interface. The surface excess was computed from the Gibbs adsorption isotherm and was found to be in good agreement with experimental results. Neither compound exhibits a free energy barrier between the bulk and the surface adsorbed state. Scattering calculations of ethanol molecules from a gas phase thermal distribution indicate that the mass accommodation coefficient is 0.98, and the molecules become thermalized within 10 ps of striking the interface. It was determined that the formation of the solvation structure around the ethanol molecule at the interface is not the rate-determining step in its uptake into water droplets. The motion of an ethanol molecule in a water lamella was followed for 30 ns. The time evolution of the probability distribution of finding an ethanol molecule that was initially located at the interface is very well described by the diffusion equation on the free energy surface.

  7. Assessing the performance of implicit solvation models at a nucleic acid surface

    PubMed Central

    Dong, Feng; Wagoner, Jason A.; Baker, Nathan A.

    2008-01-01

    Implicit solvation models are popular alternatives to explicit solvent methods due to their ability to “pre-average” solvent behavior and thus reduce the need for computationally-expensive sampling. Previously, we have demonstrated that Poisson-Boltzmann models for polar solvation and integral-based models for nonpolar solvation can reproduce explicit solvation forces in a low-charge density protein system. In the present work, we examine the ability of these continuum models to describe solvation forces at the surface of a RNA hairpin. While these models do not completely describe all of the details of solvent behavior at this highly-charged biomolecular interface, they do provide a reasonable description of average solvation forces and therefore show significant promise for developing more robust implicit descriptions of solvent around nucleic acid systems for use in biomolecular simulation and modeling. Additionally, we observe fairly good transferability in the nonpolar model parameters optimized for protein systems, suggesting its robustness for modeling general nonpolar solvation phenomena in biomolecular systems. PMID:18688533

  8. The solvation of ions in acetonitrile and acetone. II. Monte Carlo simulations using polarizable solvent models

    NASA Astrophysics Data System (ADS)

    Fischer, R.; Richardi, J.; Fries, P. H.; Krienke, H.

    2002-11-01

    Structural properties and energies of solvation are simulated for alkali and halide ions. The solvation structure is discussed in terms of various site-site distribution functions, of solvation numbers, and of orientational correlation functions of the solvent molecules around the ions. The solvent polarizability has notable effects which cannot be intuitively predicted. In particular, it is necessary to reproduce the experimental solvation numbers of small ions. The changes of solvation properties are investigated along the alkali and halide series. By comparing the solvation of ions in acetone to that in acetonitrile, it is shown that the spatial correlations among the solvent molecules around an ion result in a strong screening of the ion-solvent direct intermolecular potential and are essential to understand the changes in the solvation structures and energies between different solvents. The solvation properties derived from the simulations are compared to earlier predictions of the hypernetted chain (HNC) approximation of the molecular Ornstein-Zernike (MOZ) theory [J. Richardi, P. H. Fries, and H. Krienke, J. Chem. Phys. 108, 4079 (1998)]. The MOZ(HNC) formalism gives an overall qualitatively correct picture of the solvation and its various unexpected findings are corroborated. For the larger ions, its predictions become quantitative. The MOZ approach allows to calculate solvent-solvent and ion-solvent potentials of mean force, which shed light on the 3D labile molecular and ionic architectures in the solution. These potentials of mean force convey a unique information which is necessary to fully interpret the angle-averaged structural functions computed from the simulations. Finally, simulations of solutions at finite concentrations show that the solvent-solvent and ion-solvent spatial correlations at infinite dilution are marginally altered by the introduction of fair amounts of ions.

  9. Lithium Enolates Derived from Pyroglutaminol: Aggregation, Solvation, and Atropisomerism.

    PubMed

    Houghton, Michael J; Biok, Naomi A; Huck, Christopher J; Algera, Russell F; Keresztes, Ivan; Wright, Stephen W; Collum, David B

    2016-05-20

    Lithium enolates derived from protected pyroglutaminols were characterized by using (6)Li, (13)C, and (19)F NMR spectroscopies in conjunction with the method of continuous variations. Mixtures of tetrasolvated dimers and tetrasolvated tetramers in different proportions depend on the steric demands of the hemiaminal protecting group, tetrahydrofuran concentration, and the presence or absence of an α-fluoro moiety. The high steric demands of the substituted bicyclo[3.3.0] ring system promote dimers to an unusual extent and allow solvents and atropisomers in cubic tetramers to be observed in the slow-exchange limit. Pyridine used as a (6)Li chemical shift reagent proved useful in assigning solvation numbers. PMID:27035057

  10. Improved Dielectric Solvation Model for Electronic Structure Calculations

    SciTech Connect

    Chipman, Daniel

    2015-12-16

    This project was originally funded for the three year period from 09/01/2009 to 08/31/2012. Subsequently a No-Cost Extension was approved for a revised end date of 11/30/2013. The primary goals of the project were to develop continuum solvation models for nondielectric short-range interactions between solvent and solute that arise from dispersion, exchange, and hydrogen bonding. These goals were accomplished and are reported in the five peer-reviewed journal publications listed in the bibliography below. The secondary goals of the project included derivation of analytic gradients for the models, improvement of the cavity integration scheme, application of the models to the core-level spectroscopy of water, and several other miscellaneous items. These goals were not accomplished because they depended on completion of the primary goals, after which there was a lack of time for any additional effort.

  11. Solvation of Na+, K+, and Their Dimers in Helium

    PubMed Central

    An der Lan, Lukas; Bartl, Peter; Leidlmair, Christian; Jochum, Roland; Denifl, Stephan; Echt, Olof; Scheier, Paul

    2012-01-01

    Helium atoms bind strongly to alkali cations which, when embedded in liquid helium, form so-called snowballs. Calculations suggest that helium atoms in the first solvation layer of these snowballs form rigid structures and that their number (n) is well defined, especially for the lighter alkalis. However, experiments have so far failed to accurately determine values of n. We present high-resolution mass spectra of Na+Hen, K+Hen, Na2+Hen and K2+Hen, formed by electron ionization of doped helium droplets; the data allow for a critical comparison with several theoretical studies. For sodium and potassium monomers the spectra indicate that the value of n is slightly smaller than calculated. Na2+Hen displays two distinct anomalies at n=2 and n=6, in agreement with theory; dissociation energies derived from experiment closely track theoretical values. K2+Hen distributions are fairly featureless, which also agrees with predictions. PMID:22374575

  12. Proton Solvation and Transport in Aqueous and Biomolecular Systems

    PubMed Central

    Swanson, Jessica M. J.; Maupin, C. Mark; Chen, Hanning; Petersen, Matt K.; Xu, Jiancong; Wu, Yujie; Voth, Gregory A.

    2008-01-01

    The excess proton in aqueous media plays a pivotal role in many fundamental chemical (e.g., acid-base chemistry) and biological (e.g., bioenergetics and enzyme catalysis) processes. Understanding the hydrated proton is, therefore, crucial for chemistry, biology, and materials sciences. Although well studied for over 200 years, excess proton solvation and transport remains to this day mysterious, surprising, and perhaps even misunderstood. In this feature article various efforts to address this problem through computer modeling and simulation will be described. Applications of computer simulations to a number of important and interesting systems will be presented, highlighting the roles of charge delocalization and Grotthuss shuttling, a phenomenon unique in many ways to the excess proton in water. PMID:17429993

  13. Trimesic acid dimethyl sulfoxide solvate: space group revision

    PubMed Central

    Bernès, Sylvain; Hernández, Guadalupe; Portillo, Roberto; Gutiérrez, René

    2008-01-01

    The structure of the title solvate, C9H6O6·C2H6OS, was determined 30 years ago [Herbstein, Kapon & Wasserman (1978 ▶). Acta Cryst. B34, 1613–1617], with data collected at room temperature, and refined in the space group P21. The present redetermination, based on high-resolution diffraction data, shows that the actual space group is more likely to be P21/m. The crystal structure contains layers of trimesic acid molecules lying on mirror planes. A mirror plane also passes through the S and O atoms of the solvent molecule. The molecules in each layer are inter­connected through strong O—H⋯O hydrogen bonds, forming a two-dimensional supra­molecular network within each layer. The donor groups are the hydroxyls of the trimesic acid mol­ecules, while the acceptors are the carbonyl or the sulfoxide O atoms. PMID:21202984

  14. Solvation free energies of alanine peptides: the effect of flexibility.

    PubMed

    Kokubo, Hironori; Harris, Robert C; Asthagiri, Dilipkumar; Pettitt, B Montgomery

    2013-12-27

    The electrostatic (ΔGel), van der Waals cavity-formation (ΔGvdw), and total (ΔG) 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 fixed, extended conformations of the peptides and again for some of the peptides without constraints. The solvation free energies, ΔGel, and components ΔGvdw, and ΔG, were found to be linear in n, with the slopes of the best-fit lines being γel, γvdw, and γ, respectively. Both γel and γ were negative for fixed and flexible peptides, and γvdw was negative for fixed peptides. That γvdw was negative was surprising, as experimental data on alkanes, theoretical models, and MD computations on small molecules and model systems generally suggest that γvdw should be positive. A negative γvdw seemingly contradicts the notion that ΔGvdw drives the initial collapse of the protein when it folds by favoring conformations with small surface areas. When we computed ΔGvdw for the flexible peptides, thereby allowing the peptides to assume natural ensembles of more compact conformations, γvdw was positive. Because most proteins do not assume extended conformations, a ΔGvdw 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 find few intramolecular H-bonds but show that the intramolecular van der Waals interaction energy is more favorable for the flexible than for the extended peptides, seemingly favoring this hypothesis. The large fluctuations in the vdw energy may make attributing the collapse of the peptide to this intramolecular energy difficult. PMID:24328358

  15. Solvation Free Energies of Alanine Peptides: The Effect of Flexibility

    PubMed Central

    Kokubo, Hironori; Harris, Robert C.; Asthigiri, Dilipkumar; Pettitt, B. Montgomery

    2014-01-01

    The electrostatic (ΔGel), van der Waals cavity-formation (ΔGvdw), and total (ΔG) 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 fixed, extended conformations of the peptides and again for some of the peptides without constraints. The solvation free energies, ΔGel, and components ΔGvdw, and ΔG, were found to be linear in n, with the slopes of the best-fit lines being γel, γvdw, and γ, respectively. Both γel and γ were negative for fixed and flexible peptides, and γvdw was negative for fixed peptides. That γvdw was negative was surprising, as experimental data on alkanes, theoretical models, and MD computations on small molecules and model systems generally suggest that γvdw should be positive. A negative γvdw seemingly contradicts the notion that ΔGvdw drives the initial collapse of the protein when it folds by favoring conformations with small surface areas. When we computed ΔGvdw for the flexible peptides, thereby allowing the peptides to assume natural ensembles of more compact conformations, γvdw was positive. Because most proteins do not assume extended conformations, a ΔGvdw 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 find few intramolecular h-bonds but 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. The large fluctuations in the vdw energy may make attributing the collapse of the peptide to this intramolecular energy difficult. PMID:24328358

  16. Solvation Free Energies of Alanine Peptides: The Effect of Flexibility

    SciTech Connect

    Kokubo, Hironori; Harris, Robert C.; Asthagiri, Dilip; Pettitt, Bernard M.

    2013-12-03

    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, 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.

  17. Disentangling polar and non-polar solvation with 2D spectra

    NASA Astrophysics Data System (ADS)

    Yu, Anchi; Hybl, John; Farrow, Darcie; Jonas, David

    2002-03-01

    Polar and non-polar solvation are closely connected in polar solvents. Nonlinear spectroscopy of two structurally related cyanines (with and without a dipole moment change upon electronic excitation) were compared in several solvents. In each solvent, each relaxation timescale observed for polar solvation has a corresponding non-polar timescale. The timescales and amplitudes of the polar relaxation are always slower and larger. The fastest solvation components are extracted from two-dimensional Fourier transform spectra. The question of whether Brownian oscillator models can capture the observed relaxation will be discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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 , and second osmotic virial coefficient B 2 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.

  19. Molecular Dynamics Simulation of Ion Solvation in Polymer Melts: Effects of Dielectric Inhomogeneity and Chain Connectivity on Solvation Energy of Ions

    NASA Astrophysics Data System (ADS)

    Liu, Lijun; Nakamura, Issei

    We study the ion solvation in block copolymer melts and polymer blends using molecular dynamics simulations. In our simulations, polymers are formed through the connection of beads that provide the dielectric response. Thus, we highlight the effect of the dielectric contrast between different species on the solvation energy of ions. We demonstrate the local enrichment of higher-dielectric components near ions, which corresponds well with the result of mean-field theories. Moreover, the chain connectivity significantly affects the reorientation of molecular dipoles in response to the electrostatic field from ions. Thus, we illustrate the marked difference in the solvation energy between the block copolymer and polymer blend. Importantly, the solvation energy substantially depends on the chain length of the polymers, in stark contrast to the Born solvation energy. We also show that our simulation results exhibit striking similarity to the result of the recent self-consistent mean field theories. However, for strongly correlated dipoles and ions, our simulations provide qualitatively opposite behaviors to these results, suggesting further development of the theoretical frameworks. This work was supported by the National Natural Science Foundation of China (21474112 and 21404103). We are grateful to the Computing Center of Jilin Province for essential support.

  20. 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

    2015-06-01

    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. PMID:26049523

  1. Structure and dynamics of solvated hydrogenoxalate and oxalate anions: a theoretical study.

    PubMed

    Kroutil, Ondřej; Minofar, Babak; Kabeláč, Martin

    2016-09-01

    Hydrogenoxalate (charge -1) and oxalate (charge -2) anions and their solvated forms were studied by various computational techniques. Ab initio quantum chemical calculations in gas phase, in implicit solvent and microsolvated (up to 32 water molecules) environment were performed in order to explore a potential energy surface of both anions. The solvation envelope of water molecules around them and the role of water on the conformation of the anions was revealed by means of Born-Oppenheimer molecular dynamics simulations and optimization procedures. The structure of the anions was found to be dependent on the number of water molecules in the solvation shell. A subtle interplay between intramolecular and intermolecular hydrogen bonding dictates the final conformation and thus an explicit solvent model is necessary for a proper description of this phenomena. Graphical Abstract Solvated hydrogenoxalate and oxalate anions. PMID:27538930

  2. Unusual solvation through both p-orbital lobes of a carbene carbon

    NASA Astrophysics Data System (ADS)

    Hadad, C. Z.; Jenkins, Samantha; Flórez, Elizabeth

    2015-03-01

    As a result of a configurational space search done to explain the experimental evidence of transient specific solvation of singlet fluorocarbene amide with tetrahydrofuran, we found that the most stable structures consist in a group in which each oxygen of two tetrahydrofuran molecules act as electron donor to its respective empty p-orbital lobe of the carbene carbon atom, located at each side of the carbene molecular plane. This kind of species, which to our knowledge has not been reported before, explains very well the particular experimental characteristics observed for the transient solvation of this system. We postulate that the simultaneous interaction to both p-orbital lobes seems to confer a special stability to the solvation complexes, because this situation moves away the systems from the proximity of the corresponding transition states for the ylide products. Additionally, we present an analysis of other solvation complexes and a study of the nature of the involved interactions.

  3. Rate and Amplitude Heterogeneity in the Solvation Response of an Ionic Liquid.

    PubMed

    Verma, Sachin Dev; Corcelli, Steven A; Berg, Mark A

    2016-02-01

    In contrast with conventional liquids, ionic liquids have solvation dynamics with more rate dispersion and with average times that do not agree with dielectric measurements. A kinetic analog of multidimensional spectroscopy is introduced and used to look for heterogeneity in simulations of coumarin 153 in [Im12][BF4]. Strong heterogeneity is found in the diffusive solvation rate. An unanticipated heterogeneity in the amplitude of the inertial solvation is also seen. Both heterogeneities exchange at the same rate. This rate is similar to the mean diffusive solvation time, putting it in the intermediate-exchange region. Overall, there are multiple violations of the assumptions usually invoked in the theory of reaction dynamics. PMID:26765835

  4. 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...

  5. Unusual solvation through both p-orbital lobes of a carbene carbon

    SciTech Connect

    Hadad, C. Z.; Jenkins, Samantha; Flórez, Elizabeth

    2015-03-07

    As a result of a configurational space search done to explain the experimental evidence of transient specific solvation of singlet fluorocarbene amide with tetrahydrofuran, we found that the most stable structures consist in a group in which each oxygen of two tetrahydrofuran molecules act as electron donor to its respective empty p-orbital lobe of the carbene carbon atom, located at each side of the carbene molecular plane. This kind of species, which to our knowledge has not been reported before, explains very well the particular experimental characteristics observed for the transient solvation of this system. We postulate that the simultaneous interaction to both p-orbital lobes seems to confer a special stability to the solvation complexes, because this situation moves away the systems from the proximity of the corresponding transition states for the ylide products. Additionally, we present an analysis of other solvation complexes and a study of the nature of the involved interactions.

  6. Fast Calculations of Electrostatic Solvation Free Energy from Reconstructed Solvent Density using proximal Radial Distribution Functions

    PubMed Central

    Lin, Bin; Wong, Ka-Yiu; Hu, Char; Kokubo, Hironori; Pettitt, B. Montgomery

    2011-01-01

    Although detailed atomic models may be applied for a full description of solvation, simpler phenomenological models are particularly useful to interpret the results for scanning many, large, complex systems where a full atomic model is too computationally expensive to use. Among the most costly are solvation free energy evaluations by simulation. Here we develop a fast way to calculate electrostatic solvation free energy while retaining much of the accuracy of explicit solvent free energy simulation. The basis of our method is to treat the solvent not as a structureless dielectric continuum, but as a structured medium by making use of universal proximal radial distribution functions. Using a deca-alanine peptide as a test case, we compare the use of our theory with free energy simulations and traditional continuum estimates of the electrostatic solvation free energy. PMID:21765968

  7. Fast Calculations of Electrostatic Solvation Free Energy from Reconstructed Solvent Density Using Proximal Radial Distribution Functions

    SciTech Connect

    Lin, Bin; Wong, Ka-Yiu; Hu, Char Y.; Kokubo, Hironori; Pettitt, Bernard M.

    2011-07-07

    Although detailed atomic models may be applied for a full description of solvation, simpler phenomenologicalmodels are particularly useful to interpret the results for scanning many large, complex systems, where a full atomic model is too computationally expensive to use. Among the most costly are solvation free-energy evaluations by simulation. Here we develop a fast way to calculate electrostatic solvation free energy while retaining much of the accuracy of explicit solvent free-energy simulation. The basis of our method is to treat the solvent not as a structureless dielectric continuum but as a structured medium by making use of universal proximal radial distribution functions. Using a deca-alanine peptide as a test case, we compare the use of our theory with free-energy simulations and traditional continuum estimates of the electrostatic solvation free energy.

  8. Extended Debye-Hückel theory for studying the electrostatic solvation energy.

    PubMed

    Xiao, Tiejun

    2015-03-16

    The electrostatic part of the solvation energy has been studied by using extended Debye-Hückel (DH) theories. Specifically, our molecular Debye-Hückel theory [J. Chem. Phys. 2011, 135, 104104] and its simplified version, an energy-scaled Debye-Hückel theory, were applied to electrolytes with strong electrostatic coupling. Our theories provide a practical methodology for calculating the electrostatic solvation free energies, and the accuracy was verified for atomic and diatomic charged solutes. PMID:25640184

  9. Solvation of lithium chloride in aqueous and mixed solutions of an aprotic solvent

    NASA Astrophysics Data System (ADS)

    Zabolotskii, V. I.; Demin, A. V.; Demina, O. A.

    2013-02-01

    The dynamic hydration and solvation numbers of lithium chloride are estimated on the basis of experimental data on the limiting electrodialysis concentration of an electrolyte from aqueous and aqueousorganic solutions containing aprotic solvent N,N-dimethylacetamide. It is established that the dependence of the hydration numbers of the salt on the volume fraction of the aprotic solvent is of an extreme character, and its solvation number on N,N-dimethylacetamide does not depend on the composition of the mixed solution.

  10. Solvation thermodynamics and heat capacity of polar and charged solutes in water

    SciTech Connect

    Sedlmeier, Felix; Netz, Roland R.

    2013-03-21

    The solvation thermodynamics and in particular the solvation heat capacity of polar and charged solutes in water is studied using atomistic molecular dynamics simulations. As ionic solutes we consider a F{sup -} and a Na{sup +} ion, as an example for a polar molecule with vanishing net charge we take a SPC/E water molecule. The partial charges of all three solutes are varied in a wide range by a scaling factor. Using a recently introduced method for the accurate determination of the solvation free energy of polar solutes, we determine the free energy, entropy, enthalpy, and heat capacity of the three different solutes as a function of temperature and partial solute charge. We find that the sum of the solvation heat capacities of the Na{sup +} and F{sup -} ions is negative, in agreement with experimental observations, but our results uncover a pronounced difference in the heat capacity between positively and negatively charged groups. While the solvation heat capacity {Delta}C{sub p} stays positive and even increases slightly upon charging the Na{sup +} ion, it decreases upon charging the F{sup -} ion and becomes negative beyond an ion charge of q=-0.3e. On the other hand, the heat capacity of the overall charge-neutral polar solute derived from a SPC/E water molecule is positive for all charge scaling factors considered by us. This means that the heat capacity of a wide class of polar solutes with vanishing net charge is positive. The common ascription of negative heat capacities to polar chemical groups might arise from the neglect of non-additive interaction effects between polar and apolar groups. The reason behind this non-additivity is suggested to be related to the second solvation shell that significantly affects the solvation thermodynamics and due to its large spatial extent induces quite long-ranged interactions between solvated molecular parts and groups.

  11. 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. PMID:25093354

  12. Theoretical studies on solvation contribution to the thermodynamic stability of mutants of lysozyme T4.

    PubMed

    Deep, Shashank; Ahluwalia, J C

    2003-06-01

    Atomic solvation parameters (ASPs) are widely used to estimate the solvation contribution to the thermodynamic stability of proteins as well as the free energy of association for protein-ligand complexes. In view of discrepancies in the results of free energies of solvation of folding for various proteins obtained using different atomic solvation parameter sets, systematic studies have been carried out for the calculation of accessible surface area and the changes in free energy of solvation of folding (deltaG(s,f)) for mutants of lysozyme T4 where threonine 157 is replaced by amino acids: cysteine, aspartate, glutamate, phenylalanine, glycine, histidine, isoleucine, leucine, asparagine, arginine, serine and valine. The deviations of the calculated results from the experimental results are discussed to highlight the discrepancies in the atomic solvation parameter sets and possible reasons for them. The results are also discussed to throw light on the effect of chain free energy and hydrogen bonding on the stability of mutants. The octanol to water-based ASP sets 'Sch1' and 'EM' perform better than the vacuum to water-based ASP sets. The vacuum to water-based ASP sets 'Sch3' and 'WE' can be used to predict the stability of mutants if a proper method to calculate the hydrogen bond contribution to overall stability is in place. PMID:12874374

  13. Spicing up continuum solvation models with SaLSA: The spherically averaged liquid susceptibility ansatz

    SciTech Connect

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

    2015-02-07

    Continuum solvation models enable electronic structure calculations of systems in liquid environments, but because of the large number of empirical parameters, they are limited to the class of systems in their fit set (typically organic molecules). Here, we derive a solvation model with no empirical parameters for the dielectric response by taking the linear response limit of a classical density functional for molecular liquids. This model directly incorporates the nonlocal dielectric response of the liquid using an angular momentum expansion, and with a single fit parameter for dispersion contributions it predicts solvation energies of neutral molecules with a RMS error of 1.3 kcal/mol in water and 0.8 kcal/mol in chloroform and carbon tetrachloride. We show that this model is more accurate for strongly polar and charged systems than previous solvation models because of the parameter-free electric response, and demonstrate its suitability for ab initio solvation, including self-consistent solvation in quantum Monte Carlo calculations.

  14. Solvation-Driven Charge Transfer and Localization in Metal Complexes

    PubMed Central

    2016-01-01

    Conspectus In any physicochemical process in liquids, the dynamical response of the solvent to the solutes out of equilibrium plays a crucial role in the rates and products: the solvent molecules react to the changes in volume and electron density of the solutes to minimize the free energy of the solution, thus modulating the activation barriers and stabilizing (or destabilizing) intermediate states. In charge transfer (CT) processes in polar solvents, the response of the solvent always assists the formation of charge separation states by stabilizing the energy of the localized charges. A deep understanding of the solvation mechanisms and time scales is therefore essential for a correct description of any photochemical process in dense phase and for designing molecular devices based on photosensitizers with CT excited states. In the last two decades, with the advent of ultrafast time-resolved spectroscopies, microscopic models describing the relevant case of polar solvation (where both the solvent and the solute molecules have a permanent electric dipole and the mutual interaction is mainly dipole–dipole) have dramatically progressed. Regardless of the details of each model, they all assume that the effect of the electrostatic fields of the solvent molecules on the internal electronic dynamics of the solute are perturbative and that the solvent–solute coupling is mainly an electrostatic interaction between the constant permanent dipoles of the solute and the solvent molecules. This well-established picture has proven to quantitatively rationalize spectroscopic effects of environmental and electric dynamics (time-resolved Stokes shifts, inhomogeneous broadening, etc.). However, recent computational and experimental studies, including ours, have shown that further improvement is required. Indeed, in the last years we investigated several molecular complexes exhibiting photoexcited CT states, and we found that the current description of the formation and

  15. Was Abraham Lincoln gay?

    PubMed

    Ferguson, Michael

    2010-01-01

    Scholars and historians are blind to Lincoln's same-sex inclinations in part because of a personal aversion to male homosexuality, but more importantly because they fail to perceive the vast differences between the sexual culture of antebellum America and that of our own time, especially in regard to male-male physical and emotional intimacy. This article brings those differences to light and sets Lincoln's life in the context of the sexual culture of his own time. This enables one to see that Lincoln's same-sex sexuality was not only unproblematic, but commonplace, if not typical, in his day. Revising the Myth of Lincoln in regard to his same-sex inclinations will have a positive effect on contemporary culture, especially on the education and socialization of young boys. PMID:20924927

  16. The application of the integral equation theory to study the hydrophobic interaction

    PubMed Central

    Mohorič, Tomaž; Urbic, Tomaz; Hribar-Lee, Barbara

    2014-01-01

    The Wertheim's integral equation theory was tested against newly obtained Monte Carlo computer simulations to describe the potential of mean force between two hydrophobic particles. An excellent agreement was obtained between the theoretical and simulation results. Further, the Wertheim's integral equation theory with polymer Percus-Yevick closure qualitatively correctly (with respect to the experimental data) describes the solvation structure under conditions where the simulation results are difficult to obtain with good enough accuracy. PMID:24437891

  17. Solvation structures of water in trihexyltetradecylphosphonium-orthoborate ionic liquids

    NASA Astrophysics Data System (ADS)

    Wang, Yong-Lei; Sarman, Sten; Kloo, Lars; Antzutkin, Oleg N.; Glavatskih, Sergei; Laaksonen, Aatto

    2016-08-01

    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 orthoborate 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.

  18. Zwitterionic phosphorylated quinines as chiral solvating agents for NMR spectroscopy.

    PubMed

    Rudzińska-Szostak, Ewa; Górecki, Łukasz; Berlicki, Łukasz; Ślepokura, Katarzyna; Mucha, Artur

    2015-10-01

    Because of their unique 3D arrangement, naturally occurring Cinchona alkaloids and their synthetic derivatives have found wide-ranging applications in chiral recognition. Recently, we determined the enantioselective properties of C-9-phosphate mixed triesters of quinine as versatile chiral solvating agents in nuclear magnetic resonance (NMR) spectroscopy. In the current study, we introduce new zwitterionic members of this class of molecules containing a negatively charged phosphate moiety (i.e., ethyl, n-butyl and phenyl hydrogen quininyl phosphate). An efficient approach for synthesizing these compounds is elaborated, and full characterization, including conformational and autoaggregation phenomena studies, was performed. Therefore, their ability to induce NMR anisochrony of selected enantiomeric substrates (i.e., primarily N-DNB-protected amino acids and their methyl esters) was analyzed compared to uncharged diphenyl quininyl phosphate and its positively charged quaternary ammonium hydrochloride salt. In addition, (1) H and (13) C NMR experiments revealed their enantiodiscrimination potential toward novel analytes, such as secondary amines and nonprotected amino acids. PMID:26415853

  19. Crystallization of Esomeprazole Magnesium Water/Butanol Solvate.

    PubMed

    Skieneh, Jenna; Khalili Najafabadi, Bahareh; Horne, Stephen; Rohani, Sohrab

    2016-01-01

    The molecular structure of esomeprazole magnesium derivative in the solid-state is reported for the first time, along with a simplified crystallization pathway. The structure was determined using the single crystal X-ray diffraction technique to reveal the bonding relationships between esomeprazole heteroatoms and magnesium. The esomeprazole crystallization process was carried out in 1-butanol and water was utilized as anti-solvent. The product proved to be esomeprazole magnesium tetrahydrate with two 1-butanol molecules that crystallized in P6₃ space group, in a hexagonal unit cell. Complete characterization of a sample after drying was conducted by the use of powder X-ray diffraction (PXRD), ¹H-nuclear magnetic resonance (NMR), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), infrared spectroscopy (IR), and dynamic vapor sorption (DVS). Investigation by ¹H-NMR and TGA has shown that the solvent content in the dried sample consists of two water molecules and 0.3 butanol molecules per esomeprazole magnesium molecule. This is different from the single crystal X-ray diffraction results and can be attributed to the loss of some water and 1-butanol molecules stabilized by intermolecular interactions. The title compound, after drying, is a true solvate in terms of water; conversely, 1-butanol fills the voids of the crystal lattice in non-stoichiometric amounts. PMID:27120591

  20. Solvation structure of ice-binding antifreeze proteins

    NASA Astrophysics Data System (ADS)

    Hansen-Goos, Hendrik; Wettlaufer, John

    2009-03-01

    Antifreeze proteins (AFPs) can be found in organisms which survive at subzero temperatures. They were first discovered in polar fishes since the 1950's [1] and have been isolated meanwhile also from insects, plants, and bacteria. While AFPs shift the freezing point of water below the bulk melting point and hence can prevent recrystallization; the effect is non-colligative and there is a pronounced hysteresis between freezing and melting. For many AFPs it is generally accepted that they function through an irreversible binding to the ice-water interface which leads to a piecewise convex growth front with a lower nonequilibrium freezing point due to the Kelvin effect. Recent molecular dynamics simulations of the AFP from Choristoneura fumiferana reveal that the solvation structures of water at ice-binding and non-ice-binding faces of the protein are crucial for understanding how the AFP binds to the ice surface and how it is protected from being overgrown [2]. We use density functional theory of classical fluids in order to assess the microscopic solvent structure in the vicinity of protein faces with different surface properties. With our method, binding energies of different protein faces to the water-ice-interface can be computed efficiently in a simplified model. [1] Y. Yeh and R.E. Feeney, Chem. Rev. 96, 601 (1996). [2] D.R. Nutt and J.C. Smith, J. Am. Chem. Soc. 130, 13066 (2008).

  1. Solvation of Esters and Ketones in Supercritical CO2.

    PubMed

    Kajiya, Daisuke; Imanishi, Masayoshi; Saitow, Ken-ichi

    2016-02-01

    Vibrational Raman spectra for the C═O stretching modes of three esters with different functional groups (methyl, a single phenyl, and two phenyl groups) were measured in supercritical carbon dioxide (scCO2). The results were compared with Raman spectra for three ketones involving the same functional groups, measured at the same thermodynamic states in scCO2. The peak frequencies of the Raman spectra of these six solute molecules were analyzed by decomposition into the attractive and repulsive energy components, based on the perturbed hard-sphere theory. For all solute molecules, the attractive energy is greater than the repulsive energy. In particular, a significant difference in the attractive energies of the ester-CO2 and ketone-CO2 systems was observed when the methyl group is attached to the ester or ketone. This difference was significantly reduced in the solute systems with a single phenyl group and was completely absent in those with two phenyl groups. The optimized structures among the solutes and CO2 molecules based on quantum chemical calculations indicate that greater attractive energy is obtained for a system where the oxygen atom of the ester is solvated by CO2 molecules. PMID:26741296

  2. High throughput cherry-picking of solvated samples.

    PubMed

    Schmitt, Robert; Traphagen, Linda; Hajduk, Phillip

    2010-07-01

    Advances in the design of automated compound storage systems have made it possible to store large collections of research compounds in individual single-use aliquots dissolved in dimethyl sulfoxide and rapidly retrieve a specific group off them. This 'cherry-picking' approach offers researchers the opportunity to request large numbers of compounds desired for testing without having to also retrieve all the other compounds stored on the same rack or plate. This makes it possible to meet the increasing demand for samples from High Throughput Screening and Therapeutic Area teams without adding staff to dispense from powder each time, without the constraints imposed by storing in solvated compounds in fixed-well 96- or 384-way plates, and without sacrificing sample quality or shelf life by storing at room temperature. We describe how this approach has been implemented at Abbott Laboratories' central compound repository to provide smaller amounts of more compounds faster and with high quality. In doing so, we have been able to better support the innovation of our Drug Discovery colleagues. PMID:20426754

  3. Molecular hydrogen solvated in water – A computational study

    SciTech Connect

    Śmiechowski, Maciej

    2015-12-28

    The aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H{sub 2} molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the H{sub 2} molecule without major structural distortions and two-dimensional, radial-angular distribution functions indicate that as opposed to strictly tangential, the orientation of these water molecules is such that the solute is solvated with one of the free electron pairs of H{sub 2}O. The calculated self-diffusion coefficient of H{sub 2}(aq) agrees very well with experimental results and the time dependence of mean square displacement suggests the presence of caging on a time scale corresponding to hydrogen bond network vibrations in liquid water. Orientational correlation function of H{sub 2} experiences an extremely short-scale decay, making the H{sub 2}–H{sub 2}O interaction potential essentially isotropic by virtue of rotational averaging. The inclusion of explicit polarizability in the model allows for the calculation of Raman spectra that agree very well with available experimental data on H{sub 2}(aq) under differing pressure conditions, including accurate reproduction of the experimentally noted trends with solute pressure or concentration.

  4. Ionic strength independence of charge distributions in solvation of biomolecules.

    PubMed

    Virtanen, J J; Sosnick, T R; Freed, K F

    2014-12-14

    Electrostatic forces enormously impact the structure, interactions, and function of biomolecules. We perform all-atom molecular dynamics simulations for 5 proteins and 5 RNAs to determine the dependence on ionic strength of the ion and water charge distributions surrounding the biomolecules, as well as the contributions of ions to the electrostatic free energy of interaction between the biomolecule and the surrounding salt solution (for a total of 40 different biomolecule/solvent combinations). Although water provides the dominant contribution to the charge density distribution and to the electrostatic potential even in 1M NaCl solutions, the contributions of water molecules and of ions to the total electrostatic interaction free energy with the solvated biomolecule are comparable. The electrostatic biomolecule/solvent interaction energies and the total charge distribution exhibit a remarkable insensitivity to salt concentrations over a huge range of salt concentrations (20 mM to 1M NaCl). The electrostatic potentials near the biomolecule's surface obtained from the MD simulations differ markedly, as expected, from the potentials predicted by continuum dielectric models, even though the total electrostatic interaction free energies are within 11% of each other. PMID:25494774

  5. Solubility and solvation of monosaccharides in ionic liquids.

    PubMed

    Teles, Ana Rita R; Dinis, Teresa B V; Capela, Emanuel V; Santos, Luís M N B F; Pinho, Simão P; Freire, Mara G; Coutinho, João A P

    2016-07-20

    Herein, solubility experimental data for six monosaccharides, viz.d-(+)-glucose, d-(+)-mannose, d-(-)-fructose, d-(+)-galactose, d-(+)-xylose and l-(+)-arabinose, in four ionic liquids (ILs), at temperatures ranging from 288.2 to 348.2 K, were obtained aimed at gathering a better understanding of their solvation ability and molecular-level mechanisms which rule the dissolution process. To ascertain the chemical features that enhance the solubility of monosaccharides, ILs composed of dialkylimidazolium or tetraalkylphosphonium cations combined with the dicyanamide, dimethylphosphate or chloride anions were investigated. It was found that the ranking of the solubility of monosaccharides depends on the IL; yet, d-(+)-xylose is always the most soluble while d-(-)-fructose is the least soluble monosaccharide. The results obtained show that both the IL cation and the anion play a major role in the solubility of monosaccharides. Finally, from the determination of the respective thermodynamic properties of solution, it was found that enthalpic contributions are dominant in the solubilization process. However, the observed differences in the solubilities of monosaccharides in 1-butyl-3-methylimidazolium dicyanamide are ruled by a change in the entropy of solution. PMID:27380720

  6. Molecular hydrogen solvated in water - A computational study

    NASA Astrophysics Data System (ADS)

    Śmiechowski, Maciej

    2015-12-01

    The aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H2 molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the H2 molecule without major structural distortions and two-dimensional, radial-angular distribution functions indicate that as opposed to strictly tangential, the orientation of these water molecules is such that the solute is solvated with one of the free electron pairs of H2O. The calculated self-diffusion coefficient of H2(aq) agrees very well with experimental results and the time dependence of mean square displacement suggests the presence of caging on a time scale corresponding to hydrogen bond network vibrations in liquid water. Orientational correlation function of H2 experiences an extremely short-scale decay, making the H2-H2O interaction potential essentially isotropic by virtue of rotational averaging. The inclusion of explicit polarizability in the model allows for the calculation of Raman spectra that agree very well with available experimental data on H2(aq) under differing pressure conditions, including accurate reproduction of the experimentally noted trends with solute pressure or concentration.

  7. Ionic strength independence of charge distributions in solvation of biomolecules

    SciTech Connect

    Virtanen, J. J.; Sosnick, T. R.; Freed, K. F.

    2014-12-14

    Electrostatic forces enormously impact the structure, interactions, and function of biomolecules. We perform all-atom molecular dynamics simulations for 5 proteins and 5 RNAs to determine the dependence on ionic strength of the ion and water charge distributions surrounding the biomolecules, as well as the contributions of ions to the electrostatic free energy of interaction between the biomolecule and the surrounding salt solution (for a total of 40 different biomolecule/solvent combinations). Although water provides the dominant contribution to the charge density distribution and to the electrostatic potential even in 1M NaCl solutions, the contributions of water molecules and of ions to the total electrostatic interaction free energy with the solvated biomolecule are comparable. The electrostatic biomolecule/solvent interaction energies and the total charge distribution exhibit a remarkable insensitivity to salt concentrations over a huge range of salt concentrations (20 mM to 1M NaCl). The electrostatic potentials near the biomolecule's surface obtained from the MD simulations differ markedly, as expected, from the potentials predicted by continuum dielectric models, even though the total electrostatic interaction free energies are within 11% of each other.

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

    SciTech Connect

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

    2015-04-14

    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

  9. Short-range solvation patterns of pentachlorophenol, triethylamine, and their reaction products by cyclic ethers in cyclohexane

    NASA Astrophysics Data System (ADS)

    Van Camp, Sister Mary Josepha; Morris, Shawn; Mudge, Annmarie; Points, Richard; Knight, Jodi B.; Schullery, Stephen E.; Scott, Ronald M.

    1998-07-01

    The proton-transfer indicator reaction method is applied to the pentachlorophenol-triethylamine proton-transfer equilibrium KPT undergoing solvation by tetrahydropyran, 1,3-dioxane, and 1,4-dioxane in bulk cyclohexane. A predicted decrease in KPT occurs owing to hydrogen bonding solvation of the free phenol upon increasing ether concentration. However, the data unexpectedly suggest that hydrogen bonding solvation by the ethers to the proton of the proton-transfer adduct also occurs.

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

    SciTech Connect

    McGrath, Matthew; Kuo, I-F W.; Ngouana, Brice F.; Ghogomu, Julius N.; Mundy, Christopher J.; Marenich, Aleksandr; Cramer, Christopher J.; Truhlar, Donald G.; Siepmann, Joern I.

    2013-08-28

    The free energy of solvation and dissociation of hydrogen chloride in water is calculated through a combined molecular simulation quantum chemical approach at four temperatures between T = 300 and 450 K. The free energy is first decomposed into the sum of two components: the Gibbs free energy of transfer of molecular HCl from the vapor to the aqueous liquid phase and the standard-state free energy of acid dissociation of HCl in aqueous solution. The former quantity is calculated using Gibbs ensemble Monte Carlo simulations using either Kohn-Sham density functional theory or a molecular mechanics force field to determine the system’s potential energy. The latter free energy contribution is computed using a continuum solvation model utilizing either experimental reference data or micro-solvated clusters. The predicted combined solvation and dissociation free energies agree very well with available experimental data. CJM was supported by the US Department of Energy,Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  11. Uranyl Solvation by a Three-Dimensional Reference Interaction Site Model.

    PubMed

    Matveev, Alexei; Li, Bo; Rösch, Notker

    2015-08-13

    We report an implementation of the three-dimensional reference interaction site model (3D RISM) that in particular addresses the treatment of the long-range Coulomb field of charged species, represented by point charges and/or a distributed charge density. A comparison of 1D and 3D results for atomic ions demonstrates a reasonable accuracy, even for a moderate size of the unit cell and a moderate grid resolution. In an application to uranyl complexes with 4-6 explicit aqua ligands and an implicit bulk solvent modeled by RISM, we show that the 3D technique is not susceptible to the deficiencies of the 1D technique exposed in our previous work [Li, Matveev, Krüger, Rösch, Comp. Theor. Chem. 2015, 1051, 151]. The 3D method eliminates the artificial superposition of explicit aqua ligands and the RISM medium and predicts essentially the same values for uranyl and uranyl-water bond lengths as a state-of-the-art polarizable continuum model. With the first solvation shell treated explicitly, the observables are nearly independent of the order of the closure relationship used when solving the set of integral equations for the various distribution functions. Furthermore, we calculated the activation barrier of water exchange with a hybrid approach that combines the 3D RISM model for the bulk aqueous solvent and a quantum mechanical description (at the level of electronic density functional theory) of uranyl interacting with explicitly represented water molecules. The calculated result agrees very well with experiment and the best theoretical estimates. PMID:26167741

  12. Linear solvation energy relationships (LSER) for adsorption of organic compounds by carbon nanotubes.

    PubMed

    Ersan, Gamze; Apul, Onur G; Karanfil, Tanju

    2016-07-01

    The objective of this paper was to create a comprehensive database for the adsorption of organic compounds by carbon nanotubes (CNTs) and to use the Linear Solvation Energy Relationship (LSER) technique for developing predictive adsorption models of organic compounds (OCs) by multi-walled carbon nanotubes (MWCNTs) and single-walled carbon nanotubes (SWCNTs). Adsorption data for 123 OCs by MWCNTs and 48 OCs by SWCNTs were compiled from the literature, including some experimental results obtained in our laboratory. The roles of selected OCs properties and CNT types were examined with LSER models. The results showed that the r(2) values of the LSER models displayed small variability for aromatic compounds smaller than 220 g/mol, after which a decreasing trend was observed. The data available for aliphatics was mainly for molecular weights smaller than 250 g/mol, which showed a similar trend to that of aromatics. The r(2) values for the LSER model on the adsorption of aromatic and aliphatic OCs by SWCNTs and MWCNTs were relatively similar indicating the linearity of LSER models did not depend on the CNT types. Among all LSER model descriptors, V term (molecular volume) for aromatic OCs and B term (basicity) for aliphatic OCs were the most predominant descriptors on both type of CNTs. The presence of R term (excess molar refractivity) in LSER model equations resulted in decreases for both V and P (polarizability) parameters without affecting the r(2) values. Overall, the results demonstrate that successful predictive models can be developed for the adsorption of OCs by MWCNTs and SWCNTs with LSER techniques. PMID:27064209

  13. Measurement of solvation responses at multiple sites in a globular protein.

    PubMed

    Abbyad, Paul; Shi, Xinghua; Childs, William; McAnaney, Tim B; Cohen, Bruce E; Boxer, Steven G

    2007-07-19

    Proteins respond to electrostatic perturbations through complex reorganizations of their charged and polar groups, as well as those of the surrounding media. These solvation responses occur both in the protein interior and on its surface, though the exact mechanisms of solvation are not well understood, in part because of limited data on the solvation responses for any given protein. Here, we characterize the solvation kinetics at sites throughout the sequence of a small globular protein, the B1 domain of streptococcal protein G (GB1), using the synthetic fluorescent amino acid Aladan. Aladan was incorporated into seven different GB1 sites, and the time-dependent Stokes shift was measured over the femtosecond to nanosecond time scales by fluorescence upconversion and time-correlated single photon counting. The seven sites range from buried within the protein core to fully solvent-exposed on the protein surface, and are located on different protein secondary structures including beta-sheets, helices, and loops. The dynamics in the protein sites were compared against the free fluorophore in buffer. All protein sites exhibited an initial, ultrafast Stokes shift on the subpicosecond time scale similar to that observed for the free fluorophore, but smaller in magnitude. As the probe is moved from the surface to more buried sites, the dynamics of the solvation response become slower, while no clear correlation between dynamics and secondary structure is observed. We suggest that restricted movements of the surrounding protein residues give rise to the observed long time dynamics and that such movements comprise a large portion of the protein's solvation response. The proper treatment of dynamic Stokes shift data when the time scale for solvation is comparable to the fluorescence lifetime is discussed. PMID:17592867

  14. Measurement of Solvation Responses at Multiple Sites in a Globular Protein

    PubMed Central

    Abbyad, Paul; Shi, Xinghua; Childs, William; McAnaney, Tim B.; Cohen, Bruce E.; Boxer, Steven G.

    2008-01-01

    Proteins respond to electrostatic perturbations through complex reorganizations of their charged and polar groups, as well as those of the surrounding media. These solvation responses occur both in the protein interior and on its surface, though the exact mechanisms of solvation are not well understood, in part because of limited data on the solvation responses for any given protein. Here, we characterize the solvation kinetics at sites throughout the sequence of a small globular protein, the B1 domain of streptococcal protein G (GB1), using the synthetic fluorescent amino acid Aladan. Aladan was incorporated into seven different GB1 sites, and the time-dependent Stokes shift measured over the femtosecond to nanosecond timescales by fluorescence upconversion and time-correlated single photon counting. The seven sites range from buried within the protein core to fully solvent-exposed on the protein surface, and are located on different protein secondary structures including β-sheets, helices and loops. The dynamics in the protein sites were compared against the free fluorophore in buffer. All protein sites exhibited an initial, ultra-fast Stokes shift on the sub-picosecond timescale similar to that observed for the free fluorophore, but smaller in magnitude. As the probe is moved from the surface to more buried sites, the dynamics of the solvation response become slower, while no clear correlation between dynamics and secondary structure is observed. We suggest that restricted movements of the surrounding protein residues give rise to the observed long time dynamics and that such movements comprise a large portion of the protein’s solvation response. The proper treatment of dynamic Stokes shift data when the timescale for solvation is comparable to the fluorescence lifetime is discussed. PMID:17592867

  15. Solvation effects on the band edge positions of photocatalysts from first principles.

    PubMed

    Ping, Yuan; Sundararaman, Ravishankar; Goddard, William A

    2015-11-11

    The band edge positions of photocatalysts relative to the redox potentials of water play an important role in determining the efficiency of photoelectrochemical cells. These band positions depend on the structure of the solid-liquid interface, but direct ab initio molecular dynamics calculations of these interfaces, while expected to be accurate, are too computationally demanding for high-throughput materials screening. Thus rapid theoretical screening of new photocatalyst materials requires simplified continuum solvation models that are suitable for treating solid-liquid interfaces. In this paper, we evaluate the accuracy of the recently developed CANDLE and SaLSA continuum solvation models for predicting solvation effects on the band positions of several well-studied surfaces [Si(111), TiO2(110), IrO2(110) and WO3(001)] in water. We find that the solvation effects vary considerably, ranging from <0.5 eV for hydrophobic surfaces, 0.5-1 eV for many hydrophilic oxide surfaces, to ∼2 eV for oxygen-deficient surfaces. The solvation model predictions are in excellent agreement (within ∼0.1 eV) with ab initio molecular dynamics results where available, and in good agreement (within ∼0.2-0.3 eV) with experimental measurements. We also predict the energetics for surface oxygen vacancies and their effect on the band positions of the hydrated WO3(001) surface, leading to an explanation for why the solvation shift observed experimentally is substantially larger than predicted for the ideal surface. Based on the correlation between solvation shift and the type of surface and solvent, we suggest approaches to engineer the band positions of surfaces in aqueous and non-aqueous solutions. PMID:26513300

  16. 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). PMID:25412410

  17. Quantum Simulations of Solvated Biomolecules Using Hybrid Methods

    NASA Astrophysics Data System (ADS)

    Hodak, Miroslav

    2009-03-01

    One of the most important challenges in quantum simulations on biomolecules is efficient and accurate inclusion of the solvent, because the solvent atoms usually outnumber those in the biomolecule of interest. We have developed a hybrid method that allows for explicit quantum-mechanical treatment of the solvent at low computational cost. In this method, Kohn-Sham (KS) density functional theory (DFT) is combined with an orbital-free (OF) DFT. Kohn-Sham (KS) DFT is used to describe the biomolecule and its first solvation shells, while the orbital-free (OF) DFT is employed for the rest of the solvent. The OF part is fully O(N) and capable of handling 10^5 solvent molecules on current parallel supercomputers, while taking only ˜ 10 % of the total time. The compatibility between the KS and OF DFT methods enables seamless integration between the two. In particular, the flow of solvent molecules across the KS/OF interface is allowed and the total energy is conserved. As the first large-scale applications, the hybrid method has been used to investigate the binding of copper ions to proteins involved in prion (PrP) and Parkinson's diseases. Our results for the PrP, which causes mad cow disease when misfolded, resolve a contradiction found in experiments, in which a stronger binding mode is replaced by a weaker one when concentration of copper ions is increased, and show how it can act as a copper buffer. Furthermore, incorporation of copper stabilizes the structure of the full-length PrP, suggesting its protective role in prion diseases. For alpha-synuclein, a Parkinson's disease (PD) protein, we show that Cu binding modifies the protein structurally, making it more susceptible to misfolding -- an initial step in the onset of PD. In collaboration with W. Lu, F. Rose and J. Bernholc.

  18. Molecular dynamics simulations of solvated yeast tRNA(Asp).

    PubMed Central

    Auffinger, P; Louise-May, S; Westhof, E

    1999-01-01

    Transfer RNA molecules are involved in a variety of biological processes, implying complex recognition events with proteins and other RNAs. From a structural point of view, tRNAs constitute a reference system for studying RNA folding and architecture. A deeper understanding of their structural and functional properties will derive from our ability to model accurately their dynamical behavior. We present the first dynamical model of a fully neutralized and solvated tRNA molecule over a 500-ps time scale. Starting from the crystallographic structure of yeast tRNA(Asp), the 75-nucleotide molecule was modeled with 8055 water molecules and 74 NH4+ counterions, using the AMBER4.1 program and the particle mesh Ewald (PME) method for the treatment of long-range electrostatic interactions. The calculations led to a dynamically stable model of the tRNA molecule. During the simulation, all secondary and tertiary base pairs are maintained while a certain lability of base triples in the tRNA core is observed. This lability was interpreted as resulting from intrinsic factors associated with the "weaker" hydrogen bonding patterns seen in these base triples and from an altered ionic environment of the tRNA molecule. Calculated thermal factors are used to compare the dynamics of the tRNA in solution and in the crystal. The present molecular dynamics simulation of a complex and highly charged nucleic acid molecule attests to the fact that simulation methods are now able to investigate not only the dynamics of proteins, but also that of large RNA molecules. Thus they also provide a basis for further investigations on the structural and functional effects of chemical and posttranscriptionally modified nucleotides as well as on ionic environmental effects. PMID:9876122

  19. Effects of geometry and chemistry on hydrophobic solvation.

    PubMed

    Harris, Robert C; Pettitt, B Montgomery

    2014-10-14

    Inserting an uncharged van der Waals (vdw) cavity into water disrupts the distribution of water and creates attractive dispersion interactions between the solvent and solute. This free-energy change is the hydrophobic solvation energy (ΔG(vdw)). Frequently, it is assumed to be linear in the solvent-accessible surface area, with a positive surface tension (γ) that is independent of the properties of the molecule. However, we found that γ for a set of alkanes differed from that for four configurations of decaalanine, and γ = -5 was negative for the decaalanines. These findings conflict with the notion that ΔG(vdw) favors smaller A. We broke ΔG(vdw) into the free energy required to exclude water from the vdw cavity (ΔG(rep)) and the free energy of forming the attractive interactions between the solute and solvent (ΔG(att)) and found that γ < 0 for the decaalanines because -γ(att) > γ(rep) and γ(att) < 0. Additionally, γ(att) and γ(rep) for the alkanes differed from those for the decaalanines, implying that none of ΔG(att), ΔG(rep), and ΔG(vdw) can be computed with a constant surface tension. We also showed that ΔG(att) could not be computed from either the initial or final water distributions, implying that this quantity is more difficult to compute than is sometimes assumed. Finally, we showed that each atom's contribution to γ(rep) depended on multibody interactions with its surrounding atoms, implying that these contributions are not additive. These findings call into question some hydrophobic models. PMID:25258413

  20. Effects of geometry and chemistry on hydrophobic solvation

    PubMed Central

    Harris, Robert C.; Pettitt, B. Montgomery

    2014-01-01

    Inserting an uncharged van der Waals (vdw) cavity into water disrupts the distribution of water and creates attractive dispersion interactions between the solvent and solute. This free-energy change is the hydrophobic solvation energy (ΔGvdw). Frequently, it is assumed to be linear in the solvent-accessible surface area, with a positive surface tension (γ) that is independent of the properties of the molecule. However, we found that γ for a set of alkanes differed from that for four configurations of decaalanine, and γ = −5 was negative for the decaalanines. These findings conflict with the notion that ΔGvdw favors smaller A. We broke ΔGvdw into the free energy required to exclude water from the vdw cavity (ΔGrep) and the free energy of forming the attractive interactions between the solute and solvent (ΔGatt) and found that γ < 0 for the decaalanines because −γatt > γrep and γatt < 0. Additionally, γatt and γrep for the alkanes differed from those for the decaalanines, implying that none of ΔGatt, ΔGrep, and ΔGvdw can be computed with a constant surface tension. We also showed that ΔGatt could not be computed from either the initial or final water distributions, implying that this quantity is more difficult to compute than is sometimes assumed. Finally, we showed that each atom’s contribution to γrep depended on multibody interactions with its surrounding atoms, implying that these contributions are not additive. These findings call into question some hydrophobic models. PMID:25258413

  1. Femtosecond two-photon ionization and solvated electron geminate recombination in liquid-to-supercritical ammonia.

    PubMed

    Urbanek, Janus; Dahmen, Annika; Torres-Alacan, Joel; Königshoven, Peter; Lindner, Jörg; Vöhringer, Peter

    2012-02-23

    The first-ever femtosecond pump-probe study is reported on solvated electrons that were generated by multiphoton ionization of neat fluid ammonia. The initial ultrafast ionization was carried out with 266 nm laser pulses and was found to require two photons. The solvated electron was detected with a femtosecond probe pulse that was resonant with its characteristic near-infrared absorption band around 1.7 μm. Furthermore, the geminate recombination dynamics of the solvated electron were studied over wide ranges of temperature (227 K ≤ T ≤ 489 K) and density (0.17 g cm(-3) ≤ ρ ≤ 0.71 g cm(-3)), thereby covering the liquid and the supercritical phase of the solvent. The electron recombines in a first step with ammonium cations originating from the initial two-photon ionization thereby forming transient ion-pairs (e(am)(-)·NH(4)(+)), which subsequently react in a second step with amidogen radicals to reform neutral ammonia. The escape probability, i.e., the fraction of solvated electrons that can avoid the geminate annihilation, was found to be in quantitative agreement with the classical Onsager theory for the initial recombination of ions. When taking the sequential nature of the ion-pair-mediated recombination mechanism explicitly into account, the Onsager model provides a mean thermalization distance of 6.6 nm for the solvated electron, which strongly suggests that the ionization mechanism involves the conduction band of the fluid. PMID:22272761

  2. Binding of solvated peptide (EPLQLKM) with a graphene sheet via simulated coarse-grained approach.

    PubMed

    Sheikholeslami, Somayyeh; Pandey, R B; Dragneva, Nadiya; Floriano, Wely; Rubel, Oleg; Barr, Stephen A; Kuang, Zhifeng; Berry, Rajiv; Naik, Rajesh; Farmer, Barry

    2014-05-28

    Binding of a solvated peptide A1 ((1)E (2)P (3)L (4)Q (5)L (6)K (7)M) with a graphene sheet is studied by a coarse-grained computer simulation involving input from three independent simulated interaction potentials in hierarchy. A number of local and global physical quantities such as energy, mobility, and binding profiles and radius of gyration of peptides are examined as a function of temperature (T). Quantitative differences (e.g., the extent of binding within a temperature range) and qualitative similarities are observed in results from three simulated potentials. Differences in variations of both local and global physical quantities suggest a need for such analysis with multiple inputs in assessing the reliability of both quantitative and qualitative observations. While all three potentials indicate binding at low T and unbinding at high T, the extent of binding of peptide with the temperature differs. Unlike un-solvated peptides (with little variation in binding among residues), solvation accentuates the differences in residue binding. As a result the binding of solvated peptide at low temperatures is found to be anchored by three residues, (1)E, (4)Q, and (6)K (different from that with the un-solvated peptide). Binding to unbinding transition can be described by the variation of the transverse (with respect to graphene sheet) component of the radius of gyration of the peptide (a potential order parameter) as a function of temperature. PMID:24880319

  3. Thermodynamic Functions of Solvation of Hydrocarbons, Noble Gases, and Hard Spheres in Tetrahydrofuran-Water Mixtures.

    PubMed

    Sedov, I A; Magsumov, T I

    2015-07-16

    Thermodynamic solvation properties of mixtures of water with tetrahydrofuran at 298 K are studied. The Gibbs free energies and enthalpies of solvation of n-octane and toluene are determined experimentally. For molecular dynamics simulations of the binary solvent, we have modified a TraPPE-UA model for tetrahydrofuran and combined it with the SPC/E potential for water. The excess thermodynamic functions of neon, xenon, and hard spheres with two different radii are calculated using the particle insertion method. Simulated and real systems share the same characteristic trends for the thermodynamic functions. A maximum is present on dependencies of the enthalpy of solvation from the composition of solvent at 70-90 mol % water, making it higher than in both of the cosolvents. It is caused by a high enthalpy of cavity formation in the mixtures rich with water due to solvent reorganization around the cavity, which is shown by calculation of the enthalpy of solvation of hard spheres. Addition of relatively small amounts of tetrahydrofuran to water effectively suppresses the hydrophobic effect, leading to a quick increase of both the entropy and enthalpy of cavity formation and solvation of low polar molecules. PMID:26115405

  4. Anion Coordination Interactions in Solvates with the Lithium Salts LiDCTA and LiTDI

    SciTech Connect

    McOwen, Dennis W.; Delp, Samuel A.; Paillard, Elie; Herriot, Cristelle; Han, Sang D.; Boyle, Paul D.; Sommer, Roger D.; Henderson, Wesley A.

    2014-04-17

    Lithium 4,5-dicyano-1,2,3-triazolate (LiDCTA) and lithium 2-trifluoromethyl-4,5-dicyanoimidazole (LiTDI) are two salts proposed for lithium battery electrolyte applications, but little is known about the manner in which the DCTA- and TDI- anions coordinate Li+ cations. To explore this in-depth, crystal structures are reported here for two solvates with LiDCTA: (G2)1:LiDCTA and (G1)1:LiDCTA with diglyme and monoglyme, respectively, and seven solvates with LiTDI: (G1)2:LiTDI, (G2)2:LiTDI, (G3)1:LiTDI, (THF)1:LiTDI, (EC)1:LiTDI, (PC)1:LiTDI and (DMC)1/2:LiTDI with monoglyme, diglyme, triglyme, tetrahydrofuran, ethylene carbonate, propylene carbonate and dimethyl carbonate, respectively. These latter solvate structures are compared with the previously reported acetonitrile (AN)2:LiTDI structure. The solvates indicate that the LiTDI salt is much less associated than the LiDCTA salt and that the ions in LiTDI, when aggregated in solvates, have a very similar TDI-...Li+ cation mode of coordination through both the anion ring and cyano nitrogen atoms. Such coordination facilitates the formation of polymeric ion aggregates, instead of dimers. Insight into such ion speciation is instrumental for understanding the electrolyte properties of aprotic solvent mixtures with these salts.

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

    PubMed

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

    2016-03-15

    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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    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.

  7. 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.

  8. Free energy of solvation of carbon nanotubes in pyridinium-based ionic liquids.

    PubMed

    Chaban, Vitaly V; Fileti, Eudes Eterno

    2016-07-27

    Numerous prospective applications require the availability of individual carbon nanotubes (CNTs). Pristine CNTs, strongly hydrophobic in nature, are known to be either totally insoluble or poorly dispersible. While it is unlikely to be possible to prepare a real solution of CNTs in any solvent, the ability of certain solvents to maintain dispersions of CNTs for macroscopic times constitutes great research interest. In the present work, we characterize two pyridinium-based ionic liquids (ILs), N-butylpyridinium chloride [BPY][Cl] and N-butylpyridinium bis(trifluoromethanesulfonyl)imide [BPY][TFSI], with respect to their potential to solvate CNTs of different diameters, from the CNT (10,10) to the CNT (25,25). Using a universal methodology, we found that both ILs exhibit essentially the same solvation performance. Solvation of CNTs is strongly prohibited entropically, whereas the energy penalty increases monotonically with the CNT diameter. Weak van der Waals interactions, which guide enthalpy alteration upon the CNT solvation, are unable to compensate for the large entropic penalty from the destruction of the IL-IL electrostatic interactions. The structure of ILs inside and outside CNTs is also discussed. The reported results are necessary for gaining a fundamental understanding of the CNT solvation problems, thereby inspiring the search for more suitable solvents. PMID:27400869

  9. Kinetic equations for hopping transport and spin relaxation in a random magnetic field

    NASA Astrophysics Data System (ADS)

    Shumilin, A. V.; Kabanov, V. V.

    2015-07-01

    We derive the kinetic equations for a hopping transport that take into account an electron spin and the possibility of double occupation. In the Ohmic regime, the equations are reduced to the generalized Miller-Abrahams resistor network. We apply these equations to the problem of the magnetic moment relaxation due to the interaction with the random hyperfine fields. It is shown that in a wide range of parameters the relaxation rate is governed by the hops with the similar rates as spin precession frequency. It is demonstrated that at the large time scale spin relaxation is nonexponential. We argue that the nonexponential relaxation of the magnetic moment is related to the spin of electrons in the slow-relaxing traps. Interestingly, the traps can significantly influence the spin relaxation in the infinite conducting cluster at large times.

  10. Lorentz-Abraham-Dirac versus Landau-Lifshitz radiation friction force in the ultrarelativistic electron interaction with electromagnetic wave (exact solutions)

    SciTech Connect

    Bulanov, Sergei V.; Esirkepov, Timur Zh.; Kando, Masaki; Koga, James K.; Bulanov, Stepan S.

    2011-11-15

    When the parameters of electron-extreme power laser interaction enter the regime of dominated radiation reaction, the electron dynamics changes qualitatively. The adequate theoretical description of this regime becomes crucially important with the use of the radiation friction force either in the Lorentz-Abraham-Dirac form, which possesses unphysical runaway solutions, or in the Landau-Lifshitz form, which is a perturbation valid for relatively low electromagnetic wave amplitude. The goal of the present paper is to find the limits of the Landau-Lifshitz radiation force applicability in terms of the electromagnetic wave amplitude and frequency. For this, a class of the exact solutions to the nonlinear problems of charged particle motion in the time-varying electromagnetic field is used.

  11. Teaching Equations.

    ERIC Educational Resources Information Center

    Nibbelink, William H.

    1990-01-01

    Proposed is a gradual transition from arithmetic to the idea of an equation with variables in the elementary grades. Vertical and horizontal formats of open sentences, the instructional sequence, vocabulary, and levels of understanding are discussed in this article. (KR)

  12. 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

  13. Two and Three Dimensional Nonlocal DFT for Inhomogeneous Fluids II: Solvated Polymers as a Benchmark Problem

    SciTech Connect

    Frink, Laura J. Douglas; Salinger, Andrew G.

    1999-08-09

    In a previous companion paper, we presented the details of our algorithms for performing nonlocal density functional theory (DFT) calculations in complex 2D and 3D geometries. We discussed scaling and parallelization, but did not discuss other issues of performance. In this paper, we detail the precision of our methods with respect to changes in the mesh spacing. This is a complex issue because given a Cartesian mesh, changes in mesh spacing will result in changes in surface geometry. We discuss these issue using a series of rigid solvated polymer models including square rod polymers, cylindrical polymers, and bead-chain polymers. By comparing the results of the various models, it becomes clear that surface curvature or roughness plays an important role in determining the strength of structural solvation forces between interacting solvated polymers. The results in this paper serve as benchmarks for future application of these algorithms to complex fluid systems.

  14. 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). PMID:26067106

  15. Effect of temperature on the dynamics of benzophenone anion solvation in alcohol

    SciTech Connect

    Zhang, X.; Jonah, C.D.

    1996-04-25

    The solvation of the benzophenone anion in 1-propanol, 2-propanol, and 1-butanol has been measured over the temperature range -10 to -50{degree}C. The initial spectra of the benzophenone anion were very similar in all three alcohols. The final spectrum of the benzophenone anion in 2-propanol is less blue-shifted (17nm) than the spectrum of the anion in 1-propanol and 1-butanol. The activation energies for solvation are 22 kJ/mol for 1-propanol and 1-butanol and 16 kJ/mol for 2-propanol, which are similar to the energy for hydrogen bond breakage in the pure solvents. This suggests that the solvent H-bond breakage plays an important role in anion solvation. 37 refs., 12 figs., 1 tab.

  16. Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST.

    PubMed

    Ramsey, Steven; Nguyen, Crystal; Salomon-Ferrer, Romelia; Walker, Ross C; Gilson, Michael K; Kurtzman, Tom

    2016-08-01

    The expulsion of water from surfaces upon molecular recognition and nonspecific association makes a major contribution to the free energy changes of these processes. In order to facilitate the characterization of water structure and thermodynamics on surfaces, we have incorporated Grid Inhomogeneous Solvation Theory (GIST) into the CPPTRAJ toolset of AmberTools. GIST is a grid-based implementation of Inhomogeneous Fluid Solvation Theory, which analyzes the output from molecular dynamics simulations to map out solvation thermodynamic and structural properties on a high-resolution, three-dimensional grid. The CPPTRAJ implementation, called GIST-cpptraj, has a simple, easy-to-use command line interface, and is open source and freely distributed. We have also developed a set of open-source tools, called GISTPP, which facilitate the analysis of GIST output grids. Tutorials for both GIST-cpptraj and GISTPP can be found at ambermd.org. © 2016 Wiley Periodicals, Inc. PMID:27317094

  17. 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.

  18. Determination of Kamlet-Taft parameters for selected solvate ionic liquids.

    PubMed

    Eyckens, Daniel J; Demir, Baris; Walsh, Tiffany R; Welton, Tom; Henderson, Luke C

    2016-05-11

    The normalised polarity E and Kamlet-Taft parameters of recently described solvate ionic liquids, composed of lithium bis(trifluoromethyl)sulfonimide (LiTFSI) in tri- () or tetraglyme () have been determined and compared to the parent glyme ( and ). We show that these solvate ionic liquids have a high polarity (, (E) = 1.03; , (E) = 1.03) and display very high electron pair accepting characteristics (, α = 1.32; , α = 1.35). Molecular dynamics simulations suggest that the chelated lithium cation is responsible for this observation. The relatively small hydrogen bond acceptor (β) values for these systems (, β = 0.41; , β = 0.37) are thought to be due primarily to the TFSI anion, which is supplemented slightly by the glyme oxygen atom. In addition, these solvate ionic liquids are found to have a high polarisability (, π* = 0.94; , π* = 0.90). PMID:27122349

  19. Solvation and Deprotonation Dynamics in Reverse Micelles via Broadband Femtoseond Transient Absorption (BFTA) Spectroscopy

    NASA Astrophysics Data System (ADS)

    Cole, Richard

    2009-10-01

    Broadband femtosecond transient absorption (BFTA) spectroscopy is a useful tool in characterizing femtosecond and picosecond physical and chemical dynamics such as solvation, electron transfer, and deprotonation dynamics. This presentation will focus on our most recent results, which utilize BFTA spectroscopy in the ultraviolet-visible (UV-vis) spectral range to probe deprotonation and solvation dynamics in the nanoscopic confinement of reverse micelles. In these studies, pyranine, a `photo-acid', probes both solvation and deprotonation dynamics in reverse micelles formed from cationic (cetyl trimethylammonium bromide, CTAB), anionic (sodium dioctyl sulfosuccinate, AOT), and neutral (polyoxyethylene nonylphenylether, Igepal) surfactants. Dynamic behavior will be discussed in terms of the degree of nanoscopic confinement (micellar size) and the impact of varying interfacial environments.

  20. A new computational model for protein folding based on atomic solvation.

    PubMed Central

    Wang, Y.; Zhang, H.; Scott, R. A.

    1995-01-01

    A new model for calculating the solvation energy of proteins is developed and tested for its ability to identify the native conformation as the global energy minimum among a group of thousands of computationally generated compact non-native conformations for a series of globular proteins. In the model (called the WZS model), solvation preferences for a set of 17 chemically derived molecular fragments of the 20 amino acids are learned by a training algorithm based on maximizing the solvation energy difference between native and non-native conformations for a training set of proteins. The performance of the WZS model confirms the success of this learning approach; the WZS model misrecognizes (as more stable than native) only 7 of 8,200 non-native structures. Possible applications of this model to the prediction of protein structure from sequence are discussed. PMID:7670381

  1. Solvation of the Li+-Cl--Li+ triple ion in the gas phase

    NASA Astrophysics Data System (ADS)

    Jarek, Russell L.; Denson, Stephen C.; Shin, Seung Koo

    1998-09-01

    Fourier-transform ion cyclotron resonance (FT-ICR) spectrometry was employed to study solvations of the Li+-Cl--Li+ triple ion with oxygen-donor Lewis bases in the gas phase. The LiClLi+ triple ions were produced in an ICR cell by laser desorption ionization of a lithium chloride/dibenzo-18-crown-6-ether matrix pasted on a Teflon substrate. O-donor Lewis bases include 1,4-dioxane, 1,3-dioxane, tetrahydrofuran (THF), acetone and diethyl ether. All O-donors associate directly with LiClLi+ with the maximum solvation numbers of 3 for 1,4-dioxane, 1,3-dioxane and diethyl ether, and 4 for THF and acetone at room temperature. The rate constants for the stepwise solvations were measured, and the solvent binding energies were determined from van't Hoff plots. The structures and energetics of LiClLi+ and the 1:1 complexes of Li+ and LiClLi+ with the dioxanes, THF, and acetone were calculated at the Hartree-Fock (HF) level with a 6-311G(d,p) basis set, and those of more highly coordinated LiClLi+ complexes were calculated with a 6-31G(d) basis set. Solvation enthalpies and free energies were calculated, and solvent binding energies were compared with experiments. The mechanisms of stepwise solvations of the LiClLi+ triple ion with dioxanes, THF, and acetone are discussed in light of experimental kinetics and binding energies and theoretical structures and solvation energies.

  2. Pentaglyme-K salt binary mixtures: phase behavior, solvate structures, and physicochemical properties.

    PubMed

    Mandai, Toshihiko; Tsuzuki, Seiji; Ueno, Kazuhide; Dokko, Kaoru; Watanabe, Masayoshi

    2015-01-28

    We prepared a series of binary mixtures composed of certain K salts (KX) and pentaglyme (G5) with different salt concentrations and anionic species ([X](-): [(CF3SO2)2N](-) = [TFSA](-), [CF3SO3](-) = [TfO](-), [C4F9SO3](-) = [NfO](-), PF6(-), SCN(-)), and characterized them with respect to their phase diagrams, solvate structures, and physicochemical properties. Their phase diagrams and thermal stability strongly implied the formation of equimolar complexes. Single-crystal X-ray crystallography was performed on certain equimolar complexes, which revealed that G5 molecules coordinate to K(+) cations in a characteristic manner, like 18-crown-6 ether in the crystalline state, irrespective of the paired anions. The solvate structures in the molten state were elucidated by a combination of temperature-dependent Raman spectroscopy and X-ray crystallography. A drastic spectral variation was observed in the [K(G5)1][TfO] Raman spectra, indicating that solvate structures in the crystalline state break apart upon melting. The solvate stability of [K(G5)1]X is closely related to the ion-ion interaction of the parent salts. A stable solvate forms when the ion-dipole interaction between K(+) and G5 overwhelms the ion-ion interaction between K(+) and X(-). Furthermore, the physicochemical properties of certain equimolar mixtures were evaluated. A Walden plot clearly reflects the ionic nature of the molten equimolar complexes. Judging from the structural characteristics and dissociativity, we classified [K(G5)1]X into two groups, good and poor solvate ionic liquids. PMID:25501925

  3. Conformation of a flexible polymer in explicit solvent: Accurate solvation potentials for Lennard-Jones chains.

    PubMed

    Taylor, Mark P; Ye, Yuting; Adhikari, Shishir R

    2015-11-28

    The conformation of a polymer chain in solution is coupled to the local structure of the surrounding solvent and can undergo large changes in response to variations in solvent density and temperature. The many-body effects of solvent on the structure of an n-mer polymer chain can be formally mapped to an exact n-body solvation potential. Here, we use a pair decomposition of this n-body potential to construct a set of two-body potentials for a Lennard-Jones (LJ) polymer chain in explicit LJ solvent. The solvation potentials are built from numerically exact results for 5-mer chains in solvent combined with an approximate asymptotic expression for the solvation potential between sites that are distant along the chain backbone. These potentials map the many-body chain-in-solvent problem to a few-body single-chain problem and can be used to study a chain of arbitrary length, thereby dramatically reducing the computational complexity of the polymer chain-in-solvent problem. We have constructed solvation potentials at a large number of state points across the LJ solvent phase diagram including the vapor, liquid, and super-critical regions. We use these solvation potentials in single-chain Monte Carlo (MC) simulations with n ≤ 800 to determine the size, intramolecular structure, and scaling behavior of chains in solvent. To assess our results, we have carried out full chain-in-solvent MC simulations (with n ≤ 100) and find that our solvation potential approach is quantitatively accurate for a wide range of solvent conditions for these chain lengths. PMID:26627969

  4. Dynamic solvation shell and solubility of C60 in organic solvents.

    PubMed

    Wang, Chun I; Hua, Chi C; Chen, Show A

    2014-08-21

    The notion of (static) solvation shells has recently proved fruitful in revealing key molecular factors that dictate the solubility and aggregation properties of fullerene species in polar or ionic solvent media. Using molecular dynamics schemes with carefully evaluated force fields, we have scrutinized both the static and the dynamic features of the solvation shells of single C60 particle for three nonpolar organic solvents (i.e., chloroform, toluene, and chlorobenzene) and a range of system temperatures (i.e., T = 250-330 K). The central findings have been that, while the static structures of the solvation shell remain, in general, insensitive to the effects of changing solvent type or system temperature, the dynamic behavior of solvent molecules within the shell exhibits prominent dependence on both factors. Detailed analyses led us to propose the notion of dynamically stable solvation shell, effectiveness of which can be characterized by a new physical parameter defined as the ratio of two fundamental time constants representing, respectively, the solvent relaxation (or residence) time within the first solvation shell and the characteristic time required for the fullerene particle to diffuse a distance comparable to the shell thickness. We show that, for the five (two from the literature) different solvent media and the range of system temperatures examined herein, this parameter bears a value around unity and, in particular, correlates intimately with known trends of solubility for C60 solutions. We also provide evidence revealing that, in addition to fullerene-solvent interactions, solvent-solvent interactions play an important role, too, in shaping the dynamic solvation shell, as implied by recent experimental trends. PMID:25084556

  5. Solvation of lithium salts in protic ionic liquids: a molecular dynamics study.

    PubMed

    Méndez-Morales, Trinidad; Carrete, Jesús; Cabeza, Óscar; Russina, Olga; Triolo, Alessandro; Gallego, Luis J; Varela, Luis M

    2014-01-23

    The structure of solutions of lithium nitrate in a protic ionic liquid with a common anion, ethylammonium nitrate, at room temperature is investigated by means of molecular dynamics simulations. Several structural properties, such as density, radial distribution functions, hydrogen bonds, spatial distribution functions, and coordination numbers, are analyzed in order to get a picture of the solvation of lithium cations in this hydrogen-bonded, amphiphilically nanostructured environment. The results reveal that the ionic liquid mainly retains its structure upon salt addition, the interaction between the ammonium group of the cation and the nitrate anion being only slightly perturbed by the addition of the salt. Lithium cations are solvated by embedding them in the polar nanodomains of the solution formed by the anions, where they coordinate with the latter in a solid-like fashion reminiscent of a pseudolattice structure. Furthermore, it is shown that the average coordination number of [Li](+) with the anions is 4, nitrate coordinating [Li](+) in both monodentate and bidentate ways, and that in the second coordination layer both ethylammonium cations and other lithiums are also found. Additionally, the rattling motion of lithium ions inside the cages formed by their neighboring anions, indicative of the so-called caging effect, is confirmed by the analysis of the [Li](+) velocity autocorrelation functions. The overall picture indicates that the solvation of [Li](+) cations in this amphiphilically nanostructured environment takes place by means of a sort of inhomogeneous nanostructural solvation, which we could refer to as nanostructured solvation, and which could be a universal solvation mechanism in ionic liquids. PMID:24405468

  6. Entropy and enthalpy convergence of hydrophobic solvation beyond the hard-sphere limit

    NASA Astrophysics Data System (ADS)

    Sedlmeier, Felix; Horinek, Dominik; Netz, Roland R.

    2011-02-01

    The experimentally well-known convergence of solvation entropies and enthalpies of different small hydrophobic solutes at universal temperatures seems to indicate that hydrophobic solvation is dominated by universal water features and not so much by solute specifics. The reported convergence of the denaturing entropy of a group of different proteins at roughly the same temperature as hydrophobic solutes was consequently argued to indicate that the denaturing entropy of proteins is dominated by the hydrophobic effect and used to estimate the hydrophobic contribution to protein stability. However, this appealing picture was subsequently questioned since the initially claimed universal convergence of denaturing entropies holds only for a small subset of proteins; for a larger data collection no convergence is seen. We report extensive simulation results for the solvation of small spherical solutes in explicit water with varying solute-water potentials. We show that convergence of solvation properties for solutes of different radii exists but that the convergence temperatures depend sensitively on solute-water potential features such as stiffness of the repulsive part and attraction strength, not so much on the attraction range. Accordingly, convergence of solvation properties is only expected for solutes of a homologous series that differ in the number of one species of subunits (which attests to the additivity of solvation properties) or solutes that are characterized by similar solute-water interaction potentials. In contrast, for peptides that arguably consist of multiple groups with widely disperse interactions with water, it means that thermodynamic convergence at a universal temperature cannot be expected, in general, in agreement with experimental results.

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

    NASA Astrophysics Data System (ADS)

    Rane, Kaustubh; van der Vegt, Nico F. A.

    2016-03-01

    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 molecule 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.

  8. 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. PMID:25523643

  9. Communication: Solvation and dielectric response in ionic liquids--conductivity extension of the continuum model.

    PubMed

    Zhang, X-X; Schröder, C; Ernsting, N P

    2013-03-21

    The solvation response of a polarity probe in a conducting liquid is analyzed based on simple continuum theory. A multi-exponential description of the dynamics is inverted to give an effective dc conductivity and a generalized permittivity spectrum in terms of Debye modes. For Coumarin 153 in ionic liquids the conductivity is found to be reduced systematically from the bulk value, whereas the permittivity from GHz-THz bulk absorption measurements is well reproduced by the solvation experiment. Thus, by using a dye as molecular antenna, the dielectric dispersion of the microscopic environment can be obtained. PMID:23534620

  10. Understanding solvation in the low global warming hydrofluoroolefin HFO-1234ze propellant.

    PubMed

    Yang, Lin; da Rocha, Sandro R P

    2014-09-11

    Hydrofluoroolefins (HFOs), with zero ozone-depleting effect and very low global warming potential, are considered to be the next-generation high-pressure working fluids. They have industrial relevance in areas including refrigeration and medical aerosols. One major challenge expected in the replacement of existing working fluids with HFOs is the solubility and solvation of additives in such hydrophobic and oleophobic low dielectric semifluorinated solvents. The study of the solvation of chemistries that represent those additives by HFOs is, therefore, of great relevance. In this work, we systematically investigate how the polarity and structure of fragments (the tail, t) that represent those additives affect their binding energy (Eb) with HFO-1234ze (1,1,1,3-tetrafluoropropene) (the solvent, s; Eb(st)). We also compare and contrast those results with those for the working fluids that are most widely used in the industry, the hydrofluoroalkanes (HFAs) HFA-134a and HFA-227. Three main chemistries were investigated: alkanes, ethers, and esters. It was found that HFO-1234ze interacts quite favorably with ethers and esters, as indicated by their Eb(st), while Eb(st) with alkanes was much lower. While ether and ester groups showed little difference in Eb(st), the much lower self-interaction energy between ether tail-tail fragments (Eb(tt)) is expected to result in improved solubility/solvation of those groups in HFO-1234ze when compared with the more polar ester groups. The ratio Eb(st)/Eb(tt) is defined as the enhancement factor (Eenh) and is expected to be a better predictor of solubility/solvation of the tail fragments. The branching of the tail groups upon the addition of pendant CH3 groups did not significantly affect the solvation by the propellant. At low branching density (one CH3 pendant group), it did not affect tail-tail self-interaction either. However, at high enough branching (two CH3 groups), steric hindrance caused a significant decrease in Eb(tt) and

  11. Solvation dynamics and enzyme catalysis in a designed enzyme undergoing directed evolution

    NASA Astrophysics Data System (ADS)

    Schreck, Carl; Head-Gordon, Teresa

    2014-03-01

    We explore whether catalysis of a de novo designed enzyme-substrate complex is correlated to necessary solvent fluctuations to induce a chemical reaction. By studying a designed KEMP Eliminase as it goes through rounds of directed evolution to improve it's catalytic activity, we have found that catalytic activity correlates with an increase in density and structure of water near the active site. This suggests fluctuations in the solvation water near the active site couple to fluctuations in KEMP Eliminase to facilitate the catalytic process. To flesh this idea out, we are studying the progression of vibrational properties and cooperative fluctuations of solvation water by simulating the terahertz observable.

  12. A first-principle protocol for calculating ionization energies and redox potentials of solvated molecules and ions: Theory and application to aqueous phenol and phenolate

    PubMed Central

    Ghosh, Debashree; Roy, Anirban; Seidel, Robert; Winter, Bernd; Bradforth, Stephen; Krylov, Anna I.

    2012-01-01

    The effect of hydration on the lowest vertical ionization energy (VIE) of phenol and phenolate solvated in bulk water was characterized using the equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods (referred to as EOM/EFP), and determined experimentally by valence photo-emission measurements using microjets and synchrotron radiation. The computed solvent-induced shifts in VIEs (ΔVIE) are −0.66 eV and +5.72 eV for phenol and phenolate, respectively. Our best estimates of the absolute values of VIEs (7.9 and 7.7 eV for phenol and phenolate) agree reasonably well with the respective experimental values (7.8±0.1 eV and 7.1±0.1 eV). The EOM/EFP scheme was benchmarked against full EOM-IP-CCSD using micro-solvated phenol and phenolate clusters. A protocol for calculating redox potentials with EOM/EFP was developed based on linear response approximation (LRA) of free energy determination. The oxidation potentials of phenol and phenolate calculated using LRA and EOM/EFP are 1.32 V and 0.89 V, respectively; they agree well with experimental values. PMID:22497288

  13. Monte Carlo simulation and SAFT modeling study of the solvation thermodynamics of dimethylformamide, dimethylsulfoxide, ethanol and 1-propanol in the ionic liquid trimethylbutylammonium bis(trifluoromethylsulfonyl)imide.

    PubMed

    Vahid, A; Maginn, E J

    2015-03-21

    Understanding fundamental solvation phenomena and mixture thermodynamic properties for organic molecules in ionic liquids is essential to the development of ionic liquids in many application areas. In the present work, molecular simulations were used to compute a wide range of properties for the pure ionic liquid trimethylbutylammonium bis(trifluoromethylsulfonyl)imide as well as mixtures of this ionic liquid with ethanol, 1-propanol, dimethylformamide, and dimethylsulfoxide. A new force field for the ionic liquid was developed and validated by computing ionic liquid surface tension and density as a function of temperature. Force fields for ethanol and propanol were taken from the literature, while new force fields were developed for dimethylformamide and dimethylsulfoxide. These force fields were shown to yield vapor-liquid coexistence curves, vapor pressure curves and critical points in excellent agreement with experimental data. Absorption isotherms, enthalpies of mixing and mixture volumes were then computed and shown to agree well with available literature. The simulations help rationalize the observed trends in solubility and enthalpy of mixing in terms of the relative strength of hydrogen bonding between the solutes and the ionic liquid. It was found that the entropy of absorption plays a very important role in the solvation process. The PCIP-SAFT equation of state was able to fit the experimental data (or simulation results when experiments were unavailable) very accurately with only small adjustable binary interaction parameters. PMID:25704844

  14. 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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    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.

  15. 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

    SciTech Connect

    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.

  16. DFT SOLVATION STUDIES OF CARBOHYDRATES: THE EFFECT OF DIFFERENT HYDRATION MODELS ON THE INTERNAL COORDINATES AND ALPH/BETA-ANOMERIC RATIOS OF EPIMERS OF GLUCOSE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Solvents play an important role in carbohydrate structure. Therefore, it is important to include solvation effects in calculations to allow a better comparison with experimental data. One way to include solvation effects is via the use of continuum solvation models such as COSMO. Another possibil...

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

    SciTech Connect

    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, both 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.

  18. Beautiful equations

    NASA Astrophysics Data System (ADS)

    Viljamaa, Panu; Jacobs, J. Richard; Chris; JamesHyman; Halma, Matthew; EricNolan; Coxon, Paul

    2014-07-01

    In reply to a Physics World infographic (part of which is given above) about a study showing that Euler's equation was deemed most beautiful by a group of mathematicians who had been hooked up to a functional magnetic-resonance image (fMRI) machine while viewing mathematical expressions (14 May, http://ow.ly/xHUFi).

  19. Effects of cation and anion solvation on ion transport in functionalized perfluoropolyethers electrolytes

    NASA Astrophysics Data System (ADS)

    Timachova, Ksenia; Chintapalli, Mahati; Olsen, Kevin; Desimone, Joseph; Balsara, Nitash

    Advances in polymer electrolytes for use in lithium batteries have been limited by the incorporation of selective lithium binding groups that provide necessary solvation for the lithium but ultimately restrict the mobility of the lithium ions relative to anions. Perfluoropolyether electrolytes (PFPE) are a new class of nonflammable liquid polymer electrolytes that have been functionalized with solvating groups for both lithium ions and fluorinated anions. PFPEs with different endgroups mixed with LiN(SO2CF3)2 salt have shown substantial differences in conductivity and allows us to investigate the effects of varying solvating environments on ion transport. To study the independent motion of cations and anions in these systems, the individual diffusion coefficients of the Li + and (SO2CF3)2 - ions were measured using pulsed-field gradient nuclear magnetic resonance (PFG-NMR). Comparing conductivity calculated using these diffusion coefficients with electrochemical measurements yields an estimation for the number of charge carrier in the system. The amount of salt dissociation, not the mobility of the salt, is the primary driver of differences in electrochemical conductivities between PFPEs with different solvating groups.

  20. Solvation free energies of molecules. The most stable anionic tautomers of uracil

    PubMed Central

    Haranczyk, Maciej; Gutowski, Maciej; Warshel, Arieh

    2008-01-01

    Anionic states of nucleic acid bases are suspected to play a role in the radiation damage processes of DNA. Our recent studies suggested that the excess electron attachment to the nucleic acid bases can stabilize some rare tautomers, i.e. imine-enamine tautomers and other tautomers with a proton being transferred form nitrogen sites to carbon sites (with respect to the canonical tautomer). So far, these new anionic tautomers have been characterized by the gas phase electronic structure calculations and photoelectron spectroscopy experiments. In the current contribution we explore the effect of water solvation on the stability of the new anionic tautomers of uracil. The accurate free energies of solvation are calculated in a two step approach. The major contribution was calculated using the classical free energy perturbation adiabatic charging approach, where it is assumed that the solvated molecule has the charge distribution given by the polarizable continuum model. In the second step the free energy of solvation is refined by taking into account the real, average solvent charge distribution. This is done using our accelerated QM/MM simulations, where the QM energy of the solute is calculated in the mean potential averaged over many MD steps. We found that in water solution three of the recently identified anionic tautomers are 6.5 – 3.6 kcal/mol more stable than the anion of the canonical tautomer. PMID:18654684

  1. Solvation free-energy pressure corrections in the three dimensional reference interaction site model

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

    Solvation free energies are efficiently predicted by molecular density functional theory if one corrects the overpressure introduced by the usual homogeneous reference fluid approximation. Sergiievskyi et al. [J. Phys. Chem. Lett. 5, 1935-1942 (2014)] recently derived the rigorous compensation of this excess of pressure (referred as "pressure correction" or PC) and proposed an empirical "ideal gas" supplementary correction (referred as "advanced pressure correction" or PC+) that further enhances the calculated solvation free energies. In a recent paper [M. Misin, M. V. Fedorov, and D. S. Palmer, J. Chem. Phys. 142, 091105 (2015)], those corrections were applied to solvation free energy calculations using the three-dimensional reference interaction site model (3D-RISM). As for classical DFT, PC and PC+ improve greatly the predictions of 3D-RISM, but PC+ is described as decreasing the accuracy. In this article, we derive rigorously the expression of the pressure in 3D-RISM as well as the associated PC and PC+. This provides a consistent way to correct the solvation free-energies calculated by 3D-RISM method.

  2. Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics.

    PubMed

    Jia, Xiangyu; Wang, Meiting; Shao, Yihan; König, Gerhard; Brooks, Bernard R; Zhang, John Z H; Mei, Ye

    2016-02-01

    In this work, the solvation free energies of 20 organic molecules from the 4th Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL4) have been calculated. The sampling of phase space is carried out at a molecular mechanical level, and the associated free energy changes are estimated using the Bennett Acceptance Ratio (BAR). Then the quantum mechanical (QM) corrections are computed through the indirect Non-Boltzmann Bennett's acceptance ratio (NBB) or the thermodynamics perturbation (TP) method. We show that BAR+TP gives a minimum analytic variance for the calculated solvation free energy at the Gaussian limit and performs slightly better than NBB in practice. Furthermore, the expense of the QM calculations in TP is only half of that in NBB. We also show that defining the biasing potential as the difference of the solute-solvent interaction energy, instead of the total energy, can converge the calculated solvation free energies much faster but possibly to different values. Based on the experimental solvation free energies which have been published before, it is discovered in this study that BLYP yields better results than MP2 and some other later functionals such as B3LYP, M06-2X, and ωB97X-D. PMID:26731197

  3. Solvation structure and transport properties of alkali cations in dimethyl sulfoxide under exogenous static electric fields

    SciTech Connect

    Kerisit, Sebastien; Vijayakumar, M. E-mail: karl.mueller@pnnl.gov; Han, Kee Sung; Mueller, Karl T. E-mail: karl.mueller@pnnl.gov

    2015-06-14

    A combination of molecular dynamics simulations and pulsed field gradient nuclear magnetic resonance spectroscopy is used to investigate the role of exogenous electric fields on the solvation structure and dynamics of alkali ions in dimethyl sulfoxide (DMSO) and as a function of temperature. Good agreement was obtained, for select alkali ions in the absence of an electric field, between calculated and experimentally determined diffusion coefficients normalized to that of pure DMSO. Our results indicate that temperatures of up to 400 K and external electric fields of up to 1 V nm{sup −1} have minimal effects on the solvation structure of the smaller alkali cations (Li{sup +} and Na{sup +}) due to their relatively strong ion-solvent interactions, whereas the solvation structures of the larger alkali cations (K{sup +}, Rb{sup +}, and Cs{sup +}) are significantly affected. In addition, although the DMSO exchange dynamics in the first solvation shell differ markedly for the two groups, the drift velocities and mobilities are not significantly affected by the nature of the alkali ion. Overall, although exogenous electric fields induce a drift displacement, their presence does not significantly affect the random diffusive displacement of the alkali ions in DMSO. System temperature is found to have generally a stronger influence on dynamical properties, such as the DMSO exchange dynamics and the ion mobilities, than the presence of electric fields.

  4. Role of Local Response in Ion Solvation: Born Theory and Beyond.

    PubMed

    Remsing, Richard C; Weeks, John D

    2016-07-01

    The nature of ion solvation has drawn the interest of scientists for over a century, yet a thorough theoretical understanding is still lacking. In this work, we focus on the microscopic origins underlying ionic charge asymmetric and nonlinear response contributions to ion solvation free energies. We first derive an exact expression for the charging component of the ionic free energy, the free energy change when the Coulomb interactions between a fixed ion and the solvent are gradually "turned on". We then introduce the concept of a Gaussian test charge distribution, a generalization of the classical electrostatic point test charge that can be used to probe dielectric response in atomically detailed models. This enables the study of a thermodynamic cycle that isolates a linear and charge-symmetric contribution to the free energy that is well-described by Born-model-like dielectric continuum theories. We give a simple physical derivation of the classic Born model that locally relates the induced charge density in a linear dielectric model to the applied ionic charge distribution. The nonlinear response and charge asymmetric contributions to the ion solvation free energy are then examined in the remaining steps of the cycle and compared to classic thermodynamic cycles for this process using computer simulations. The insights provided by this work will aid the development of quantitative theories for the solvation of charged solutes. PMID:27183036

  5. Experimental and computational studies of polar solvation. Third year progress report, 1989--1991

    SciTech Connect

    Not Available

    1991-12-31

    Many articles and papers were published; a few are still in preparation or will be published. The solvation dynamics studies will be extended to ionic solutions. Computer simulations were also performed. A new line of research was begun on excited-state proton-transfer reactions catalyzed by alcohol solvents. (DLC)

  6. Structure and photoabsorption properties of cationic alkali dimers solvated in neon clusters.

    PubMed

    Zanuttini, D; Douady, J; Jacquet, E; Giglio, E; Gervais, B

    2010-11-01

    We present a theoretical investigation of the structure and optical absorption of M(2)(+) alkali dimers (M=Li,Na,K) solvated in Ne(n) clusters for n=1 to a few tens Ne atoms. For all these alkali, the lowest-energy isomers are obtained by aggregation of the first Ne atoms at the extremity of the alkali molecule. This particular geometry, common to other M(2)(+)-rare gas clusters, is intimately related to the shape of the electronic density of the X  (2)Σ(g)(+) ground state of the bare M(2)(+) molecules. The structure of the first solvation shell presents equilateral Ne(3) and capped pentagonal Ne(6) motifs, which are characteristic of pure rare gas clusters. The size and geometry of the complete solvation shell depend on the alkali and were obtained at n=22 with a D(4h) symmetry for Li and at n=27 with a D(5h) symmetry for Na. For K, our study suggests that the closure of the first solvation shell occurs well beyond n=36. We show that the atomic arrangement of these clusters has a profound influence on their optical absorption spectrum. In particular, the XΣ transition from the X  (2)Σ(g)(+) ground state to the first excited (2)Σ(u)(+) state is strongly blueshifted in the Frank-Condon area. PMID:21054047

  7. The charge-asymmetric nonlocally determined local-electric (CANDLE) solvation model.

    PubMed

    Sundararaman, Ravishankar; Goddard, William A

    2015-02-14

    Many important applications of electronic structure methods involve molecules or solid surfaces in a solvent medium. Since explicit treatment of the solvent in such methods is usually not practical, calculations often employ continuum solvation models to approximate the effect of the solvent. Previous solvation models either involve a parametrization based on atomic radii, which limits the class of applicable solutes, or based on solute electron density, which is more general but less accurate, especially for charged systems. We develop an accurate and general solvation model that includes a cavity that is a nonlocal functional of both solute electron density and potential, local dielectric response on this nonlocally determined cavity, and nonlocal approximations to the cavity-formation and dispersion energies. The dependence of the cavity on the solute potential enables an explicit treatment of the solvent charge asymmetry. With four parameters per solvent, this "CANDLE" model simultaneously reproduces solvation energies of large datasets of neutral molecules, cations, and anions with a mean absolute error of 1.8 kcal/mol in water and 3.0 kcal/mol in acetonitrile. PMID:25681887

  8. Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces.

    PubMed

    Herron, Jeffrey A; Morikawa, Yoshitada; Mavrikakis, Manos

    2016-08-23

    Using ab initio molecular dynamics as implemented in periodic, self-consistent (generalized gradient approximation Perdew-Burke-Ernzerhof) density functional theory, we investigated the mechanism of methanol electrooxidation on Pt(111). We investigated the role of water solvation and electrode potential on the energetics of the first proton transfer step, methanol electrooxidation to methoxy (CH3O) or hydroxymethyl (CH2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), whereas the binding energies of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C-H and O-H bonds in methanol were calculated through a Blue Moon Ensemble using constrained ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Water solvation reduces the barriers for both C-H and O-H bond activation steps with respect to their vapor-phase values, although the effect is more pronounced for C-H bond activation, due to less disruption of the hydrogen bond network. The calculated activation energy barriers show that breaking the C-H bond of methanol is more facile than the O-H bond on solvated negatively biased or uncharged Pt(111). However, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation. PMID:27503889

  9. Structure prediction, disorder and dynamics in a DMSO solvate of carbamazepine.

    PubMed

    Cruz-Cabeza, Aurora J; Day, Graeme M; Jones, William

    2011-07-28

    We have applied crystal structure prediction methods to understand and predict the formation of a DMSO solvate of the anti-convulsant drug carbamazepine (CBZ), in which the DMSO molecules are disordered. Crystal structure prediction calculations on the 1:1 CBZ:DMSO solvate revealed the generation of two similar low energy structures which differ only in the orientation of the DMSO molecules. Analysis of crystal energy landscapes generated at 0 K suggests the possibility of solvent disorder. A combined computational and experimental study of the changes in the orientation of the DMSO within the crystal structure revealed that the nature of the disorder changes with temperature. At low temperature, the DMSO disorder is static whilst at high temperature the DMSO configurations can interconvert by a 180° rotation of the DMSO molecules within the lattice. This 180° rotation of the DMSO molecules drives a phase change from a high temperature dynamically disordered phase to a low temperature phase with static disorder. Crystallisation of a DMSO solvate of the related molecule epoxycarbamazepine resulted in a different degree of DMSO disorder in the crystal structure, despite the similarity of the carbamazepine and epoxycarbamazepine molecules. We believe consideration of disorder and its contribution to entropy and crystal free energies at temperature other than 0 K is fundamental for the accuracy of future energy rankings in crystal structure prediction calculations of similar solvated structures. PMID:21670828

  10. Solvation structure and dynamics of Na+ in liquid ammonia studied by ONIOM-XS MD simulations

    NASA Astrophysics Data System (ADS)

    Sripradite, Jarukorn; Tongraar, Anan; Kerdcharoen, Teerakiat

    2015-12-01

    The molecular dynamics (MD) technique based on the ONIOM-XS method, known as the ONIOM-XS MD, has been applied to investigate the solvation structure and dynamics of Na+ in liquid ammonia. Regarding the ONIOM-XS MD results, it is observed that Na+ is able to order the surrounding ammonia molecules to form its specific first and second solvation shells with the average coordination numbers of 5.1 and 11.2, respectively. The first solvation shell of Na+ is rather well-defined, forming a preferred 5-fold coordinated complex with a distorted square pyramidal geometry. In this respect, the most preferential Na+(NH3)5 species could convert back and forth to the lower probability Na+(NH3)6 and Na+(NH3)4 configurations. The second solvation shell of Na+ is detectable, in which a number of ammonia molecules, ranging from 7 to 14, are involved in this layer and they are arranged according to recognizable influence of the ion.

  11. Femtosecond solvation dynamics in a neat ionic liquid and ionic liquid microemulsion: excitation wavelength dependence.

    PubMed

    Adhikari, Aniruddha; Sahu, Kalyanasis; Dey, Shantanu; Ghosh, Subhadip; Mandal, Ujjwal; Bhattacharyya, Kankan

    2007-11-01

    Solvation dynamics in a neat ionic liquid, 1-pentyl-3-methyl-imidazolium tetra-flouroborate ([pmim][BF4]) and its microemulsion in Triton X-100 (TX-100)/benzene is studied using femtosecond up-conversion. In both the neat ionic liquid and the microemulsion, the solvation dynamics is found to depend on excitation wavelength (lambda(ex)). The lambda(ex) dependence is attributed to structural heterogeneity in neat ionic liquid (IL) and in IL microemulsion. In neat IL, the heterogeneity arises from clustering of the pentyl groups which are surrounded by a network of cation and anions. Such a nanostructural organization is predicted in many recent simulations and observed recently in an X-ray diffraction study. In an IL microemulsion, the surfactant (TX-100) molecules aggregate in form of a nonpolar peripheral shell around the polar pool of IL. The micro-environment in such an assembly varies drastically over a short distance. The dynamic solvent shift (and average solvation time) in neat IL as well as in IL microemulsions decreases markedly as lambda(ex) increases from 375 to 435 nm. In a [pmim][BF4]/water/TX-100/benzene quaternary microemulsion, the solvation dynamics is slower than that in a microemulsion without water. This is ascribed to the smaller size of the water containing microemulsion. The anisotropy decay in an IL microemulsion is found to be faster than that in neat IL. PMID:17944511

  12. Models of Ion Solvation Thermodynamics in Ethylene Carbonate and Propylene Carbonate.

    PubMed

    Arslanargin, Ayse; Powers, August; Beck, Thomas L; Rick, Steven W

    2016-03-01

    Ethylene carbonate (EC) and propylene carbonate (PC) are organic solvents used extensively in energy storage applications such as lithium-ion batteries and supercapacitors. Using statistical mechanical theory and computer simulations, this paper compares and contrasts the thermodynamics of ion solvation in EC and PC with the behavior observed in water. The EC and PC solvents are modeled with the AMBER (GAFF) force field. Ion-solvent interactions are treated with two point-charge models: one using an existing Lennard-Jones ion parameter set optimized for solvation in water, and the other based on high-level quantum calculations on ion-solvent dimers and fitting to a Buckingham-type potential form. The second model produces a coordination number for the Li(+) ion in closer agreement with experiment. Neither model yields consistently accurate solvation thermodynamic quantities (free energies, enthalpies, and entropies), however. The simulations and thermodynamic analysis illustrate key physical aspects of the solvation; the studies also point to necessary modifications of these simple models. In particular, the calculations show that polarization and associated dispersion forces are important and that well-optimized polarizable or quantum models are likely required to accurately reproduce condensed-phase properties of ions in these technologically important solvents. PMID:26292974

  13. Solvation Phenomena in Dilute Solutions: Formal, Experimental Evidence, and Modeling Implications

    SciTech Connect

    Chialvo, Ariel A

    2013-01-01

    We review the fundamentals underlying a general molecular-based formalism for the microscopic interpretation of the solvation phenomena involving sparingly soluble solutes in compressible media, an approach that hinges around the unambiguous splitting of the species correlation function integrals into short-(finite) and long-ranged (diverging) contributions at infinite dilution, where this condition is taken as the reference system for the derivation of composition expansions. Then, we invoke the formalism (a) to illustrate the well-behaved nature of the solvation contributions to the mechanical partial molecular properties of solutes at infinite dilution, (b) to guide the development of, and provide molecular-based support to, the macroscopic modeling of high-temperature dilute aqueous-electrolyte solutions, (c) to study solvation effects on the kinetic rate constants of reactions in near-critical solvents in an attempt to understand from a microscopic perspective the macroscopic evidence regarding the thermodynamic pressure effects, and (d) to interpret the microscopic mechanism behind synergistic solvation effects involving either co-solutes or co-solvents, and provide a molecular argument on the unsuitability of the van der Waals one-fluid (vdW-1f) mixing rules for the 2 description of weakly attractive solutes in compressible solvents. Finally, we develop thermodynamically consistent perturbation expansions, around the infinite dilution reference, for the species residual properties in binary and ternary mixtures, and discuss the theoretical and modeling implications behind ad hoc first-order truncated expansions.

  14. The charge-asymmetric nonlocally determined local-electric (CANDLE) solvation model

    SciTech Connect

    Sundararaman, Ravishankar; Goddard, William A.

    2015-02-14

    Many important applications of electronic structure methods involve molecules or solid surfaces in a solvent medium. Since explicit treatment of the solvent in such methods is usually not practical, calculations often employ continuum solvation models to approximate the effect of the solvent. Previous solvation models either involve a parametrization based on atomic radii, which limits the class of applicable solutes, or based on solute electron density, which is more general but less accurate, especially for charged systems. We develop an accurate and general solvation model that includes a cavity that is a nonlocal functional of both solute electron density and potential, local dielectric response on this nonlocally determined cavity, and nonlocal approximations to the cavity-formation and dispersion energies. The dependence of the cavity on the solute potential enables an explicit treatment of the solvent charge asymmetry. With four parameters per solvent, this “CANDLE” model simultaneously reproduces solvation energies of large datasets of neutral molecules, cations, and anions with a mean absolute error of 1.8 kcal/mol in water and 3.0 kcal/mol in acetonitrile.

  15. Mutagenicity of Tween 80-solvated mild gasification products in the Ames salmonella microsomal assay system

    SciTech Connect

    Not Available

    1992-01-13

    The results of the Tween 80-solvated Ames testing of six mild gasification samples indicate significant mutagenic activity only in the composite materials (MG-119 and MG-120), previously suspected from the DMSO-solvated assays, which had shown some variable but ultimately insignificant mutagenic responses. The activity of these samples from the Tween 80-solvated assays was quite low when compared to either the positive controls or the SRC-II HD coal-liquefaction reference material. The class of mutagenic activity expressed by these samples solvated in Tween 80 was that of an indirect-acting, frameshift mutagen(s) since significant activity was found only on tester strain TA98 in the presence of the metabolic activation fraction (S9). Because DMSO and other solvents have been shown to affect the mutagenic activity of certain pure chemicals, the possibility of solvent/mutagen interactions in complex mixtures such as coal-derived liquids exists. Thus, the testing of the genotoxic activity of undefined, chemically complex compounds may require the use of at least two solvent systems to reduce the possibility of artifactual findings. 10 refs., 4 tabs.

  16. 6,6'-Dimethoxygossypol: molecular structure, crystal polymorphism, and solvate formation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    6,6´-Dimethoxygossypol (DMG) is a naturally produced derivative of gossypol that is found in relatively high concentration in some Gossypium barbadense cotton varieties. Like gossypol, DMG forms an equimolar solvate with acetic acid, but it was not clear if, like gossypol, the compound would form c...

  17. IR SPECTRA BY DFT FOR GLUCOSE AND ITS EPIMERS: A COMPARISON BETWEEN VACUUM AND SOLVATED SPECTRA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Infrared spectra were calculated for the low energy geometry optimized structures of glucose and all of its epimers, at B3LYP/6-311++G** level of theory. Calculations were performed both in vacuo and using the COSMO solvation method. Frequencies, zero point energies, enthalpies, entropies, and rel...

  18. DFT molecular simulations of solvated glucose dimers: explicit vs. implicit water

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The behavior of Glucose dimers in solution is investigated at the DFT level of theory via optimization and constant energy DFT molecular dynamics. The effect of the solvent on the dimer is treated two different ways: using the implicit solvation method COSMO alone to treat the bulk water behavior an...

  19. Solvation and Acid Strength Effects on Catalysis by Faujasite Zeolites

    SciTech Connect

    Gounder, Rajamani P.; Jones, Andrew J.; Carr, Robert T.; Iglesia, Enrique

    2012-02-01

    Kinetic, spectroscopic, and chemical titration data indicate that differences in monomolecular isobutane cracking and dehydrogenation and methanol dehydration turnover rates (per H+) among FAU zeolites treated thermally with steam (H-USY) and then chemically with ammonium hexafluorosilicate (CDHUSY) predominantly reflect differences in the size and solvating properties of their supercage voids rather than differences in acid strength. The number of protons on a given sample was measured consistently by titrations with Na+, with CH3 groups via reactions of dimethyl ether, and with 2,6-di-tert-butylpyridine during methanol dehydration catalysis; these titration values were also supported by commensurate changes in acidic OH infrared band areas upon exposure to titrant molecules. The number of protons, taken as the average of the three titration methods, was significantly smaller than the number of framework Al atoms (Alf) obtained from X-ray diffraction and 27Al magic angle spinning nuclear magnetic resonance spectroscopy on H-USY (0.35 H+/Alf) and CD-HUSY (0.69 H+/Alf). These data demonstrate that the ubiquitous use of Alf sites as structural proxies for active H+ sites in zeolites can be imprecise, apparently because distorted Al structures that are not associated with acidic protons are sometimes detected as Alf sites. Monomolecular isobutane cracking and dehydrogenation rate constants, normalized non-rigorously by the number of Alf species, decreased with increasing Na+ content on both H-USY and CD-HUSY samples and became undetectable at sub-stoichiometric exchange levels (0.32 and 0.72 Na+/Alf ratios, respectively), an unexpected finding attributed incorrectly in previous studies to the presence of minority ‘‘super-acidic’’ sites. These rate constants, when normalized rigorously by the number of residual H+ sites were independent of Na+ content on both H-USY and CD-HUSY samples, reflecting the stoichiometric replacement of protons that are uniform in

  20. Marcus equation

    DOE R&D Accomplishments Database

    1998-09-21

    In the late 1950s to early 1960s Rudolph A. Marcus developed a theory for treating the rates of outer-sphere electron-transfer reactions. Outer-sphere reactions are reactions in which an electron is transferred from a donor to an acceptor without any chemical bonds being made or broken. (Electron-transfer reactions in which bonds are made or broken are referred to as inner-sphere reactions.) Marcus derived several very useful expressions, one of which has come to be known as the Marcus cross-relation or, more simply, as the Marcus equation. It is widely used for correlating and predicting electron-transfer rates. For his contributions to the understanding of electron-transfer reactions, Marcus received the 1992 Nobel Prize in Chemistry. This paper discusses the development and use of the Marcus equation. Topics include self-exchange reactions; net electron-transfer reactions; Marcus cross-relation; and proton, hydride, atom and group transfers.

  1. Marcus equation

    SciTech Connect

    1998-11-01

    In the late 1950s to early 1960s Rudolph A. Marcus developed a theory for treating the rates of outer-sphere electron-transfer reactions. Outer-sphere reactions are reactions in which an electron is transferred from a donor to an acceptor without any chemical bonds being made or broken. (Electron-transfer reactions in which bonds are made or broken are referred to as inner-sphere reactions.) Marcus derived several very useful expressions, one of which has come to be known as the Marcus cross-relation or, more simply, as the Marcus equation. It is widely used for correlating and predicting electron-transfer rates. For his contributions to the understanding of electron-transfer reactions, Marcus received the 1992 Nobel Prize in Chemistry. This paper discusses the development and use of the Marcus equation. Topics include self-exchange reactions; net electron-transfer reactions; Marcus cross-relation; and proton, hydride, atom and group transfers.

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

    PubMed

    Pliego, Josefredo R; Miguel, Elizabeth L M

    2013-05-01

    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. PMID:23570440

  3. Competitive lithium solvation of linear and cyclic carbonates from quantum chemistry.

    PubMed

    Borodin, Oleg; Olguin, Marco; Ganesh, P; Kent, Paul R C; Allen, Joshua L; Henderson, Wesley A

    2016-01-01

    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)-LiPF6 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-LiPF6 solvates in the gas-phase and for an implicit solvent (as a function of the solvent dielectric constant) indicated that the DMC-containing Li(+) solvates were stabilized relative to (EC4)-Li(+) and (EC)3-LiPF6 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)LiPF6 mixed solvent electrolyte was studied using the BOMD simulations. PMID:26601903

  4. Solvation chemical shifts of perylenic antenna molecules from molecular dynamics simulations.

    PubMed

    Özcan, Nergiz; Mareš, Jiří; Sundholm, Dage; Vaara, Juha

    2014-10-28

    Solvation-induced shifts in molecular properties can be realistically simulated by employing a dynamic model with explicit solvent molecules. In this work, (13)C NMR chemical shifts of various candidate antenna molecules for dye-sensitised solar cells have been studied by using density-functional theory calculations both in vacuo and by employing a dynamic solvation model. The solvent effects were investigated using instantaneous molecular dynamics snapshots containing the antenna molecule and surrounding acetonitrile solvent molecules. Such calculations take into account the main mechanisms of solvation-induced chemical shifts. We have analysed the contributions to the solvent shift due to the solvent susceptibility anisotropy, changes in the density of the virtual orbital space and the accessibility of the excited states to the pronouncedly local magnetic hyperfine operator. We present Lorentzian-broadened chemical shift stick spectra in which a comparison of the in vacuo and dynamic-solvation model results is graphically illustrated. The results show that the solvent-accessible atoms at the perimeter of the solute are influenced by the virtual states of the solvent molecules, which are visible to the hyperfine operators of the perimeter nuclei. This enables efficient coupling of the ground state of the solute to the magnetically allowed excited states, resulting in a positive chemical shift contribution of the perimeter nuclei. As a result of solvation, the chemical shift signals of perimeter nuclei are found to be displaced towards larger chemical shift values, whereas the nuclei of the inner region of the solute molecules show the opposite trend. The solvent susceptibility anisotropy is found to cause a small and practically constant contribution. PMID:25222796

  5. Competitive lithium solvation of linear and cyclic carbonates from quantum chemistry

    SciTech Connect

    Kent, Paul R. C.; Ganesh, Panchapakesan; Borodin, Oleg; Olguin, Marco; Allen, Joshua L.; Henderson, Wesley A.

    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)–LiPF6 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–LiPF6 solvates in the gas-phase and for an implicit solvent (as a function of the solvent dielectric constant) indicated that the DMC-containing Li+ solvates were stabilized relative to (EC4)–Li+ and (EC)3–LiPF6 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)LiPF6 mixed solvent electrolyte was studied using the BOMD simulations.

  6. Picosecond solvation dynamics—A potential viewer of DMSO—Water binary mixtures

    SciTech Connect

    Banik, Debasis; Kundu, Niloy; Kuchlyan, Jagannath; Roy, Arpita; Banerjee, Chiranjib; Ghosh, Surajit; Sarkar, Nilmoni

    2015-02-07

    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 X{sub D} = 0.12–0.17 and X{sub D} = 0.27–0.35, respectively. Among them, the second region (X{sub D} = 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:2H{sub 2}O complexes, hydration around the probe C480 decreases, as a result of which solvation time increases.

  7. Competitive lithium solvation of linear and cyclic carbonates from quantum chemistry

    DOE PAGESBeta

    Kent, Paul R. C.; Ganesh, Panchapakesan; Borodin, Oleg; Olguin, Marco; Allen, Joshua L.; Henderson, Wesley A.

    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)–LiPF6 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–LiPF6 solvates in the gas-phase and for an implicit solvent (as a function of the solvent dielectricmore » constant) indicated that the DMC-containing Li+ solvates were stabilized relative to (EC4)–Li+ and (EC)3–LiPF6 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)LiPF6 mixed solvent electrolyte was studied using the BOMD simulations.« less

  8. Picosecond solvation dynamics--a potential viewer of DMSO-water binary mixtures.

    PubMed

    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. PMID:25662652

  9. Deciphering the photochemical mechanisms describing the UV-induced processes occurring in solvated guanine monophosphate

    NASA Astrophysics Data System (ADS)

    Altavilla, Salvatore; Segarra-Martí, Javier; Nenov, Artur; Conti, Irene; Rivalta, Ivan; Garavelli, Marco

    2015-04-01

    The photophysics and photochemistry of water-solvated guanine monophosphate (GMP) are here characterized by means of a multireference quantum-chemical/molecular mechanics theoretical approach (CASPT2//CASSCF/AMBER) in order to elucidate the main photo-processes occurring upon UV-light irradiation. The effect of the solvent and of the phosphate group on the energetics and structural features of this system are evaluated for the first time employing high-level ab initio methods and thoroughly compared to those in vacuo previously reported in the literature and to the experimental evidence to assess to which extent they influence the photoinduced mechanisms. Solvated electronic excitation energies of solvated GMP at the Franck-Condon (FC) region show a red shift for the ππ* La and Lb states, whereas the energy of the oxygen lone-pair nπ* state is blue-shifted. The main photoinduced decay route is promoted through a ring-puckering motion along the bright lowest-lying La state towards a conical intersection (CI) with the ground state, involving a very shallow stationary point along the minimum energy pathway in contrast to the barrierless profile found in gas-phase, the point being placed at the end of the minimum energy path (MEP) thus endorsing its ultrafast deactivation in accordance with time-resolved transient and photoelectron spectroscopy experiments. The role of the nπ* state in the solvated system is severely diminished as the crossings with the initially populated La state and also with the Lb state are placed too high energetically to partake prominently in the deactivation photo-process. The proposed mechanism present in solvated and in vacuo DNA/RNA chromophores validates the intrinsic photostability mechanism through CI-mediated non-radiative processes accompanying the bright excited-state population towards the ground state and subsequent relaxation back to the FC region.

  10. Simultaneous permeation of tamoxifen and gamma linolenic acid across excised human skin. Further evidence of the permeation of solvated complexes.

    PubMed

    Karia, Clare; Harwood, John L; Morris, Andy P; Heard, Charles M

    2004-03-01

    Tamoxifen is the hormonal treatment of choice in women who have hormone-dependent breast cancer and its efficacy in those women considered to have a high risk of developing breast cancer, has also been established. Gamma linolenic acid (GLA) has been shown to decrease the invasion of breast cancer and recent studies have demonstrated that GLA can enhance the oestrogen receptor down-regulation induced by tamoxifen. However, tamoxifen is associated with serious side-effects due mainly to systemic delivery, and targeted delivery of both tamoxifen and GLA would be highly beneficial. This work was a preliminary study for the development of a transcutaneous system to simultaneously deliver both tamoxifen and GLA directly to the breast. Full thickness human skin was dosed with 500 microl saturated solution of tamoxifen in borage oil (25% GLA) and the simultaneous permeation of the two actives determined. There was rapid flux with minimal lag time, the cumulative permeation at 24 h was 764.3 +/- 94.2 microg cm(-2) for GLA and 5.44 +/- 0.67 microg cm(-2) for tamoxifen: the latter being comparable to the amount of tamoxifen associated with cancerous breast tissue from a 20 mg oral dose. The ratio of GLA/tamoxifen permeated at different timepoints was quite consistent, both in terms of mass (mean 138, S.D. 15.1) and mols (mean 184, S.D. 20.3). It was determined that 2.5 molecules of GLA were associated with each molecule of tamoxifen in the permeation process, equating to a solvation cage of three molecules of triacylglycerol. This study has demonstrated the feasibility of administering simultaneously tamoxifen and GLA using borage oil as vehicle, which warrants further investigation as a novel topical two-component system in relation to or prophylaxis of those perceived at high risk of developing breast cancer. The study also provides further evidence of the permeation of solvated complexes across skin, rather than discrete penetrant molecules. PMID:15129999

  11. LDS-750 as a probe of solvation dynamics: a femtosecond time-resolved fluorescence study in liquid aniline

    NASA Astrophysics Data System (ADS)

    Smith, Neil A.; Meech, Stephen R.; Rubtsov, Igor V.; Yoshihara, Keitaro

    1999-04-01

    The dynamics of the fluorescence Stokes shift of the styryl dye LDS-750 have been measured in liquid aniline with sub-100 fs time resolution. The shape of the time-resolved spectra are time dependent, which is not consistent with the predictions of a solvation dynamics mechanism. However, the measured spectral shift correlation function is reasonably well described by the dynamical mean spherical approximation model of solvation dynamics. It is suggested that these observations are consistent if solvent dynamics is the rate controlling process in both solvation of the increased dipole moment of the excited state of LDS-750 and the stabilisation of a distribution of solute conformers in the excited state.

  12. Development of three-dimensional site-site Smoluchowski-Vlasov equation and application to electrolyte solutions

    SciTech Connect

    Kasahara, Kento; Sato, Hirofumi

    2014-06-28

    Site-site Smoluchowski-Vlasov (SSSV) equation enables us to directly calculate van Hove time correlation function, which describes diffusion process in molecular liquids. Recently, the theory had been extended to treat solute-solvent system by Iida and Sato [J. Chem. Phys. 137, 034506 (2012)]. Because the original framework of SSSV equation is based on conventional pair correlation function, time evolution of system is expressed in terms of one-dimensional solvation structure. Here, we propose a new SSSV equation to calculate time evolution of solvation structure in three-dimensional space. The proposed theory was applied to analyze diffusion processes in 1M NaCl aqueous solution and in lithium ion battery electrolyte solution. The results demonstrate that these processes are properly described with the theory, and the computed van Hove functions are in good agreement with those in previous works.

  13. Development of three-dimensional site-site Smoluchowski-Vlasov equation and application to electrolyte solutions

    NASA Astrophysics Data System (ADS)

    Kasahara, Kento; Sato, Hirofumi

    2014-06-01

    Site-site Smoluchowski-Vlasov (SSSV) equation enables us to directly calculate van Hove time correlation function, which describes diffusion process in molecular liquids. Recently, the theory had been extended to treat solute-solvent system by Iida and Sato [J. Chem. Phys. 137, 034506 (2012)]. Because the original framework of SSSV equation is based on conventional pair correlation function, time evolution of system is expressed in terms of one-dimensional solvation structure. Here, we propose a new SSSV equation to calculate time evolution of solvation structure in three-dimensional space. The proposed theory was applied to analyze diffusion processes in 1M NaCl aqueous solution and in lithium ion battery electrolyte solution. The results demonstrate that these processes are properly described with the theory, and the computed van Hove functions are in good agreement with those in previous works.

  14. Theory for the solvation of nonpolar solutes in water.

    PubMed

    Urbic, T; Vlachy, V; Kalyuzhnyi, Yu V; Dill, K A

    2007-11-01

    We recently developed an angle-dependent Wertheim integral equation theory (IET) of the Mercedes-Benz (MB) model of pure water [Silverstein et al., J. Am. Chem. Soc. 120, 3166 (1998)]. Our approach treats explicitly the coupled orientational constraints within water molecules. The analytical theory offers the advantage of being less computationally expensive than Monte Carlo simulations by two orders of magnitude. Here we apply the angle-dependent IET to studying the hydrophobic effect, the transfer of a nonpolar solute into MB water. We find that the theory reproduces the Monte Carlo results qualitatively for cold water and quantitatively for hot water. PMID:17994825

  15. Theory for the solvation of nonpolar solutes in water

    NASA Astrophysics Data System (ADS)

    Urbic, T.; Vlachy, V.; Kalyuzhnyi, Yu. V.; Dill, K. A.

    2007-11-01

    We recently developed an angle-dependent Wertheim integral equation theory (IET) of the Mercedes-Benz (MB) model of pure water [Silverstein et al., J. Am. Chem. Soc. 120, 3166 (1998)]. Our approach treats explicitly the coupled orientational constraints within water molecules. The analytical theory offers the advantage of being less computationally expensive than Monte Carlo simulations by two orders of magnitude. Here we apply the angle-dependent IET to studying the hydrophobic effect, the transfer of a nonpolar solute into MB water. We find that the theory reproduces the Monte Carlo results qualitatively for cold water and quantitatively for hot water.

  16. The Assassination of Abraham Lincoln and the Evolution of Neuro-Trauma Care: Would the 16th President Have Survived in the Modern Era?

    PubMed

    Yan, Sandra C; Smith, Timothy R; Bi, Wenya Linda; Brewster, Ryan; Gormley, William B; Dunn, Ian F; Laws, Edward R

    2015-11-01

    Abraham Lincoln was the 16(th) President of the United States of America. On April 14, 1865, shortly after his re-election and the conclusion of the Civil War, Lincoln was shot and killed by John Wilkes Booth. Although numerous physicians tended to the President shortly after his injury, he passed away the next morning. Today, we recognize Lincoln as one of the greatest Presidents in American history. His assassination profoundly influenced the future of the United States, especially as the country was coming back together again following the Civil War. Testaments to his lasting legacy can be seen in many places, from the stone carving of him on Mount Rushmore to his image gracing the $5 bill. What if the President had survived his injury? Would he have had a different outcome utilizing current critical care treatment? Neurotrauma care in 1865 was not yet developed, and head wounds such as the one Lincoln sustained were almost always fatal. The medical attention he received is considered by historians and physicians today to be excellent for that time. We look at the evolution of neurotrauma care during the last 150 years in the US. Particular focus is paid to the advancement of care for penetrating brain injuries in modern trauma centers. PMID:26092530

  17. Li(+) Local Structure in Hydrofluoroether Diluted Li-Glyme Solvate Ionic Liquid.

    PubMed

    Saito, Soshi; Watanabe, Hikari; Ueno, Kazuhide; Mandai, Toshihiko; Seki, Shiro; Tsuzuki, Seiji; Kameda, Yasuo; Dokko, Kaoru; Watanabe, Masayoshi; Umebayashi, Yasuhiro

    2016-04-01

    Hydrofluoroethers have recently been used as the diluent to a lithium battery electrolyte solution to increase and decrease the ionic conductivity and the solution viscosity, respectively. In order to clarify the Li(+) local structure in the 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether (HFE) diluted [Li(G4)][TFSA] (G4, tetraglyme; TFSA, bis(trifluoromethanesulfonyl)amide) solvate ionic liquid, Raman spectroscopic study has been done with the DFT calculations. It has turned out that the HFE never coordinates to the Li(+) directly, and that the solvent (G4) shared ion pair of Li(+) with TFSA anion (SSIP) and the contact ion pair between Li(+) and TFSA anion (CIP) are found in the neat and HFE diluted [Li(G4)][TFSA] solvate ionic liquid. It is also revealed that the two kinds of the CIP in which TFSA anion coordinates to the Li(+) in monodentate and bidentate manners (hereafter, we call them the monodentate CIP and the bidentate CIP, respectively) exist with the SSIP of predominant [Li(G4)](+) ion-pair species in the neat [Li(G4)][TFSA] solvate ionic liquid, and that the monodentate CIP decreases as diluting with the HFE. To obtain further insight, X-ray total scattering experiments (HEXTS) were carried out with the aid of MD simulations, where the intermolecular force field parameters, mainly partial atomic charges, have been newly proposed for the HFE and glymes. A new peak appeared at around 0.6-0.7 Å(-1) in X-ray structure factors, which was ascribed to the correlation between the [Li(G4)][TFSA] ion pairs. Furthermore, MD simulations were in good agreement with the experiments, from which it is suggested that the terminal oxygen atoms of the G4 in [Li(G4)](+) solvated cation frequently repeat coordinating/uncoordinating to the Li(+), although almost all of the G4 coordinates to the Li(+) to form [Li(G4)](+) solvated cation in the neat and HFE diluted [Li(G4)][TFSA] solvate ionic liquid. PMID:26959344

  18. Importance of polar solvation and configurational entropy for design of antiretroviral drugs targeting HIV-1 protease.

    PubMed

    Kar, Parimal; Lipowsky, Reinhard; Knecht, Volker

    2013-05-16

    Both KNI-10033 and KNI-10075 are high affinity preclinical HIV-1 protease (PR) inhibitors with affinities in the picomolar range. In this work, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method has been used to investigate the potency of these two HIV-1 PR inhibitors against the wild-type and mutated proteases assuming that potency correlates with the affinity of the drugs for the target protein. The decomposition of the binding free energy reveals the origin of binding affinities or mutation-induced affinity changes. Our calculations indicate that the mutation I50V causes drug resistance against both inhibitors. On the other hand, we predict that the mutant I84V causes drug resistance against KNI-10075 while KNI-10033 is more potent against the I84V mutant compared to wild-type protease. Drug resistance arises mainly from unfavorable shifts in van der Waals interactions and configurational entropy. The latter indicates that neglecting changes in configurational entropy in the computation of relative binding affinities as often done is not appropriate in general. For the bound complex PR(I50V)-KNI-10075, an increased polar solvation free energy also contributes to the drug resistance. The importance of polar solvation free energies is revealed when interactions governing the binding of KNI-10033 or KNI-10075 to the wild-type protease are compared to the inhibitors darunavir or GRL-06579A. Although the contributions from intermolecular electrostatic and van der Waals interactions as well as the nonpolar component of the solvation free energy are more favorable for PR-KNI-10033 or PR-KNI-10075 compared to PR-DRV or PR-GRL-06579A, both KNI-10033 and KNI-10075 show a similar affinity as darunavir and a lower binding affinity relative to GRL-06579A. This is because of the polar solvation free energy which is less unfavorable for darunavir or GRL-06579A relative to KNI-10033 or KNI-10075. The importance of the polar solvation as revealed here

  19. 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

  20. Polarization effects on the solvation dynamics of coumarin C153 in ionic liquids: Components and their cross-correlations

    NASA Astrophysics Data System (ADS)

    Schmollngruber, Michael; Schröder, Christian; Steinhauser, Othmar

    2013-05-01

    The solvation dynamics of coumarin C153 dissolved in three selected molecular ionic liquids - EMIM+BF_4^-, EMIM+TfO-, and BMIM+BF_4^- - was studied by molecular dynamics simulations including polarization forces. The solvation response function was decomposed with respect to permanent and induced charge distributions, cationic and anionic contributions, and translational and non-translational motions. The latter decomposition was accomplished by an appropriate multipole expansion. Furthermore, the difference in solvation energy was resolved radially. The dynamics in the sub-picosecond regime was elucidated as the mutual translational motion of the solute and the cage formed by the first solvation shell. For a qualitative interpretation, solvent molecules can be reduced to "quasi-atomic" ions carrying a net charge at their molecular center of mass. Towards a quantitative description, the dipole moment serves as a measure of charge anisotropy.

  1. 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

    2016-01-01

    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. PMID:26706441

  2. Solvent effects of 1-ethyl-3-methylimidazolium acetate: solvation and dynamic behavior of polar and apolar solutes.

    PubMed

    Lesch, Volker; Heuer, Andreas; Holm, Christian; Smiatek, Jens

    2015-04-01

    We study the solvation properties of the ionic liquid 1-ethyl-3-methylimidazolium acetate ([EMIM](+)[ACE](-)) and the resulting dynamic behavior for differently charged model solutes at room temperature via atomistic molecular dynamics (MD) simulations of 300 ns length and 200 ns equilibration time. The solutes are simple model spheres which are either positively or negatively charged with a valency of one, or uncharged. The numerical findings indicate a distinct solvation behavior with the occurrence of well-pronounced solvation shells whose composition significantly depends on the charge of the solute. All the results of our simulations evidence the existence of a long-range perturbation effect in presence of the solutes. Our findings validate the dominance of electrostatic interactions with regard to unfavorable entropic ordering effects which elucidates the enthalpic character of the solvation process in ionic liquids for charged solutes. PMID:25680082

  3. A modification of the generalized Born theory for improved estimates of solvation energies and pK shifts

    NASA Astrophysics Data System (ADS)

    Jayaram, B.; Liu, Y.; Beveridge, D. L.

    1998-07-01

    We present herein an appraisal on the performance of the generalized Born (GB) model in estimating the solvation energies of small molecules and pKa shifts of dicarboxylic acids. The quality of the solvation energy results obtained with the GB model was exceedingly good as already reported in the literature but the pKa shift estimates fell short of expectations. Analysis of the problem on a simple prototype system revealed that with the GB model, the estimates of the two components, viz. the shielding and the self-energy terms, to be somewhat in error. These errors compensate each other in the calculation of solvation energies but affect the intramolecular interaction energies and hence pK shifts differently. We examine here the feasibility of introducing modifications to the GB model for a simultaneous evaluation of both solvation and intramolecular interaction energies.

  4. Computing solvent-induced forces in the solvation approach called Semi Explicit Assembly

    NASA Astrophysics Data System (ADS)

    Brini, Emiliano; Hummel, Michelle H.; Coutsias, Evangelos A.; Fennell, Christopher J.; Dill, Ken A.

    2014-03-01

    Many biologically relevant processes (e.g. protein folding) are often too big and slow to be simulated by computer methods that model atomically detailed water. Faster physical models of water are needed. We have developed an approach called Semi Explicit Assembly (SEA) [C.J. Fennell, C.W. Kehoe, K.A. Dill, PNAS, 108, 3234 (2011)]. It is physical because it uses pre-simulations of explicit-solvent models, and it is fast because at runtime, we just combine the pre-simulated results in rapid computations. SEA has also now been proven physically accurate in two blind tests called SAMPL. Here, we describe the computation of solvation forces in SEA, so that this solvation procedure can be incorporated into standard molecular dynamics codes. We describe experimental tests.

  5. Probing micro-solvation in "numbers": the case of neutral dipeptides in water.

    PubMed

    Takis, Panteleimon G; Papavasileiou, Konstantinos D; Peristeras, Loukas D; Melissas, Vasilios S; Troganis, Anastassios N

    2013-05-21

    How many solvent molecules and in what way do they interact directly with biomolecules? This is one of the most challenging questions regarding a deep understanding of biomolecular functionalism and solvation. We herein present a novel NMR spectroscopic study, achieving for the first time the quantification of the directly interacting water molecules with several neutral dipeptides. Our proposed method is supported by both molecular dynamics simulations and density functional theory calculations, advanced analysis of which allowed the identification of the direct interactions between solute-solvent molecules in the zwitterionic L-alanyl-L-alanine dipeptide-water system. Beyond the quantification of dipeptide-water molecule direct interactions, this NMR technique could be useful for the determination and elucidation of small to moderate bio-organic molecular groups' direct interactions with various polar solvent molecules, shedding light on the biomolecular micro-solvation processes and behaviour in various solvents. PMID:23579285

  6. Influence of Solvation and Structural Contributions on Fluorescence of Dipyrrine Dyes.

    PubMed

    Ksenofontov, A A; Guseva, G B; Antina, E V; Vyugin, A I; Nuraneeva, E N

    2015-11-01

    The results of quantum-chemical and spectral researches of zinc((II)) complexes with alkylated dipyrrine and 3,3'-, 2,3'- and 2,2'-bis(dipyrrine)s in non-polar and polar solvents and their binary mixtures are presented. It was investigated the efficiency of the fluorescence quenching of fluorophores depending on of the solvation and structural contributions. Found that 3,3'-bis(dipyrrinato)zinc((II)) demonstrates the highest sensitivity of the fluorescence to the presence of the electron-donor component compared with the studied complexes. The obtained results allow to offer dipyrrine and bis(dipyrrine) zinc((II)) complexes as new, highly sensitive and selective fluorescent sensors of the N- and O-containing toxicants. Graphical Abstract Influence of solvation and structural contributions on fluorescence of dipyrrine dyes. PMID:26439931

  7. Solvation in highly nonideal solutions: A study of aqueous 1-propanol using the coumarin 153 probe

    NASA Astrophysics Data System (ADS)

    Shirota, Hideaki; Castner, Edward W.

    2000-02-01

    We have investigated the anomalous behavior of aqueous 1-propanol binary solutions using a typical fluorescence probe molecule, coumarin 153. We present data on the fluorescence lifetimes, fluorescence anisotropies, and solvent reorganization dynamics, as well as the steady-state absorption and emission spectra of coumarin 153 in the binary solutions. The rotational diffusion and solvation time constants depend strongly on the content of 1-propanol, especially at low 1-propanol mole fractions. Spectroscopic results presented here are consistent with prior light scattering [G. H. Großmann and K. H. Ebert, Ber. Bunsenges. Phys. Chem. 85, 1026 (1981)], small angle x-ray scattering [H. Hayashi, K. Nishikawa, and T. Iijima, J. Phys. Chem. 94, 8334 (1990)], and dielectric relaxation [S. Mashimo, T. Umehara, and H. Redlin, J. Chem. Phys. 95, 6257 (1991)] data. The anomalous dynamics features likely arise from the effect of the preferential solvation due to the 1-propanol clustering.

  8. Simulation of peptide folding with explicit water--a mean solvation method.

    PubMed

    Wu, X W; Sung, S S

    1999-02-15

    A new approach to efficiently calculate solvent effect in computer simulation of macromolecular systems has been developed. Explicit solvent molecules are included in the simulation to provide a mean solvation force for the solute conformational search. Simulations of an alanine dipeptide in aqueous solution showed that the new approach is significantly more efficient than conventional molecular dynamics method in conformational search, mainly because the mean solvation force reduced the solvent damping effect. This approach allows the solute and solvent to be simulated separately with different methods. For the macromolecule, the rigid fragment constraint dynamics method we developed previously allows large time-steps. For the solvent, a combination of a modified force-bias Monte Carlo method and a preferential sampling can efficiently sample the conformational space. A folding simulation of a 16-residue peptide in water showed high efficiency of the new approach. PMID:10024017

  9. Solvation structure around ruthenium(II) tris(bipyridine) in lithium halide solutions

    PubMed Central

    Josefsson, Ida; Eriksson, Susanna K.; Rensmo, Håkan; Odelius, Michael

    2016-01-01

    The solvation of the ruthenium(II) tris(bipyridine) ion ([Ru(bpy)3]2+) is investigated with molecular dynamics simulations of lithium halide solutions in polar solvents. The anion distribution around the [Ru(bpy)3]2+ complex exhibits a strong solvent dependence. In aqueous solution, the iodide ion forms a solvent shared complex with [Ru(bpy)3]2+, but not in the other solvents. Between Cl– and [Ru(bpy)3]2+, the strong hydration of the chloride ion results in a solvent separated complex where more than one solvent molecule separates the anion from the metal center. Hence, tailored solvation properties in electrolytes is a route to influence ion-ion interactions and related electron transfer processes. PMID:26798838

  10. Role of Presolvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport.

    PubMed

    Biswas, Rajib; Tse, Ying-Lung Steve; Tokmakoff, Andrei; Voth, Gregory A

    2016-03-01

    Results from condensed phase ab initio molecular dynamics (AIMD) simulations suggest a proton transfer reaction is facilitated by "presolvation" in which the hydronium is transiently solvated by four water molecules, similar to the typical solvation structure of water, by accepting a weak hydrogen bond from the fourth water molecule. A new version 3.2 multistate empirical valence bond (MS-EVB 3.2) model for the hydrated excess proton incorporating this presolvation behavior is therefore developed. The classical MS-EVB simulations show similar structural properties as those of the previous model but with significantly improved diffusive behavior. The inclusion of nuclear quantum effects in the MS-EVB also provides an even better description of the proton diffusion rate. To quantify the influence of anharmonicity, a second model (aMS-EVB 3.2) is developed using the anharmonic aSPC/Fw water model, which provides similar structural properties but improved spectroscopic responses at high frequencies. PMID:26575795

  11. Femtosecond pump-probe measurements of solvation by hydrogen-bonding interactions.

    PubMed

    Pines, Ehud; Pines, Dina; Ma, Ying-Zhong; Fleming, Graham R

    2004-09-20

    An additional ultrafast blue shift in the transient absorption spectra of hydrogen-bonding complexes of a strong photoacid, 8-hydroxypyrene 1,3,6-trisdimethylsulfonamide (HPTA), over the solvation response of the uncomplexed HPTA and also over that of the methoxy derivative of the photoacid (MPTA) in the presence of the hydrogen-bonding base was observed on optical excitation of the photoacid. The additional 55 +/- 10 fs solvation response was found to be about 35 % and 19% of the total C(t) of HPTA in dichloromethane (DCM) when it was hydrogen-bonded to dimethylsulfoxide (DMSO) and dioxane, respectively, and about 29% of the total C(t) of HPTA in dichloroethane (DCE) when it was hydrogen-bonded to DMSO. We have assigned this additional dynamic spectral shift to a transient change in the hydrogen bond (O-H...O) that links HPTA to the complexing base, after the electronic excitation of the photoacid. PMID:15499848

  12. Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy

    NASA Astrophysics Data System (ADS)

    Zhang, Bo; Peng, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai; Lu, Benzhuo

    2015-05-01

    We present PAFMPB, an updated and parallel version of the AFMPB software package for fast calculation of molecular solvation-free energy. The new version has the following new features: (1) The adaptive fast multipole method and the boundary element methods are parallelized; (2) A tool is embedded for automatic molecular VDW/SAS surface mesh generation, leaving the requirement for a mesh file at input optional; (3) The package provides fast calculation of the total solvation-free energy, including the PB electrostatic and nonpolar interaction contributions. PAFMPB is implemented in C and Fortran programming languages, with the Cilk Plus extension to harness the computing power of both multicore and vector processing. Computational experiments demonstrate the successful application of PAFMPB to the calculation of the PB potential on a dengue virus system with more than one million atoms and a mesh with approximately 20 million triangles.

  13. Structural studies of several solvated potassium salts of tenatoprazole crystallizing as conglomerates

    NASA Astrophysics Data System (ADS)

    Tauvel, G.; Sanselme, M.; Coste-Leconte, S.; Petit, S.; Coquerel, G.

    2009-11-01

    Despite the weak acidic character of tenatoprazole it is possible to crystallize, in strong alkaline media, different solvated salts of this active pharmaceutical ingredient. Among these solid phases, some potassium salts exhibiting non congruent solubilities, form stable conglomerates in equilibrium with their mother liquors without detectable partial solid solutions between the enantiomers. The crystal structures of the ethanol and the ethylene glycol stoichiometric solvates of potassium salts have been determined by single crystal X-ray diffraction, revealing that the solvent molecules play an important role in the crystal cohesion. They participate to the coordination polyhedra of the potassium cations and also contribute to strong periodic bond chains. Moreover, there is no direct link between the tenatoprazole anions and the potassium cations, so the solvent molecules act as electrostatic relays between ions of opposite charges.

  14. Copper extraction from chloride solutions with mixtures of solvating and chelating reagents

    SciTech Connect

    Borowiak-Resterna, A.; Szymanowski, J.

    2000-01-01

    Equimolar mixtures of N,N,N{prime},N{prime}-tetrahexylpyridine-3,5-dicarboxamide (L) with 2-hydroxy-5-t-octylbenzophenone oxime or 1-phenyldecane-1,3-dione (HB), were used to extract copper from chloride solutions of various concentration of chloride ions. Chloride ions were then scrubbed out with water or ammoniacal solutions and copper was transferred from the solvate CuCl{sub 2}L{sub 2} to chelate CuB{sub 2}. Both studied systems permit effective extraction of copper and removal of chloride ions from the organic phase. Some protonation of solvating reagent L occurs, however, when copper is stripped from the chelate with hydroxyoxime. This negative effect can be suppressed when 1-phenyldecane-1,3-dione is used as a chelating agent. The scrubbing of chloride ions must be then carried out with ammoniacal solutions to avoid simultaneous stripping of copper.

  15. Electrolyte Solvation and Ionic Association. VI. Acetonitrile-Lithium Salt Mixtures. Highly Associated Salts Revisited

    SciTech Connect

    Borodin, Oleg; Han, Sang D.; Daubert, James S.; Seo, D. M.; Yun, Sung-Hyun; Henderson, Wesley A.

    2015-01-14

    Molecular dynamics (MD) simulations of acetonitrile (AN) mixtures with LiBF4, LiCF3SO3 and LiCF3CO2 provide extensive details about the molecular- and mesoscale-level solution interactions and thus explanations as to why these electrolytes have very different thermal phase behavior and electrochemical/physicochemical properties. The simulation results are in full accord with a previous experimental study of these (AN)n-LiX electrolytes. This computational study reveals how the structure of the anions strongly influences the ionic association tendency of the ions, the manner in which the aggregate solvates assemble in solution and the length of time in which the anions remain coordinated to the Li+ cations in the solvates which result in dramatic variations in the transport properties of the electrolytes.

  16. 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

  17. Solvation dynamics in ionic fluids: an extended Debye-Hückel dielectric continuum model.

    PubMed

    Song, Xueyu

    2009-07-28

    Motivated by our recent proposition on the possibility of using dielectric continuum models to interpret experimental measurements of solvation dynamics in room temperature ionic liquids [J. Phys. Chem. A 110, 8623 (2006)], some detailed simulation studies are performed to test the validity of our proposition. From these simulation studies, it seems to be justified that an extended Debye-Hückel continuum model can be used to understand the solvation dynamics of ionic fluids. The theoretical underpinning of such an extended Debye-Hückel model is presented from the general dispersion relation in electrodynamics. The connection with the static extension from the dressed ion theory of electrolyte solutions is also discussed. Such a connection between the Debye-Hückel theory and the dispersion relation may be exploited to enhance our understanding of the electric double layer problem not only for the static case but also for dynamic situations. PMID:19655890

  18. 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.

  19. Absolute Hydration Free Energies of Blocked Amino Acids: Implications for Protein Solvation and Stability

    PubMed Central

    König, Gerhard; Bruckner, Stefan; Boresch, Stefan

    2013-01-01

    Most proteins perform their function in aqueous solution. The interactions with water determine the stability of proteins and the desolvation costs of ligand binding or membrane insertion. However, because of experimental restrictions, absolute solvation free energies of proteins or amino acids are not available. Instead, solvation free energies are estimated based on side chain analog data. This approach implies that the contributions to free energy differences are additive, and it has often been employed for estimating folding or binding free energies. However, it is not clear how much the additivity assumption affects the reliability of the resulting data. Here, we use molecular dynamics–based free energy simulations to calculate absolute hydration free energies for 15 N-acetyl-methylamide amino acids with neutral side chains. By comparing our results with solvation free energies for side chain analogs, we demonstrate that estimates of solvation free energies of full amino acids based on group-additive methods are systematically too negative and completely overestimate the hydrophobicity of glycine. The largest deviation of additive protocols using side chain analog data was 6.7 kcal/mol; on average, the deviation was 4 kcal/mol. We briefly discuss a simple way to alleviate the errors incurred by using side chain analog data and point out the implications of our findings for the field of biophysics and implicit solvent models. To support our results and conclusions, we calculate relative protein stabilities for selected point mutations, yielding a root-mean-square deviation from experimental results of 0.8 kcal/mol. PMID:23442867

  20. Highly effective configurational assignment using bisthioureas as chiral solvating agents in the presence of DABCO.

    PubMed

    Bian, Guangling; Fan, Hongjun; Huang, Huayin; Yang, Shiwei; Zong, Hua; Song, Ling; Yang, Genjin

    2015-03-20

    A highly effective (1)H NMR method for determining the absolute configurations of various chiral α-hydroxyl acids and their derivatives has been developed with the use of bisthioureas (R)-CSA 1 and (S)-CSA 1 as chiral solvating agents in the presence of DABCO, giving distinguishable proton signals with up to 0.66 ppm chemical shift nonequivalence. Computational modeling studies were performed with Gaussian09 to reveal the chiral recognition mechanism. PMID:25751415

  1. Solvated electrons at the atmospheric pressure plasma–water anodic interface

    NASA Astrophysics Data System (ADS)

    Gopalakrishnan, R.; Kawamura, E.; Lichtenberg, A. J.; Lieberman, M. A.; Graves, D. B.

    2016-07-01

    We present results from a particle-in-cell/Monte Carlo model of a dc discharge in argon at atmospheric pressure coupled with a fluid model of an aqueous electrolyte acting as anode to the plasma. The coupled models reveal the structure of the plasma–electrolyte interface and near-surface region, with a special emphasis on solvated or hydrated electrons. Results from the coupled models are in generally good agreement with the experimental results of Rumbach et al (2016 Nat. Commun. 6 7248). Electrons injected from the plasma into the water are solvated, then lost by reaction with water within about 10–20 nm from the surface. The major reaction products are OH‑ and H2. The solvated electron density profile is controlled by the injected electron current density and subsequent reactions with water, and is relatively independent of the external plasma electric field and the salt concentration in the aqueous electrolyte. Simulations of the effects of added scavenger compounds (H2O2, \\text{NO}2- , \\text{NO}2- and H+) on near-surface solvated electron density generally match the experimental results. The generation of near-surface OH‑ following electron-water decomposition in the presence of bulk acid creates a highly basic region (pH ~ 11) very near the surface. In the presence of bulk solution acidity, pH can vary from a very acidic pH 2 away from the surface to a very basic pH 11 over a distance of ~200 nm. High near-surface gradients in aqueous solution properties could strongly affect plasma-liquid applications and challenge theoretical understanding of this complex region.

  2. ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions

    PubMed Central

    Vitalis, Andreas; Pappu, Rohit V.

    2009-01-01

    A new implicit solvation model for use in Monte Carlo simulations of polypeptides is introduced. The model is termed ABSINTH for self-Assembly of Biomolecules Studied by an Implicit, Novel, and Tunable Hamiltonian. It is designed primarily for simulating conformational equilibria and oligomerization reactions of intrinsically disordered proteins in aqueous solutions. The paradigm for ABSINTH is conceptually similar to the EEF1 model of Lazaridis and Karplus (Proteins: Struct. Func. Genet., 1999, 35: 133-152). In ABSINTH, the transfer of a polypeptide solute from the gas phase into a continuum solvent is the sum of a direct mean field interaction (DMFI), and a term to model the screening of polar interactions. Polypeptide solutes are decomposed into a set of distinct solvation groups. The DMFI is a sum of contributions from each of the solvation groups, which are analogs of model compounds. Continuum-mediated screening of electrostatic interactions is achieved using a framework similar to the one used for the DMFI. Promising results are shown for a set of test cases. These include the calculation of NMR coupling constants for short peptides, the assessment of the thermal stability of two small proteins, reversible folding of both an alpha-helix and a beta-hairpin forming peptide, and the polymeric properties of intrinsically disordered polyglutamine peptides of varying lengths. The tests reveal that the computational expense for simulations with the ABSINTH implicit solvation model increase by a factor that is in the range of 2.5-5.0 with respect to gas-phase calculations. PMID:18506808

  3. Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge.

    PubMed

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

    2014-03-01

    Here, we test a method, called semi-explicit assembly (SEA), that computes the solvation free energies of molecules in water in the SAMPL4 blind test challenge. SEA was developed with the intention of being as accurate as explicit-solvent models, but much faster to compute. It is accurate because it uses pre-simulations of simple spheres in explicit solvent to obtain structural and thermodynamic quantities, and it is fast because it parses solute free energies into regionally additive quantities. SAMPL4 provided us the opportunity to make new tests of SEA. Our tests here lead us to the following conclusions: (1) The newest version, called Field-SEA, which gives improved predictions for highly charged ions, is shown here to perform as well as the earlier versions (dipolar and quadrupolar SEA) on this broad blind SAMPL4 test set. (2) We find that both the past and present SEA models give solvation free energies that are as accurate as TIP3P. (3) Using a new approach for force field parameter optimization, we developed improved hydroxyl parameters that ensure consistency with neat-solvent dielectric constants, and found that they led to improved solvation free energies for hydroxyl-containing compounds in SAMPL4. We also learned that these hydroxyl parameters are not just fixing solvent exposed oxygens in a general sense, and therefore do not improve predictions for carbonyl or carboxylic-acid groups. Other such functional groups will need their own independent optimizations for potential improvements. Overall, these tests in SAMPL4 indicate that SEA is an accurate, general and fast new approach to computing solvation free energies. PMID:24474161

  4. Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber

    PubMed Central

    Luchko, Tyler; Gusarov, Sergey; Roe, Daniel R.; Simmerling, Carlos; Case, David A.; Tuszynski, Jack; Kovalenko, Andriy

    2010-01-01

    We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multi-time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package, and is illustrated here on alanine dipeptide and protein G. PMID:20440377

  5. Ultrafast dynamics of solvation and charge transfer in a DNA-based biomaterial.

    PubMed

    Choudhury, Susobhan; Batabyal, Subrata; Mondol, Tanumoy; Sao, Dilip; Lemmens, Peter; Pal, Samir Kumar

    2014-05-01

    Charge migration along DNA molecules is a key factor for DNA-based devices in optoelectronics and biotechnology. The association of a significant amount of water molecules in DNA-based materials for the intactness of the DNA structure and their dynamic role in the charge-transfer (CT) dynamics is less documented in contemporary literature. In the present study, we have used a genomic DNA-cetyltrimethyl ammonium chloride (CTMA) complex, a technological important biomaterial, and Hoechest 33258 (H258), a well-known DNA minor groove binder, as fluorogenic probe for the dynamic solvation studies. The CT dynamics of CdSe/ZnS quantum dots (QDs; 5.2 nm) embedded in the as-prepared and swollen biomaterial have also been studied and correlated with that of the timescale of solvation. We have extended our studies on the temperature-dependent CT dynamics of QDs in a nanoenvironment of an anionic, sodium bis(2-ethylhexyl)sulfosuccinate reverse micelle (AOT RMs), whereby the number of water molecules and their dynamics can be tuned in a controlled manner. A direct correlation of the dynamics of solvation and that of the CT in the nanoenvironments clearly suggests that the hydration barrier within the Arrhenius framework essentially dictates the charge-transfer dynamics. PMID:24665050

  6. Ejection of solvated ions from electrosprayed methanol/water nanodroplets studied by molecular dynamics simulations.

    PubMed

    Ahadi, Elias; Konermann, Lars

    2011-06-22

    The ejection of solvated small ions from nanometer-sized droplets plays a central role during electrospray ionization (ESI). Molecular dynamics (MD) simulations can provide insights into the nanodroplet behavior. Earlier MD studies have largely focused on aqueous systems, whereas most practical ESI applications involve the use of organic cosolvents. We conduct simulations on mixed water/methanol droplets that carry excess NH(4)(+) ions. Methanol is found to compromise the H-bonding network, resulting in greatly increased rates of ion ejection and solvent evaporation. Considerable differences in the water and methanol escape rates cause time-dependent changes in droplet composition. Segregation occurs at low methanol concentration, such that layered droplets with a methanol-enriched periphery are formed. This phenomenon will enhance the partitioning of analyte molecules, with possible implications for their ESI efficiencies. Solvated ions are ejected from the tip of surface protrusions. Solvent bridging prior to ion secession is more extensive for methanol/water droplets than for purely aqueous systems. The ejection of solvated NH(4)(+) is visualized as diffusion-mediated escape from a metastable basin. The process involves thermally activated crossing of a ~30 kJ mol(-1) free energy barrier, in close agreement with the predictions of the classical ion evaporation model. PMID:21591733

  7. Probing Solvation Dynamics around Aromatic and Biological Molecules at the Single-Molecular Level.

    PubMed

    Dopfer, Otto; Fujii, Masaaki

    2016-05-11

    Solvation processes play a crucial role in chemical reactions and biomolecular recognition phenomena. Although solvation dynamics of interfacial or biological water has been studied extensively in aqueous solution, the results are generally averaged over several solvation layers and the motion of individual solvent molecules is difficult to capture. This review describes the development and application of a new experimental approach, namely, picosecond time-resolved pump-probe infrared spectroscopy of size- and isomer-selected aromatic clusters, in which for the first time the dynamics of a single individual solvent molecule can be followed in real time. The intermolecular isomerization reaction is triggered by resonant photoionization (pump), and infrared photodissociation (probe) at variable delay generates the spectroscopic signature of salient properties of the reaction, including rates, yields, pathways, branching ratios of competing reactions, existence of reaction intermediates, occurrence of back reactions, and time scales of energy relaxation processes. It is shown that this relevant information can reliably be decoded from the experimental spectra by sophisticated molecular dynamics simulations. This review covers a description of the experimental strategies and spectroscopic methods along with all applications to date, which range from aromatic clusters with nonpolar solvent molecules to aromatic monohydrated biomolecules. PMID:27054835

  8. Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation.

    PubMed

    Khandogin, Jana; Gregersen, Brent A; Thiel, Walter; York, Darrin M

    2005-05-19

    The present paper describes the extension of a recently developed smooth conductor-like screening model for solvation to a d-orbital semiempirical framework (MNDO/d-SCOSMO) with analytic gradients that can be used for geometry optimizations, transition state searches, and molecular dynamics simulations. The methodology is tested on the potential energy surfaces for separating ions and the dissociative phosphoryl transfer mechanism of methyl phosphate. The convergence behavior of the smooth COSMO method with respect to discretization level is examined and the numerical stability of the energy and gradient are compared to that from conventional COSMO calculations. The present method is further tested in applications to energy minimum and transition state geometry optimizations of neutral and charged metaphosphates, phosphates, and phosphoranes that are models for stationary points in transphosphorylation reaction pathways of enzymes and ribozymes. The results indicate that the smooth COSMO method greatly enhances the stability of quantum mechanical geometry optimization and transition state search calculations that would routinely fail with conventional solvation methods. The present MNDO/d-SCOSMO method has considerable computational advantages over hybrid quantum mechanical/molecular mechanical methods with explicit solvation, and represents a potentially useful tool in the arsenal of multi-scale quantum models used to study biochemical reactions. PMID:16852180

  9. Properties of solvate shells and the mobility of ions, according to molecular dynamics data

    NASA Astrophysics Data System (ADS)

    Lankin, A. V.; Norman, G. E.; Orekhov, M. A.

    2016-05-01

    The solvate shells of an ion, its velocity autocorrelation function, and diffusion coefficient D are found, and the interrelations between them are analyzed. A single ion in the system of atoms of a liquid is considered a model system. The interaction between the ion and atoms of the liquid is described by polarization potential U( r); the interaction between atoms of the liquid alone is described by the Lennard-Jones potential. A classical molecular dynamics method is used. Five solvate shells around the ion are found, and the lifetimes of atoms on each shell are calculated. It is found that the velocity autocorrelation function is of a vibrating nature. The spectrum of the autocorrelator and the frequency of cluster vibrations in a linear approximation are compared. Dependences D on parameters of potential U( r) are found. No dependence D on the ion mass is found; this is explained by solvation. The Einstein-Stokes formula and the HSK approximation are used in discussing the results. It is shown that at small radii of the ion, dependence D on parameters U( r) is described by such a model. When the ion radius is increased, the deviation from this dependence and an increase in D are observed. The results are compared to experimental mobilities of O 2 - and Ar 2 + ions in liquid argon.

  10. Solvation Behavior of Short-chain Polystyrene Sulfonate in Aqueous Electrolyte Solutions: A Molecular Dyamics Study

    SciTech Connect

    Chialvo, Ariel A; Simonson, J Michael {Mike}

    2005-01-01

    We analyze the solvation behavior of short-chain polystyrene sulfonate (PSS) in aqueous electrolyte solutions by isothernal-isochoric molecular dynamics simulation to determine the solvation effects on the structure and conformation of the polyelectrolyte as a function of the aqueous environment. To that end, we study these aqueous systems including the explicit atomistic description of water, the PSS chain, and their interactions with all species in solution. In addition, we investigate the effect of the degree of sulfonation and its distribution along the PSS chain on the resulting conformation as well as solvation structure. Moreover, we assess the impact of added salts on the net charge of the PSS backbone, placing emphasis on the valence of the counterion and the extent of the ion-pair formation between the sulfonate group and the counterions. Finally, we present evidence for the so-called like-charge attraction between sulfonate groups through the formation of counterion-mediated interchain sulfonate-sulfonate and water-mediated intrachain sulfonate-sulfonate bridges, as well as between unlike counterion-counterion interactions.

  11. Band offsets across solid-liquid interfaces from continuum solvation methods

    NASA Astrophysics Data System (ADS)

    Sundararaman, Ravishankar; Ping, Yuan; Galli, Giulia A.; Goddard, William A., III

    2015-03-01

    The band edge positions of photo-electrodes relative to water redox potentials play an important role in determining the efficiency of the photo-electrochemical cell. Direct theoretical calculations of solid-liquid interfaces are expensive and simplified models are desirable for rapid theoretical screening of new materials. However, traditional solvation models are extensively fit to describe organic solutes and hence extrapolate poorly to highly-polar inorganic surfaces. We develop minimally-empirical continuum solvation models suitable for treating such surfaces and present theoretical predictions of the band positions of rutile TiO2 (110) and WO3 (001) surfaces in water. We obtain non-negligible solvation effects ~ 1-2 eV, in good agreement with experimental results. This material is based upon work performed by the Joint Center for Artificial Photosynthesis, a DOE Energy Innovation Hub, supported through the Office of Science of the U.S. Department of Energy under Award Number DE-SC0004993.

  12. A metallacage encapsulating chloride as a probe for a solvation scale in ionic liquids.

    PubMed

    Daguenet, Corinne; Dyson, Paul J

    2007-01-22

    With the purpose of assessing the reactivity of chloride ions dissolved in ionic liquids (ILs), a relative scale for the solvation of chloride is given for a series of ILs based on the bis(trifluoromethane)sulfonimide ([Tf(2)N]) anion and different cations, 1-butyl-3-methylimidazolium ([bmim]), 1-butyl-2,3-dimethylimidazolium ([bdmim]), 1-butyl-1-methylpyrrolidinium ([bmpy]), 1-butylpyridinium ([bpy]), 1-pentyl-1,1,1-triethylammonium ([C(5)e(3)am]), and 1-(2-hydroxy)ethyl-3-methylimidazolium ([mimeOH]). Insights into the solvation of chloride are achieved by the thermodynamic study of the reaction of dissociation of a chloride-templated nickel(II) metallacage performed at various temperatures by UV-visible spectroscopy in each IL. The order of chloride solvation [C(5)e(3)am][Tf(2)N] < [bmpy][Tf(2)N] < [bmim][Tf(2)N]

  13. Wavelength Dependence of UV Photoemission from Solvated Electrons in Bulk Water, Methanol, and Ethanol.

    PubMed

    Yamamoto, Yo-ichi; Karashima, Shutaro; Adachi, Shunsuke; Suzuki, Toshinori

    2016-03-01

    We have measured the wavelength dependence (340-215 nm) of one-photon photoemission from the ground electronic state of solvated electrons in bulk water, methanol, and ethanol. In every case, the vertical electron binding energy (VBE) gradually increased with photon energy, indicating that the photoelectron kinetic energy diminishes as a result of electron-vibration inelastic scattering prior to emission from the liquid surface. In contrast, the VBE of the Rydberg electron in DABCO (1,4-diazabicyclo[2,2,2]octane), which has a surface-excess density, revealed no clear wavelength dependence. These results suggest that the solvated electrons are created predominantly in the bulk and that VBEs measured using UV photoemission spectroscopy of liquids generally require energy corrections to account for inelastic scattering effects. From the wavelength dependence, we have re-estimated the VBEs of solvated electrons in bulk water, methanol, and ethanol to be 3.3, 3.1, and 3.1 eV, respectively. Hydrated electrons were also identified by photoemission spectroscopy using 90 nm radiation. PMID:26836447

  14. 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. PMID:24425837

  15. Structural and aggregate analyses of (Li salt + glyme) mixtures: the complex nature of solvate ionic liquids.

    PubMed

    Shimizu, Karina; Freitas, Adilson A; Atkin, Rob; Warr, Gregory G; FitzGerald, Paul A; Doi, Hiroyuki; Saito, Soshi; Ueno, Kazuhide; Umebayashi, Yasuhiro; Watanabe, Masayoshi; Canongia Lopes, José N

    2015-09-14

    The structure and interactions of different (Li salt + glyme) mixtures, namely equimolar mixtures of lithium bis(trifluoromethylsulfonyl)imide, nitrate or trifluoroacetate salts combined with either triglyme or tetraglyme molecules, are probed using Molecular Dynamics simulations. structure factor functions, calculated from the MD trajectories, confirmed the presence of different amounts of lithium-glyme solvates in the aforementioned systems. The MD results are corroborated by S(q) functions derived from diffraction and scattering data (HEXRD and SAXS/WAXS). The competition between the glyme molecules and the salt anions for the coordination to the lithium cations is quantified by comprehensive aggregate analyses. Lithium-glyme solvates are dominant in the lithium bis(trifluoromethylsulfonyl)imide systems and much less so in systems based on the other two salts. The aggregation studies also emphasize the existence of complex coordination patterns between the different species (cations, anions, glyme molecules) present in the studied fluid media. The analysis of such complex behavior is extended to the conformational landscape of the anions and glyme molecules and to the dynamics (solvate diffusion) of the bis(trifluoromethylsulfonyl)imide plus triglyme system. PMID:26245295

  16. 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

  17. Solvation of benzophenone anion radical in ethanol and ethanol/2-methyltetrahydrofuran mixture

    SciTech Connect

    Ichikawa, T.; Ishikawa, Y.; Yoshida, H.

    1988-01-28

    The electron spin-echo modulations and the absoprtion spectra of benzophenone anion radicals generated by ..gamma..-irradiation in the glassy matrices of ethanol and ethanol2-methyltetrahydrofuran mixtures have been measured for elucidating the mechanism of spectral shift observed during the solvation of the anion radicals in alcohols. The anion radical generated at 4.2 K in the ethanol matrix maintains the same solvation structure as that of neutral benzophenone. At 77 K ethanol molecules solvate the anion radical by orienting the O-H dipoles toward the anion radical. The anion radical is hydrogen-bonded by two ethanol molecules through the p/sub z/ orbital on the benzophenone oxygen which composes the ..pi.. orbitals of anion radical. Three kinds of anion radicals are observed in the mixed matrix at 77 K. Two of them are essentially the same as those observed in the ethanol matrix at 4.2 and 77 K. The third has the absorption maximum at 700 nm and is attributed to the anion radical hydrogen-bonded by one ethanol molecule through the p/sub z/ orbital. It is concluded that the spectral shift observed in alcohols is caused by the stabilization of a SOMO ..pi..* orbital induced by the hydrogen bonding with the (RO)H--O--H(OR) angle perpendicular to the molecular plane of the anion radical

  18. Development of a solvate as an active pharmaceutical ingredient: Developability, crystallisation and isolation challenges

    NASA Astrophysics Data System (ADS)

    Douillet, Julien; Stevenson, Neil; Lee, Mei; Mallet, Franck; Ward, Richard; Aspin, Peter; Dennehy, Daniel Robert; Camus, Laure

    2012-03-01

    The preclinical development of an active pharmaceutical ingredient (API) begins with the selection of a solid state form. A solvate may be selected for development if it is sufficiently stable and if the solvent quantity administered to the patient is lower than the tolerated potential daily exposure (PDE). The selection and process development of a solvate is presented here. The initial crystallisation process gave poor control over the particle size distribution (PSD) and inclusion of additional crystallisation solvent in the crystal lattice. These two API attributes were controlled using micronised seeds and optimising the crystallisation conditions. After filtration, slurry washing with a second solvent was used to replace the high boiling point crystallisation solvent to improve the drying efficiency. The slurry washing was modelled and studied in the laboratory to control the level of unbound crystallisation solvent in the API. The API desolvation during slurry washing was studied by considering thermodynamics, by construction of the ternary phase diagram, and kinetics aspects. This work provides useful approaches and considerations to assess the risks specific to the controlled production of a solvate that are rarely presented in the literature.

  19. Minimalistic predictor of protein binding energy: contribution of solvation factor to protein binding.

    PubMed

    Choi, Jeong-Mo; Serohijos, Adrian W R; Murphy, Sean; Lucarelli, Dennis; Lofranco, Leo L; Feldman, Andrew; Shakhnovich, Eugene I

    2015-02-17

    It has long been known that solvation plays an important role in protein-protein interactions. Here, we use a minimalistic solvation-based model for predicting protein binding energy to estimate quantitatively the contribution of the solvation factor in protein binding. The factor is described by a simple linear combination of buried surface areas according to amino-acid types. Even without structural optimization, our minimalistic model demonstrates a predictive power comparable to more complex methods, making the proposed approach the basis for high throughput applications. Application of the model to a proteomic database shows that receptor-substrate complexes involved in signaling have lower affinities than enzyme-inhibitor and antibody-antigen complexes, and they differ by chemical compositions on interfaces. Also, we found that protein complexes with components that come from the same genes generally have lower affinities than complexes formed by proteins from different genes, but in this case the difference originates from different interface areas. The model was implemented in the software PYTHON, and the source code can be found on the Shakhnovich group webpage: http://faculty.chemistry.harvard.edu/shakhnovich/software. PMID:25692584

  20. Conformational properties of trans-2-halo-acetoxycyclohexanes: 1H NMR, solvation and theoretical investigation

    NASA Astrophysics Data System (ADS)

    Freitas, Matheus P.; Tormena, Cláudio F.; Rittner, Roberto; Abraham, Raymond J.

    2005-01-01

    Conformational analyses of trans-2-halo-acetoxycyclohexanes have been performed through NMR, theoretical calculations and solvation theory. The solvent dependence of coupling constants analysed together with solvation parameters of the main calculated geometries allowed the determination of both the individual couplings and difference energies between the possible ax-ax and eq-eq conformations. For all the halo-compounds eq-eq is the most stable form in the vapour phase and in solution. The molar fractions ( naa) of the ax-ax conformer are 0.28, 0.30, 0.28 and 0.22 in the vapour phase for fluoro ( 1), chloro ( 2), bromo ( 3) and iodo ( 4) derivatives, respectively, decreasing to 0.06, 0.10, 0.12 and 0.12 in DMSO, calculated through MODELS and BESTFIT, using the solvation theory. The governing factors of these conformational equilibria are the classical steric and electrostatic interactions, as well as the ' gauche effect', especially for the fluoro compound. The acetoxy group effect has also been compared with previous results for the hydroxy and methoxy derivatives.

  1. Solvation of Dimethyl Succinate in a Sodium Hydroxide Aqueous Solution. A Computational Study

    SciTech Connect

    Sun, Xiuquan; Chang, Tsun-Mei; Cao, Yang; Niwayama, Satomi; Hase, William L.; Dang, Liem X.

    2009-05-07

    Molecular dynamics simulations were carried out to study dimethyl-succinate/water/NaOH solutions. The potential of mean force method is used to determine the transport mechanism of a dimethyl-succinate (a diester) molecule across the aqueous/vapor interface. The computed number density profiles show a strong propensity for the diester molecules to congregate at the interface with the solubility of the diester increasing with increasing NaOH concentration. It is observed that the major contribution to the interfacial solvation free energy minimum is from van der Waals interactions. Thus, even at higher NaOH concentrations, the increasing electrostatic interaction between the diester and ions is not large enough to overcome the Lennard-Jones (LJ) interactions to favor the solvation of diester in bulk solutions. The calculated solvation free energies are found to be -2.6 ~ -3.5 kcal/mol in variant concentrations of NaOH aqueous solutions. These values are in qualitative agreement with the corresponding experimental measurements. The computed surface potential indicates that the contribution of diester molecules to the total surface potential is about 25%, with the major contribution from interfacial water molecules. This work was supported by the US Department of Energy (DOE) Office of Basic Energy Sciences, Chemical Sciences program. Pacific Northwest National Laboratory is operated by Battelle for DOE.

  2. Electronic Structure Insights into the Solvation of Magnesium Ions with Cyclic and Acyclic Carbonates.

    PubMed

    Shakourian-Fard, Mehdi; Kamath, Ganesh; Sankaranarayanan, Subramanian K R S

    2015-12-01

    A computational framework to rank the solvation behavior of Mg(2+) in carbonates by using molecular dynamics simulations and density functional theory is reported. Based on the binding energies and enthalpies of solvation calculated at the M06-2X/6-311++G(d,p) level of theory and the free energies of solvation from ABF-MD simulations, we find that ethylene carbonate (EC) and the ethylene carbonate:propylene carbonate (EC:PC) binary mixture are the best carbonate solvents for interacting with Mg(2+) . Natural bond orbital and quantum theory of atoms in molecules analyses support the thermochemistry calculations with the highest values of charge transfer, perturbative stabilization energies, electron densities, and Wiberg bond indices being observed in the Mg(2+) (EC) and Mg(2+) (EC:PC) complexes. The plots of the noncovalent interactions indicate that those responsible for the formation of Mg(2+) carbonate complexes are strong-to-weak attractive interactions, depending on the regions that are interacting. Finally, density of state calculations indicate that the interactions between Mg(2+) and the carbonate solvents affects the HOMO and LUMO states of all carbonate solvents and moves them to more negative energy values. PMID:26395020

  3. Solvated ions as defects in liquid water: A first-principles perspective

    NASA Astrophysics Data System (ADS)

    Schwegler, Eric; Pham, Tuan Anh; Govoni, Marco; Galli, Giulia

    Understanding the electronic properties of solvated ions is crucial in order to control and engineer aqueous electrolytes for a wide variety of emerging energy and environmental technologies, including photocatalytic water splitting. In this talk, we present a strategy to evaluate electronic energy levels of simple solvated ions in aqueous solutions, using a combination of first-principles molecular dynamics simulations and many-body perturbation theory within the GW approximation. We considered CO32- , HCO3-,NO3-,NO2-ions and we show that by analogy to defects in semiconductors, these solvated ions may be classified as deep or shallow defects in liquid water. In particular CO32- and NO2-ions behave as shallow defects, while HCO3-and NO3-as deep ones. We also show that the inclusion of many-body corrections constitutes significant improvement over conventional density functional theory calculations, yielding satisfactory agreement with photoemission experiments. Part of this work was supported by the U.S. Department of Energy at the LLNL under Contract DE-AC52-07NA27344. T.A.P acknowledge the support from the Lawrence Fellowship. Part of this work was supported by LDRD at ANL.

  4. Drug design for cardiovascular disease: the effect of solvation energy on Rac1-ligand interactions.

    PubMed

    Maggi, Norbert; Arrigo, Patrizio; Ruggiero, Carmelina

    2011-01-01

    'OMICS' techniques have deeply changed the drug discovery process. The availability of many different potential druggable genes, generated by these new techniques, have exploited the complexity of new lead compounds screening. 'Virtual screening', based on the integration of different analytical tools on high performance hardware platforms, has speeded up the search for new chemical entities suitable for experimental validation. Docking is a key step in the screening process. The aim of this paper is the evaluation of binding differences due to solvation. We have compared two commonly used software, one of which takes into account solvation, on a set of small molecules (Morpholines, flavonoids and imidazoles) which are able to target the RAC1 protein--a cardiovascular target. We have evaluated the degree of agreement between the two different programs using a machine learning approach combined with statistical test. Our analysis, on a sample of small molecules, has pointed out that 35% of the molecules seem to be sensitive to solvation. This result, even though quite preliminary, stresses the need to combine different algorithms to obtain a more reliable filtered set of ligands. PMID:22255029

  5. Enabling forbidden processes: quantum and solvation enhancement of nitrate anion UV absorption.

    PubMed

    Svoboda, Ondřej; Kubelová, Lucie; Slavíček, Petr

    2013-12-01

    We present simulated electronic absorption spectra of isolated and solvated nitrate anion in the UV region, focusing primarily on the absorption into the first absorption band around 300 nm. This weak absorption band in this spectral region is responsible for the generation of NOx in the polar areas or OH(•) radicals in the hydrosphere. The 300 nm absorption band is symmetrically strongly forbidden and coupling of at least two vibrational modes is needed to allow the transition in the isolated nitrate anion. Further symmetry breaking is provided by solvation. In this study we model the absorption spectra of nitrate-water clusters using the combined reflection principle path integral molecular dynamics (RP-PIMD) method. Condensed phase UV spectra are modeled within a cluster-continuum model. The calculated spectra are compared with experimental bulk phase measurements and reasonable agreement is found. We also provide a benchmarking of the DFT functionals to be used for a description of the electronically excited states of solvated nitrate anion. PMID:24237180

  6. The single crystal X-ray structure of β-hematin DMSO solvate grown in the presence of chloroquine, a β-hematin growth-rate inhibitor

    PubMed Central

    Gildenhuys, Johandie; le Roex, Tanya; Egan, Timothy J.; de Villiers, Katherine A.

    2012-01-01

    Single crystals of solvated β-hematin were grown from a DMSO solution containing the antimalarial drug chloroquine, a known inhibitor of β-hematin formation. In addition, a kinetics study employing biomimetic lipid-water emulsion conditions was undertaken to further investigate the effect of chloroquine and quinidine on the formation of β-hematin. Scanning electron microscopy shows that the external morphology of the β-hematin DMSO solvate crystals is almost indistinguishable from that of malaria pigment (hemozoin) and single crystal X-ray diffraction confirms the presence of μ-propionato coordination dimers of iron(III) protoporphyrin IX. The free propionic acid functional groups of adjacent dimers hydrogen bond to included DMSO molecules, rather than forming carboxylic acid dimers. The observed exponential kinetics were modeled using the Avrami equation, with an Avrami constant equal to 1. The decreased rate of β-hematin formation observed at low concentrations of both drugs could be accounted for by assuming a mechanism of drug adsorption to sites on the fastest growing face of β-hematin. This behavior was modeled using the Langmuir isotherm. Higher concentrations of drug resulted in decreased final yields of β-hematin, and an irreversible drug-induced precipitation of iron(III) protoporphyrin IX was postulated to account for this. The model permits determination of the equilibrium adsorption constant (Kads). The values for chloroquine (log Kads = 5.55 ± 0.03) and quinidine (log Kads = 4.92 ± 0.01) suggest that the approach may be useful as a relative probe of the mechanism of action of novel antimalarial compounds. PMID:23253048

  7. SAMPL4, a blind challenge for computational solvation free energies: the compounds considered.

    PubMed

    Guthrie, J Peter

    2014-03-01

    For the fifth time I have provided a set of solvation energies (1 M gas to 1 M aqueous) for a SAMPL challenge. In this set there are 23 blind compounds and 30 supplementary compounds of related structure to one of the blind sets, but for which the solvation energy is readily available. The best current values of each compound are presented along with complete documentation of the experimental origins of the solvation energies. The calculations needed to go from reported data to solvation energies are presented, with particular attention to aspects which are new to this set. For some compounds the vapor pressures (VP) were reported for the liquid compound, which is solid at room temperature. To correct from VPsubcooled liquid to VPsublimation requires ΔSfusion, which is only known for mannitol. Estimated values were used for the others, all but one of which were benzene derivatives and expected to have very similar values. The final compound for which ΔSfusion was estimated was menthol, which melts at 42 °C so that modest errors in ΔSfusion will have little effect. It was also necessary to look into the effects of including estimated values of ΔCp on this correction. The approximate sizes of the effects of inclusion of ΔCp in the correction from VPsubcooled liquid to VPsublimation were estimated and it was noted that inclusion of ΔCp invariably makes ΔGS more positive. To extend the set of compounds for which the solvation energy could be calculated we explored the use of boiling point (b.p.) data from Reaxys/Beilstein as a substitute for studies of the VP as a function of temperature. B.p. data are not always reliable so it was necessary to develop a criterion for rejecting outliers. For two compounds (chlorinated guaiacols) it became clear that inclusion represented overreach; for each there were only two independent pressure, temperature points, which is too little for a trustworthy extrapolation. For a number of compounds the extrapolation from

  8. Computations of absolute solvation free energies of small molecules using explicit and implicit solvent model.

    SciTech Connect

    Shivakumar, D.; Deng, Y.; Roux, B.; Biosciences Division; Univ. of Chicago

    2009-01-01

    Accurate determination of absolute solvation free energy plays a critical role in numerous areas of biomolecular modeling and drug discovery. A quantitative representation of ligand and receptor desolvation, in particular, is an essential component of current docking and scoring methods. Furthermore, the partitioning of a drug between aqueous and nonpolar solvents is one of the important factors considered in pharmacokinetics. In this study, the absolute hydration free energy for a set of 239 neutral ligands spanning diverse chemical functional groups commonly found in drugs and drug-like candidates is calculated using the molecular dynamics free energy perturbation method (FEP/MD) with explicit water molecules, and compared to experimental data as well as its counterparts obtained using implicit solvent models. The hydration free energies are calculated from explicit solvent simulations using a staged FEP procedure permitting a separation of the total free energy into polar and nonpolar contributions. The nonpolar component is further decomposed into attractive (dispersive) and repulsive (cavity) components using the Weeks-Chandler-Anderson (WCA) separation scheme. To increase the computational efficiency, all of the FEP/MD simulations are generated using a mixed explicit/implicit solvent scheme with a relatively small number of explicit TIP3P water molecules, in which the influence of the remaining bulk is incorporated via the spherical solvent boundary potential (SSBP). The performances of two fixed-charge force fields designed for small organic molecules, the General Amber force field (GAFF), and the all-atom CHARMm-MSI, are compared. Because of the crucial role of electrostatics in solvation free energy, the results from various commonly used charge generation models based on the semiempirical (AM1-BCC) and QM calculations [charge fitting using ChelpG and RESP] are compared. In addition, the solvation free energies of the test set are also calculated using

  9. Relating pressure tuned coupled column ensembles with the solvation parameter model for tunable selectivity in gas chromatography.

    PubMed

    Sharif, Khan M; Kulsing, Chadin; Chin, Sung-Tong; Marriott, Philip J

    2016-07-15

    The differential pressure drop of carrier gas by tuning the junction point pressure of a coupled column gas chromatographic system leads to a unique selectivity of the overall separation, which can be tested using a mixture of compounds with a wide range of polarity. This study demonstrates a pressure tuning (PT) GC system employing a microfluidic Deans switch located at the mid-point of the two capillary columns. This PT system allowed variations of inlet-outlet pressure differences of the two columns in a range of 52-17psi for the upstream column and 31-11psi for the downstream column. Peak shifting (differential migration) of compounds due to PT difference are related to a first order regression equation in a Plackett-Burman factorial study. Increased first (upstream) column pressure drop makes the second column characteristics more significant in the coupled column retention behavior, and conversely increased second (downstream) column pressure drop makes the first column characteristics more apparent; such variation can result in component swapping between polar and non-polar compounds. The coupled column system selectivity was evaluated in terms of linear solvation energy relationship (LSER) parameters, and their relation with different pressure drop effects has been constructed by applying multivariate principle component analysis (PCA). It has been found that the coupled column PT system descriptors provide a result that shows a clear clustering of different pressure settings, somewhat intermediate between those of the two commercial columns. This is equivalent to that obtained from a conventional single-column GC analysis where the interaction energy contributed from the stationary phases can be significantly adjusted by choice of midpoint PT. This result provides a foundation for pressure differentiation for selectivity enhancement. PMID:27302688

  10. Deuterium isotope effect on femtosecond solvation dynamics in an ionic liquid microemulsion: an excitation wavelength dependence study.

    PubMed

    Sasmal, Dibyendu Kumar; Mojumdar, Supratik Sen; Adhikari, Aniruddha; Bhattacharyya, Kankan

    2010-04-01

    The deuterium isotope effect on the solvation dynamics and the anisotropy decay of coumarin 480 (C480) in a room temperature ionic liquid (RTIL) microemulsion is studied by femtosecond up-conversion. The microemulsion consists of the RTIL 1-pentyl-3-methyl-imidazolium tetra-fluoroborate ([pmim][BF(4)]) in triton X-100 (TX-100)/benzene. Replacement of H(2)O by D(2)O in the microemulsion causes retardation of solvation dynamics. The average solvation time of C480 (tau(s)) in RTIL microemulsion with 5 wt % D(2)O is approximately 1.5-1.7 times slower compared to that in the H(2)O containing RTIL microemulsion. This suggests that the main species in the microemulsion responsible for solvation is the water molecules. In both D(2)O and H(2)O containing RTIL microemulsion, the solvation dynamics exhibits marked dependence on the excitation wavelength (lambda(ex)) and becomes about 15 times faster as lambda(ex) increases from 375 to 435 nm. This is ascribed to the structural heterogeneity in the RTIL microemulsion. For lambda(ex) = 375 nm, the region near the TX-100 surfactant is probed where bound water molecules cause slow solvation dynamics. At 435 nm, the RTIL pool is selected where the water molecules are more mobile and hence gives rise to faster solvation. The average time constant of anisotropy decay shows opposite dependence on lambda(ex) and increases about 2.5-fold from 180 ps at lambda(ex) = 375 nm to 500 ps at lambda(ex) = 435 nm for D(2)O containing RTIL microemulsion. The slower anisotropy decay at lambda(ex) = 435 nm is ascribed to the higher viscosity of RTIL which causes greater friction at the core. PMID:20235504

  11. Extended rate equations

    SciTech Connect

    Shore, B.W.

    1981-01-30

    The equations of motion are discussed which describe time dependent population flows in an N-level system, reviewing the relationship between incoherent (rate) equations, coherent (Schrodinger) equations, and more general partially coherent (Bloch) equations. Approximations are discussed which replace the elaborate Bloch equations by simpler rate equations whose coefficients incorporate long-time consequences of coherence.

  12. Maxwell's macroscopic equations, the energy-momentum postulates, and the Lorentz law of force.

    PubMed

    Mansuripur, Masud; Zakharian, Armis R

    2009-02-01

    We argue that the classical theory of electromagnetism is based on Maxwell's macroscopic equations, an energy postulate, a momentum postulate, and a generalized form of the Lorentz law of force. These seven postulates constitute the foundation of a complete and consistent theory, thus eliminating the need for actual (i.e., physical) models of polarization P and magnetization M , these being the distinguishing features of Maxwell's macroscopic equations. In the proposed formulation, P(r,t) and M(r,t) are arbitrary functions of space and time, their physical properties being embedded in the seven postulates of the theory. The postulates are self-consistent, comply with the requirements of the special theory of relativity, and satisfy the laws of conservation of energy, linear momentum, and angular momentum. One advantage of the proposed formulation is that it sidesteps the long-standing Abraham-Minkowski controversy surrounding the electromagnetic momentum inside a material medium by simply "assigning" the Abraham momentum density E(r,t)xH(r,t)/c2 to the electromagnetic field. This well-defined momentum is thus taken to be universal as it does not depend on whether the field is propagating or evanescent, and whether or not the host medium is homogeneous, transparent, isotropic, dispersive, magnetic, linear, etc. In other words, the local and instantaneous momentum density is uniquely and unambiguously specified at each and every point of the material system in terms of the E and H fields residing at that point. Any variation with time of the total electromagnetic momentum of a closed system results in a force exerted on the material media within the system in accordance with the generalized Lorentz law. PMID:19391864

  13. A systematic study of chloride ion solvation in water using van der Waals inclusive hybrid density functional theory

    NASA Astrophysics Data System (ADS)

    Bankura, Arindam; Santra, Biswajit; DiStasio, Robert A., Jr.; Swartz, Charles W.; Klein, Michael L.; Wu, Xifan

    2015-09-01

    In this work, the solvation and electronic structure of the aqueous chloride ion solution was investigated using density functional theory (DFT) based ab initio molecular dynamics (AIMD). From an analysis of radial distribution functions, coordination numbers, and solvation structures, we found that exact exchange (Exx) and non-local van der Waals (vdW) interactions effectively weaken the interactions between the Cl- ion and the first solvation shell. With a Cl-O coordination number in excellent agreement with experiment, we found that most configurations generated with vdW-inclusive hybrid DFT exhibit sixfold coordinated distorted trigonal prism structures, which is indicative of a significantly disordered first solvation shell. By performing a series of band structure calculations on configurations generated from AIMD simulations with varying DFT potentials, we found that the solvated ion orbital energy levels (unlike the band structure of liquid water) strongly depend on the underlying molecular structures. In addition, these orbital energy levels were also significantly affected by the DFT functional employed for the electronic structure; as the fraction of Exx was increased, the gap between the highest occupied molecular orbital of Cl- and the valence band maximum of liquid water steadily increased towards the experimental value.

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

    SciTech Connect

    Allen, Joshua L.; Borodin, Oleg; Seo, D. M.; Henderson, Wesley A.

    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. Commercially 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.

  15. Different Spin-State Behaviors in Isostructural Solvates of a Molecular Iron(II) Complex.

    PubMed

    Cook, Laurence J Kershaw; Kulmaczewski, Rafal; Cespedes, Oscar; Halcrow, Malcolm A

    2016-01-26

    The complex [FeL2][BF4]2 (1; L=4-(isopropylsulfanyl)-2,6-di(pyrazol-1-yl)pyridine) forms solvate crystals 1⋅solv (solv=MeNO2, MeCN, EtCN, or Me2 CO). Most of these materials lose their solvent sluggishly on heating. However, heating 1⋅MeNO2 at 450 K, or storing 1⋅EtCN under ambient conditions, leads to single-crystal to single-crystal exchange of the organic solvent for atmospheric moisture, forming 1⋅H2O. Solvent-free 1 (1⋅sf) can be generated in situ by annealing 1⋅H2O at 370 K in the diffractometer or magnetometer. The different forms of 1 are isostructural (P21 /c, Z=4) and most of them exhibit spin-crossover (SCO) at 141 ≤ T1/2 ≤ 212 K, depending on their solvent content. The exception is the EtCN solvate, whose pristine crystals remain high-spin between 3-300 K. The cooperativity of the spin-transitions depends on the solvent, ranging from gradual and incomplete when solv=acetone to abrupt with 17 K hysteresis when solv=MeCN. Our previously proposed relationship between molecular structure and SCO explains some of these observations, but there is no single structural feature that correlates with SCO in all the 1⋅solv materials. However, changes to the unit cell dimensions during SCO differ significantly between the solvates, and correlate with the SCO cooperativity. In particular, the percentage change in unit cell volume during SCO for the most cooperative material, 1⋅MeCN, is 10 times smaller than for the other 1⋅solv crystals. PMID:26691772

  16. Structure and solvation forces in confined films: Linear and branched alkanes

    SciTech Connect

    Gao, J.; Luedtke, W.D.; Landman, U.

    1997-03-01

    Equilibrium structures, solvation forces, and conformational dynamics of thin confined films of n-hexadecane and squalane are investigated using a new grand canonical ensemble molecular dynamics method for simulations of confined liquids. The method combines constant pressure simulations with a computational cell containing solid surfaces and both bulk and confined liquid regions in equilibrium with each other. Layered density oscillations in the confined films are found for various widths of the confining gap. The solvation force oscillations as a function of the gap width for the straight chain n-hexadecane liquid are more pronounced exhibiting attractive and repulsive regions, while for the branched alkane the solvation forces are mostly repulsive, with the development of shallow local attractive regions for small values of the gap width. Furthermore, the nature of the transitions between well-formed layered configurations is different in the two systems. The n-hexadecane film exhibits solid-like characteristics portrayed by step-like variations in the number of confined segments occurring in response to a small decrease in the gap width, starting from well-layered states of the film; the behavior of the squalane film is liquid-like, exhibiting a monotonic continuous decrease in the number of confined segments as the gap width is decreased. These characteristics are correlated with structural properties of the confined films which, for n-hexadecane, exhibit enhanced layered ordering and in-plane ordered molecular arrangements, as well as with the relatively high tendency for interlayer molecular interdigitation in the squalane films. Reduced conformational (trans-guache) transition rates in the confined films, compared to their bulk values, are found, and their oscillatory dependence on the degree of confinement is analyzed, showing smaller transition rates for the well-formed layered states of the films. {copyright} {ital 1997 American Institute of Physics.}

  17. Lieb-Liniger-like model of quantum solvation in CO-4HeN clusters

    NASA Astrophysics Data System (ADS)

    Farrelly, D.; Iñarrea, M.; Lanchares, V.; Salas, J. P.

    2016-05-01

    Small 4He clusters doped with various molecules allow for the study of "quantum solvation" as a function of cluster size. A peculiarity of quantum solvation is that, as the number of 4He atoms is increased from N = 1, the solvent appears to decouple from the molecule which, in turn, appears to undergo free rotation. This is generally taken to signify the onset of "microscopic superfluidity." Currently, little is known about the quantum mechanics of the decoupling mechanism, mainly because the system is a quantum (N + 1)-body problem in three dimensions which makes computations difficult. Here, a one-dimensional model is studied in which the 4He atoms are confined to revolve on a ring and encircle a rotating CO molecule. The Lanczos algorithm is used to investigate the eigenvalue spectrum as the number of 4He atoms is varied. Substantial solvent decoupling is observed for as few as N = 5 4He atoms. Examination of the Hamiltonian matrix, which has an almost block diagonal structure, reveals increasingly weak inter-block (solvent-molecule) coupling as the number of 4He atoms is increased. In the absence of a dopant molecule the system is similar to a Lieb-Liniger (LL) gas and we find a relatively rapid transition to the LL limit as N is increased. In essence, the molecule initially—for very small N—provides a central, if relatively weak, attraction to organize the cluster; as more 4He atoms are added, the repulsive interactions between the identical bosons start to dominate as the solvation ring (shell) becomes more crowded which causes the molecule to start to decouple. For low N, the molecule pins the atoms in place relative to itself; as N increases the atom-atom repulsion starts to dominate the Hamiltonian and the molecule decouples. We conclude that, while the notion of superfluidity is a useful and correct description of the decoupling process, a molecular viewpoint provides complementary insights into the quantum mechanism of the transition from a molecular

  18. Amphipathic solvation of indole: implications for the role of tryptophan in membrane proteins.

    PubMed

    Johnston, Andrew J; Zhang, Yapei Rosie; Busch, Sebastian; Pardo, Luis Carlos; Imberti, Silvia; McLain, Sylvia E

    2015-05-14

    The microscopic structure of the tryptophan side chain, indole, in an amphiphilic environment has been investigated using a combination of neutron diffraction measurements and simulations in solution. The results show that indole is preferentially solvated by hydrogen bonding interactions between water and alcohol -OH groups rather than the interaction being dominated by indole-methyl interactions. This has implications for understanding how tryptophan interacts with the amphipathic membrane environment to anchor proteins into membranes, where the results here suggest that the benzene ring of tryptophan interacts directly with the interfacial water at the membrane surface rather than being buried into the hydrophobic regions of the membrane bilayer. PMID:25893741

  19. Molecular jet study of the solvation of toluene by methane, ethane, and propanea)

    NASA Astrophysics Data System (ADS)

    Schauer, Mark; Law, K. S.; Bernstein, E. R.

    1985-01-01

    Two color time of flight mass spectroscopy studies of toluene solvated by methane, ethane, and propane in a supersonic molecular jet have been carried out. This work is quite similar to the studies in the preceding paper on benzene. The conclusions and finding in the benzene investigation are strengthened and elaborated. The comparison of calculations and experiments has yielded information on binding enegy, geometry, and spectral shift. A strong correlation is found between observed cluster transition intensity and cluster nucleation processes and a tentative nucleation scheme for the molecular jet formation of solute-solvent clusters is presented.

  20. Lieb-Liniger-like model of quantum solvation in CO-(4)HeN clusters.

    PubMed

    Farrelly, D; Iñarrea, M; Lanchares, V; Salas, J P

    2016-05-28

    Small (4)He clusters doped with various molecules allow for the study of "quantum solvation" as a function of cluster size. A peculiarity of quantum solvation is that, as the number of (4)He atoms is increased from N = 1, the solvent appears to decouple from the molecule which, in turn, appears to undergo free rotation. This is generally taken to signify the onset of "microscopic superfluidity." Currently, little is known about the quantum mechanics of the decoupling mechanism, mainly because the system is a quantum (N + 1)-body problem in three dimensions which makes computations difficult. Here, a one-dimensional model is studied in which the (4)He atoms are confined to revolve on a ring and encircle a rotating CO molecule. The Lanczos algorithm is used to investigate the eigenvalue spectrum as the number of (4)He atoms is varied. Substantial solvent decoupling is observed for as few as N = 5 (4)He atoms. Examination of the Hamiltonian matrix, which has an almost block diagonal structure, reveals increasingly weak inter-block (solvent-molecule) coupling as the number of (4)He atoms is increased. In the absence of a dopant molecule the system is similar to a Lieb-Liniger (LL) gas and we find a relatively rapid transition to the LL limit as N is increased. In essence, the molecule initially-for very small N-provides a central, if relatively weak, attraction to organize the cluster; as more (4)He atoms are added, the repulsive interactions between the identical bosons start to dominate as the solvation ring (shell) becomes more crowded which causes the molecule to start to decouple. For low N, the molecule pins the atoms in place relative to itself; as N increases the atom-atom repulsion starts to dominate the Hamiltonian and the molecule decouples. We conclude that, while the notion of superfluidity is a useful and correct description of the decoupling process, a molecular viewpoint provides complementary insights into the quantum mechanism of the transition from a

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

    PubMed

    Yadav, Hari O S; Shrivastav, Gourav; Agarwal, Manish; Chakravarty, Charusita

    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 Au140(SC10H21)62 nanoparticles in n-alkane solvents, specifically hexane, octane, decane and dodecane, 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

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

    NASA Astrophysics Data System (ADS)

    Yadav, Hari O. S.; Shrivastav, Gourav; Agarwal, Manish; Chakravarty, Charusita

    2016-06-01

    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 Au140(SC10H21)62 nanoparticles in n-alkane solvents, specifically hexane, octane, decane and dodecane, 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

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

    SciTech Connect

    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 the 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

  4. Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble.

    PubMed

    Deighan, Michael; Bonomi, Massimiliano; Pfaendtner, Jim

    2012-07-10

    Herein, we report significant reduction in the cost of combined parallel tempering and metadynamics simulations (PTMetaD). The efficiency boost is achieved using the recently proposed well-tempered ensemble (WTE) algorithm. We studied the convergence of PTMetaD-WTE conformational sampling and free energy reconstruction of an explicitly solvated 20-residue tryptophan-cage protein (trp-cage). A set of PTMetaD-WTE simulations was compared to a corresponding standard PTMetaD simulation. The properties of PTMetaD-WTE and the convergence of the calculations were compared. The roles of the number of replicas, total simulation time, and adjustable WTE parameter γ were studied. PMID:26588950

  5. Solvation force induced by short range, exact dissipative particle dynamics effective surfaces on a simple fluid and on polymer brushes.

    PubMed

    Goicochea, Armando Gama; Alarcón, Francisco

    2011-01-01

    The thermodynamic properties of a simple fluid confined by effective wall forces are calculated using Monte Carlo simulations in the grand canonical ensemble. The solvation force produced by polymer brushes of two different lengths is obtained also. For the particular type of model interactions used, known as the dissipative particle dynamics method, we find that it is possible to obtain an exact, simple expression for the effective force induced by a planar wall composed of identical particles that interact with those in the fluid. We show that despite the short range of all forces in the model, the solvation force can be finite at relatively large distances and therefore does not depend only on the range of the interparticle or solvent-surface forces. As for the polymer brushes, we find that the shape of the solvation force profiles is in fair agreement with scaling and self-consistent field theories. The applications and possible extensions of this work are discussed. PMID:21219016

  6. Two- and three-dimensional nonlocal density functional theory for inhomogeneous fluids. 2. Solvated polymers as a benchmark problem

    SciTech Connect

    Frink, L.J.D.; Salinger, A.G.

    2000-04-10

    In a previous companion paper, the authors presented the details of the algorithms for performing nonlocal density functional theory calculations in complex two- and three-dimensional geometries. The authors discussed scaling and parallelization, but did not discuss other issues of performance. In this paper, they detail the precision of the methods with respect to changes in the mesh spacing. This is a complex issue because given a Cartesian mesh, changes in mesh spacing will result in changes in surface geometry. The authors discuss these issues using a series of rigid solvated polymer models including square rod polymers, cylindrical polymers, and bead-chain polymers. In comparing the results of the various models, it becomes clear that surface curvature or roughness plays an important role in determining the strength of structural solvation forces between interacting solvated polymers. The results in this paper serve as benchmarks for future applications of these algorithms to complex fluid systems.

  7. Electrostatic Solvation Free Energy of Amino Acid Side Chain Analogs: Implications for the Validity of Electrostatic Linear Response in Water

    SciTech Connect

    Lin, Bin; Pettitt, Bernard M.

    2011-04-15

    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 confirms that success of the approximate methods for electrostatic solvation free energies comes from their ability to evaluate free energy differences accurately.

  8. DFT studies of carbohydrate solvation: II. MD-DFTr of a super-molecule complex of glucose, explicit waters, and an implicit solvent (COSMO)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    MD-DFTr studies are carried out on the super-molecule solvated complexes of glucose described in paper I. Included were ten explicit water molecules and an implicit solvation model, COSMO, superimposed upon the complex. Starting configurations were taken from DFTr optimized complexes resulting from ...

  9. Spin field equations and Heun's equations

    NASA Astrophysics Data System (ADS)

    Jiang, Min; Wang, Xuejing; Li, Zhongheng

    2015-06-01

    The Kerr-Newman-(anti) de Sitter metric is the most general stationary black hole solution to the Einstein-Maxwell equation with a cosmological constant. We study the separability of the equations of the massless scalar (spin s=0), neutrino ( s=1/2), electromagnetic ( s=1), Rarita-Schwinger ( s=3/2), and gravitational ( s=2) fields propagating on this background. We obtain the angular and radial master equations, and show that the master equations are transformed to Heun's equation. Meanwhile, we give the condition of existence of event horizons for Kerr-Newman-(anti) de Sitter spacetime by using Sturm theorem.

  10. Solvation of [alpha]-hydroxydiphenylmethyl radical in room temperature ionic liquids studied by transient FT-EPR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kawai, Akio; Hidemori, Takehiro; Shibuya, Kazuhiko

    2005-10-01

    To understand solvation in room temperature ionic liquids (RTILs), an FT-EPR spectrum of α-hydroxydiphenylmethyl (HDPM) radical was measured in several RTILs of tert-alkylammonium or alkylimidazolium salts with anions of PF6-, BF4-, (CF 3SO 2) 2N -, CF3SO3-,WO42-, Cl - and Br -. The hyperfine coupling constant of the hydroxyl proton depends on Gutmann's donor number of the anions, while the constants of phenyl α-protons are essentially the same for these RTILs. This result suggests the electron donor character of anions is important in HDPM solvation in RTILs through the anion-OH group hydrogen-bond.

  11. Direct Observation of the Dynamics of Self-Assembly of Individual Solvation Layers in Molecularly Confined Liquids

    NASA Astrophysics Data System (ADS)

    Relat-Goberna, Josep; Garcia-Manyes, Sergi

    2015-06-01

    Confined liquids organize in solidlike layers at the liquid-substrate interface. Here we use force-clamp spectroscopy AFM to capture the equilibrium dynamics between the broken and reformed states of an individual solvation layer in real time. Kinetic measurements demonstrate that the rupture of each individual solvation layer in structured liquids is driven by the rupture of a single interaction for 1-undecanol and by two interactions in the case of the ionic liquid ethylammonium nitrate. Our results provide a first description of the energy landscape governing the molecular motions that drive the packing and self-assembly of each individual liquid layer.

  12. Study of solvation dynamics in the interior of staphylococcal nuclease (SNase) using picosecond-resolved emission spectra of tryptophan

    NASA Astrophysics Data System (ADS)

    Gao, Guangyu; Li, Yu; Wang, Wei; Men, Jing; Zhong, Dongping; Wang, ShuFeng; Gong, Qihuang

    2014-09-01

    We report here our study on ultrafast spectral dynamics in the interior of SNase using picosecond-resolved emission spectra of tryptophan through site-directed mutagenesis. By probing the solvation dynamics in the nucleotide binding pocket and the Ca2+ binding pocket as well as in the interior of hydrophobic core, two robust relaxation time scales on a few picoseconds and on tens of picoseconds have been observed. Both two time scales are strongly correlated with local structural and chemical properties of protein. These distinct differences in solvation dynamics reflect the intimate relationship between the dynamic structures and the functions of enzyme.

  13. The relation between the structure of the first solvation shell and the IR spectra of aqueous solutions.

    PubMed

    Kumar, Revati; Keyes, Tom

    2012-01-01

    The spectroscopic signatures of solvated anions and cations, in the O-H stretch region of water, are studied using the POLIR potential. Shifts in the spectra are shown to correlate very well with the distribution of a particular hydrogen bond angle for the waters in the first solvation shell. The results indicate that the spectral shifts might be predicted from MD simulations in a computationally convenient fashion, avoiding an explicit calculation of the spectra, as first suggested by Sharp et al. (J Chem Phys 114(4):1791-1796, 2001). PMID:23277671

  14. Infrared and vibrational CD spectra of partially solvated alpha-helices: DFT-based simulations with explicit solvent.

    PubMed

    Turner, David R; Kubelka, Jan

    2007-02-22

    Theoretical simulations are used to investigate the effects of aqueous solvent on the vibrational spectra of model alpha-helices, which are only partly exposed to solvent to mimic alpha-helices in proteins. Infrared absorption (IR) and vibrational circular dichroism (VCD) amide I' spectra for 15-amide alanine alpha-helices are simulated using density functional theory (DFT) calculations combined with the property transfer method. The solvent is modeled by explicit water molecules hydrogen bonded to the solvated amide groups. Simulated spectra for two partially solvated model alpha-helices, one corresponding to a more exposed and the other to a more buried structure, are compared to the fully solvated and unsolvated (gas phase) simulations. The dependence of the amide I spectra on the orientation of the partially solvated helix with respect to the solvent and effects of solvation on the amide I' of 13C isotopically substituted alpha-helices are also investigated. The partial exposure to solvent causes significant broadening of the amide I' bands due to differences in the vibrational frequencies of the explicitly solvated and unsolvated amide groups. The different degree of partial solvation is reflected primarily in the frequency shifts of the unsolvated (buried) amide group vibrations. Depending on which side of the alpha-helix is exposed to solvent, the simulated IR band-shapes exhibit significant changes, from broad and relatively featureless to distinctly split into two maxima. The simulated amide I' VCD band-shapes for the partially solvated alpha-helices parallel the broadening of the IR and exhibit more sign variation, but generally preserve the sign pattern characteristic of the alpha-helical structures and are much less dependent on the alpha-helix orientation with respect to the solvent. The simulated amide I' IR spectra for the model peptides with explicitly hydrogen-bonded water are consistent with the experimental data for small alpha-helical proteins

  15. Basic lubrication equations

    NASA Technical Reports Server (NTRS)

    Hamrock, B. J.; Dowson, D.

    1981-01-01

    Lubricants, usually Newtonian fluids, are assumed to experience laminar flow. The basic equations used to describe the flow are the Navier-Stokes equation of motion. The study of hydrodynamic lubrication is, from a mathematical standpoint, the application of a reduced form of these Navier-Stokes equations in association with the continuity equation. The Reynolds equation can also be derived from first principles, provided of course that the same basic assumptions are adopted in each case. Both methods are used in deriving the Reynolds equation, and the assumptions inherent in reducing the Navier-Stokes equations are specified. Because the Reynolds equation contains viscosity and density terms and these properties depend on temperature and pressure, it is often necessary to couple the Reynolds with energy equation. The lubricant properties and the energy equation are presented. Film thickness, a parameter of the Reynolds equation, is a function of the elastic behavior of the bearing surface. The governing elasticity equation is therefore presented.

  16. A Dialogue with Abraham Maslow.

    ERIC Educational Resources Information Center

    Hardeman, Mildred

    1979-01-01

    This question-and-answer session was conducted at the New School for Social Research in the spring of 1962. Maslow comments on creativity, peak experiences, drug use, self-actualization, religion, and his psychology of Being. (SJL)

  17. Study of dispersion forces with quantum Monte Carlo: toward a continuum model for solvation.

    PubMed

    Amovilli, Claudio; Floris, Franca Maria

    2015-05-28

    We present a general method to compute dispersion interaction energy that, starting from London's interpretation, is based on the measure of the electronic electric field fluctuations, evaluated on electronic sampled configurations generated by quantum Monte Carlo. A damped electric field was considered in order to avoid divergence in the variance. Dispersion atom-atom C6 van der Waals coefficients were computed by coupling electric field fluctuations with static dipole polarizabilities. The dipole polarizability was evaluated at the diffusion Monte Carlo level by studying the response of the system to a constant external electric field. We extended the method to the calculation of the dispersion contribution to the free energy of solvation in the framework of the polarizable continuum model. We performed test calculations on pairs of some atomic systems. We considered He in ground and low lying excited states and Ne in the ground state and obtained a good agreement with literature data. We also made calculations on He, Ne, and F(-) in water as the solvent. Resulting dispersion contribution to the free energy of solvation shows the reliability of the method illustrated here. PMID:25535856

  18. Multidimensional infrared spectroscopy reveals the vibrational and solvation dynamics of isoniazid

    NASA Astrophysics Data System (ADS)

    Shaw, Daniel J.; Adamczyk, Katrin; Frederix, Pim W. J. M.; Simpson, Niall; Robb, Kirsty; Greetham, Gregory M.; Towrie, Michael; Parker, Anthony W.; Hoskisson, Paul A.; Hunt, Neil T.

    2015-06-01

    The results of infrared spectroscopic investigations into the band assignments, vibrational relaxation, and solvation dynamics of the common anti-tuberculosis treatment Isoniazid (INH) are reported. INH is known to inhibit InhA, a 2-trans-enoyl-acyl carrier protein reductase enzyme responsible for the maintenance of cell walls in Mycobacterium tuberculosis but as new drug-resistant strains of the bacterium appear, next-generation therapeutics will be essential to combat the rise of the disease. Small molecules such as INH offer the potential for use as a biomolecular marker through which ultrafast multidimensional spectroscopies can probe drug binding and so inform design strategies but a complete characterization of the spectroscopy and dynamics of INH in solution is required to inform such activity. Infrared absorption spectroscopy, in combination with density functional theory calculations, is used to assign the vibrational modes of INH in the 1400-1700 cm-1 region of the infrared spectrum while ultrafast multidimensional spectroscopy measurements determine the vibrational relaxation dynamics and the effects of solvation via spectral diffusion of the carbonyl stretching vibrational mode. These results are discussed in the context of previous linear spectroscopy studies on solid-phase INH and its usefulness as a biomolecular probe.

  19. 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. PMID:27558719

  20. Computational 17O-NMR spectroscopy of organic acids and peracids: comparison of solvation models.

    PubMed

    Baggioli, Alberto; Crescenzi, Orlando; Field, Martin J; Castiglione, Franca; Raos, Guido

    2013-01-28

    We examine several computational strategies for the prediction of the (17)O-NMR shielding constants for a selection of organic acids and peracids in aqueous solution. In particular, we consider water (the solvent and reference for the chemical shifts), hydrogen peroxide, acetic acid, lactic acid and peracetic acid. First of all, we demonstrate that the PBE0 density functional in combination with the 6-311+G(d,p) basis set provides an excellent compromise between computational cost and accuracy in the calculation of the shielding constants. Next, we move on to the problem of the solvent representation. Our results confirm the shortcomings of the Polarizable Continuum Model (PCM) in the description of systems susceptible to strong hydrogen bonding interactions, while at the same time they demonstrate its usefulness within a molecular-continuum approach, whereby PCM is applied to describe the solvation of the solute surrounded by some explicit solvent molecules. We examine different models of the solvation shells, sampling their configurations using both energy minimizations of finite clusters and molecular dynamics simulations of bulk systems. Hybrid molecular dynamics simulations, in which the solute is described at the PM6 semiempirical level and the solvent by the TIP3P model, prove to be a promising sampling method for medium-to-large sized systems. The roles of solvent shell size and structure are also briefly discussed. PMID:23223608

  1. Investigations of structure and dynamics of water solvation of the type I antifreeze protein

    NASA Astrophysics Data System (ADS)

    Cui, Jun; Battle, Keith; Wierzbicki, Andrzej; Madura, Jeffry D.

    We use molecular dynamics simulations to study the water structure and dynamics around the winter flounder antifreeze protein (AFP) and its two mutant forms in which the four key threonine residues of the winter flounder AFP are mutated to alanines and serines, respectively. The TIP4P-Ew water model is used to better describe the water interactions and water structure; all simulations are performed at 245.5 K, a temperature near the freezing point of the TIP4P-Ew water model. Analysis of structural and dynamic properties of the water around the threonines in the winter flounder AFP reveals that the water structure is ordered around the threonine residues, especially in the second-solvation shell. Alanine and serine mutations instead promote water hydration in the first-solvation shell. Also our calculations show that in the close vicinity of the threonine residues of the wild-type AFP, the mobility of water molecules is substantially decreased. A smaller effect is observed for the weakly active alanine-substituted mutant, and no effect is observed for the inactive serine-substituted mutant. The results of this study suggest that water ordering and immobilization play important roles in the recognition and adsorption of the antifreeze protein to ice.

  2. Solvation structure around the Li(+) ion in succinonitrile-lithium salt plastic crystalline electrolytes.

    PubMed

    Shen, Yuneng; Deng, Gang-Hua; Ge, Chuanqi; Tian, Yuhuan; Wu, Guorong; Yang, Xueming; Zheng, Junrong; Yuan, Kaijun

    2016-06-01

    Herein, we discuss the study of solvation dynamics of lithium-succinonitrile (SN) plastic crystalline electrolytes by ultrafast vibrational spectroscopy. The infrared absorption spectra indicated that the CN stretch of the Li(+) bound and unbound succinonitrile molecules in a same solution have distinct vibrational frequencies (2276 cm(-1)vs. 2253 cm(-1)). The frequency difference allowed us to measure the rotation decay times of solvent molecules bound and unbound to Li(+) ion. The Li(+) coordination number of the Li(+)-SN complex was found to be 2 in the plastic crystal phase (22 °C) and 2.5-3 in the liquid phase (80 °C), which is independent of the concentration (from 0.05 mol kg(-1) to 2 mol kg(-1)). The solvation structures along with DFT calculations of the Li(+)-SN complex have been discussed. In addition, the dissociation percentage of lithium salt was also determined. In 0.5 mol kg(-1) LiBF4-SN solutions at 80 °C, 60% ± 10% of the salt dissociates into Li(+), which is bound by 2 or 3 solvent molecules. In the 0.5 mol kg(-1) LiClO4-SN solutions at 80 °C, the salt dissociation ratio can be up to 90% ± 10%. PMID:27189266

  3. Relativistic and Solvation Effects on the Stability of Gold(III) Halides in Aqueous Solution.

    PubMed

    Theilacker, Kolja; Schlegel, H Bernhard; Kaupp, Martin; Schwerdtfeger, Peter

    2015-10-19

    The redox stability of gold halide complexes in aqueous solution has been examined quantum-chemically by a systematic comparison of scalar- and nonrelativistic pseudopotential calculations, using both COSMO and D-COSMO-RS solvent models for water. After a computational benchmarking of density-functional methods against CCSD(T) results for the gas phase decomposition AuX4(-) → AuX2(-) + X2, B3LYP calculations have been used to establish solvent contributions. While relativity clearly enhances the stability of AuX4(-) (X = F, Cl, Br, I) complexes against X2 elimination, solvation favors the lower oxidation state. Solvation and relativity are nonadditive, due to the relativistic reduction of bond polarity. At scalar relativistic D-COSMO-RS level, the reaction AuX4(-) ⇌ AuX2(-) + X2 is computed to be endergonic, except for X = I, where it is slightly exergonic. Under the chosen conditions, partial hydrolysis of AuCl4(-) to AuCl3OH(-) is exergonic. The latter complex in turn is stable against Cl2 elimination. The disproportionation 3 AuCl2(-) ⇌ AuCl4(-) + 2 Au(s) + 2 Cl(-) is clearly exergonic. All of the computed reaction energies at scalar relativistic D-COSMO-RS level agree well with the observed speciation in dilute pH-neutral solutions at ambient temperatures. PMID:26421633

  4. Observing Solvation Dynamics with Simultaneous Femtosecond X-ray Emission Spectroscopy and X-ray Scattering.

    PubMed

    Haldrup, Kristoffer; Gawelda, Wojciech; Abela, Rafael; Alonso-Mori, Roberto; Bergmann, Uwe; Bordage, Amélie; Cammarata, Marco; Canton, Sophie E; Dohn, Asmus O; van Driel, Tim Brandt; Fritz, David M; Galler, Andreas; Glatzel, Pieter; Harlang, Tobias; Kjær, Kasper S; Lemke, Henrik T; Møller, Klaus B; Németh, Zoltán; Pápai, Mátyás; Sas, Norbert; Uhlig, Jens; Zhu, Diling; Vankó, György; Sundström, Villy; Nielsen, Martin M; Bressler, Christian

    2016-02-18

    In liquid phase chemistry dynamic solute-solvent interactions often govern the path, ultimate outcome, and efficiency of chemical reactions. These steps involve many-body movements on subpicosecond time scales and thus ultrafast structural tools capable of capturing both intramolecular electronic and structural changes, and local solvent structural changes are desired. We have studied the intra- and intermolecular dynamics of a model chromophore, aqueous [Fe(bpy)3](2+), with complementary X-ray tools in a single experiment exploiting intense XFEL radiation as a probe. We monitored the ultrafast structural rearrangement of the solute with X-ray emission spectroscopy, thus establishing time zero for the ensuing X-ray diffuse scattering analysis. The simultaneously recorded X-ray diffuse scattering patterns reveal slower subpicosecond dynamics triggered by the intramolecular structural dynamics of the photoexcited solute. By simultaneous combination of both methods only, we can extract new information about the solvation dynamic processes unfolding during the first picosecond (ps). The measured bulk solvent density increase of 0.2% indicates a dramatic change of the solvation shell around each photoexcited solute, confirming previous ab initio molecular dynamics simulations. Structural changes in the aqueous solvent associated with density and temperature changes occur with ∼1 ps time constants, characteristic for structural dynamics in water. This slower time scale of the solvent response allows us to directly observe the structure of the excited solute molecules well before the solvent contributions become dominant. PMID:26783685

  5. The effects of charge transfer on the aqueous solvation of ions

    SciTech Connect

    Soniat, Marielle; Rick, Steven W.

    2012-07-28

    Ab initio-based charge partitioning of ionic systems results in ions with non-integer charges. This charge-transfer (CT) effect alters both short- and long-range interactions. Until recently, the effects of CT have been mostly neglected in molecular dynamics (MD) simulations. The method presented in this paper for including charge transfer between ions and water is consistent with ab initio charge partitioning and does not add significant time to the simulation. The ions of sodium, potassium, and chloride are parameterized to reproduce dimer properties and aqueous structures. The average charges of the ions from MD simulations (0.900, 0.919, and -0.775 for Na{sup +}, K{sup +}, and Cl{sup -}, respectively) are consistent with quantum calculations. The hydration free energies calculated for these ions are in agreement with experimental estimates, which shows that the interactions are described accurately. The ions also have diffusion constants in good agreement with experiment. Inclusion of CT results in interesting properties for the waters in the first solvation shell of the ions. For all ions studied, the first shell waters acquire a partial negative charge, due to the difference between water-water and water-ion charge-transfer amounts. CT also reduces asymmetry in the solvation shell of the chloride anion, which could have important consequences for the behavior of chloride near the air-water interface.

  6. The thermoelectrochemistry of lithium-glyme solvate ionic liquids: towards waste heat harvesting.

    PubMed

    Black, Jeffrey J; Murphy, Thomas; Atkin, Rob; Dolan, Andrew; Aldous, Leigh

    2016-07-27

    Thermoelectrochemistry offers a simple, scalable technique for direct conversion of waste heat into useful electricity. Here the thermoelectrochemical properties of lithium-glyme solvate ionic liquids, as well as their dilute electrolyte analogues, have been investigated using mixtures of tetraglyme (G4, tetraethylene glycol dimethyl ether) and lithium bis(trifluoromethylsulfonyl)imide (Li[NTf2]). The thermoelectrochemical process is entropically-driven by release of the glyme from the lithium-glyme complex cation, due to electrodeposition of lithium metal at the hotter lithium electrode with concomitant electrodissolution at the cooler lithium electrode. The optimum ratio for thermochemical electricity generation is not the solvate ionic liquid (equimolar mixture of Li[NTf2] and glyme), but rather one Li[NTf2] to four G4, due to the mixtures relatively high ionic conductivity and good apparent Seebeck coefficient (+1.4 mV K(-1)). Determination of the lithium-glyme mixture thermal conductivity enabled full assessment of the Figure of Merit (ZT), and the efficiency relative to the Carnot efficiency to be determined. As the lithium electrodeposits are porous, alternating the temperature gradient results in a system that actually improves with repeated use. PMID:27412130

  7. Polymorphs, hydrates and solvates of a co-crystal of caffeine with anthranilic acid.

    PubMed

    Madusanka, Nadeesh; Eddleston, Mark D; Arhangelskis, Mihails; Jones, William

    2014-02-01

    A polymorph screen on a new 1:1 co-crystal of caffeine, C8H10N4O2, with anthranilic acid, C7H7NO2, has revealed a rich diversity of crystal forms (two polymorphs, two hydrates and seven solvates, including two sets of isostructural solvates). These forms were prepared by liquid-assisted grinding and solution crystallization, and the crystal structures of nine of these forms have been solved using either single-crystal or powder X-ray data. The structures contain O-H...N and N-H...O hydrogen bonds through which caffeine and anthranilic acid molecules assemble to form zigzag-type chains. These chains can interact in an anti-parallel and offset manner to form cage- or channel-type skeletons within which solvent molecules can be located, giving rise to the diversity of forms observed for this co-crystal. In contrast, an equivalent series of liquid-assisted grinding and solution crystallization experiments with the closely related system of theobromine, C7H8N4O2, and anthranilic acid resulted in the formation of only one 1:1 co-crystal form. PMID:24441130

  8. Modeling solvation effects in real-space and real-time within density functional approaches

    SciTech Connect

    Delgado, Alain; Corni, Stefano; Pittalis, Stefano; Rozzi, Carlo Andrea

    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 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.

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

    PubMed

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

    2016-04-19

    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)Nature437(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

  10. Surface of active polarons: A semiexplicit solvation method for biomolecular dynamics

    NASA Astrophysics Data System (ADS)

    Kimura, S. Roy; Brower, Richard C.; Zhang, Chao; Sugimori, Masamichi

    2000-05-01

    We present a strategy for solvating biomolecules in molecular dynamics or Monte Carlo simulations. The method employs a thin layer (often monomolecular) of explicit water with additional external forces representing the electrostatics, pressure, fluctuations, and dissipations caused by the neglected bulk. Long-range electrostatic corrections are supplied through a set of variable surface charges (polarons) that recreates the mean reaction field (or dielectric properties) of an infinite solvent. We refer to this "fictitious" boundary layer as a "surface of active polarons" (or SOAP). Test simulations of the solvation free energies of 15 amino acid analogs and nine ions are in good agreement with experiment (correlation coefficients: 0.995 and 1.000, respectively) despite the use of unaltered published force-fields with only one adjustable parameter. Dynamical capabilities of SOAP are illustrated by application to a six residue peptide with a stable conformation (SYPFDV), as well as a flexible nine residue HIV-1 gp120 peptide (TLTSCNTSV from PDB 1hhg). Future extensions, calibrations, and applications are discussed briefly.

  11. Collective vibrations of water-solvated hydroxide ions investigated with broadband 2DIR spectroscopy

    NASA Astrophysics Data System (ADS)

    Mandal, Aritra; Ramasesha, Krupa; De Marco, Luigi; Tokmakoff, Andrei

    2014-05-01

    The infrared spectra of aqueous solutions of NaOH and other strong bases exhibit a broad continuum absorption for frequencies between 800 and 3500 cm-1, which is attributed to the strong interactions of the OH- ion with its solvating water molecules. To provide molecular insight into the origin of the broad continuum absorption feature, we have performed ultrafast transient absorption and 2DIR experiments on aqueous NaOH by exciting the O-H stretch vibrations and probing the response from 1350 to 3800 cm-1 using a newly developed sub-70 fs broadband mid-infrared source. These experiments, in conjunction with harmonic vibrational analysis of OH-(H2O)n (n = 17) clusters, reveal that O-H stretch vibrations of aqueous hydroxides arise from coupled vibrations of multiple water molecules solvating the ion. We classify the vibrations of the hydroxide complex by symmetry defined by the relative phase of vibrations of the O-H bonds hydrogen bonded to the ion. Although broad and overlapping spectral features are observed for 3- and 4-coordinate ion complexes, we find a resolvable splitting between asymmetric and symmetric stretch vibrations, and assign the 2850 cm-1 peak infrared spectra of aqueous hydroxides to asymmetric stretch vibrations.

  12. Collective Vibrations of Water-Solvated Hydroxide Ions Investigated with Broadband 2DIR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Mandal, Aritra; Ramasesha, Krupa; De Marco, Luigi; Thämer, Martin; Tokmakoff, Andrei

    2014-06-01

    The infrared spectra of aqueous solutions of NaOH and other strong bases exhibit a broad continuum absorption for frequencies between 800-3500 cm-1, which is attributed to the strong interactions of the hydroxide ion with its solvating water molecules. To provide molecular insight into the origin of the broad continuum absorption feature, we have performed ultrafast pump-probe and 2DIR experiments on aqueous NaOH by exciting the O—H stretch vibrations and probing the response from 1350-3800 cm-1 using a newly developed sub-70 fs broadband mid-infrared source. These experiments, in conjunction with harmonic vibrational analysis of OH-(H2O)n clusters, reveal that O—H stretch vibrations of aqueous hydroxides arise from coupled vibrations of multiple water molecules solvating the ion. We classify the vibrations of the hydroxide complex by symmetry defined by the relative phase of vibrations of the O—H bonds hydrogen bonded to the ion. Although spectral broadening does not allow us to distinguish 3- and 4-coordinate ion complexes, we find a resolvable splitting between asymmetric and symmetric stretch vibrations, and assign the 2850 cm-1 peak infrared spectra of aqueous hydroxides to asymmetric stretch vibrations.

  13. Multidimensional infrared spectroscopy reveals the vibrational and solvation dynamics of isoniazid.

    PubMed

    Shaw, Daniel J; Adamczyk, Katrin; Frederix, Pim W J M; Simpson, Niall; Robb, Kirsty; Greetham, Gregory M; Towrie, Michael; Parker, Anthony W; Hoskisson, Paul A; Hunt, Neil T

    2015-06-01

    The results of infrared spectroscopic investigations into the band assignments, vibrational relaxation, and solvation dynamics of the common anti-tuberculosis treatment Isoniazid (INH) are reported. INH is known to inhibit InhA, a 2-trans-enoyl-acyl carrier protein reductase enzyme responsible for the maintenance of cell walls in Mycobacterium tuberculosis but as new drug-resistant strains of the bacterium appear, next-generation therapeutics will be essential to combat the rise of the disease. Small molecules such as INH offer the potential for use as a biomolecular marker through which ultrafast multidimensional spectroscopies can probe drug binding and so inform design strategies but a complete characterization of the spectroscopy and dynamics of INH in solution is required to inform such activity. Infrared absorption spectroscopy, in combination with density functional theory calculations, is used to assign the vibrational modes of INH in the 1400-1700 cm(-1) region of the infrared spectrum while ultrafast multidimensional spectroscopy measurements determine the vibrational relaxation dynamics and the effects of solvation via spectral diffusion of the carbonyl stretching vibrational mode. These results are discussed in the context of previous linear spectroscopy studies on solid-phase INH and its usefulness as a biomolecular probe. PMID:26049421

  14. 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. PMID:25563344

  15. 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. PMID:27487964

  16. Physical and Chemical Aspects of Pharmaceutical Solids: Fundamentals of Polymorphs, Hydrates and Solvates

    NASA Astrophysics Data System (ADS)

    Reutzel-Edens, Susan

    2007-03-01

    Crystal polymorphs are solid phases of a given compound resulting from the possibility of at least two different arrangements of the molecules of that compound in the solid state. Solvates form when the solvent is incorporated in the crystal structure of a compound; hydrates form when water is the solvent of crystallization. The potential effects of crystal polymorphism and hydration on the quality and performance of drug products is widely recognized by the pharmaceutical industry. Investigations of crystal polymorphism and hydration are usually conducted early in drug development to optimize the physical properties of a pharmaceutical solid. Although the thermodynamically most stable crystal form is generally selected for commercial development to mitigate the risk of undesired phase transformations, form selection oftentimes involves a compromise among different physical properties of various drug crystal forms. Controlling polymorph (or hydrate) appearance must be accomplished through careful evaluation of both thermodynamic (tendency toward the formation of more stable crystal forms) and kinetic parameters (which lead to the formation of metastable forms) in the crystallization process. In this presentation, fundamental aspects of polymorphs and solvates (hydrates) will be explored. Particular attention will be given to the structure and stability relationships between polymorphs and hydrates, kinetic vs. thermodynamic transitions, and the impact of polymorphism and hydration on the chemical and physical stability of an active pharmaceutical ingredient.

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

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

    This paper extends the image charge solvation model (ICSM) [Y. Lin, A. Baumketner, S. Deng, Z. Xu, D. Jacobs, W. Cai, An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions, J. Chem. Phys. 131 (2009) 154103], 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.

  18. Ultrafast Spectroscopic and AB Initio Computational Investigations on Solvation Dynamics of Neutral and Deprotonated Tyrosine.

    NASA Astrophysics Data System (ADS)

    Fujiwara, Takashige; Zgierski, Marek Z.

    2015-06-01

    We have studied one of the aromatic amino acids, tyrosine, regarding its photophysical properties in various solvent conditions by using a femtosecond fluorescence up-conversion technique and high-level TDDFT and CC2 computations. In this talk, profound details not only on ultrafast solvation dynamics on a neutral tyrosine in various solvents, but also on the excited-state dynamics for a single- (or doubly-) deprotonated tyrosine under various pH solutions will be presented. In high basicity, a tyrosine shows different absorption/emission spectra, and a total spectrum consists of a combination of these individual spectra that depend on the pH of the solution. The time scale of acid--base equilibrium is essential in solvation dynamics; whereas the protonation is simply controlled by diffusion, the de-protonation is considered to be slow process such that acid--base equilibrium may not be reached in the short-lived excited state after photo-excitation. Experimental and computational approaches taken and insights obtained in this concerted work will be described.

  19. Final Progress Report for Linking Ion Solvation and Lithium Battery Electrolyte Properties

    SciTech Connect

    Henderson, Wesley

    2014-08-29

    The research objective of this proposal was to provide a detailed analysis of how solvent and anion structure govern the solvation state of Li+ cations in solvent-LiX mixtures and how this, in turn, dictates the electrolyte physicochemical and electrochemical properties which govern (in part) battery performance. Lithium battery electrolytes remain a poorly understood and hardly studied topic relative to the research devoted to battery electrodes. This is due to the fact that it is the electrodes which determine the energy (capacity) of the battery. The electrolyte, however, plays a crucial role in the practical energy density, power, low and/or high temperature performance, lifetime, safety, etc. which is achievable. The development within this project of a "looking glass" into the molecular interactions (i.e., solution structure) in bulk electrolytes through a synergistic experimental approach involving three research thrusts complements work by other researchers to optimize multi-solvent electrolytes and efforts to understand/control the electrode-electrolyte interfaces, thereby enabling the rational design of electrolytes for a wide variety of battery chemistries and applications (electrolytes-on-demand). The three research thrusts pursued include: (1) conduction of an in-depth analysis of the thermal phase behavior of diverse solvent-LiX mixtures, (2) exploration of the ionic association/solvate formation behavior of select LiX salts with a wide variety of solvents, and (3) linking structure to properties-determination of electrolyte physicochemical and electrochemical properties for comparison with the ionic association and phase behavior.

  20. Is the uptake of alcohols by H2O droplets governed by equilibrium solvation dynamics?

    SciTech Connect

    Taylor, R.S.; Dang, Liem, X.; Garret, B.C.

    1997-12-31

    Heterogeneous processes are important components of the earth`s atmospheric system. Experiments suggest that the interaction of small gas phase molecules with the liquid/vapor interface of aqueous droplets and their subsequent accommodation into the bulk of droplet is an integral part of these processes. A recently devised, molecular-level model predicts that this mass accommodation process is solely dependent on the rates of solvation and desorption of the impinging molecule and that the molecule must cross a large energy barrier before becoming solvated in the bulk water. In this work, we are using molecular dynamics computer simulations to examine this model. Due to the availability of experimental data, the ethanol-water and ethylene glycol-water systems have been chosen as prototypes for the mass accommodation process of non-reacting molecules. The potential of mean force technique is used to explore the equilibrium free energy surface for inserting these alcohols into bulk water from its vapor. These free energy profiles do not correspond to those predicted by the above mentioned model. The non-equilibrium aspects of this process are also explored.

  1. Exploring Conformation Selective Far Infrared Action Spectroscopy of Isolated Molecules and Solvated Clusters

    NASA Astrophysics Data System (ADS)

    Bakker, Daniël; Rijs, Anouk; Mahé, Jérôme; Gaigeot, Marie-Pierre

    2015-06-01

    Far-Infrared (IR) spectroscopy has been labeled as a promising method for identifying structural motifs in large molecules. However, several hurdles have kept this promising spectral region from breaking through to widespread use for gas phase experiments. Normal modes in the far-IR mostly have weak intensities, and high brightness sources of far-IR radiation are rare. Moreover, standard density functional theory - applied to identify the specific molecular structure responsible for the measured IR spectra - does not reproduce features in the far-IR well. This mismatch can be attributed to the high degree of anharmonicity of many of the normal modes present in the far-IR. We have overcome these hurdles by combining an advanced laser source with novel experiments and high-level dynamical calculations. We present far-IR spectra of a family of phenolic molecules and solvated clusters, obtained using the free electron laser FELIX. By employing IR-UV ion-dip spectroscopy in the gas phase, we are able to obtain conformer specific far-IR spectra of isolated molecules or solvated clusters. The studied systems display both intra- and intermolecular hydrogen bonding, enabling us to study the merits of far-IR action spectroscopy for direct probing of these weak interactions. Moreover, the combination of far-IR experiments with quantum chemical calculations allows us to test the limits of the harmonic approximation in DFT calculations, and to test the possibilities of employing a more sophisticated technique, namely Born-Oppenheimer molecular dynamics.

  2. Phase behavior and second osmotic virial coefficient for competitive polymer solvation in mixed solvent solutions

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

    We apply our recently developed generalized Flory-Huggins (FH) type theory for the competitive solvation of polymers by two mixed solvents to explain general trends in the variation of phase boundaries and solvent quality (quantified by the second osmotic virial coefficient B 2 ) with solvent composition. The complexity of the theoretically predicted miscibility patterns for these ternary mixtures arises from the competitive association between the polymer and the solvents and from the interplay of these associative interactions with the weak van der Waals interactions between all components of the mixture. The main focus here lies in determining the influence of the free energy parameters for polymer-solvent association (solvation) and the effective FH interaction parameters {χαβ} (driving phase separation) on the phase boundaries (specifically the spinodals), the second osmotic virial coefficient B 2 , and the relation between the positions of the spinodal curves and the theta temperatures at which B 2 vanishes. Our classification of the predicted miscibility patterns is relevant to numerous applications of ternary polymer solutions in industrial formulations and the use of mixed solvent systems for polymer characterization, such as chromatographic separation where mixed solvents are commonly employed. A favorable comparison of B 2 with experimental data for poly(methyl methacrylate)/acetonitrile/methanol (or 1-propanol) solutions only partially supports the validity of our theoretical predictions due to the lack of enough experimental data and the neglect of the self and mutual association of the solvents.

  3. Accuracy of exchange-correlation functionals and effect of solvation on the surface energy of copper

    NASA Astrophysics Data System (ADS)

    Fishman, Matthew; Zhuang, Houlong L.; Mathew, Kiran; Dirschka, William; Hennig, Richard G.

    2013-06-01

    Surface energies are important for predicting the shapes of nanocrystals and describing the faceting and roughening of surfaces. Copper surfaces are of particular interest in recent years since they are the preferred surfaces for growing graphene using chemical vapor deposition. In this study we calculate the surface energies of copper for the three low-index facets (111), (100), and (110) and one high-index facet, (210), using density-functional theory with both the local-density approximation and various parametrizations of the generalized-gradient approximation to the exchange-correlation functional. To assess the accuracy of the different functionals, we obtain the average surface energies of an isotropic crystal using a broken-bond model. We use this method, which can be generalized to other crystal structures, to compare calculated surface energies to experimental surface energies for fcc crystals. We find that the recent exchange-correlation functionals AM05 and PBEsol are the most accurate functionals for calculating the surface energies of copper. To determine how solvents affect the surface energies of copper, we perform calculations using a continuum solvation model. We find that aqueous solvation changes the overall magnitude of the surface energies only slightly but leads to more isotropic surface energies.

  4. Simulated Solvation of Organic Ions II: Study of Linear Alkylated Carboxylate Ions in Water Nanodrops and in Liquid Water. Propensity for Air/Water Interface and Convergence to Bulk Solvation Properties.

    PubMed

    Houriez, Céline; Meot-Ner Mautner, Michael; Masella, Michel

    2015-09-10

    We investigated the solvation of carboxylate ions from formate to hexanoate, in droplets of 50 to 1000 water molecules and neat water, by computations using standard molecular dynamics and sophisticated polarizable models. The carboxylate ions from methanoate to hexanoate show strong propensity for the air/water interface in small droplets. Only the ions larger than propanoate retain propensity for the interface in larger droplets, where their enthalpic stabilization by ion/water dispersion is reduced there by 3 kcal mol(-1) per CH2 group. This is compensated by entropy effects over +3.3 cal mol(-1) K(-1) per CH2 group. On the surface, the anionic headgroups are strongly oriented toward the aqueous core, while the hydrophobic alkyl chains are repelled into air and lose their structure-making effects. These results reproduce the structure-making effects of alkyl groups in solution, and suggest that the hydrocarbon chains of ionic headgroups and alkyl substituents solvate independently. Extrapolation to bulk solution using standard extrapolation schemes yields absolute carboxylate solvation energies. The results for formate and acetate yield a proton solvation enthalpy of about 270 kcal mol(-1), close to the experiment-based value. The largest carboxylate ions yield a value smaller by about 10 kcal mol(-1), which requires studies in much larger droplets. PMID:26287943

  5. Chemical Equation Balancing.

    ERIC Educational Resources Information Center

    Blakley, G. R.

    1982-01-01

    Reviews mathematical techniques for solving systems of homogeneous linear equations and demonstrates that the algebraic method of balancing chemical equations is a matter of solving a system of homogeneous linear equations. FORTRAN programs using this matrix method to chemical equation balancing are available from the author. (JN)

  6. Equations and closure methods

    NASA Technical Reports Server (NTRS)

    1977-01-01

    Basic differential equations governing compressible turbulent boundary layer flow are reviewed, including conservation of mass and energy, momentum equations derived from Navier-Stokes equations, and equations of state. Closure procedures were broken down into: (1) simple or zeroth-order methods, (2) first-order or mean field closure methods, and (3) second-order or mean turbulence field methods.

  7. Structural Effects of Solvation by 18-Crown-6 on Gaseous Peptides and TrpCage after Electrospray Ionization

    NASA Astrophysics Data System (ADS)

    Bonner, James G.; Hendricks, Nathan G.; Julian, Ryan R.

    2016-08-01

    Significant effort is being employed to utilize the inherent speed and sensitivity of mass spectrometry for rapid structural determination of proteins; however, a thorough understanding of factors influencing the transition from solution to gas phase is critical for correct interpretation of the results from such experiments. It was previously shown that combined use of action excitation energy transfer (EET) and simulated annealing can reveal detailed structural information about gaseous peptide ions. Herein, we utilize this method to study microsolvation of charged groups by retention of 18-crown-6 (18C6) in the gas phase. In the case of GTP (CEGNVRVSRE LAGHTGY), solvation of the 2+ charge state leads to reduced EET, whereas the opposite result is obtained for the 3+ ion. For the mini-protein C-Trpcage, solvation by 18C6 leads to dramatic increase in EET for the 3+ ion. Examination of structural details probed by molecular dynamics calculations illustrate that solvation by 18C6 alleviates the tendency of charged side chains to seek intramolecular solvation, potentially preserving native-like structures in the gas phase. These results suggest that microsolvation may be an important tool for facilitating examination of native-like protein structures in gas phase experiments.

  8. Electron spin echo studies of the solvation structure of O/sub 2//sup -/ in methanol and ethanol

    SciTech Connect

    Narayana, P.A.; Suryanarayana, D.; Kevan, L.

    1982-07-08

    Electron spin echo modulation studies of O/sub 2//sup -/ in specifically deuterated methanol and ethanol glasses have been carried out at 4.2/sup 0/K to determine the solvation structure around O/sub 2//sup -/. The results of the analysis indicate that in both the cases each O/sub 2//sup -/ is solvated by four alcohol molecules. In the case of methanol, the solvent molecules have their H-O bonds oriented toward the II* orbitals of O/sub 2//sup -/ to maximize hydrogen-bonding interactions. This is similar to the O/sub 2//sup -/ solvation structure in water. However, in ethanol the H-O bonds are tilted away from the II* orbitals so that partial molecular dipole orientation of ethanol occurs. As the polar solvent molecule becomes bulkier it appears that molecular dipole orientation becoms more important. This tend is compared with results for solvated electrons in the same solvents. 9 figures, 1 table.

  9. Structural Stability and Deformation of Solvated Sm@C2(45)-C90 under High Pressure

    NASA Astrophysics Data System (ADS)

    Cui, Jinxing; Yao, Mingguang; Yang, Hua; Liu, Ziyang; Liu, Shijie; Du, Mingrun; Li, Quanjun; Liu, Ran; Cui, Tian; Liu, Bingbing

    2016-08-01

    Solvated fullerenes recently have been shown to exhibit novel compression behaviors compared with the pristine fullerenes. However, less attention has been focused on the large cage endohedral metallofullerenes. Here, we have firstly synthesized solvated Sm@C90 microrods by a solution drop-drying method, and then studied the transformations under high pressure. The pressure-induced structural evolutions of Sm@C90 molecules both undergo deformation and collapse. The band gaps of both samples decrease with increasing pressure. The trapped Sm atom plays a role in restraining the compression of the adjacent bonds. The solvent plays a role in protecting Sm@C90 against collapse in the region of 12–20 GPa, decreasing and postponing the change of band gap. Above 30 GPa, the carbon cages collapse. Released from 45 GPa, the compressed solvated Sm@C90 forms a new ordered amorphous carbon cluster (OACC) structure with metal atoms trapped in the units of amorphous carbon clusters, which is different from the OACC structure formed by compressing solvated C60 and C70. This discovery opens the door for the creation of new carbon materials with desirable structural and physical properties when suitable starting materials are selected.

  10. Solvation effects for polymers at an interface: a hybrid self-consistent field-density functional theory approach.

    PubMed

    Bryk, Paweł; MacDowell, Luis G

    2011-11-28

    Using polyatomic density functional theory of Kierlik and Rosinberg, we show that Wertheim's thermodynamic perturbation theory (TPT) incorporates solvation effects in a systematic, although simplified form. We derive two approximate solvation potentials, which require the knowledge of the correlation function in the reference unbonded fluid only. The theoretical predictions are tested against many-chain Monte Carlo simulations for moderate chain lengths. The predictions of the end-to-end distance in the bulk are in a reasonable agreement with simulations for the TPT(M-1) approximation, while the simpler TPT2_e approximation leads to the solvation potential that is shorter ranged and considerably less accurate. The resulting conformations are used in the subsequent self-consistent field theory calculations of hard-sphere polymers at a hard wall. While the incorporation of the solvation effects has little impact on the density profiles, the predictions of the components of the end-to-end distance vector as a function of the distance to the wall are much improved. PMID:22128953

  11. Structural Stability and Deformation of Solvated Sm@C2(45)-C90 under High Pressure.

    PubMed

    Cui, Jinxing; Yao, Mingguang; Yang, Hua; Liu, Ziyang; Liu, Shijie; Du, Mingrun; Li, Quanjun; Liu, Ran; Cui, Tian; Liu, Bingbing

    2016-01-01

    Solvated fullerenes recently have been shown to exhibit novel compression behaviors compared with the pristine fullerenes. However, less attention has been focused on the large cage endohedral metallofullerenes. Here, we have firstly synthesized solvated Sm@C90 microrods by a solution drop-drying method, and then studied the transformations under high pressure. The pressure-induced structural evolutions of Sm@C90 molecules both undergo deformation and collapse. The band gaps of both samples decrease with increasing pressure. The trapped Sm atom plays a role in restraining the compression of the adjacent bonds. The solvent plays a role in protecting Sm@C90 against collapse in the region of 12-20 GPa, decreasing and postponing the change of band gap. Above 30 GPa, the carbon cages collapse. Released from 45 GPa, the compressed solvated Sm@C90 forms a new ordered amorphous carbon cluster (OACC) structure with metal atoms trapped in the units of amorphous carbon clusters, which is different from the OACC structure formed by compressing solvated C60 and C70. This discovery opens the door for the creation of new carbon materials with desirable structural and physical properties when suitable starting materials are selected. PMID:27503144

  12. Aqueous solvation of amphiphilic molecules by extended depolarized light scattering: the case of trimethylamine-N-oxide.

    PubMed

    Comez, L; Paolantoni, M; Corezzi, S; Lupi, L; Sassi, P; Morresi, A; Fioretto, D

    2016-04-01

    Hydrophilic and hydrophobic interactions strongly affect the solvation dynamics of biomolecules. To understand their role, small model systems are generally employed to simplify the investigations. In this study the amphiphile trimethylamine N-oxide (TMAO) is chosen as an exemplar, and studied by means of extended frequency range depolarized light scattering (EDLS) experiments as a function of solute concentration. This technique proves to be a suitable tool for investigating different aspects of aqueous solvation, being able at the same time to provide information about relaxation processes and vibrational modes of solvent and solute. In the case study of TMAO, we find that the relaxation dynamics of hydration water is moderately retarded compared to the bulk, and the perturbation induced by the solute on surrounding water is confined to the first hydration shell. The results highlight the hydrophobic character of TMAO in its interaction with water. The number of molecules taking part in the solvation process decreases as the solute concentration increases, following a trend consistent with the hydration water-sharing model, and suggesting that aggregation between solute molecules is negligible. Finally, the analysis of the resonant modes in the THz region and the comparison with the corresponding results obtained for the isosteric molecule tert-butyl alcohol (TBA) allow us to provide new insights into the different solvating properties of these two biologically relevant molecules. PMID:26958663

  13. Structural Stability and Deformation of Solvated Sm@C2(45)-C90 under High Pressure

    PubMed Central

    Cui, Jinxing; Yao, Mingguang; Yang, Hua; Liu, Ziyang; Liu, Shijie; Du, Mingrun; Li, Quanjun; Liu, Ran; Cui, Tian; Liu, Bingbing

    2016-01-01

    Solvated fullerenes recently have been shown to exhibit novel compression behaviors compared with the pristine fullerenes. However, less attention has been focused on the large cage endohedral metallofullerenes. Here, we have firstly synthesized solvated Sm@C90 microrods by a solution drop-drying method, and then studied the transformations under high pressure. The pressure-induced structural evolutions of Sm@C90 molecules both undergo deformation and collapse. The band gaps of both samples decrease with increasing pressure. The trapped Sm atom plays a role in restraining the compression of the adjacent bonds. The solvent plays a role in protecting Sm@C90 against collapse in the region of 12–20 GPa, decreasing and postponing the change of band gap. Above 30 GPa, the carbon cages collapse. Released from 45 GPa, the compressed solvated Sm@C90 forms a new ordered amorphous carbon cluster (OACC) structure with metal atoms trapped in the units of amorphous carbon clusters, which is different from the OACC structure formed by compressing solvated C60 and C70. This discovery opens the door for the creation of new carbon materials with desirable structural and physical properties when suitable starting materials are selected. PMID:27503144

  14. Characterizing the dissolution profiles of supersaturable salts, cocrystals, and solvates to enhance in vivo oral absorption.

    PubMed

    Hisada, Nozomi; Takano, Ryusuke; Takata, Noriyuki; Shiraki, Koji; Ueto, Takamitsu; Tanida, Satoshi; Kataoka, Makoto; Yamashita, Shinji

    2016-06-01

    The purposes of this study were to elucidate the type-specific characteristics of salt, cocrystal, and solvate formulations upon dissolution and precipitation, and to clarify their effect on enhancing oral absorption. Several types of solid formulations (dantrolene sodium salt [DAN-NA], pioglitazone hydrochloride salt [PIO-HCL], megestrol acetate saccharin cocrystal [MEG-SA], and an in-house compound ZR ethanolate [ZR-ETH]) that induce supersaturation of BCS class II drugs were compared to their crystalline free forms. An in vitro miniscale dissolution test in biorelevant media was used to characterize their dissolution profiles and residue forms. Both salts (DAN-NA and PIO-HCL) rapidly reached the maximum concentration within 5min, whereas the cocrystal (MEG-SA) did so slowly. After the maximum concentration had been reached, the dissolved concentrations of DAN-NA, PIO-HCL, and MEG-SA decreased, but that of ZR-ETH did not. Time-dependent XRPD analysis revealed that the initial solid state of each salt dissolved within 5min, whereas the cocrystal remained for more than 10min, and the solvate remained for 4h. It also revealed that PIO-HCL and MEG-SA precipitated to the stable free form, while DAN-NA precipitated to the metastable form, which maintains a higher concentration than the stable free form continuously. In vivo absorption in beagle dogs was also examined. The plasma AUC of DAN-NA, MEG-SA, and ZR-ETH was respectively 1.5-, 2.1-, and 11-fold more than each free form. On the other hand, the absorption of PIO-HCL was not enhanced compared with its free form. The results in the present study clarified that not only the precipitation rate and the form of precipitation but also the retention of the initial solid state in the absorption process contribute to enhancing the in vivo absorption of Class II drugs from solid formulations such as salts, solvates, and cocrystals. PMID:27060622

  15. Why are ionic liquids liquid? A simple explanation based on lattice and solvation energies.

    PubMed

    Krossing, Ingo; Slattery, John M; Daguenet, Corinne; Dyson, Paul J; Oleinikova, Alla; Weingärtner, Hermann

    2006-10-18

    We have developed a simple and quantitative explanation for the relatively low melting temperatures of ionic liquids (ILs). The basic concept was to assess the Gibbs free energy of fusion (Delta(fus)G) for the process IL(s) --> IL(l), which relates to the melting point of the IL. This was done using a suitable Born-Fajans-Haber cycle that was closed by the lattice (i.e., IL(s) --> IL(g)) Gibbs energy and the solvation (i.e., IL(g) --> IL(l)) Gibbs energies of the constituent ions in the molten salt. As part of this project we synthesized and determined accurate melting points (by DSC) and dielectric constants (by dielectric spectroscopy) for 14 ionic liquids based on four common anions and nine common cations. Lattice free energies (Delta(latt)G) were estimated using a combination of Volume Based Thermodynamics (VBT) and quantum chemical calculations. Free energies of solvation (Delta(solv)G) of each ion in the bulk molten salt were calculated using the COSMO solvation model and the experimental dielectric constants. Under standard ambient conditions (298.15 K and 10(5) Pa) Delta(fus)G degrees was found to be negative for all the ILs studied, as expected for liquid samples. Thus, these ILs are liquid under standard ambient conditions because the liquid state is thermodynamically favorable, due to the large size and conformational flexibility of the ions involved, which leads to small lattice enthalpies and large entropy changes that favor melting. This model can be used to predict the melting temperatures and dielectric constants of ILs with good accuracy. A comparison of the predicted vs experimental melting points for nine of the ILs (excluding those where no melting transition was observed and two outliers that were not well described by the model) gave a standard error of the estimate (s(est)) of 8 degrees C. A similar comparison for dielectric constant predictions gave s(est) as 2.5 units. Thus, from very little experimental and computational data it is

  16. Characterization of volatile organic compound adsorption on multiwall carbon nanotubes under different levels of relative humidity using linear solvation energy relationship.

    PubMed

    Li, Mei-Syue; Wu, Siang Chen; Shih, Yang-Hsin

    2016-09-01

    Multiwall carbon nanotubes (MWCNTs) have been used as an adsorbent for evaluating the gas/solid partitioning of selected volatile organic compounds (VOCs). In this study, 15 VOCs were probed to determine their gas/solid partitioning coefficient (LogKd) using inverse gas chromatography at different relative humidity (RH) levels. Interactions between MWCNTs and VOCs were analyzed by regressing the observed LogKd with the linear solvation energy relationship (LSER). The results demonstrate that the MWCNT carbonyl and carboxyl groups provide high adsorption capacity for the VOCs (LogKd 3.72-5.24g/kg/g/L) because of the π-/n-electron pair interactions and hydrogen-bond acidity. The increasing RH gradually decreased the LogKd and shifted the interactions to dipolarity/polarizability, hydrogen-bond basicity, and cavity formation. The derived LSER equations provided adequate fits of LogKd, which is useful for VOC-removal processes and fate prediction of VOC contaminants by MWCNT adsorption in the environment. PMID:27152974

  17. Computational Investigation of the First Solvation Shell Structure of Interfacial and Bulk Aqueous Chloride and Iodide Ions

    SciTech Connect

    Wick, Collin D.; Xantheas, Sotiris S.

    2009-04-02

    Molecular dynamics simulations with polarizable interaction potentials were carried out to understand the solvation structure of chloride and iodide anions in bulk and interfacial water, showing qualitative similarities between the first solvation shell structures at the interface and bulk. For the more polarizable iodide, its solvation structure was more anisotropic than chloride, and this trend persisted at both the interface and in the bulk. Furthermore it was found that the first few clusters of water with iodide were quite different than the corresponding ones with chloride, with the former exhibiting more anisotropic configurations than the latter. The anisotropy of the solvation structure correlated with polarizability, but it was also found to inversely correlate with anion size. When polarizability was reduced to near zero, a very small anisotropy in the water solvation structure around the ion still persisted. Polarizable anions were found to have on average an induced dipole in the bulk that was significantly larger than zero. This induced dipole resulted in the water hydrogen atoms having stronger interactions with the anions on one side of them, in which the dipole was pointing at. In contrast, the other side of the anions, in which the induced dipole was pointing away from, had fewer water molecules present and, for the case of iodide, was rather devoid of water molecules all together at both the interface and in the bulk. This region formed a small cavity in the bulk, while at the air-water interface was simply part of the air interface. In the bulk, this small cavity may be viewed as somewhat hydrophobic, and the need for the extinction of this cavity may be one of the major driving forces for polarizable anions to reside at the air-water interface. This work was supported by the U.S. Department of Energy's (DOE) Office of Basic Energy Sciences, Chemical Sciences program. The Pacific Northwest National Laboratory is operated by Battelle for DOE.

  18. A first principles molecular dynamics study of lithium atom solvation in binary liquid mixture of water and ammonia: Structural, electronic, and dynamical properties

    NASA Astrophysics Data System (ADS)

    Pratihar, Subha; Chandra, Amalendu

    2011-01-01

    The preferential solvation of solutes in mixed solvent systems is an interesting phenomenon that plays important roles in solubility and kinetics. In the present study, solvation of a lithium atom in aqueous ammonia solution has been investigated from first principles molecular dynamics simulations. Solvation of alkali metal atoms, like lithium, in aqueous and ammonia media is particularly interesting because the alkali metal atoms release their valence electrons in these media so as to produce solvated electrons and metal counterions. In the present work, first principles simulations are performed employing the Car-Parrinello molecular dynamics method. Spontaneous ionization of the Li atom is found to occur in the mixed solvent system. From the radial distribution functions, it is found that the Li ^+ ion is preferentially solvated by water and the coordination number is mostly four in its first solvation shell and exchange of water molecules between the first and second solvation shells is essentially negligible in the time scale of our simulations. The Li ^+ ion and the unbound electron are well separated and screened by the polar solvent molecules. Also the unbound electron is primarily captured by the hydrogens of water molecules. The diffusion rates of Li ^+ ion and water molecules in its first solvation shell are found to be rather slow. In the bulk phase, the diffusion of water is found to be slower than that of ammonia molecules because of strong ammonia-water hydrogen bonds that participate in solvating ammonia molecules in the mixture. The ratio of first and second rank orientational correlation functions deviate from 3, which suggests a deviation from the ideal Debye-type orientational diffusion. It is found that the hydrogen bond lifetimes of ammonia-ammonia pairs is very short. However, ammonia-water H-bonds are found to be quite strong when ammonia acts as an acceptor and these hydrogen bonds are found to live longer than even water-water hydrogen

  19. Understanding the Role of Solvation Forces on the Preferential Attachment of Nanoparticles in Liquid.

    PubMed

    Welch, David A; Woehl, Taylor J; Park, Chiwoo; Faller, Roland; Evans, James E; Browning, Nigel D

    2016-01-26

    Optimization of colloidal nanoparticle synthesis techniques requires an understanding of underlying particle growth mechanisms. Nonclassical growth mechanisms are particularly important as they affect nanoparticle size and shape distributions, which in turn influence functional properties. For example, preferential attachment of nanoparticles is known to lead to the formation of mesocrystals, although the formation mechanism is currently not well-understood. Here we employ in situ liquid cell scanning transmission electron microscopy and steered molecular dynamics (SMD) simulations to demonstrate that the experimentally observed preference for end-to-end attachment of silver nanorods is a result of weaker solvation forces occurring at rod ends. SMD reveals that when the side of a nanorod approaches another rod, perturbation in the surface-bound water at the nanorod surface creates significant energy barriers to attachment. Additionally, rod morphology (i.e., facet shape) effects can explain the majority of the side attachment effects that are observed experimentally. PMID:26588243

  20. Resonant two-photon ionization spectroscopy of Al atoms and dimers solvated in helium nanodroplets

    SciTech Connect

    Krasnokutski, Serge A.; Huisken, Friedrich

    2015-02-28

    Resonant two-photon ionization (R2PI) spectroscopy has been applied to investigate the solvation of Al atoms in helium droplets. The R2PI spectra reveal vibrational progressions that can be attributed to Al–He{sub n} vibrations. It is found that small helium droplets have very little chance to pick up an aluminum atom after collision. However, the pick-up probability increases with the size of the helium droplets. The absorption band that is measured by monitoring the ions on the mass of the Al dimer is found to be very little shifted with respect to the Al monomer band (∼400 cm{sup −1}). However, using the same laser wavelength, we were unable to detect any Al{sub n} photoion with n larger than two.