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Sample records for abraham solvation equations

  1. Reduced-order Abraham-Lorentz-Dirac equation and the consistency of classical electromagnetism

    NASA Astrophysics Data System (ADS)

    Steane, Andrew M.

    2015-03-01

    It is widely believed that classical electromagnetism is either unphysical or inconsistent, owing to pathological behavior when self-force and radiation reaction are non-negligible. We argue that there is no inconsistency as long as it is recognized that certain types of charge distribution are simply impossible, such as, for example, a point particle with finite charge and finite inertia. This is owing to the fact that negative inertial mass is an unphysical concept in classical physics. It remains useful to obtain an equation of motion for small charged objects that describes their motion to good approximation without requiring knowledge of the charge distribution within the object. We give a simple method to achieve this, leading to a reduced-order form of the Abraham-Lorentz-Dirac equation, essentially as proposed by Eliezer, Landau, and Lifshitz and derived by Ford and O'Connell.

  2. Analysis of the Henderson-Abraham-Barker equation in the case of a polar liquid near a neutral hard wall

    NASA Astrophysics Data System (ADS)

    Badiali, J. P.; Russier, V.; Holovko, M. E.

    1993-11-01

    The physical content of the wall-particle direct correlation function cw(1), defined from the Ornstein-Zernike equation in the framework of the Henderson-Abraham-Barker approach, is analyzed in the case of a dipolar-hard-sphere fluid near a pure and dielectric neutral wall. The exact asymptotic behavior of cw(1) is established and we show that it is not related to simple physical concepts as, e.g., the image potential. We show that the exact Henderson-Abraham-Barker equation introduces some bridge diagrams which are more simple graphs in another approach. Due to this fact, at least for systems with long range interactions, it is misleading to use the usual closures of the theory of homogeneous liquids for cw(1). In the case of a dielectric wall, we emphasize that the diagrammatic structure of cw(1) requires the introduction of a three-body Mayer function. The dipolar-hard-sphere liquid is a good candidate for analyzing cw(1) because some exact results are known and related to simple electrostatic effects; however, the present results are not restricted to this system.

  3. Solvation!

    SciTech Connect

    Adamovic, Ivana

    2004-01-01

    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, C6 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 SN2 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- • Arn (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.

  4. 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.

  5. Abraham-Lorentz versus Landau-Lifshitz

    NASA Astrophysics Data System (ADS)

    Griffiths, David J.; Proctor, Thomas C.; Schroeter, Darrell F.

    2010-04-01

    The classical Abraham-Lorentz formula for the radiation reaction on a point charge suffers from two notorious defects: runaways and preacceleration. Recently, several authors have advocated as an alternative the Landau-Lifshitz formula, which has neither fault. The latter formula is often presented as an approximation to Abraham-Lorentz, raising the delicate question of how an approximation can be considered more accurate than the original. For a spherical shell of finite size, the equation for the radiation reaction is noncontroversial. We begin there, obtain the Abraham-Lorentz and Landau-Lifshitz expressions as limiting cases, and undertake some numerical studies to determine which is superior.

  6. 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.

  7. Abraham Colles: Colles' fracture.

    PubMed

    Ellis, Harold

    2012-08-01

    Every reader of this journal will be all too familiar with Colles' fracture; either seeing patients with it in A & E, helping with its reduction and splinting or being part of the anaesthetics team involved in its management. On an icy winter's day there might be half a dozen patients with this injury in your accident unit, mostly elderly ladies. Yet it was not until 1814 that Abraham Colles accurately described this injury and its treatment in his paper 'On the fracture of the carpal extremity of the radius', published in the Edinburgh Medical and Surgical Journal of that year.

  8. 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

  9. 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)

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

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

    PubMed

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

    2016-11-01

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

  13. [Salzburg 1908. Karl Abraham caught between Freud and Jung].

    PubMed

    van Schoonheten, Anna Bentinck

    2010-01-01

    The first psychoanalytic congress in Salzburg has often been described as a great success with one blemish: a conflict between Jung and Abraham, mainly caused by the rivalry in Abraham's behaviour. A new study of the material, and taking Abraham's perspective, provides a different view. Abraham, still a beginner in psychoanalysis, got in the way of Freud and Jung who at that time had a deep theoretical disagreement. In the end they both blamed Abraham.

  14. 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)

  15. 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…

  16. The Political Novels of Peter Abrahams

    ERIC Educational Resources Information Center

    Ogunghesan, Kolawole

    1973-01-01

    Abrahams' theme is the attempt of black men to regain their manhood and self-respect, which alone can help them to achieve true freedom in a world dominated by white men: how this is to be done is the subject of three novels, using three different political situations. (Author/JM)

  17. 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)…

  18. 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…

  19. Integral Equation Theory of Molecular Solvation Coupled with Quantum Mechanical/Molecular Mechanics Method in NWChem Package

    SciTech Connect

    Chuev, Gennady N.; Valiev, Marat; Fedotova, Marina V.

    2012-04-10

    We have developed a hybrid approach based on a combination of integral equation theory of molecular liquids and QM/MM methodology in NorthWest computational Chemistry (NWChem) software package. We have split the evaluations into conse- quent QM/MM and statistical mechanics calculations based on the one-dimensional reference interaction site model, which allows us to reduce signicantly the time of computation. The method complements QM/MM capabilities existing in the NWChem package. The accuracy of the presented method was tested through com- putation of water structure around several organic solutes and their hydration free energies. We have also evaluated the solvent effect on the conformational equilibria. The applicability and limitations of the developed approach are discussed.

  20. 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

  1. 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.

  2. [Karl Abraham, Freud's scapegoat and, guide to understanding the truth].

    PubMed

    Cremerius, J

    1997-01-01

    The history of the relationship between Freud and Abraham is characterized by the presence of third parties. There was always another, more favored one of Freud's disciples between Freud and Abraham. The first of these, from 1907 to 1912, was C.G. Jung. The second, fifteen years later, was Otto Rank. (I will omit Ferenczi, because his relationship with Freud only entered its dramatic final stage after Abraham's death.) Both Jung and Rank eventually showed signs of deviating from Freud's theories, and Abraham, as the guardian of those teachings, called attention to this. As a result, complicated triangles arose between Freud, Abraham and the favored son of the moment. Because of Freud's preference for these psychoanalytic sons, a preference of which he himself was not consciously aware, he resisted Abraham's attacks on them and felt them to be unfounded and destructive. Confusing cause with effect he blamed Abraham for the danger to the psychoanalytic movement which ensued from three conflicts. Freud loved and protected the apostates and made the defender of his theories into a scapegoat. When, however, the apostasy eventually became apparent, Freud renounced whoever was concerned and rehabilitated Abraham. However, until the final separation from the love object, Freud wavered between rejection and affection, hope and disappointment. Then, feeling deceived and betrayed, Freud's love turned to hate.

  3. 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

  4. Can the Abraham Light Momentum and Energy in a Medium Constitute a Lorentz Four-Vector?

    NASA Astrophysics Data System (ADS)

    Wang, Changbiao

    2013-08-01

    By analyzing the Einstein-box thought experiment with the principle of relativity, it is shown that Abraham's light momentum and energy in a medium cannot constitute a Lorentz four-vector, and they consequentially break global momentum and energy conservation laws. In contrast, Minkowski's momentum and energy always constitute a Lorentz four-vector no matter whether in a medium or in vacuum, and the Minkowski's momentum is the unique correct light momentum. A momentum-associated photon mass in a medium is exposed, which explains why only the Abraham's momentum is derived in the traditional "center-of-mass-energy" approach. The EM boundary-condition matching approach, combined with Einstein light-quantum hypothesis, is proposed to analyze this thought experiment, and it is found for the first time that only from Maxwell equations without resort to the relativity, the correctness of light momentum definitions cannot be identified. Optical pulling effect is studied as well.

  5. Parameter optimization in differential geometry based solvation models

    PubMed Central

    Wang, Bao; Wei, G. W.

    2015-01-01

    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

  6. Abraham Colles and his contributions to anatomy.

    PubMed

    Shayota, Brian J; Oelhafen, Kim; Shoja, Mohammadali; Tubbs, R Shane; Loukas, Marios

    2014-07-01

    Abraham Colles is known among the medical community for his detailed description of Colles' fracture, one of the most common occurring skeletal injuries. It is remarkable that something as seemingly simple as the diagnosis of Colles' fracture had not been established until nearly 200 years ago. While that may have been his most well known accomplishment, Colles made several other contributions to medicine across multiple fields of practice. In the field of anatomy, he is also credited for his discovery and description of Colles' fascia and Colles' ligament. Less commonly known, however, are his clinical observations and offered treatment regimens for syphilis, as well as his achievement in performing the first surgery for axillary artery aneurysm. The current paper will review the life and contributions of this early surgeon and anatomist.

  7. 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…

  8. 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.

  9. 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.

  10. 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.

  11. 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...

  12. Macroscopic model for solvated ion dynamics

    NASA Astrophysics Data System (ADS)

    Chen, J.-H.; Adelman, S. A.

    1980-02-01

    A macroscopic treatment of solvated ion dynamics is developed and applied to calculate the limiting (zero concentration) conductance of cations in several aprotic solvents. The theory is based on a coupled set of electrostatic and hydrodynamic equations for the density, flow, and polarization fields induced in the polar solvent by a moving ion. These equations, which are derived by the Mori projection technique, include crucial local solvent structure (ion solvation) effects through solvent compressibility, and local constitutive parameters. If solvent structure is suppressed, the equations reduce to those derived previously by Onsager and Hubbard [J. B. Hubbard and L. Onsager, J. Chem. Phys. 67, 4850 (1977)]. The macroscopic equations are approximately decoupled into electrostatic and hydrodynamic parts. The decoupled equations are solved assuming a step density, viscosity, and dielectric constant model for the local solvent structure and dynamics. This yields analytic expressions for the viscous, ζV, and dielectric ζD, contributions to the ion friction coefficient. These expressions generalize, respectively, the Stokes and Zwanzig results for the (slip) viscous and dielectric friction so as to account for ion solvation effects. The friction coefficients involve a desolvation function Δ which depends on the local structure (density) and dynamics of the solvent. The drag coefficient results reduce in form to those of Zwanzig (within a flow gradient correction factor of 2/3) and Stokes for both weak (Δ→1) and strong (Δ→0) ion-solvent interaction. For Δ→1 the true ionic radius Ri appears in the drag formulas while for Δ→0 a renormalized solvated ion radius σ=Ri+2Rs (where Rs=solvent molecule radius) appears. The theory is fit to experimental cation conductances in pyridine, acetone, and acetonitrile by representing Δ by a two parameter switching function. Agreement between the model and experiment is satisfactory for all three solvents. Moreover

  13. 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…

  14. "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…

  15. Differential geometry based solvation model. III. Quantum formulation.

    PubMed

    Chen, Zhan; Wei, Guo-Wei

    2011-11-21

    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. Resolution of the Abraham-Minkowski debate: Implications for the electromagnetic wave theory of light in matter

    NASA Astrophysics Data System (ADS)

    Kemp, B. A.

    2011-06-01

    A century has now passed since the origins of the Abraham-Minkowski controversy pertaining to the correct form of optical momentum in media. Experiment and theory have been applied at both the classical and quantum levels in attempt to resolve the debate. The result of these efforts is the identification of Abraham's kinetic momentum as being responsible for the overall center of mass translations of a medium and Minkowski's canonical or wave momentum as being responsible for translations within or with respect to a medium. In spite of the recent theoretical developments, much confusion still exists regarding the appropriate theory required to predict experimental outcomes and to develop new applications. In this paper, the resolution of the longstanding Abraham-Minkowski controversy is reviewed. The resolution is presented using classical electromagnetic theory and logical interpretation of experiments disseminated over the previous century. Emphasis is placed on applied physics applications: modeling optical manipulation of cells and particles. Although the basic interpretation of optical momentum has been resolved, there is still some uncertainly regarding the complete form of the momentum continuity equation describing electromagnetics. Thus, while a complete picture of electrodynamics has still yet to be fully interpreted, this correspondence should help clarify the state-of-the-art view.

  17. Ultrafast underdamped solvation: Agreement between computer simulation and various theories of solvation dynamics

    NASA Astrophysics Data System (ADS)

    Roy, Srabani; Bagchi, Biman

    1993-07-01

    A theoretical analysis of the three currently popular microscopic theories of solvation dynamics, namely, the dynamic mean spherical approximation (DMSA), the molecular hydrodynamic theory (MHT), and the memory function theory (MFT) is carried out. It is shown that in the underdamped limit of momentum relaxation, all three theories lead to nearly identical results when the translational motions of both the solute ion and the solvent molecules are neglected. In this limit, the theoretical prediction is in almost perfect agreement with the computer simulation results of solvation dynamics in the model Stockmayer liquid. However, the situation changes significantly in the presence of the translational motion of the solvent molecules. In this case, DMSA breaks down but the other two theories correctly predict the acceleration of solvation in agreement with the simulation results. We find that the translational motion of a light solute ion can play an important role in its own solvation. None of the existing theories describe this aspect. A generalization of the extended hydrodynamic theory is presented which, for the first time, includes the contribution of solute motion towards its own solvation dynamics. The extended theory gives excellent agreement with the simulations where solute motion is allowed. It is further shown that in the absence of translation, the memory function theory of Fried and Mukamel can be recovered from the hydrodynamic equations if the wave vector dependent dissipative kernel in the hydrodynamic description is replaced by its long wavelength value. We suggest a convenient memory kernel which is superior to the limiting forms used in earlier descriptions. We also present an alternate, quite general, statistical mechanical expression for the time dependent solvation energy of an ion. This expression has remarkable similarity with that for the translational dielectric friction on a moving ion.

  18. Resolution of a Challenge for Solvation Modeling: Calculation of Dicarboxylic Acid Dissociation Constants Using Mixed Discrete-Continuum Solvation Models

    SciTech Connect

    Marenich, Aleksandr; Ding, Wendu; Cramer, Christopher J.; Truhlar, Donald G.

    2012-06-07

    First and second dissociation constants (pKa values) of oxalic acid, malonic acid, and adipic acid were computed by using a number of theoretical protocols based on density functional theory and using both continuum solvation models and mixed discrete-continuum solvation models. We show that fully implicit solvation models (in which the entire solvent is represented by a dielectric continuum) fail badly for dicarboxylic acids with mean unsigned errors averaged over six pKa values) of 2.4-9.0 log units, depending on the particular implicit model used. The use of water-solute clusters and accounting for multiple conformations in solution significantly improve the performance of both generalized Born solvation models and models that solve the nonhomogeneous dielectric Poisson equation for bulk electrostatics. The four most successful models have mean unsigned errors of only 0.6-0.8 log units.

  19. 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.

  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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    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 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

  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. Solvated dissipative electro-elastic network model of hydrated proteins.

    PubMed

    Martin, Daniel R; Matyushov, Dmitry V

    2012-10-28

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

  5. Solvation Energetics of Biomolecules

    NASA Astrophysics Data System (ADS)

    Williams, Evan

    2002-03-01

    The gas phase offers a unique environment in which to study the intrinsic structure and reactivity of molecules and ions. The intrinsic structure of a wide range of biomolecules, ranging from individual amino acids to large biomolecule complexes has been investigated. From differences observed between the gas phase and solution phase behavior, one can infer the role of solvent. Hydrated ions can be easily generated by electrospray ionization and stored in the cell of a Fourier-transform ion cyclotron resonance spectrometer. Water binding energies can be determined using blackbody infrared radiative dissociation (BIRD) and from these energies, structures can be inferred. For cationized valine, we show that the gas-phase complex exists as a charge-solvated structure. Addition of one water molecule does not change the structure or relative energy of this structure. However, the addition of three water molecules is sufficient to change valine in this complex into its solution phase zwitterionic structure. By studying such hydrated ions, one water molecule at a time, we hope that a detailed understanding of the role of water on biomolecule structure can be obtained.

  6. Domain decomposition for implicit solvation models.

    PubMed

    Cancès, Eric; Maday, Yvon; Stamm, Benjamin

    2013-08-07

    This article is the first of a series of papers dealing with domain decomposition algorithms for implicit solvent models. We show that, in the framework of the COSMO model, with van der Waals molecular cavities and classical charge distributions, the electrostatic energy contribution to the solvation energy, usually computed by solving an integral equation on the whole surface of the molecular cavity, can be computed more efficiently by using an integral equation formulation of Schwarz's domain decomposition method for boundary value problems. In addition, the so-obtained potential energy surface is smooth, which is a critical property to perform geometry optimization and molecular dynamics simulations. The purpose of this first article is to detail the methodology, set up the theoretical foundations of the approach, and study the accuracies and convergence rates of the resulting algorithms. The full efficiency of the method and its applicability to large molecular systems of biological interest is demonstrated elsewhere.

  7. Reactivity of transition metal solvates

    NASA Astrophysics Data System (ADS)

    Berezin, Boris D.

    1991-09-01

    Reactivity data are generalised for one of the most important classes of complexes, solvates, which are quantitatively nearly unstudied. Various approaches to studying and describing the reactivity are compared with respect to solvation of the reagents and the transition state. The specifics and mechanism of ligand substitution in pure and mixed organic solvents are found. The reactivity of simple (homoleptic) and mixed solvates toward macrocycles is examined in detail using porphyrins as an example. The kinetic method of indicator reactions is applied to porphyrins in order to study the state of transition metal salts in organic solvents and the stability of the coordination spheres of acidosalts (MXnn-2), acidosolvates (MX2Sn-2) and their transition states. The concentration dependence of the rate constant of an indicator reaction is demonstrated to be due to a change in the inner coordination sphere and a shift of equilibria between the various coordination complexes. The bibliography includes 38 references.

  8. Flecainide acetate acetic acid solvates.

    PubMed

    Veldre, Kaspars; Actiņs, Andris; Eglite, Zane

    2011-02-01

    Flecainide acetate forms acetic acid solvates with 0.5 and 2 acetic acid molecules. Powder X-ray diffraction, differential thermal analysis/thermogravimetric, infrared, and potentiometric titration were used to determine the composition of solvates. Flecainide acetate hemisolvate with acetic acid decomposes to form a new crystalline form of flecainide acetate. This form is less stable than the already known polymorphic form at all temperatures, and it is formed due to kinetic reasons. Both flecainide acetate nonsolvated and flecainide acetate hemisolvate forms crystallize in monoclinic crystals, but flecainide triacetate forms triclinic crystals. Solvate formation was not observed when flecainide base was treated with formic acid, propanoic acid, and butanoic acid. Only nonsolvated flecainide salts were obtained in these experiments.

  9. 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

  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. 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

  12. 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

    NASA Astrophysics Data System (ADS)

    Omelyan, Igor; Kovalenko, Andriy

    2013-12-01

    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

  13. Preparation of cerium halide solvate complexes

    SciTech Connect

    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.

  14. 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)

  15. 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.

  16. Incorporating the excluded solvent volume and surface charges for computing solvation free energy.

    PubMed

    Yang, Pei-Kun

    2014-01-05

    Gauss's law or Poisson's equation is conventionally used to calculate solvation free energy. However, the near-solute dielectric polarization from Gauss's law or Poisson's equation differs from that obtained from molecular dynamics (MD) simulations. To mimic the near-solute dielectric polarization from MD simulations, the first-shell water was treated as two layers of surface charges, the densities of which are proportional to the electric field at the solvent molecule that is modeled as a hard sphere. The intermediate water was treated as a bulk solvent. An equation describing the solvation free energy of ions using this solvent scheme was derived using the TIP3P water model.

  17. 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.

  18. 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

  19. Ponderomotive forces in electrodynamics of moving media: The Minkowski and Abraham approaches

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    In the general setting of the problem, the explicit compact formulae are derived for the ponderomotive forces in the macroscopic electrodynamics of moving media in the Minkowski and Abraham approaches. Taking account of the Minkowski constitutive relations and making use of a special representation for the Abraham energy-momentum tensor enable one to obtain a compact expression for the Abraham force in the case of arbitrary dependence of the medium velocity on spatial coordinates and the time and for nonstationary external electromagnetic field. We term the difference between the ponderomotive forces in the Abraham and Minkowski approaches as the Abraham force not only under consideration of media at rest but also in the case of moving media. The Lorentz force is found which is exerted by external electromagnetic field on the conduction current in a medium, the covariant Ohm law, and the constitutive Minkowski relations being taken into account. The physical argumentation is traced for the definition of the 4-vector of the ponderomotive force as the 4-divergence of the energy-momentum tensor of electromagnetic field in a medium.

  20. 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...

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

    SciTech Connect

    Odake, Satoru; Sasaki, Ryu

    2013-10-15

    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.

  2. 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…

  3. Solvation and electrostatic model for specific electrolyte adsorption

    NASA Astrophysics Data System (ADS)

    Sahai, Nita; Sverjensky, Dimitri A.

    1997-07-01

    A solvation and electrostatic model has been developed for estimating electrolyte adsorption from physical and chemical properties of the system, consistent with the triple-layer model. The model is calibrated on experimental surface titration data for ten oxides and hydroxides in ten electrolytes over a range of ionic strengths from 0.001 M-2.9 M (Sahai and Sverjensky, 1997a). The model assumes the presence of a single type of surface site, >SOH. It is proposed that for a 1:1 electrolyte of the type M +L -, the logarithms of the adsorption constants ( Ks,M +and Ks,L -) representing the equilibria > SO- + Maq+ = > SO- - M+and> SOH2+ + Laq- = > SOH2+ - L- contain contributions from an ion-intrinsic component and a solvation component. According to Born solvation theory, log Ks,M + and log Ks, L - can be linearly correlated with inverse dielectric constant of the k-th mineral ( 1/ɛ k) resulting in the equations log K s,M + = - δω M +/2.303 RT1/ɛ k + log Kii,M+″and log K s,L - = - δω L -/2.303 RT1/ɛ k + log K ii,L +″ The ion-intrinsic part (log Kii ″) is a linear function of the inverse electrostatic radius ( 1/r e,j ) of the j-th aqueous ion, where, in general, j = M + or L -. The interfacial solvation coefficient ( Δ, Ω j) associated with the solvation component is linearly related to the inverse effective radius ( 1/R e,j ) of the adsorbed ion and to the charge ( Zj) on the ion. The model is consistent with surface protonation constants ( Ks,1and Ks,2) calculated from experimental points of zero charge and values of ΔpK predicted from the Pauling bond-strength per unit bond-length ( s/r >S-OH) of the bulk mineral (Sahai and Sverjensky, 1997a), site-densities ( Ns) from isotopic-exchange data, and outer-layer capacitance (C 2) equal to 0.2 F m -2. As a first approximation, we also find an empirical trend between capacitance (C 1) of the inner-layer and 1/(r e,ML·ω ML) where re,ML is the electrostatic radius and ω ML is the solvation coefficient of

  4. 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

  5. A continuum theory of solvation in quadrupolar solvents. I. Formulation

    NASA Astrophysics Data System (ADS)

    Jeon, Jonggu; Kim, Hyung J.

    2003-10-01

    A continuum theory to describe equilibrium and nonequilibrium solvation in polarizable, nondipolar, quadrupolar solvents is developed. By employing the densities of the solvent quadrupole and induced dipole moments as primary field variables, a reaction field theory formulation for quadrupolar solvents is constructed with account of their electronic polarizability. Nonequilibrium solvation aspects are effected via the solvent coordinate description for the quadrupole moment density. It is found that the theory is consistent with the macroscopic Maxwell equations and satisfies the continuity of the electric potential across the cavity boundaries. Solvation stabilization arising from the solvent quadrupoles is captured via novel reaction field factors analogous to those for dipolar solvents. Comparison is made with the dielectric continuum description of the polarizable, dipolar solvents as well as with previous theories of the quadrupolar solvents. Extensions and applications of the current theoretical formulation to study free energetics and dynamics of reactive and spectroscopic processes in the quadrupolar solvents are reported in the following paper [J. Jeon and H. J. Kim, J. Chem. Phys. 119, 8626 (2003)].

  6. 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

  7. Differential geometry based solvation model I: Eulerian formulation

    PubMed Central

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

    2010-01-01

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

  8. 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…

  9. Abraham's discovery of the 'bad mother'. A contribution to the history of the theory of depression.

    PubMed

    May, U

    2001-04-01

    The author shows how, after Freud struggled in vain from the 1890s to develop a theory of depression, Abraham succeeded for the first time in finding an approach to the understanding of depression a few years before the publication of Freud's 'Mourning and melancholia'. It is contained in his study of the painter Giovanni Segantini (1911), which also includes a description, imbued with a new atmospheric quality, of the mother-son relationship that centres on the concept of the 'bad mother'. The author points out that Abraham's 'good/bad' dimension is effectively absent from Freud's published work up to 1911 and is also at variance with his view of the relationship between son and mother. In later contributions, too, Abraham maintained that unconscious hate directed at the mother, who is experienced as 'bad' but longed for as 'good', was a central factor in the aetiology of depression, a view he had to defend vis-à-vis Freud. The author contends that in the Segantini paper Abraham was describing an inner world similar to that evinced by the work of Melanie Klein and significantly different from Freud's. It is characterised by hate, revenge, death wishes and guilt feelings on the one hand and tranquillity and inner peace on the other.

  10. 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…

  11. 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,…

  12. 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…

  13. 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)

  14. Paul Abraham: A Forgotten Scholar of the Prussian Academy of Sciences and Humanities

    ERIC Educational Resources Information Center

    Thiel, Jens

    2004-01-01

    Paul Abraham, one of the Berlin Academy's most experienced researchers, was deported to Auschwitz in 1943. The fate of this Jewish scholar reveals much about the inner life of the Academy, and its treatment of Jewish staff, during the World War II. This paper describes his life, against a backdrop of war, revolution, and dictatorship, and in the…

  15. 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…

  16. A two-dimensional-reference interaction site model theory for solvation structure near solid-liquid interface.

    PubMed

    Iida, Kenji; Sato, Hirofumi

    2011-12-28

    We develop a new equation to describe solvation structure near solid-liquid interface at the atomic-level. The developed equation focuses on anisotropy of solvation structure near the interface by using two-dimensional density distribution of solvent along two directions, one of which is perpendicular to the interface and the other is parallel to the interface. As a first application of the equation, we treat a system where a solid modeled by an atomistic wall is immersed in solvent water. The preferential adsorption position of water molecules and the change of water orientation by charging the wall are discussed.

  17. Anion Solvation in Carbonate-Based Electrolytes

    SciTech Connect

    von Wald Cresce, Arthur; Gobet, Mallory; Borodin, Oleg; Peng, Jing; Russell, Selena M.; Wikner, Emily; Fu, Adele; Hu, Libo; Lee, Hung-Sui; Zhang, Zhengcheng; Yang, Xiao-Qing; Greenbaum, Steven; Amine, Khalil; Xu, Kang

    2015-11-16

    The correlation between Li+ solvation and interphasial chemistry on anodes firmly established in Li-ion batteries, the effect of cation–solvent interaction has gone beyond bulk thermodynamic and transport properties and become an essential element that determines the reversibility of electrochemistry and kinetics of Li-ion intercalation chemistries. Now, most studies are dedicated to the solvation of Li+, and the solvation of anions in carbonate-based electrolytes and its possible effect on the electrochemical stability of such electrolytes remains little understood. Moreover, as a mirror effort to prior Li+ solvation studies, this work focuses on the interactions between carbonate-based solvents 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.

  18. Anion Solvation in Carbonate-Based Electrolytes

    DOE PAGES

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

    2015-11-16

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

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

    PubMed

    Nguyen, Duc D; Wei, Guo-Wei

    2017-01-05

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

  20. Measurement of the Abraham force and its predicted QED corrections in crossed electric and magnetic fields.

    PubMed

    Rikken, G L J A; van Tiggelen, B A

    2011-10-21

    We report the observation by a new method of mechanical momentum transferred to gas phase atoms and molecules upon application of crossed oscillating electric and static magnetic fields. We identify this momentum as the microscopic analogue of the classical Abraham force. Two QED predictions of additional magnetoelectrically induced mechanical momentum are addressed. One of them is experimentally refuted; the other is found to be currently below our experimental detection.

  1. 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

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

    SciTech Connect

    Wei, Guowei; Baker, Nathan A.

    2016-11-11

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

  3. 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.

  4. Solvation and Reaction in Ionic Liquids

    SciTech Connect

    Maroncelli, Mark

    2010-10-15

    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.

  5. 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.)

  6. Retrapping and solvation dynamics after femtosecond UV excitation of the solvated electron in water

    NASA Astrophysics Data System (ADS)

    Assel, M.; Laenen, R.; Laubereau, A.

    1999-10-01

    We report on a novel investigation of the solvated electron with excitation into the continuum band. The subsequent localization process of quasifree electrons in neat water is studied by femtosecond probe spectroscopy in the spectral range between 580 nm and 990 nm. Excitation is achieved by a pump pulse at 310 nm promoting equilibrated solvated electrons to well-defined levels in the continuum band approximately 0.7 eV above the band edge. The subsequent retrapping and solvation of the electron occurs via two observed intermediates with time constants of τ2=300±50 fs and τs=1.0±0.2 ps. The absorption bands of the two intermediates are derived by the help of a 4-level energy scheme. Comparison with investigations of the solvated electron after excitation with 2 eV visible pulses gives strong evidence that the second intermediate in the UV-excitation experiment is identical to the modified ground state s″ occupied after excitation in the visible. The present study with excitation of the solvated electrons to continuum states sheds also new light on the generation process of localized electrons in neat water. Our data present strong evidence that the so-called "wet electron" is the solvated electron in a modified, hot ground state.

  7. Analysis of the Nucleophilic Solvation Effects in Isopropyl Chlorothioformate Solvolysis

    PubMed Central

    D’Souza, Malcolm J.; Mahon, Brian P.; Kevill, Dennis N.

    2010-01-01

    Correlation of the solvent effects through application of the extended Grunwald-Winstein equation to the solvolysis of isopropyl chlorothioformate results in a sensitivity value of 0.38 towards changes in solvent nucleophilicity (l) and a sensitivity value of 0.72 towards changes in solvent ionizing power (m). This tangible l value coupled with the negative entropies of activation observed indicates a favorable predisposition towards a modest rear-side nucleophilic solvation of a developing carbocation. Only in 100% ethanol was the bimolecular pathway dominant. These observations are very different from those obtained for the solvolysis of isopropyl chloroformate, where dual reaction channels were proposed, with the addition-elimination reaction favored in the more nucleophilic solvents and a unimolecular fragmentation-ionization mechanism favored in the highly ionizing solvents. PMID:20717524

  8. [Karl Abraham's revolution. From sensual sucking to oral-aggressive destruction wishes].

    PubMed

    May, Ulrike

    2010-01-01

    The author argues that Abraham's paper on "The first pregenital stage of the libido" (1916-17) expounds a new conception of orality, i. e. the idea of a purposeful oral aggression directed against an object. This conception is shown to be contrary to Freud's view of orality as elaborated in his Three Essays as well as in other writings of late 1914 and early 1915. It ignores fundamental dimensions of Freud's thinking, namely the difference between autoerotism/narcissism and object love on the one hand and between libido and aggression on the other, thus representing a basic theoretical change that also had consequences for analytical practice.

  9. Relativistic Dynamics of a Charged Sphere: Updating the Lorentz-Abraham Model

    DTIC Science & Technology

    1992-02-01

    and is approved for publication. APPROVED: V Y~t C w ROBERT V. McGAHAN, Chief Applied Electromagnetics Division FOR THE COMMANDER: d JOHN K. SCHINDLER...Abraham derivation reveals that the self electromagnetic force must be modified during the short time interval after the external force is first applied ...Newton’s secondI law of mot ion. arid Lu"Ist em’s mt ass-energy relation. (The latter twvo laws of phyisics were( not dIiscoveredI until after t lie

  10. Molecular density functional theory: application to solvation and electron-transfer thermodynamics in polar solvents.

    PubMed

    Borgis, Daniel; Gendre, Lionel; Ramirez, Rosa

    2012-03-01

    A molecular density functional theory of solvation is presented. The solvation properties of an arbitrary solute in a given solvent, both described by a molecular force field, can be obtained by minimization of a position- and orientation-dependent free-energy density functional. In the homogeneous reference fluid approximation, the unknown excess term of the functional can be approximated by the angular-dependent direct correlation function of the pure solvent. This function can be extracted from a preliminary MD simulation of the pure solvent by computing the angular-dependent pair distribution function and solving subsequently the molecular Ornstein-Zernike equation. The corresponding functional can then be minimized on a three-dimensional cubic grid for positions and a Gauss-Legendre angular grid for orientations to provide the solvation free energy of embedded molecules at the same time as the solvent three-dimensional microscopic structure. This functional minimization procedure is much more efficient than direct molecular dynamics simulations combined with thermodynamic integration schemes. The approach is shown to be also pertinent to the molecular-level determination of electron-transfer properties such as reaction free energy and reorganization energy. It is illustrated for molecular solvation and photochemical electron-transfer reactions in acetonitrile, a prototypical polar aprotic solvent.

  11. 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.

  12. Electron trapping in polar-solvated zeolites.

    PubMed

    Ellison, Eric H

    2005-11-03

    Of current interest in our laboratory is the nature of photoinduced processes in the cavities of zeolites completely submerged in polar solvents, or polar-solvated zeolites (PSZ). The present study addresses the nature of electron trapping in PSZ with emphasis on the zeolites NaX and NaY. Free electrons were generated by two-photon, pulsed-laser excitation of either pyrene or naphthalene included in zeolite cavities. Trapped electrons were monitored by diffuse transmittance, transient absorption spectroscopy at visible wavelengths. In anhydrous alcohols, electron trapping by Na(4)(4+) ion clusters was observed in both NaX and NaY. The resulting trapped electrons decayed over the course of tens of milliseconds. No evidence for alcohol-solvated electrons was found. More varied results were observed in solvents containing water. In NaX submerged in CH(3)OH containing 5% or higher water, species having microsecond lifetimes characteristic of solvated electrons were observed. By contrast, a 2 h exposure of NaY to 95/5 CH(3)OH/H(2)O had no effect on electron trapping relative to anhydrous CH(3)OH. The difference between NaX and NaY was explained by how fast water migrates into the sodalite cage. Prolonged exposure to water at room temperature or exposure to water at elevated temperatures was necessary to place water in the sodalite cages of NaY and deactivate Na(4)(4+) as an electron trap. Additional studies in NaY revealed that solvent clusters eventually become lower energy traps than Na(4)(4+) as the water content in methanol increases. In acetonitrile-water mixtures, electron trapping by Na(4)(4+) was eliminated and no equivalent species characteristic of solvated electrons in methanol-water mixtures was observed. This result was explained by the formation of low energy solvated electrons which cannot be observed in the visible region of the spectrum. Measurements of the rate of O(2) quenching in anhydrous solvents revealed rate constants for the quenching of ion

  13. Graphene Oxide Demonstrates Experimental Confirmation of Abraham Pressure on Solid Surface.

    PubMed

    Kundu, Anirban; Rani, Renu; Hazra, Kiran S

    2017-02-13

    The century-old controversy over two contradicting theories on radiation pressure of light proposed by Abraham and Minkowski can come to an end if there is a direct method to measure the surface deformation of the target material due to momentum transfer of photons. Here we have investigated the effect of radiation pressure on the surface morphology of Graphene Oxide (GO) film, experienced due to low power focused laser irradiation. In-depth investigation has been carried out to probe the bending of the GO surface due to radiation pressure by Atomic Force Microscopy (AFM) and subsequently the uniaxial strain induced on the GO film has been probed by Raman Spectroscopy. Our results show GO film experience an inward pressure due to laser radiation resulting in inward bending of the surface, which is consistent with the Abraham theory. The bending diameter and depth of the irradiated spot show linear dependence with the laser power while an abrupt change in depth and diameter of the irradiated spot is observed at the breaking point. Such abrupt change in depth is attributed to the thinning of the GO film by laser irradiation.

  14. Sir Edward Abraham's contribution to the development of the cephalosporins: a reassessment.

    PubMed

    Hamilton-Miller, J M

    2000-08-01

    This paper is based on an invited lecture given at the 21st International Congress of Chemotherapy in July 1999, as part of a Symposium entitled '50 years of cephalosporins: their use the next 50 years', (Hamilton-Miller JMT, Cephalosporins: from mould to drug. Sardinia to Oxford and beyond, J Antimicr Chemother 1999;44(A):26). Celebration of this Golden Anniversary was made more poignant by the death of the last major participant, Sir Edward Abraham, in May 1999. This history has been told before, but mainly by Sir Edward, who being a very modest man (to which his obituaries graphically attest) consistently underplayed the role that he and Newton had in the discovery of cephalosporin C, that led to all the cephalosporins now in use. I had the privilege of working at the Dunn School from 1967 to 1970, with Abraham and Newton, where I met Brotzu, Florey and Dorothy Hodgkin, all of whom had important roles in this story. Other workers at the Dunn School at that time, e.g. Heatley, Sanders and Jennings (who became Lady Florey), helped develop penicillin. Such a galaxy of stars of the antibiotic firmament will never again be assembled. "Let us now praise famous men... these were honoured in their generation, and were the glory of their times" - Ecclesiasticus XLIV. vv 1.7.

  15. Graphene Oxide Demonstrates Experimental Confirmation of Abraham Pressure on Solid Surface

    PubMed Central

    Kundu, Anirban; Rani, Renu; Hazra, Kiran S.

    2017-01-01

    The century-old controversy over two contradicting theories on radiation pressure of light proposed by Abraham and Minkowski can come to an end if there is a direct method to measure the surface deformation of the target material due to momentum transfer of photons. Here we have investigated the effect of radiation pressure on the surface morphology of Graphene Oxide (GO) film, experienced due to low power focused laser irradiation. In-depth investigation has been carried out to probe the bending of the GO surface due to radiation pressure by Atomic Force Microscopy (AFM) and subsequently the uniaxial strain induced on the GO film has been probed by Raman Spectroscopy. Our results show GO film experience an inward pressure due to laser radiation resulting in inward bending of the surface, which is consistent with the Abraham theory. The bending diameter and depth of the irradiated spot show linear dependence with the laser power while an abrupt change in depth and diameter of the irradiated spot is observed at the breaking point. Such abrupt change in depth is attributed to the thinning of the GO film by laser irradiation. PMID:28211901

  16. Graphene Oxide Demonstrates Experimental Confirmation of Abraham Pressure on Solid Surface

    NASA Astrophysics Data System (ADS)

    Kundu, Anirban; Rani, Renu; Hazra, Kiran S.

    2017-02-01

    The century-old controversy over two contradicting theories on radiation pressure of light proposed by Abraham and Minkowski can come to an end if there is a direct method to measure the surface deformation of the target material due to momentum transfer of photons. Here we have investigated the effect of radiation pressure on the surface morphology of Graphene Oxide (GO) film, experienced due to low power focused laser irradiation. In-depth investigation has been carried out to probe the bending of the GO surface due to radiation pressure by Atomic Force Microscopy (AFM) and subsequently the uniaxial strain induced on the GO film has been probed by Raman Spectroscopy. Our results show GO film experience an inward pressure due to laser radiation resulting in inward bending of the surface, which is consistent with the Abraham theory. The bending diameter and depth of the irradiated spot show linear dependence with the laser power while an abrupt change in depth and diameter of the irradiated spot is observed at the breaking point. Such abrupt change in depth is attributed to the thinning of the GO film by laser irradiation.

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

    NASA Astrophysics Data System (ADS)

    Yang, Pei-Kun

    2014-10-01

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

  18. Preferential Solvation of an Asymmetric Redox Molecule

    SciTech Connect

    Han, Kee Sung; Rajput, Nav Nidhi; Vijayakumar, M.; Wei, Xiaoliang; Wang, Wei; Hu, Jianzhi; Persson, Kristin A.; Mueller, Karl T.

    2016-12-15

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

  19. 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

  20. 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

  1. 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

  2. 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…

  3. Thermochemistry of solvation: A self-consistent three-dimensional reference interaction site model approach

    NASA Astrophysics Data System (ADS)

    Kovalenko, Andriy; Truong, Thanh N.

    2000-11-01

    We developed a self-consistent three-dimensional reference interaction site model integral equation theory with the molecular hypernetted chain closure (SC-3D-RISM/HNC) for studying thermochemistry of solvation of ionic solutes in a polar molecular solvent. It is free from the inconsistency in the positions of the ion-solvent site distribution peaks, peculiar to the conventional RISM/HNC approach and improves the predictions for the solvation thermodynamics. The SC-3D-RISM treatment can be readily generalized to the case of finite ionic concentrations, including the consistent dielectric corrections to provide a consistent description of the dielectric properties of ion-molecular solution. The proposed theory is tested for hydration of the Na+ and Cl- ions in ambient water at infinite dilution. An improved agreement of the ion hydration structure and thermodynamics with molecular simulation results is found as compared to the conventional RISM/HNC treatment.

  4. Quantum mechanical continuum solvation models for ionic liquids.

    PubMed

    Bernales, Varinia S; Marenich, Aleksandr V; Contreras, Renato; Cramer, Christopher J; Truhlar, Donald G

    2012-08-02

    The quantum mechanical SMD continuum universal solvation model can be applied to predict the free energy of solvation of any solute in any solvent following specification of various macroscopic solvent parameters. For three ionic liquids where these descriptors are readily available, the SMD solvation model exhibits a mean unsigned error of 0.48 kcal/mol for 93 solvation free energies of neutral solutes and a mean unsigned error of 1.10 kcal/mol for 148 water-to-IL transfer free energies. Because the necessary solvent parameters are not always available for a given ionic liquid, we determine average values for a set of ionic liquids over which measurements have been made in order to define a generic ionic liquid solvation model, SMD-GIL. Considering 11 different ionic liquids, the SMD-GIL solvation model exhibits a mean unsigned error of 0.43 kcal/mol for 344 solvation free energies of neutral solutes and a mean unsigned error of 0.61 kcal/mol for 431 water-to-IL transfer free energies. As these errors are similar in magnitude to those typically observed when applying continuum solvation models to ordinary liquids, we conclude that the SMD universal solvation model may be applied to ionic liquids as well as ordinary liquids.

  5. Predicting solvent-water partitioning of charged organic species using quantum-chemically estimated Abraham pp-LFER solute parameters.

    PubMed

    Davis, Craig Warren; Di Toro, Dominic M

    2016-12-01

    Methods for obtaining accurate predictions of solvent-water partitioning for neutral organic chemicals (e.g., Kow) are well-established. However, methods that provide comparable accuracy are not available for predicting the solvent-water partitioning of ionic species. Previous methods for addressing charge contributions to solvent-water partitioning rely on charged solute descriptors which are obtained from regressions to neutral species descriptors as well as charged descriptors which are specific to unique charge-functionalities and structural moieties. This paper presents a method for obtaining Abraham poly-parameter linear free energy relationship (pp-LFER) descriptors using quantum chemical calculations and molecular structure, only. The method utilizes a large number of solvent-water systems to overcome large errors in individual quantum chemical computations of ionic solvent-water partition coefficients. The result is a single set of quantum-chemically estimated Abraham solute parameters (QCAP) which are solvent-independent, and can be used to predict the solvent-water partitioning of ionic species. Predictions of solvent-water partition coefficients for ionic species using quantum-chemically estimated Abraham parameters (QCAPs) are shown to provide improved accuracy compared over both existing Absolv-estimated Abraham solute parameters (AAP) as well as direct a priori quantum chemical (QC) calculations for partitioning of anionic solutes in 4 organic solvent-water systems (RMS = 0.740, 2.48 and 0.426 for the Absolv, QC and QCAP methods, respectively). For quaternary amine cations in the octanol-water system the RMS errors of the solvent-water partition coefficients were larger and similar between the two Abraham models (RMSE = 0.997 and 1.16, for the AAP and QCAP methods, respectively). Both methods showed significant improvement over direct QC calculations (RMSE = 2.82).

  6. Momentum Exchange between Light and a Single Atom: Abraham or Minkowski?

    PubMed

    Hinds, E A; Barnett, Stephen M

    2009-02-06

    We consider forces on an atom due to a plane-wave light pulse. The standard view of the optical dipole force indicates that red-detuned light should attract the atom towards high intensity. While the atom is inside the pulse, this would increase the average momentum per photon from p_{0} to p_{0}n, where n is the average refractive index due to the presence of the atom. We show, however, that this is the wrong conclusion and that the dispersive forces repel the atom from the light in this particular case, giving the photons a momentum p_{0}/n. This leads us to identify Abraham's optical momentum with the kinetic momentum transfer. The form due to Minkowski is similarly associated with the canonical momentum. We consider the possibility of demonstrating this in the laboratory, and we note an unexpected connection with the Aharonov-Casher effect.

  7. 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.

  8. 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…

  9. 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.

  10. Nonlinear Poisson equation for heterogeneous media.

    PubMed

    Hu, Langhua; Wei, Guo-Wei

    2012-08-22

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

  11. Nonlinear Poisson Equation for Heterogeneous Media

    PubMed Central

    Hu, Langhua; Wei, Guo-Wei

    2012-01-01

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

  12. KECSA-Movable Type Implicit Solvation Model (KMTISM).

    PubMed

    Zheng, Zheng; Wang, Ting; Li, Pengfei; Merz, Kenneth M

    2015-02-10

    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).

  13. 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

  14. Simulations of solvation free energies and solubilities in supercritical solvents

    NASA Astrophysics Data System (ADS)

    Su, Zemin; Maroncelli, Mark

    2006-04-01

    Computer simulations are used to study solvation free energies and solubilities in supercritical solvents. Solvation free energies are calculated using the particle insertion method. The equilibrium solvent configurations required for these calculations are based on molecular dynamics simulations employing model solvent potentials previously tuned to reproduce liquid-vapor coexistence properties of the fluids Xe, C2H6, CO2, and CHF3. Solutes are represented by all-atom potentials based on ab initio calculations and the OPLS-AA parameter set. Without any tuning of the intermolecular potentials, such calculations are found to reproduce the solvation free energies of a variety of typical solid solutes with an average accuracy of ±2kJ /mol. Further calculations on simple model solutes are also used to explore general aspects of solvation free energies in supercritical solvents. Comparisons of solutes in Lennard-Jones and hard-sphere representations of Xe show that solvation free energies and thus solubilities are not significantly influenced by solvent density fluctuations near the critical point. The solvation enthalpy and entropy do couple to these fluctuations and diverge similarly to solute partial molar volumes. Solvation free energies are also found to be little affected by the local density augmentation characteristic of the compressible regime. In contrast to solute-solvent interaction energies, which often provide a direct measure of local solvent densities, solvation free energies are remarkably insensitive to the presence of local density augmentation.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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.

  16. 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

  17. Solvation of polymers as mutual association. II. Basic thermodynamic properties

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

    The theory of equilibrium solvation of polymers B by a relatively low molar mass solvent A, developed in the simplest form in Paper I, is used to explore some essential trends in basic thermodynamic properties of solvated polymer solutions, such as the equilibrium concentrations of solvated polymers AiB and free solvent molecules A, the mass distribution φ _{{AiB}}(i) of solvated clusters, the extent of solvation of the polymer Φsolv, the solvation transition lines T_{solv}(φ _{{B}}o), the specific heat CV, the osmotic second virial coefficient B2, phase stability boundaries, and the critical temperatures associated with closed loop phase diagrams. We discuss the differences between the basic thermodynamic properties of solvated polymers and those derived previously for hierarchical mutual association processes involving the association of two different species A and B into AB complexes and the subsequent polymerization of these AB complexes into linear polymeric structures. The properties of solvated polymer solutions are also compared to those for solutions of polymers in a self-associating solvent. Closed loop phase diagrams for solvated polymer solutions arise in the theory from the competition between the associative and van der Waals interactions, a behavior also typical for dispersed molecular and nanoparticle species that strongly associate with the host fluid. Our analysis of the temperature dependence of the second osmotic virial coefficient reveals that the theory must be generalized to describe the association of multiple solvent molecules with each chain monomer, and this complex extension of the present model will be developed in subsequent papers aimed at a quantitative rather than qualitative treatment of solvated polymer solutions.

  18. The role of solvation in the binding selectivity of the L-type calcium channel.

    PubMed

    Boda, Dezső; Henderson, Douglas; Gillespie, Dirk

    2013-08-07

    We present grand canonical Monte Carlo simulation results for a reduced model of the L-type calcium channel. While charged residues of the protein amino acids in the selectivity filter are treated explicitly, most of the degrees of freedom (including the rest of the protein and the solvent) are represented by their dielectric response, i.e., dielectric continua. The new aspect of this paper is that the dielectric coefficient in the channel is different from that in the baths. The ions entering the channel, thus, cross a dielectric boundary at the entrance of the channel. Simulating this case has been made possible by our recent methodological development [D. Boda, D. Henderson, B. Eisenberg, and D. Gillespie, J. Chem. Phys. 135, 064105 (2011)]. Our main focus is on the effect of solvation energy (represented by the Born energy) on monovalent vs. divalent ion selectivity in the channel. We find no significant change in selectivity by changing the dielectric coefficient in the channel because the larger solvation penalty is counterbalanced by the enhanced Coulomb attraction inside the channel as soon as we use the Born radii (fitted to experimental hydration energies) to compute the solvation penalty from the Born equation.

  19. 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

  20. 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.

  1. Wave-particle interactions in a resonant system of photons and ion-solvated water

    NASA Astrophysics Data System (ADS)

    Konishi, Eiji

    2017-02-01

    We investigate a laser model for a resonant system of photons and ion cluster-solvated rotating water molecules in which ions in the cluster are identical and have very low, non-relativistic velocities and direction of motion parallel to a static electric field induced in a single direction. This model combines Dicke superradiation with wave-particle interaction. As the result, we find that the equations of motion of the system are expressed in terms of a conventional free electron laser system. This result leads to a mechanism for dynamical coherence, induced by collective instability in the wave-particle interaction.

  2. Dipole solvation in nondipolar solvents: Experimental studies of reorganization energies and solvation dynamics

    SciTech Connect

    Reynolds, L.; Gardecki, J.A.; Frankland, S.J.V.; Horng, M.L.; Maroncelli, M.

    1996-06-13

    Steady-state and time-resolved emission measurements of the solvatochromic probe coumarin 153 are used to study solvation of a dipolar solute in nondipolar solvents such as benzene and 1,4-dioxane. Contrary to the predictions of dielectric continuum theories, the Stokes shifts (or nuclear reorganization energies) that accompany electronic excitation of this solute are substantial in such solvents (nearly 1000 cm{sup -1}). The magnitudes of the shifts observed in both nondipolar and dipolar solvents can be consistently understood in terms of the relative strength of the interactions between the permanent charge distributions of the solute and solvent molecules. (Information concerning these charge distributions is derived from extensive ab initio calculations on the solute and 31 common solvents). The dynamics of solvation in nondipolar solvents, as reflected in the time dependence of the Stokes shifts, is qualitatively like that observed in polar solvents. But, whereas the dynamics in polar solvents can be rather simply modeled using the solvents dielectric response as empirical input, no simple theories of this sort are currently capable of predicting the solvation dynamics in nondipolar solvents 52 refs., 14 figs., 4 tabs.

  3. Nonperiodic boundary conditions for solvated systems.

    PubMed

    Petraglio, Gabriele; Ceccarelli, Matteo; Parrinello, Michele

    2005-07-22

    The simulation of charged and/or strongly polar solutes represents a challenge for standard molecular-dynamics techniques. The use of periodic boundary conditions (PBCs) leads to artifacts due to the interaction between two replicas in the presence of the long-range Coulomb forces. A way to avoid these problems is the use of nonperiodic boundary conditions. A possible realization is to consider a finite system, a sphere, embedded in a reaction field described by the method of the images. In the present work the modified image approximation has been implemented in a molecular-dynamics code and optimized for the use of two standard solvents, water and acetonitrile. The methodology has then been applied to investigate the conformational changes in water-solvated alanine dipeptide. The free-energy surface calculated with this method is comparable to that obtained with PBC.

  4. Application of the Mean Spherical Approximation to Describe the Entropy of Solvation of Spherical Ions in Polar Solvents

    DTIC Science & Technology

    1993-01-15

    the radius of the ion, and No, the Avogadro constant . The dimensionless parameter, ýi, which depends on the solvent and the ion, is given by 4i = rs...of infinite dilution, the MSA requires only two parameters to describe the Gibbs solvation energy, namely, the dielectric constant of the pure...the temperature derivatives of both the dielectric constant of the solvent and the polarization parameter, k. According to the Wertheim equation

  5. 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

  6. 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.

  7. [Abraham Horwitz (1910-2000): a Leading Man of Pan American Public Health].

    PubMed

    Jiménez de la Jara, Jorge

    2003-08-01

    The Chilean physician Abraham B Horwitz (1910-2000) was an outstanding personality of World and Pan American public health during the second half of the twentieth century. He was member of a family that, emigrating due to ethnic persecutions in Russia, took refuge in Chile. He became a relevant physician, a specialist in infectious diseases and public health. He was highly influential in the birth of the Public Health School at the University of Chile and the Chilean Health Service. He became Executive Director of the Pan American Health Organization, holding that position for 16 years. During this period, the institution experienced a great development. He stimulated research in the areas of basic sanitation, nutrition and eradication of transmissible diseases. He also opened unexplored areas such as the relation between economy, modern administration and health. During his last years, he chaired a successful Nutrition Committee at the United Nations. The most outstanding achievement of this Committee was the promotion of widespread vitamin A use. His intellectual and social deed is continued by The Pan American Foundation for Health and Education and this institution established an annual prize in his memory.

  8. 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.

  9. 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.

  10. Solvation of lithium ion in dimethoxyethane and propylene carbonate

    NASA Astrophysics Data System (ADS)

    Chaban, Vitaly

    2015-07-01

    Solvation of the lithium ion (Li+) in dimethoxyethane (DME) and propylene carbonate (PC) is of scientific significance and urgency in the context of lithium-ion batteries. I report PM7-MD simulations on the composition of Li+ solvation shells (SH) in a few DME/PC mixtures. The equimolar mixture features preferential solvation by PC, in agreement with classical MD studies. However, one DME molecule is always present in the first SH, supplementing the cage formed by five PC molecules. As PC molecules get removed, DME gradually substitutes vacant places. In the PC-poor mixtures, an entire SH is populated by five DME molecules.

  11. 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.

  12. Polar solvation dynamics in water and methanol: search for molecularity.

    PubMed

    Sajadi, Mohsen; Weinberger, Michael; Wagenknecht, Hans-Achim; Ernsting, Nikolaus P

    2011-10-21

    Time-dependent Stokes shifts (TDSS) were measured for diverse polarity probes in water, heavy water, methanol, and benzonitrile, by broadband fluorescence up-conversion with 85 fs time resolution. In water the spectral dynamics is solute-independent and quantitatively described by simple dielectric continuum theory of solvation. In methanol the slower part of the TDSS is solute-dependent. A correlation with anisotropy decay suggests that methanol solvation dynamics is modulated by orientational solute diffusion. An empirical power law which links the solvation relaxation function of a mobile solute to that of an immobile solute is experimentally verified. Activation energies for the average relaxation rate are also given. Solvation dynamics in H(2)O and D(2)O are identical at and above 20 °C but diverge below.

  13. Zero-point energy effects in anion solvation shells.

    PubMed

    Habershon, Scott

    2014-05-21

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

  14. Nonexponential Solvation Dynamics of Simple Liquids and Mixtures

    DTIC Science & Technology

    1991-05-06

    femto- solvent. One important point of view that has re- second (fwhm) instrument response function. ceived a lot of attention is the so-called Onsager ...population is negligibly small during the i7(t) during the solvation process in a single solvent %,aclength can be found for which the emission in- lar ...re- solxed in these expcriments. Unfortunately. molecu- lar dynamics calculations on solvation in water and methanol predict that there should be

  15. Photo-detrapping of solvated electrons in an ionic liquid

    NASA Astrophysics Data System (ADS)

    Takahashi, Kenji; Suda, Kayo; Seto, Takafumi; Katsumura, Yosuke; Katoh, Ryuzi; Crowell, Robert A.; Wishart, James F.

    2009-12-01

    We studied the dynamics of photo-detrapped solvated electrons in the ionic liquid trimethyl- N-propylammonium bis(trifluoromethanesulfonyl)imide (TMPA-TFSI) using laser flash photolysis. The solvated electrons were produced by the electron photodetachment from iodide via a 248 nm KrF excimer laser. The solvated electron decayed by first-order kinetics with a lifetime of about 240 ns. The spectrum of the solvated electron in the ionic liquid TMPA-TFSI is very broad with a peak around 1100 nm. After the 248 nm pulse, a 532 nm pulse was used to subsequently detrap the solvated electrons. After the detrapping pulse, quasi-permanent bleaching was observed. The relative magnitude of the bleaching in the solvated electron absorbance was measured from 500 to 1000 nm. The amount of bleaching depends on the probe wavelength. The fraction of bleached absorbance was larger at 500 nm than that at 1000 nm, suggesting that there are at least two species that absorb 532 nm light. We discuss the present results from viewpoint of the heterogeneity of ionic liquids.

  16. Perfusion calorimetry in the characterization of solvates forming isomorphic desolvates.

    PubMed

    Baronsky, Julia; Preu, Martina; Traeubel, Michael; Urbanetz, Nora Anne

    2011-09-18

    In this study, the potential of perfusion calorimetry in the characterization of solvates forming isomorphic desolvates was investigated. Perfusion calorimetry was used to expose different hydrates forming isomorphic desolvates (emodepside hydrates II-IV, erythromycin A dihydrate and spirapril hydrochloride monohydrate) to stepwise increasing relative vapour pressures (RVP) of water and methanol, respectively, while measuring thermal activity. Furthermore, the suitability of perfusion calorimetry to distinguish the transformation of a desolvate into an isomorphic solvate from the adsorption of solvent molecules to crystal surfaces as well as from solvate formation that is accompanied by structural rearrangement was investigated. Changes in the samples were confirmed using FT-Raman and FT-IR spectroscopy. Perfusion calorimetry indicates the transformation of a desolvate into an isomorphic solvate by a substantial exothermic, peak-shaped heat flow curve at low RVP which reflects the rapid incorporation of solvent molecules by the desolvate to fill the structural voids in the lattice. In contrast, adsorption of solvent molecules to crystal surfaces is associated with distinctly smaller heat changes whereas solvate formation accompanied by structural changes is characterized by an elongated heat flow. Hence, perfusion calorimetry is a valuable tool in the characterization of solvates forming isomorphic desolvates which represents a new field of application for the method.

  17. Water-enhanced solvation of organics

    SciTech Connect

    Lee, Jane 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 γs vs xw/xs curve. From graph shape Δ(log γs) 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 Δ(log γacid)/Δ(xw/xacid) = -0.25. In methylcyclohexanone, the decrease of the activity coefficient of propionic acid was -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.

  18. Structure of solvated Fe(CO)5: complex formation during solvation in alcohols.

    PubMed

    Lessing, Joshua; Li, Xiaodi; Lee, Taewoo; Rose-Petruck, Christoph G

    2008-03-20

    The equilibrium structure of iron pentacarbonyl, Fe(CO)5, solvated in various alcohols has been investigated by Fourier transform infrared (FTIR) measurements and density functional theory calculations. This system was studied because it is prototypical of a larger class of monometallic systems, which are electronically saturated but not sterically crowded. Upon solvation, the Fe(CO)5 is not just surrounded by a solvation shell. Instead, solute-solvent complexes are formed with the oxygen of the alcohol oriented toward an axial ligand of the Fe(CO)5 giving a formation energy on the order of -5 kJ/mol. This complexation is not a chemical reaction but rather a "preassembly" of the solute molecules with a single solvent molecule. For instance, at room temperature the interaction between Fe(CO)5 and ethanol results in 87% of all Fe(CO)5 molecules being complexated with a single ethanol molecule. This complexation was found in all the alcohol systems studied in this paper. The stability of these complexes was found to depend on the alcohol chain length and branching. The observed complexation mechanism is accompanied by an electron density shift from the complexed alcohol molecule toward Fe(CO)5 where it induces a dipole moment. The finding that Fe(CO)5 forms a complex with the hydroxyl group of a single solvent molecule might have significant implications for ligand substitution reactions. This implies that ligand substitution reactions do not have to proceed via a dissociative mechanism. Instead, the reaction might proceed through a concerted mechanism with the leaving CO simultaneously being replaced by the incoming alcohol that was complexed to Fe(CO)5 prior to the photoexcitation.

  19. Aqueous solvation dynamics at metal oxide surfaces.

    PubMed

    Portuondo-Campa, Erwin; Tortschanoff, Andreas; van Mourik, Frank; Moser, Jacques-Edouard; Kornherr, Andreas; Chergui, Majed

    2006-04-20

    Broadband transient absorption (TA) spectroscopy, three-pulse photon echo peak shift (3PEPS), and anisotropy decay measurements were used to study the solvation dynamics in bulk water and interfacial water at ZrO(2) surfaces, using Eosin Y as a probe. The 3PEPS results show a multiexponential behavior with two subpicosecond components that are similar in bulk and interfacial water, while a third component of several picoseconds is significantly lengthened at the interface. The bandwidth correlation function from TA spectra exhibits the same behavior, and the TA spectra are well reproduced using the doorway-window picture with the time constants from PEPS. Our results suggest that interfacial water is restricted to a thickness of less than 5 A. Also the high-frequency collective dynamics of water does not seem to be affected by the interface. On the other hand, the increase of the third component may point to a slowing down of diffusional motion at the interface, although other effects, may play a role, which are discussed.

  20. Ligand Entropy in Gas-Phase, Upon Solvation and Protein Complexation. Fast Estimation with Quasi-Newton Hessian.

    PubMed

    Wlodek, S; Skillman, A G; Nicholls, A

    2010-07-13

    A method of rapid entropy estimation for small molecules in vacuum, solution, and inside a protein receptor is proposed. We show that the Hessian matrix of second derivatives built by a quasi-Newton optimizer during geometry optimization of a molecule with a classical molecular potential in these three environments can be used to predict vibrational entropies. We also show that a simple analytical solvation model allows for no less accurate entropy estimation of molecules in solution than a physically rigorous but computationally more expensive model based on Poisson's equation. Our work also suggests that scaled particle theory more precisely estimates the hydrophobic part of solvation entropy than the using a simple surface area term.

  1. 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.

  2. 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

  3. 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

  4. How accurate are continuum solvation models for drug-like molecules?

    NASA Astrophysics Data System (ADS)

    Kongsted, Jacob; Söderhjelm, Pär; Ryde, Ulf

    2009-07-01

    We have estimated the hydration free energy for 20 neutral drug-like molecules, as well as for three series of 6-11 inhibitors to avidin, factor Xa, and galectin-3 with four different continuum solvent approaches (the polarised continuum method the Langevin dipole method, the finite-difference solution of the Poisson equation, and the generalised Born method), and several variants of each, giving in total 24 different methods. All four types of methods have been thoroughly calibrated for a number of experimentally known small organic molecules with a mean absolute deviation (MAD) of 1-6 kJ/mol for neutral molecules and 4-30 kJ/mol for ions. However, for the drug-like molecules, the accuracy seems to be appreciably worse. The reason for this is that drug-like molecules are more polar than small organic molecules and that the uncertainty of the methods is proportional to the size of the solvation energy. Therefore, the accuracy of continuum solvation methods should be discussed in relative, rather than absolute, terms. In fact, the mean unsigned relative deviations of the best solvation methods, 0.09 for neutral and 0.05 for ionic molecules, correspond to 2-20 kJ/mol absolute error for the drug-like molecules in this investigation, or 2-3,000 in terms of binding constants. Fortunately, the accuracy of all methods can be improved if only relative energies within a series of inhibitors are considered, especially if all of them have the same net charge. Then, all except two methods give MADs of 2-5 kJ/mol (corresponding to an uncertainty of a factor of 2-7 in the binding constant). Interestingly, the generalised Born methods typically give better results than the Poison-Boltzmann methods.

  5. Solvation forces between silica bodies in supercritical carbon dioxide.

    PubMed

    Vishnyakov, Aleksey; Shen, Yangyang; Tomassone, M Silvina

    2008-12-02

    We report Monte Carlo simulations of the solvation pressure between two planar surfaces, which represent the interface of spherical silica nanoparticles in supercritical carbon dioxide. Carbon dioxide (CO2) was modeled as an atomistic dumbbell or a spherical Lennard-Jones particle. The interaction between CO2 molecules and silica surfaces was characterized by the standard Steele potential with energetic heterogeneities representing the hydrogen bonds. The parameters for the solid-fluid interaction potentials were obtained by fitting our simulations to the experimental isotherms of CO2 sorption on mesoporous siliceous materials. We studied the dependence of the solvation force on the distance between planar silica surfaces at T = 318 K, at equilibrium bulk pressures p(bulk) ranging from 69 to 200 atm. At 69 atm, we observed a long-range attraction between the two surfaces, and it vanished when the pressure was increased to 102 and then 200 atm. The results obtained with different fluid models were consistent with each other. According to our observations, energetic heterogeneities of the surface have negligible influence on the solvation pressure. Using the Derjaguin approximation, we calculated the solvation forces between spherical silica nanoparticles in supercritical CO2 from the solvation pressures between the planar surfaces.

  6. 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.

  7. Characterisation and evaluation of pharmaceutical solvates of Atorvastatin calcium by thermoanalytical and spectroscopic studies

    PubMed Central

    2012-01-01

    Background Atorvastatin calcium (ATC), an anti-lipid biopharmaceutical class II drug, is widely prescribed as a cholesterol-lowering agent and is presently the world’s best-selling medicine. A large number of crystalline forms of ATC have been published in patents. A variety of solid forms may give rise to different physical properties. Therefore, the discovery of new forms of this unusual molecule, ATC, may still provide an opportunity for further improvement of advantageous properties. Results In the present work, eight new solvates (Solvate I-VIII) have been discovered by recrystallization method. Thermal behaviour of ATC and its solvates studied by DSC and TGA indicate similar pattern suggesting similar mode of entrapment of solvent molecules. The type of solvent present in the crystal lattice of the solvates is identified by GC-MS analysis and the stoichiometric ratio of the solvents is confirmed by 1HNMR. The high positive value of binding energy determined from thermochemical parameters indicates deep inclusion of the solvent molecules into the host cavity. The XRPD patterns point towards the differences in their crystallanity, however, after desolvation solvate II, III, IV, V and VIII transform to isostructral amorphous desolvated solvates. The order of crystallinity was confirmed by solution calorimetric technique as the enthalpy of solution is an indirect measure of lattice energy. All the solvates behaved endothermically following the order solvate-VIII (1-butanol solvate) < solvate-I (isoproplyate) < solvate-V (methanol solvate) < solvate-III (ethonalate) < solvate-VI (acetone ethanol solvate) < solvate-IV (t-butanol solvate) < solvate-II (THF solvate) < solvate-VII (mixed hemi-ethanol hydrate). The positive value of the heat capacity of the solvate formation provides information about the state of solvent molecules in the host lattice. The solvents molecules incorporated in the crystal lattice induced local chemical environment changes in the drug

  8. 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.

  9. Prediction of solvation enthalpy of gaseous organic compounds in propanol

    NASA Astrophysics Data System (ADS)

    Golmohammadi, Hassan; Dashtbozorgi, Zahra

    2016-09-01

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

  10. 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.

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

    DOE PAGES

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

    2015-09-16

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

  12. 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.

  13. 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

  14. 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

  15. Density profiles and solvation forces for a Yukawa fluid in a slit pore.

    PubMed

    Karanikas, S; Dzubiella, J; Moncho-Jordá, A; Louis, A A

    2008-05-28

    The effect of varying wall-particle and particle-particle interactions on the density profiles near a single wall and the solvation forces between two walls immersed in a fluid of particles is investigated by grand canonical Monte Carlo simulations. Attractive and repulsive particle-particle and particle-wall interactions are modeled by a versatile hard-core Yukawa form. These simulation results are compared to theoretical calculations using the hypernetted chain integral equation technique, as well as with fundamental measure density functional theory (DFT), where particle-particle interactions are either treated as a first order perturbation using the radial distribution function or else with a DFT based on the direct-correlation function. All three theoretical approaches reproduce the main trends fairly well, but exhibit inconsistent accuracy, particularly for attractive particle-particle interactions. We show that the wall-particle and particle-particle attractions can couple together to induce a nonlinear enhancement of the adsorption and a related "repulsion through attraction" effect for the effective wall-wall forces. We also investigate the phenomenon of bridging, where an attractive wall-particle interaction induces strongly attractive solvation forces.

  16. Continuous surface charge polarizable continuum models of solvation. I. General formalism.

    PubMed

    Scalmani, Giovanni; Frisch, Michael J

    2010-03-21

    Continuum solvation models are appealing because of the simplified yet accurate description they provide of the solvent effect on a solute, described either by quantum mechanical or classical methods. The polarizable continuum model (PCM) family of solvation models is among the most widely used, although their application has been hampered by discontinuities and singularities arising from the discretization of the integral equations at the solute-solvent interface. In this contribution we introduce a continuous surface charge (CSC) approach that leads to a smooth and robust formalism for the PCM models. We start from the scheme proposed over ten years ago by York and Karplus and we generalize it in various ways, including the extension to analytic second derivatives with respect to atomic positions. We propose an optimal discrete representation of the integral operators required for the determination of the apparent surface charge. We achieve a clear separation between "model" and "cavity" which, together with simple generalizations of modern integral codes, is all that is required for an extensible and efficient implementation of the PCM models. Following this approach we are now able to introduce solvent effects on energies, structures, and vibrational frequencies (analytical first and second derivatives with respect to atomic coordinates), magnetic properties (derivatives with respect of magnetic field using GIAOs), and in the calculation more complex properties like frequency-dependent Raman activities, vibrational circular dichroism, and Raman optical activity.

  17. Morphometric approach to thermodynamic quantities of solvation of complex molecules: extension to multicomponent solvent.

    PubMed

    Kodama, Ryota; Roth, Roland; Harano, Yuichi; Kinoshita, Masahiro

    2011-07-28

    The morphometric approach (MA) is a powerful tool for calculating a solvation free energy (SFE) and related quantities of solvation thermodynamics of complex molecules. Here, we extend it to a solvent consisting of m components. In the integral equation theories, the SFE is expressed as the sum of m terms each of which comprises solute-component j correlation functions (j = 1,..., m). The MA is applied to each term in a formally separate manner: The term is expressed as a linear combination of the four geometric measures, excluded volume, solvent-accessible surface area, and integrated mean and Gaussian curvatures of the accessible surface, which are calculated for component j. The total number of the geometric measures or the coefficients in the linear combinations is 4m. The coefficients are determined in simple geometries, i.e., for spherical solutes with various diameters in the same multicomponent solvent. The SFE of the spherical solutes are calculated using the radial-symmetric integral equation theory. The extended version of the MA is illustrated for a protein modeled as a set of fused hard spheres immersed in a binary mixture of hard spheres. Several mixtures of different molecular-diameter ratios and compositions and 30 structures of the protein with a variety of radii of gyration are considered for the illustration purpose. The SFE calculated by the MA is compared with that by the direct application of the three-dimensional integral equation theory (3D-IET) to the protein. The deviations of the MA values from the 3D-IET values are less than 1.5%. The computation time required is over four orders of magnitude shorter than that in the 3D-IET. The MA thus developed is expected to be best suited to analyses concerning the effects of cosolvents such as urea on the structural stability of a protein.

  18. Morphometric approach to thermodynamic quantities of solvation of complex molecules: Extension to multicomponent solvent

    NASA Astrophysics Data System (ADS)

    Kodama, Ryota; Roth, Roland; Harano, Yuichi; Kinoshita, Masahiro

    2011-07-01

    The morphometric approach (MA) is a powerful tool for calculating a solvation free energy (SFE) and related quantities of solvation thermodynamics of complex molecules. Here, we extend it to a solvent consisting of m components. In the integral equation theories, the SFE is expressed as the sum of m terms each of which comprises solute-component j correlation functions (j = 1, …, m). The MA is applied to each term in a formally separate manner: The term is expressed as a linear combination of the four geometric measures, excluded volume, solvent-accessible surface area, and integrated mean and Gaussian curvatures of the accessible surface, which are calculated for component j. The total number of the geometric measures or the coefficients in the linear combinations is 4m. The coefficients are determined in simple geometries, i.e., for spherical solutes with various diameters in the same multicomponent solvent. The SFE of the spherical solutes are calculated using the radial-symmetric integral equation theory. The extended version of the MA is illustrated for a protein modeled as a set of fused hard spheres immersed in a binary mixture of hard spheres. Several mixtures of different molecular-diameter ratios and compositions and 30 structures of the protein with a variety of radii of gyration are considered for the illustration purpose. The SFE calculated by the MA is compared with that by the direct application of the three-dimensional integral equation theory (3D-IET) to the protein. The deviations of the MA values from the 3D-IET values are less than 1.5%. The computation time required is over four orders of magnitude shorter than that in the 3D-IET. The MA thus developed is expected to be best suited to analyses concerning the effects of cosolvents such as urea on the structural stability of a protein.

  19. Residue length and solvation model dependency of elastinlike polypeptides.

    PubMed

    Bilsel, Mustafa; Arkin, Handan

    2010-05-01

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

  20. Residue length and solvation model dependency of elastinlike polypeptides

    NASA Astrophysics Data System (ADS)

    Bilsel, Mustafa; Arkin, Handan

    2010-05-01

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

  1. Lithium solvation in bis(trifluoromethanesulfonyl)imide-based ionic liquids.

    PubMed

    Lassègues, Jean-Claude; Grondin, Joseph; Talaga, David

    2006-12-28

    The lithium solvation in (1 -x)(EMI-TFSI), xLiTFSI ionic liquids where EMI(+) is the 1-ethyl-3-methylimidazolium cation and TFSI(-) the bis(trifluoromethanesulfonyl)imide anion, is shown by Raman spectroscopy to involve essentially [Li(TFSI)(2)](-) anionic clusters for 0 < x < 0.4, but addition of stoichiometric amounts of solvents S such as oligoethers changes the lithium solvation into [Li(S)(m)](+) cationic clusters; the lithium transference number in TFSI-based ionic liquid electrolytes for lithium batteries should thus be strongly improved.

  2. 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...

  3. Determination of partial unfolding enthalpy for lysozyme upon interaction with dodecyltrimethylammonium bromide using an extended solvation model.

    PubMed

    Behbehani, G Rezaei; Saboury, A A; Taleshi, E

    2008-01-01

    The interactions of dodecyltrimethylammonium bromides (DTABs) with hen egg lysozyme have been investigated at pH = 7.0 and 27 degrees C in phosphate buffer by isothermal titration calorimetry. DTAB interacts endothermically and activate lysozyme. The endothermicity of the lysozyme-DTAB interaction is in marked contrast to the exothermic interactions between sodium dodecyl sulphate (SDS) and lysozyme which have been attributed to specific binding between the anionic sulphate head groups and cationic amino acid residues. The enthalpies of interaction between the cationic surfactant (DTAB) and lysozyme are dominated by the endothermic unfolding of the native structure followed by an exothermic solvation of the lysozyme-DTAB complex by the addition of extra DTAB. A new direct calorimetric method to follow protein denaturation, and the effect of surfactants on the stability of proteins was introduced. The extended solvation model was used to reproduce the enthalpies of lysozyme-DTAB interaction over the whole range of DTAB concentrations. The solvation parameters recovered from the new equation, attributed to the structural change of lysozyme and its biological activity. At low concentrations of DTAB, the binding is mainly electrostatic, with some simultaneous interaction of the hydrophobic tail with nearby hydrophobic patches on the lysozyme. These initial interactions presumably cause some protein unfolding and expose additional hydrophobic sites. The DTAB-induced denaturation enthalpy of lysozyme is 86.46 +/- 0.02 kJ mol(-1).

  4. Molecular thermodynamics of metabolism: hydration quantities and the equation-of-state approach.

    PubMed

    Panayiotou, C; Mastrogeorgopoulos, S; Ataman, M; Hadadi, N; Hatzimanikatis, V

    2016-11-30

    The present work is part of a series of papers aiming at a thorough understanding of the thermodynamics of metabolism over a broad range of external conditions. The focus here is on the systematic study of solvation/hydration of a variety of fluids via an equation-of-state approach. This approach permits the study not only of the overall free energy, enthalpy or entropy of hydration but also their key components from cavitation, charging, and solute conformations/solvent restructuring contributions. These latter components shed light into the mechanism of hydration and contribute to our understanding of solvation phenomena at remote conditions of temperature and pressure. Hydrogen bonding is of central importance in this respect and is handled via the partial solvation parameter (PSP) approach. The developed solvation model is used for the estimation of the hydration quantities of key metabolites. The challenges and perspectives of this equation-of-state approach are critically discussed.

  5. 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

  6. 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…

  7. 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…

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

    PubMed

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

    2016-09-08

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

  9. 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.}

  10. 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.

  11. Surfactant solvation effects and micelle formation in ionic liquids.

    PubMed

    Anderson, Jared L; Pino, Verónica; Hagberg, Erik C; Sheares, Valerie V; Armstrong, Daniel W

    2003-10-07

    The formation of micelles in 1-butyl-3-methyl imidazolium chloride (BMIM-Cl) and hexafluorophosphate (BMIM-PF6) were explored using different surfactants and the solvation behavior of the new micellar-ionic liquid solutions examined using inverse gas chromatography.

  12. 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

  13. 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.

  14. Gauge-origin-independent magnetizabilities of solvated molecules using the polarizable continuum model

    NASA Astrophysics Data System (ADS)

    Ferrighi, Lara; Marchesan, Domenico; Ruud, Kenneth; Frediani, Luca; Coriani, Sonia

    2005-11-01

    We present an implementation of the polarizable continuum model in its integral equation formulation for the calculation of the magnetizabilities of solvated molecules. The gauge-origin independence of the calculated magnetizabilities and the fast basis set convergence are ensured through the use of London atomic orbitals. Our implementation can use Hartree-Fock and multiconfigurational self-consistent-field (MCSCF) wave functions as well as density-functional theory including hybrid functionals such as B3LYP. We present the results of dielectric continuum effects on water and pyridine using MCSCF wave functions, as well as dielectric medium effects on the magnetizability of the aromatic amino acids as a model for how a surrounding protein environment affects the magnetizability of these molecules. It is demonstrated that the dielectric medium effects on the magnetizability anisotropies of the aromatic amino acids may be substantial, being as large as 25% in the case of tyrosine.

  15. 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

    2016-04-07

    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.

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

    PubMed

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

    2009-05-07

    We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the "D" stands for "density" to denote that the full solute electron density is used without defining partial atomic charges. "Continuum" denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where "universal" denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which a few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonhomogeneous Poisson equation for electrostatics in terms of the integral-equation-formalism polarizable continuum model (IEF-PCM). The cavities for the bulk electrostatic calculation are defined by superpositions of nuclear-centered spheres. The second component is called the cavity-dispersion-solvent-structure term and is the contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. This contribution is a sum of terms that are proportional (with geometry-dependent proportionality constants called atomic surface tensions) to the solvent-accessible surface areas of the individual atoms of the solute. The SMD model has been parametrized with a training set of 2821 solvation data including 112 aqueous ionic solvation free energies, 220 solvation free energies for 166 ions in acetonitrile, methanol, and dimethyl sulfoxide, 2346 solvation free energies for 318 neutral solutes in 91 solvents (90 nonaqueous

  17. Power-Law Solvation Dynamics in G-Quadruplex DNA: Role of Hydration Dynamics on Ligand Solvation inside DNA.

    PubMed

    Pal, Nibedita; Shweta, Him; Singh, Moirangthem Kiran; Verma, Sachin Dev; Sen, Sobhan

    2015-05-07

    G-quadruplex DNA (GqDNA) structures act as promising anticancer targets for small-molecules (ligands). Solvation dynamics of a ligand (DAPI: 4',6-diamidino-2-phenylindole) inside antiparallel-GqDNA is studied through direct comparison of time-resolved experiments to molecular dynamics (MD) simulation. Dynamic Stokes shifts of DAPI in GqDNA prepared in H2O buffer and D2O are compared to find the effect of water on ligand solvation. Experimental dynamics (in H2O) is then directly compared with the dynamics computed from 65 ns simulation on the same DAPI-GqDNA complex. Ligand solvation follows power-law relaxation (summed with fast exponential relaxation) from ~100 fs to 10 ns. Simulation results show relaxation below ~5 ps is dominated by water motion, while both water and DNA contribute comparably to dictate long-time power-law dynamics. Ion contribution is, however, found to be negligible. Simulation results also suggest that anomalous solvation dynamics may have origin in subdiffusive motion of perturbed water near GqDNA.

  18. 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

  19. Subpicosecond measurements of polar solvation dynamics: Coumarin 153 revisited

    SciTech Connect

    Horng, M.L.; Gardecki, J.A.; Papazyan, A.; Maroncelli, M.

    1995-11-30

    Time-resolved emission measurements of the solute coumarin 153 (C153) are used to probe the time dependence of solvation in 24 common solvents at room temperature. Significant improvements in experimental time resolution ({approx}100 fs instrument response) as well as corresponding improvements in analysis methods provide confidence that all of the spectral evolution (including both the inertial and the diffusive parts of the response) are observed in these measurements. Extensive data concerning the steady-state solvatochromism of C153, coupled to an examination of the effects of vibrational relaxation, further demonstrate that the spectral dynamics being observed accurately monitor the dynamics of nonspecific solvation. Comparisons to theoretical predictions show that models based on the dielectric response of the pure solvent provide a semiquantitative understanding of the dynamics observed. 156 refs., 26 figs., 5 tabs.

  20. 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

  1. 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

  2. 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

  3. The Absorption Spectrum of an Electron Solvated in Sodalite

    DTIC Science & Technology

    1992-05-15

    S. FUNDING NUMBERS The Absorption Spectrum of an Electron N00014-90-J-1159 Solvated in Sodalite C AUTHOR(S) K. Haug, V. Srdanov, G. Stucky, and H...words) We use a simple model to study the color change taking place when sodium atoms are absorbed in the zeolite sodalite . The Hamiltonian is that...the absorption spectrum on the magnitude of framework charges, the orientation of the Na 4 cluster in the sodalite cells, the localization of the

  4. Polaron theory of electrons solvated in molten salts

    NASA Astrophysics Data System (ADS)

    Malescio, G.; Parrinello, M.

    1987-01-01

    A suitably modified version of the polaron theory of Chandler et al. [J. Chem. Phys. 81, 1975 (1984)] is applied to the study of the solvation of electrons in molten salts. The results obtained compare favorably with recent numerical simulations and confirm the picture of the formation in the melt of an F-center analog. A novel expression for the explicit evaluation of the electron kinetic energy is given.

  5. On the solvation of L-aspartic acid

    NASA Astrophysics Data System (ADS)

    Paxton, A. T.; Harper, J. B.

    2004-01-01

    We use molecular statics and dynamics to study the stability of L-aspartic acid both in vacuo and solvated by polar and non-polar molecules using density functional theory in the generalized gradient approximation. We find that structures stable in vacuo are unstable in aqueous solution and vice versa. From our simulations we are able to come to some conclusions about the mechanism of stabilisation of zwitterions by polar protic solvents, water and methanol.

  6. Resolving Ultrafast Photoinduced Deactivations in Water-solvated Pyrimidine Nucleosides.

    PubMed

    Pepino, Ana J; Segarra-Martí, Javier; Nenov, Artur; Improta, Roberto; Garavelli, Marco

    2017-03-27

    For the first time, ultrafast deactivations of photo-excited water-solvated pyrimidine nucleosides are mapped employing hybrid QM(CASPT2)/MM(AMBER) optimizations that account for explicit solvation, sugar effects and dynamically correlated potential energy surfaces. Low energy S1/S0 ring-puckering and ring-opening conical intersections (CIs) are suggested to drive the ballistic coherent sub-ps (<200fs) decays observed in each pyrimidine, the energetics controlling this processes correlating with the lifetimes observed. A second bright 1π2π* state, promoting excited-state population branching and leading towards a third CI with the ground state, is proposed to be involved in the slower ultrafast decay component observed in Thd/Cyd. The transient spectroscopic signals of the competitive deactivation channels are computed for the first time. A general unified scheme for ultrafast deactivations, spanning the sub-to-few ps time domain, is eventually delivered, with computed data that matches the experiments and elucidates the intrinsic photo-protection mechanism in solvated pyrimidine nucleosides.

  7. 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.

  8. Hydroxide Solvation and Transport in Anion Exchange Membranes

    SciTech Connect

    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.

  9. Enthalpy-entropy compensation: the role of solvation.

    PubMed

    Dragan, Anatoliy I; Read, Christopher M; Crane-Robinson, Colyn

    2017-05-01

    Structural modifications to interacting systems frequently lead to changes in both the enthalpy (heat) and entropy of the process that compensate each other, so that the Gibbs free energy is little changed: a major barrier to the development of lead compounds in drug discovery. The conventional explanation for such enthalpy-entropy compensation (EEC) is that tighter contacts lead to a more negative enthalpy but increased molecular constraints, i.e., a compensating conformational entropy reduction. Changes in solvation can also contribute to EEC but this contribution is infrequently discussed. We review long-established and recent cases of EEC and conclude that the large fluctuations in enthalpy and entropy observed are too great to be a result of only conformational changes and must result, to a considerable degree, from variations in the amounts of water immobilized or released on forming complexes. Two systems exhibiting EEC show a correlation between calorimetric entropies and local mobilities, interpreted to mean conformational control of the binding entropy/free energy. However, a substantial contribution from solvation gives the same effect, as a consequence of a structural link between the amount of bound water and the protein flexibility. Only by assuming substantial changes in solvation-an intrinsically compensatory process-can a more complete understanding of EEC be obtained. Faced with such large, and compensating, changes in the enthalpies and entropies of binding, the best approach to engineering elevated affinities must be through the addition of ionic links, as they generate increased entropy without affecting the enthalpy.

  10. 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.

  11. 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.

  12. Solvation dynamics in a Brownian dipolar lattice. Comparison between computer simulation and various molecular theories of solvation dynamics

    NASA Astrophysics Data System (ADS)

    Komath, Sneha Sudha; Bagchi, Biman

    1993-06-01

    Several recent theoretical and computer simulation studies have considered solvation dynamics in a Brownian dipolar lattice which provides a simple model solvent for which detailed calculations can be carried out. In this article a fully microscopic calculation of the solvation dynamics of an ion in a Brownian dipolar lattice is presented. The calculation is based on the non-Markovian molecular hydrodynamic theory developed recently. The main assumption of the present calculation is that the two-particle orientational correlation functions of the solid can be replaced by those of the liquid state. It is shown that such a calculation provides an excellent agreement with the computer simulation results. More importantly, the present calculations clearly demonstrate that the frequency-dependent dielectric friction plays an important role in the long time decay of the solvation time correlation function. We also find that the present calculation provides somewhat better agreement than either the dynamic mean spherical approximation (DMSA) or the Fried-Mukamel theory which use the simulated frequency-dependent dielectric function. It is found that the dissipative kernels used in the molecular hydrodynamic approach and in the Fried-Mukamel theory are vastly different, especially at short times. However, in spite of this disagreement, the two theories still lead to comparable results in good agreement with computer simulation, which suggests that even a semiquantitatively accurate dissipative kernel may be sufficient to obtain a reliable solvation time correlation function. A new wave vector and frequency-dependent dissipative kernel (or memory function) is proposed which correctly goes over to the appropriate expressions in both the single particle and the collective limits. This form is expected to lead to better results than all the existing descriptions.

  13. Revisiting the crisis in Freud's libido theory and Abraham's concept of the oral-sadistic phase as a way out of it.

    PubMed

    Dahl, Gerhard

    2016-10-01

    The now available unabridged correspondence between Freud and Abraham leads to a re-evaluation of the significance of Abraham's work. The author proposes the thesis that clinical observations by Karl Abraham of the ambivalence of object relations and the destructive-sadistic aspects of orality have an important influence on the advancement of psychoanalytical theory. The phantasy problem of the Wolf Man and the question of the pathogenic relevance of early actual, or merely imagined traumata led Freud to doubt the validity of his theory. He attempted repeatedly to solve this problem using libido theory, but failed because of his problematic conception of oral erotics. The pathogenic effect of presymbolic traumatizations cannot be demonstrated scientifically because of the still underdeveloped brain in the early stage of the child's development. Consequently, the important empirical evidence of a scientific neurosis theory could not be provided. A revision of the theory of the instincts thus became necessary. With Abraham's clinical contributions and other pathologic evidence, Freud was, with some reservation, forced to modify his idea of oral erotics by ascribing to it a status of a merely constructed and fictive phase of oral organization. A solution was eventually facilitated via recognition of non-erotic aggression and destruction, thereby opening libido theory to fundamental revisions. Driven by the desire to develop a scientific theory, Freud initially had, in his first theory of the instincts, assumed a strongly causal-deterministic view on Psychic Function. His third revision of theory of the instincts, Beyond the Pleasure Principle including the death instinct hypothesis, considered the hermeneutic aspect of psychoanalytic theory, which had previously existed only implicitly in his theory. Further development of the death instinct hypothesis by Melanie Klein and her successors abandoned quantitative-economic and causal-deterministic principles, and instead

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  15. 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.

  16. a New Supersymmetric Version of the Abraham-Moses Method for Symmetric Potentials

    NASA Astrophysics Data System (ADS)

    Casahorrán, J.

    Starting from the one-dimensional Schrodinger equation with symmetric potential Vs(x), a general method is presented in order to obtain a family of partially isospectral hamiltonians. Arguments concerning supersymmetric transformations, factorization procedures and Riccati equations are invoked along the article. As a result of the appearance of singular superpotentials, the physical meaning of our method can be summarized as follows: only the odd wave-functions of the original potential Vs(x) are transported via supersymmetry into the Hilbert space associated with the partner Vp(x). In such a case the degeneracy of energy levels is partially broken. Supersymmetry is neither exact nor spontaneously broken but realizes itself acting on wave functions vanishing at x=0. While the domain of the original hamiltonian H extends along the whole real axis, the susy partner Hp reduces to the half-line (x≤0 or x≥0). To illustrate how the procedure works in practice we resort to a symmetric potential in the Posch-Teller class containing both discrete and continuous spectra.

  17. 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).

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

    PubMed Central

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

    2006-01-01

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

  19. Topological and spatial aspects of the hydration of solutes of extreme solvation entropy

    NASA Astrophysics Data System (ADS)

    Bergman, Dan L.; Lyubartsev, Alexander P.; Laaksonen, Aatto

    1999-10-01

    The hydration of charged Lennard-Jones spheres by simple point charge water is considered. Molecular dynamics and expanded ensemble simulations were used to compare the hydration structures surrounding solutes with extreme solvation entropy. The variations in the solvation entropy were analyzed in terms of changes in the spatial and topological structure of the hydration shells. The solvation entropy was found to be maximal for solutes that can replace water molecules in the hydrogen-bond network. Further, using a Kirkwood-type factorization, the solvation entropy was expanded as a sum over the partial n-body distribution functions. The two-body solute-water contribution to the solvation entropy was found to exceed the full solvation entropy for solutes with low charge, whereas the converse is true for the other solutes. This is consistent with the idea that water-water correlations are enhanced by solvation of, for example, noble gases, whereas they are disrupted by solvation of ions. Further, the orientational and radial parts of the two-body solute-water entropy were calculated as functions of the charge of the solute. The orientational part has a single maximum, whereas the radial part maintains the bimodal form of the full solvation entropy.

  20. The Gordon Gordon-Taylor Memorial Lecture: surgical giants and giants among surgeons--the case of Abraham Colles.

    PubMed

    Little, Miles

    2006-12-01

    Sir Gordon Gordon-Taylor was a surgical giant and a giant among surgeons. There's a distinction between the two. Surgical giants are technical geniuses who pave the way for others and set the standards against which others can measure their performance. Giants among surgeons contribute other things to the science and practice of surgery and sometimes to fields outside surgery. By these measures, Abraham Colles was not a surgical giant. He thought, wrote and taught about his interests. He enhanced the reputation of Irish surgery. In retrospect, his science and his ethics seem flawed by modern standards, but by the measures of his own time he was a model investigator and a man of outstanding moral probity. He is remembered for the eponymous Colles's fracture and for Colles's fascia and ligament. He held the Chair of Anatomy and Surgery in Dublin for 32 years and drew the admiration and affection of his contemporaries, colleagues and students. He was a giant among surgeons, and his name deserves commemoration.

  1. Energetics and structure in solvent: A dielectric continuum model of solvation combined with molecular mechanics, Ab Initio, and Semi-empirical molecular orbital treatments of the solute

    SciTech Connect

    Tawa, G.J.; Pratt, L.R.; Martin, R.L.

    1996-12-31

    We present a method for computing the electrostatic component of the solvation free energy, {Delta}G{sup el}, of a solute molecule in the presence of solvent modeled as a dielectric continuum. The method is based on an integral form of Poisson`s equation which is solved to obtain a distribution of induced polarization charge at the solute-solvent dielectric interface. The solution of Poisson`s equation is obtained by application of a boundary element procedure. The method is tested by comparing its predictions of {Delta}G{sup el} to exact values for several model problems. The method is then used in a variety of contexts to assess its qualitative prediction ability. It is first combined with a molecular mechanics treatment of the solute to evaluate the effects of aqueous solvent on the conformational equilibria of several small molecules of interest-these are N-methyl acetamide and alanine dipeptide. For both molecules dielectric continuum solvation predicts torsional free energies of solvation that are in accord with other more complete treatments of solvation. The method is then combined with ab initio and semi-empirical molecular orbital theory for the solute. Self consistent reaction field calculations (SCRF) are performed to evaluate the correlation is in general very good. Relative agreement with experiment is best for ions where electrostatics predominate and worst for non-polar neutral molecules were electrostatics are minor. Semi-empirical configuration interaction SCRF calculations are also performed in the presence of solvent in order to determine ground-to-excited state absorption energy shifts for formaldehyde and indole mine ground-to-excited state absorption energy shifts for formaldehyde and indole when placed in water. We find a rough correlation between transition energy shifts and the dipole moments of the initial and final states involved in the transition.

  2. Homogeneous solvation controlled photoreduction of cobalt(III) complexes in aqueous 2-methyl-2-propanol solutions. Linear solvation energy relationship and cyclic voltammetric analyses

    NASA Astrophysics Data System (ADS)

    Anbalagan, K.; Lydia, I. Sharmila

    2008-03-01

    The effect of solvent participation on the ligand-to-metal charge transfer (LMCT, L → Co III) reduction of the of Co III(en) 2Br(RC 6H 4NH 2) 2+ where R = m-OCH 3, p-F, H, m-CH 3, p-CH 3,p-OC 2H 5 and p-OCH 3 were examined in aqueous 2-methyl-2-propanol (Bu tOH) solutions. The change in the reduction behavior of Co III centre was also examined through cyclic voltammetric studies. The observed reduction in quantum yield due to LMCT excitation can mainly be accounted using linear solvation energy relationship (LSER) comprising model correlation equations. These consist of empirical parameters such as Grunwald-Winstein's solvent ionizing power, Y, Dimroth-Richardt's solvent micro-polarity parameter, ETN, Gutmann's donor number, DN N, along with Kamlet-Taft's solvatochromic parameters (hydrogen bond acceptor acidity/basicity α/ β and solvent dipolarity/polarizability, π*). The origin of solvent effect is found to be due to microscopic interaction between the solvent donor and the nitrogen-bound hydrogen of the ligand. Cyclic voltammograms show an irreversible reduction of Co III in DMF using Glassy Carbon Electrode, GCE, the redox peaks for the aniline complexes appear at -0.20 and 0.525 V. Irradiation of the complexes with UV light ( λ = 254 nm) in binary mixtures produce Co IIaq and the concentration of this species are highly dependent on xalc ( xalc = mole fraction of alcohol). The observed quantum yield (log ΦCo(II)) is found to be linearly related to mole fraction of organic co-solvent added in the mixture, therefore, log ΦCo(II) = 26.41 × 10 -2 when x2 = 0.0094 and 43.75 × 10 -2 when x2 = 0.076 for a typical complex Co III(en) 2Br( p-OCH 3C 6H 4NH 2) 2+ in aqueous 2-methyl-2-propanol at 300 K. Cyclic voltammetry and LSER analyses illustrate the variation of reduction property of Co(III) by the aryl ligand and homogeneous solvation of the excited state of the complex Co III(en) 2Br(RC 6H 4NH 2) 2+ in H 2O/Bu tOH mixtures.

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

    The intensity of the ultra-short pulse lasers has reached 1022 W/cm2 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.

  5. 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.

  6. 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.

  7. Relationship between Solvation Thermodynamics from IST and DFT Perspectives.

    PubMed

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

    2017-02-28

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

  8. Conformational analysis of [Met5]-enkephalin: Solvation and ionization considerations

    NASA Astrophysics Data System (ADS)

    Carlacci, Louis

    1998-03-01

    [Met5]-Enkephalin has the sequence Tyr-Gly-Gly-Phe-Met. Only the extended conformation of the peptide has been observed by X-ray crystallography. Nuclear magnetic resonance spectroscopy supports the presence of a turn at Gly 3 and Phe 4 in dimethyl sulfoxide. In this study, the peptide conformational states and thermodynamic properties are understood in terms of ionization state and solvent environment. In the calculation, final conformations obtained from multiple independent Monte Carlo simulated annealing conformational searches are starting points for molecular dynamics simulations. In an aqueous environment given by the use of solvation free energy and the zwitterionic state, dominant structural motifs computed are G-P Type II' bend, G-G Type II' bend, and G-G Type I' bend motifs, in order of increasing free energy. In the calculation of the peptide with neutral N- and C-termini and solvation free energy, the extended conformer dominates (by at least a factor of 2.5), and the conformation of another low free energy conformer superimposes well on the pharmacophoric groups of morphine. Neutralization of charge and solvation induce and stabilize the extended conformation, respectively. A mechanism of inter-conversion between the extended conformer and three bent conformers is supported by φ/ψ-scatter plots, and by the conformer relative free energies. An estimate of the entropy change of receptor unbinding is 8.3 cal K-1 mol-1, which gives rise to a -2.5 kcal/mol entropy contribution to the free energy of unbinding at 25 °C. The conformational analysis methodology described here should be useful in studies on short peptides and flexible protein surface loops that have important biological implications.

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

    PubMed

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

    2015-04-07

    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.

  10. First Principals and Classical Molecular Dynamics Simulations of Solvated Benzene

    SciTech Connect

    Allesch, M; Lightstone, F; Schwegler, E; Galli, G

    2007-09-11

    We have performed extensive ab initio and classical MD simulations of benzene in water in order to examine the unique solvation structures that are formed. Qualitative differences between classical and ab initio MD simulations are found and the importance of various technical simulation parameters is examined. Our comparison indicates that non-polarizable classical models are not capable of describing the solute-water interface correctly if local interactions become energetically comparable to water hydrogen bonds. In addition, a comparison is made between a rigid water model and fully flexible water within ab initio MD simulations which shows that both models agree qualitatively for this challenging system.

  11. CO2 solvation free energy using quasi-chemical theory

    NASA Astrophysics Data System (ADS)

    Jiao, Dian; Rempe, Susan B.

    2011-06-01

    Accumulation of greenhouse gases, especially carbon dioxide, is believed to be the key factor in global climate change. To develop effective ways to remove CO2 from the atmosphere, it is helpful to understand the mechanism of CO2 solvation first. Here we investigate the thermodynamics of CO2 hydration using quasi-chemical theory. Two approaches for estimating hydration free energy are carried out. Both agree reasonably well with experimental measurements. Analysis of the free energy components reveals that the weak hydration free energy results from a balance of unfavorable molecular packing and favorable chemical association.

  12. Protein Folding, Stability, and Solvation Structure in Osmolyte Solutions

    PubMed Central

    Rösgen, Jörg; Pettitt, B. Montgomery; Bolen, David Wayne

    2005-01-01

    An understanding of the impact of the crowded conditions in the cytoplasm on its biomolecules is of clear importance to biochemical, medical, and pharmaceutical science. Our previous work on the use of small biochemical compounds to crowd protein solutions indicates that a quantitative description of their nonideal behavior is possible and straightforward. Here, we show the structural origin of the nonideal solution behavior. We discuss the consequences of these findings regarding protein folding stability and solvation in crowded solutions through a structural analysis of the m-value or the change in free-energy difference of a macromolecule in solution with respect to the concentration of a third component. PMID:16113118

  13. Solvation of Coumarin 480 within nano-confining environments: Structure and dynamics

    NASA Astrophysics Data System (ADS)

    Elola, M. Dolores; Rodriguez, Javier

    2014-01-01

    Equilibrium and dynamical characteristics pertaining to the solvation of the fluorescent probe Coumarin 480 within different confining environments are investigated using molecular dynamics simulations. Three kinds of confining systems are examined: (i) the cetyltrimethylammonium bromide (CTAB)/isooctane/1-hexanol/water; cationic inverse micelle (IM) (ii) a CTAB/water direct micelle (DM), and (iii) a silica-surfactant nanocomposite, comprising a cylindrical silica pore (SP) containing small amounts of water and CTAB species adsorbed at the pore walls. The solvation structures in the three environments differ at a qualitative level: an exchange between bulk- and interface-like solvation states was found in the IM, whereas in the DM, the solvation states of the probe are characterized by its embedding at the interface, trapped among the surfactant heads and tails. Within the SP structure, the coumarin exhibits alternations between internal and interfacial solvation states that occur on a ˜20 ns time scale and operate via 90° rotations of its molecular plane. The solvation responses of the environment following a vertical excitation of the probe are also investigated. Solvation times resulted between 2 and 1000 times longer than those found in bulk water, with a fast-to-slow trend IM→DM→SP, which can be interpreted in terms of the solvation structures that prevail in each case.

  14. Spectroscopic studies of solvated hydrogen and hydroxide ions at aqueous surfaces.

    PubMed

    Tarbuck, Teresa L; Ota, Stephanie T; Richmond, Geraldine L

    2006-11-15

    Measuring the molecular properties of the surface of acidic and basic aqueous solutions is essential to understanding a wide range of important biological, chemical, and environmental processes on our planet. In the present studies, vibrational sum-frequency spectroscopy (VSFS) is employed in combination with isotopic dilution experiments at the vapor/water interface to elucidate the interfacial water structure as the pH is varied with HCl and NaOH. In acidic solutions, solvated proton species are seen throughout the interfacial region, and they alter the hydrogen bonding between water molecules in ways that reflect their depth in the interfacial region. At the higher frequencies of the OH stretch region, there is spectral evidence for solvated proton species residing in the topmost layers of the interfacial region. As reported in previous VSF studies, more strongly bound solvated proton species are observed at lower OH stretching frequencies. The solvated proton species that have stronger hydrogen bonding are similar in structure to those found in bulk acid solutions and likely reside somewhat deeper in the interfacial region. There is also evidence of OH stretching from solvated protons and relatively strong hydrogen bonding in the solvation sphere that is similar to other solvated ions. In contrast, water molecules solvating OH(-) ions show relatively weak hydrogen bonding and significantly less interfacial order. VSF spectra are acquired under multiple polarizations to provide crucial information for the interpretation of the spectra and for the determination of interfacial structure.

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

    PubMed

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

    2016-12-21

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

  16. 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.

  17. Solvation structure and dynamics of Li+ ion in liquid water, methanol and ethanol: A comparison study

    NASA Astrophysics Data System (ADS)

    Zeng, Yongping; Wang, Chunfeng; Zhang, Xiaobin; Ju, Shengui

    2014-03-01

    Car-Parrinello molecular dynamics was performed on Li+ in water, methanol and ethanol. Structural and dynamical properties of Li+ were studied and compared with experimental data. Excellent agreement was obtained with the experimental data for the structure of the first solvation shell. The results show the Li+ has a more stable tetrahedral coordination in water and methanol than that in ethanol. The diffusion of water in its first solvation shell was rather slow. Compared to water and methanol, the ethanol in the first solvation shell diffuses slower. The decay of orientational profiles of the solvent molecules in the solvation shell shows slower relaxation for first and second rank correlations compared to bulk water and methanol. The decay of orientational correlations for solvation shell molecules shows faster relaxation compared to that of bulk ethanol. Spectral of bound solvent molecules are compared to those of the bulk. Reasonable agreement is obtained with experiments.

  18. Molecular Thermodynamics of Methane Solvation in tert-Butanol-Water Mixtures.

    PubMed

    Lee, Maeng-Eun; Van der Vegt, Nico F A

    2007-01-01

    We studied solvation structure and thermodynamics of methane in mixtures of tert-butanol and water using computer simulations. We show that for alcohol mole fractions below 20%, methane is preferentially solvated by hydrated alcohol clusters. Because methane expels water molecules from these clusters, a large endothermic solvent reorganization enthalpy occurs. This process is responsible for the experimentally observed maximum of the heat of methane solvation close to 5% alcohol in the mixture and contributes to a positive entropy change relative to solvation in pure water. Because the structural solvent reorganization enthalpy is enthalpy-entropy compensating, the methane solvation free energy is a smoothly varying function of the alcohol/water solution composition.

  19. 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.

  20. Femtosecond infrared studies of solvation by directly probing the solvent

    SciTech Connect

    Yang, H.; Lian, T.; Asplund, M.

    1996-12-31

    In this paper, we report studies of solvation dynamics by directly probing solvent vibrational motions. The IR spectral changes in the CN stretching mode region of a series of nitrile solvents were studied after excitation of solute dye molecules from the S{sub 0} to S{sub 1} state. For LDS750 molecules that have a large dipole moment change from the ground to excited state, the observed signal consists of (1) a time-dependent spectral shift of the CN stretching band, and (2) a broad feature with an instrument response limited rise and multiexponential decays. The decay time constants correspond well to the solvation times of these solvents. However, these solvent spectral changes were not observed for dye molecules that have small dipole moment changes such as R6G, or short lived (<1 ps) excited states such as phenol blue. We assign these signals to the change of solvent vibrational spectra in response to the change of solute dipole field, although the origin of these solvents modes is still not clear. Presently, these solvent responses are being studied by molecular dynamics simulations that include solvent vibrational modes.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. "I am the Author and Must Take Full Responsibility": Abraham Verghese, Physicians as the Storytellers of the Body, and the Renewal of Medicine.

    PubMed

    Nussbaum, Abraham M

    2016-12-01

    Abraham Verghese proposes to renew medicine by training physicians to read the right texts-literary fiction and patients' bodies-with skilled attention. Analyzing Verghese's proposal with reference to Foucault's idea of the "clinical gaze," I find that Verghese conceives of patients as texts that only physicians can read, meaning that physicians become the storytellers of the bodies, lives, and deaths of the people they meet as patients. I conclude that Verghese's project is unsustainable and alternatively propose thinking analogically of physicians as ship captains who maintain therapeutic distance to reopen interpretative spaces for communities outside of medicine.

  6. 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.

  7. Modeling drug-melanin interaction with theoretical linear solvation energy relationships.

    PubMed

    Lowrey, A H; Famini, G R; Loumbev, V; Wilson, L Y; Tosk, J M

    1997-10-01

    The affinity of drugs and other xenobiotic agents for melanin is a well-known phenomenon, often occurring with serious physiological consequences. For example, the interaction of anti-psychotic drugs with neuromelanin may play a pivotal role in the induction of extrapyramidal movement disorders associated with the chronic administration of phenothiazine and other neuroleptic agents. Little, however, is known about the complete nature of melanin-drug binding and the impact of these interactions on the physico-chemical properties of melanin. Data, such as binding affinities, can be analyzed using recently developed computational methods that combine mathematical models of chemical structure with statistical analysis. In particular, theoretical linear solvation energy relationships provide a convenient model for understanding and predicting biological, chemical, and physical properties. By using this modeling technique, drug-melanin binding of a set of 16 compounds has been analyzed with correlation analysis and a set of theoretical molecular parameters in order to better understand and characterize drug-melanin interactions. The resulting correlation equation supports a charge transfer model for drug-melanin complex formation and can also be used to estimate binding constants for related compounds.

  8. 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.

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

    SciTech Connect

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

    1986-04-01

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

  10. The conformational free-energy map for solvated neocarrabiose.

    PubMed

    Ueda, Kazuyoshi; Ueda, Tatsuro; Sato, Taiken; Nakayama, Haruo; Brady, John W

    2004-08-02

    A Ramachandran map of the conformational potential of mean force (pmf) for neocarrabiose in water was obtained using molecular dynamics (MD) simulations with umbrella sampling. The potential energy map calculated in a previous study for this molecule in vacuum exhibited a global minimum located at (phi = 81 degrees, psi = -141 degrees). However, the global minimum on the new pmf map in aqueous solution is located in an area centered around (phi = 175 degrees, psi = 180 degrees), indicating a considerable solvent shift. This new global minimum-energy solution conformation was found to correspond to the experimental value obtained from NMR-NOE measurements, and is also consistent with the experimental crystal structure for neocarrabiose and the fiber diffraction conformation for iota-carrageenan. The global minimum of the solution pmf and its local topology were found to be approximately reproduced by quick vacuum conformational energy mapping using several approximations that mimic solvation effects by de-emphasizing intramolecular hydrogen bonding.

  11. 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

  12. Protein folding, stability, and solvation structure in osmolyte solutions hydrophobicity

    NASA Astrophysics Data System (ADS)

    Montgomery Pettitt, B.

    2008-03-01

    The hydrophobic effect between solutes in aqueous solutions plays a central role in our understanding of recognition and folding of proteins and self assembly of lipids. Hydrophobicity induces nonideal solution behavior which plays a role in many aspects of biophysics. Work on the use of small biochemical compounds to crowd protein solutions indicates that a quantitative description of their non-ideal behavior is possible and straightforward. Here, we will show what the structural origin of this non-ideal solution behavior is from expression derived from a semi grand ensemble approach. We discuss the consequences of these findings regarding protein folding stability and solvation in crowded solutions through a structural analysis of the m-value or the change in free energy difference of a macromolecule in solution with respect to the concentration of a third component. This effect has recently been restudied and new mechanisms proposed for its origins in terms of transfer free energies and hydrophobicity.

  13. Improved Dielectric Solvation Model for Electronic Structure Calculations

    SciTech Connect

    Chipman, Daniel M.

    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.

  14. 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.

  15. Calculating Free Energy Changes in Continuum Solvation Models

    SciTech Connect

    Ho, Junming; Ertem, Mehmed Z.

    2016-02-27

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

  16. Molecular dynamics simulation of solvated protein at high pressure.

    PubMed

    Kitchen, D B; Reed, L H; Levy, R M

    1992-10-20

    We have completed a molecular dynamics simulation of protein (bovine pancreatic trypsin inhibitor, BPTI) in solution at high pressure (10 kbar). The structural and energetic effects of the application of high pressure to solvated protein are analyzed by comparing the results of the high-pressure simulation with a corresponding simulation at low pressure. The volume of the simulation cell containing one protein molecule plus 2943 water molecules decreases by 24.7% at high pressure. This corresponds to a compressibility for the protein solution of beta = 1.8 x 10(-2) kbar-1. The compressibility of the protein is estimated to be about one-tenth that of bulk water, while the protein hydration layer water is found to have a greater compressibility as compared to the bulk, especially for water associated with hydrophobic groups. The radius of gyration of BPTI decreases by 2% and there is a one third decrease in the protein backbone atomic fluctuations at high pressure. We have analyzed pressure effects on the hydration energy of the protein. The total hydration energy is slightly (4%) more favorable at high pressure even though the surface accessibility of the protein has decreased by a corresponding amount. Large pressure-induced changes in the structure of the hydration shell are observed. Overall, the solvation shell waters appear more ordered at high pressure; the pressure-induced ordering is greatest for nonpolar surface groups. We do not observe evidence of pressure-induced unfolding of the protein over the 100-ps duration of the high-pressure simulation. This is consistent with the results of high-pressure optical experiments on BPTI.(ABSTRACT TRUNCATED AT 250 WORDS)

  17. Calculating Free Energy Changes in Continuum Solvation Models

    DOE PAGES

    Ho, Junming; Ertem, Mehmed Z.

    2016-02-27

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

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

    PubMed

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

    2017-01-31

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

  19. A morphometric approach for the accurate solvation thermodynamics of proteins and ligands.

    PubMed

    Harano, Yuichi; Roth, Roland; Chiba, Shuntaro

    2013-09-05

    We have developed a versatile method for calculating solvation thermodynamic quantities for molecules, starting from their atomic coordinates. The contribution of each atom to the thermodynamic quantities is estimated as a linear combination of four fundamental geometric measures of the atomic species, which are defined by Hadwiger's theorem, and the coefficients reflecting their solvation properties. This treatment enables us to calculate the solvation free energy with high accuracy despite of the limited computational load. The method can readily be applied to macromolecules in an all-atom molecular model, allowing the stability of these molecules' structures in solution to be evaluated.

  20. 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.

  1. The catalytic diversity of zeolites: confinement and solvation effects within voids of molecular dimensions.

    PubMed

    Gounder, Rajamani; Iglesia, Enrique

    2013-05-04

    The ability of molecular sieves to control the access and egress of certain reactants and products and to preferentially contain certain transition states while excluding others based on size were captured as shape selectivity concepts early in the history of zeolite catalysis. The marked consequences for reactivity and selectivity, specifically in acid catalysis, have since inspired and sustained many discoveries of novel silicate frameworks and driven the engineering of hierarchical structures and void size to influence catalysis. The catalytic diversity of microporous voids is explored and extended here in the context of their solvating environments, wherein voids act as hosts and stabilize guests, whether reactive intermediates or transition states, by van der Waals forces. We use specific examples from acid catalysis, including activation of C-C and C-H bonds in alkanes, alkylation and hydrogenation of alkenes, carbonylation of dimethyl ether, and elimination and homologation reactions of alkanols and ethers, which involve transition states and adsorbed precursors of varying size and composition. Mechanistic interpretations of measured turnover rates enable us to assign precise chemical origins to kinetic and thermodynamic constants in rate equations and, in turn, to identify specific steps and intermediates that determine the free energy differences responsible for chemical reactivity and selectivity. These free energy differences reflect the stabilization of transition states and their relevant precursors via electrostatic interactions that depend on acid strength and van der Waals interactions that depend on confinement within voids. Their respective contributions to activation free energies are examined by Born-Haber thermochemical cycles by considering plausible transition states and the relevant precursors. These examples show that zeolite voids solvate transition states and precursors differently, and markedly so for guest moieties of different size and

  2. 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.

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

    PubMed

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

    2015-06-07

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

  4. Potential of mean force in confined colloids: integral equations with fundamental measure bridge functions.

    PubMed

    Ayadim, A; Malherbe, J G; Amokrane, S

    2005-06-15

    The potential of mean force for uncharged macroparticles suspended in a fluid confined by a wall or a narrow pore is computed for solvent-wall and solvent-macroparticle interactions with attractive forces. Bridge functions taken from Rosenfeld's density-functional theory are used in the reference hypernetted chain closure of the Ornstein-Zernike integral equations. The quality of this closure is assessed by comparison with simulation. As an illustration, the role of solvation forces is investigated. When the "residual" attractive tails are given a range appropriate to "hard sphere-like" colloids, the unexpected role of solvation forces previously observed in bulk colloids is confirmed in the confinement situation.

  5. Controlled Formation and Vibrational Characterization of Large Solvated Ionic Clusters in Cryogenic Ion Traps

    NASA Astrophysics Data System (ADS)

    Garand, Etienne; Marsh, Brett; Voss, Jonathan; Duffy, Erin M.

    2016-06-01

    An experimental approach for the formation of solvated ionic clusters and their vibrational spectroscopy will be presented. This recently developed apparatus combines an electrospray ionization source, two temperature controlled cryogenic ion traps and a time-of-flight infrared photofragmentation spectrometer, to allow for a universal and controlled formation and characterization of solvent clusters around ionic core as well as product of ion-molecule reaction. Recent results on the spectroscopy of such solvated ions, will be presented and discussed. In particular, this talk will present the structural evolution of glycylglycine as a function of stepwise solvation, and show how the presence of just a few water can modify the geometry of this model peptide. I will also present results solvation of ion that do not form hydrogen bond or strongly interactions with the solvent.

  6. 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.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

  9. 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...

  10. 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.

  11. Preferable solvatation of decane and benzene in 1-octanol- N, N-dimethylformamide mixed solvent

    NASA Astrophysics Data System (ADS)

    Kustov, A. V.; Smirnova, N. L.; Berezin, M. B.

    2014-01-01

    Heat effects of the dissolution of decane and benzene in a model system of 1-octanol (OctOH)- N, N-dimethylformamide are measured at 298 and 318 K using a variable temperature calorimeter with an isotermic shell. The state of hydrocarbon molecules in the mixed solvent is studied using an extended coordination model and is compared to earlier data for ethyl acetate (EtOAc), DMF, OctOH, and tetramethyl hematoporphyrin (TMHP). It is shown that the polar carboxylic groups of porphyrin are preferably solvated by amide molecules due to stronger interaction with DMF, while nonpolar aliphatic groups are solvated by alcohol molecules. We conclude that a solvate shell of aromatic benzene is strongly enriched with DMF over the range of compositions, suggesting that the weakening of the preferable solvatation of porphyrin relative to EtOAc is due primarily to the influence of nonpolar substituents.

  12. Spicing up continuum solvation models with SaLSA: the spherically averaged liquid susceptibility ansatz.

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

    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. 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.

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

    SciTech Connect

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

    2014-10-07

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

  16. Hydrophobic hydration: Heat capacity of solvation from computer simulations and from an information theory approximation

    NASA Astrophysics Data System (ADS)

    Arthur, Jonathan W.; Haymet, A. D. J.

    1999-03-01

    Hydrophobic hydration is studied with an information theory approximation, using the first two moments of the number of solvent centers in a cavity in liquid water, calculated from the density and the pair correlation function. The excess chemical potential, entropy, and heat capacity of solvation are determined for three cases: the two-dimensional MB model of water, in both the (i) NPT and (ii) NVT ensembles, and (iii) the central force CF1 model of water in the NPT ensemble. The results are compared with Monte Carlo simulations and experimental measurements from the literature. The information theory approximation, using only the first two moments, accurately determines the excess chemical potential and entropy of solvation but is unable to predict the excess heat capacity of solvation. Little difference is found between the results obtained using the uniform prior and the ideal gas prior. Molecular dynamics simulations are performed to calculate the excess chemical potential of solvation of soft-spheres as a function of solute size. These results are compared with the solvation of a hard sphere using the information theory approximation and previous molecular dynamics simulations of Lennard-Jones spheres in water. The information theory approximation is found to predict the free energy of solvation as a function of size accurately up to a cavity diameter of approximately 3.5 Å.

  17. Footprinting molecular electrostatic potential surfaces for calculation of solvation energies.

    PubMed

    Calero, Christian Solis; Farwer, Jochen; Gardiner, Eleanor J; Hunter, Christopher A; Mackey, Mark; Scuderi, Serena; Thompson, Stuart; Vinter, Jeremy G

    2013-11-07

    A liquid is composed of an ensemble of molecules that populate a large number of different states, so calculation of the solvation energy of a molecule in solution requires a method for summing the interactions with the environment over all of these states. The surface site interaction model for the properties of liquids at equilibrium (SSIMPLE) simplifies the surface of a molecule to a discrete number of specific interaction sites (SSIPs). The thermodynamic properties of these interaction sites can be characterised experimentally, for example, through measurement of association constants for the formation of simple complexes that feature a single H-bonding interaction. Correlation of experimentally determined solution phase H-bond parameters with gas phase ab initio calculations of maxima and minima on molecular electrostatic potential surfaces (MEPS) provides a method for converting gas phase calculations on isolated molecules to parameters that can be used to estimate solution phase interaction free energies. This approach has been generalised using a footprinting technique that converts an MEPS into a discrete set of SSIPs (each described by a polar interaction parameter, εi). These SSIPs represent the molecular recognition properties of the entire surface of the molecule. For example, water is described by four SSIPs, two H-bond donor sites and two H-bond acceptor sites. A liquid mixture is described as an ensemble of SSIPs that represent the components of the mixture at appropriate concentrations. Individual SSIPs are assumed to be independent, so speciation of SSIP contacts can be calculated based on properties of the individual SSIP interactions, which are given by the sum of a polar (εiεj) and a non-polar (E(vdW)) interaction term. Results are presented for calculation the free energies of transfer of a range of organic molecules from the pure liquid into water, from the pure liquid into n-hexadecane, from n-hexadecane into water, from n-octanol into

  18. 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

  19. FAMBE-pH: a fast and accurate method to compute the total solvation free energies of proteins.

    PubMed

    Vorobjev, Yury N; Vila, Jorge A; Scheraga, Harold A

    2008-09-04

    A fast and accurate method to compute the total solvation free energies of proteins as a function of pH is presented. The method makes use of a combination of approaches, some of which have already appeared in the literature; (i) the Poisson equation is solved with an optimized fast adaptive multigrid boundary element (FAMBE) method; (ii) the electrostatic free energies of the ionizable sites are calculated for their neutral and charged states by using a detailed model of atomic charges; (iii) a set of optimal atomic radii is used to define a precise dielectric surface interface; (iv) a multilevel adaptive tessellation of this dielectric surface interface is achieved by using multisized boundary elements; and (v) 1:1 salt effects are included. The equilibrium proton binding/release is calculated with the Tanford-Schellman integral if the proteins contain more than approximately 20-25 ionizable groups; for a smaller number of ionizable groups, the ionization partition function is calculated directly. The FAMBE method is tested as a function of pH (FAMBE-pH) with three proteins, namely, bovine pancreatic trypsin inhibitor (BPTI), hen egg white lysozyme (HEWL), and bovine pancreatic ribonuclease A (RNaseA). The results are (a) the FAMBE-pH method reproduces the observed pK a's of the ionizable groups of these proteins within an average absolute value of 0.4 p K units and a maximum error of 1.2 p K units and (b) comparison of the calculated total pH-dependent solvation free energy for BPTI, between the exact calculation of the ionization partition function and the Tanford-Schellman integral method, shows agreement within 1.2 kcal/mol. These results indicate that calculation of total solvation free energies with the FAMBE-pH method can provide an accurate prediction of protein conformational stability at a given fixed pH and, if coupled with molecular mechanics or molecular dynamics methods, can also be used for more realistic studies of protein folding, unfolding, and

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    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.

  2. Infinite dilution activity coefficients from ab initio solvation calculations

    SciTech Connect

    Lin, S.T.; Sandler, S.I.

    1999-12-01

    A Group Contribution Solvation (GCS) model was developed to calculate infinite dilution activity coefficients ({gamma}{sup {chi}}) based on modern computational chemistry. The GCS model results in an average error of 7% in {gamma}{sup {chi}} for the limited number of data points among water, n-hexane, acetonitrile and n-octanol, whereas the errors are 47% and 52% with the UNIFAC model and the modified UNIFAC model, respectively. GCS was also used to calculate infinite dilution partition coefficients, which can be used to determine how a dilute solute partitions between two solvents. Solutes were examined in three different liquid-liquid systems: water/n-hexane, water/acetonitrile, and water/n-octanol. With GCS, the average errors are 22% (for 18 solutes), 18% (for 14 solutes) and 14% (for 15 solutes) for these solvent systems, while comparable errors are 237%, 286% and 226% with UNIFAC; and 342%, 414% and 306% with modified UNIFAC. The GCS model is a powerful new tool to predict the octanol-water partition coefficients.

  3. Solvation of Na+, K+, and their dimers in helium.

    PubMed

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

    2012-04-02

    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(+)He(n), K(+)He(n), Na(2)(+)He(n) and K(2)(+)He(n), 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. Na(2)(+)He(n) displays two distinct anomalies at n=2 and n=6, in agreement with theory; dissociation energies derived from experiment closely track theoretical values. K(2)(+)He(n) distributions are fairly featureless, which also agrees with predictions.

  4. 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).

  5. 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.

  6. 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

  7. Internal energy effects on the solvation and reactivity of multiply charged biomolecules for electrospray ionization mass spectroscopy. [Bovine ubiquitin

    SciTech Connect

    Light-Wahl, K.J.; Winger, B.E.; Rockwood, A.L.; Smith, R.D.

    1992-06-01

    Mild (capillary) interface conditions which do not completely desolvate the ions of proteins in electrospray ionization mass spectrometry (ESI-MS) may be required to probe the higher order structures and weak associations. For the small protein bovine ubiquitin, two ion distributions (unsolvated ions and unresolved solvated ions) were observed. The resolvable solvation for leucine-enkephalin with methanol and water shows that the use of countercurrent N{sub 2} flow at the capillary affects the solvation observed. 2 figs. (DLC)

  8. Internal energy effects on the solvation and reactivity of multiply charged biomolecules for electrospray ionization mass spectroscopy

    SciTech Connect

    Light-Wahl, K.J.; Winger, B.E.; Rockwood, A.L.; Smith, R.D.

    1992-06-01

    Mild (capillary) interface conditions which do not completely desolvate the ions of proteins in electrospray ionization mass spectrometry (ESI-MS) may be required to probe the higher order structures and weak associations. For the small protein bovine ubiquitin, two ion distributions (unsolvated ions and unresolved solvated ions) were observed. The resolvable solvation for leucine-enkephalin with methanol and water shows that the use of countercurrent N{sub 2} flow at the capillary affects the solvation observed. 2 figs. (DLC)

  9. 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.

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

    PubMed

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

    2011-11-01

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

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

    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.

  12. Equation poems

    NASA Astrophysics Data System (ADS)

    Prentis, Jeffrey J.

    1996-05-01

    One of the most challenging goals of a physics teacher is to help students see that the equations of physics are connected to each other, and that they logically unfold from a small number of basic ideas. Derivations contain the vital information on this connective structure. In a traditional physics course, there are many problem-solving exercises, but few, if any, derivation exercises. Creating an equation poem is an exercise to help students see the unity of the equations of physics, rather than their diversity. An equation poem is a highly refined and eloquent set of symbolic statements that captures the essence of the derivation of an equation. Such a poetic derivation is uncluttered by the extraneous details that tend to distract a student from understanding the essential physics of the long, formal derivation.

  13. Penetration equations

    SciTech Connect

    Young, C.W.

    1997-10-01

    In 1967, Sandia National Laboratories published empirical equations to predict penetration into natural earth materials and concrete. Since that time there have been several small changes to the basic equations, and several more additions to the overall technique for predicting penetration into soil, rock, concrete, ice, and frozen soil. The most recent update to the equations was published in 1988, and since that time there have been changes in the equations to better match the expanding data base, especially in concrete penetration. This is a standalone report documenting the latest version of the Young/Sandia penetration equations and related analytical techniques to predict penetration into natural earth materials and concrete. 11 refs., 6 tabs.

  14. 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).

  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.

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

    PubMed

    Oliveira, Ivan P; Martínez, Leandro

    2016-08-21

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

  17. Ultrafast solvation dynamics in water: Isotope effects and comparison with experimental results

    NASA Astrophysics Data System (ADS)

    Nandi, Nilashis; Roy, Srabani; Bagchi, Biman

    1995-01-01

    A detailed theoretical study of solvation dynamics in water is presented. The motivation of the present study comes from the recent experimental observation that the dynamics of solvation of an ion in water is ultrafast and the solvation time correlation function decays with a time constant of about 55 fs. The slower decay in the long time can be described by a sum of two exponentials with time constants equal to 126 and 880 fs. The molecular theory (developed earlier) predicts a time constant equal to 52 fs for the initial Gaussian decay and time constants equal to 134 and 886 fs for the two exponential components at the long time. This nearly perfect agreement is obtained by using the most detailed dynamical information available in the literature. The present study emphasizes the importance of the intermolecular vibrational band originating from the O...O stretching mode of the O-H...O units in the initial dynamics and raises several interesting questions regarding the nature of the decay of this mode. We have also studied the effects of isotope substitution on solvation dynamics. It is predicted that a significant isotope effect may be observed in the long time. The experimental results have also been compared with the prediction of the dynamic mean spherical approximation (DMSA); the agreement is not satisfactory at the long time. It is further found that the molecular theory and the DMSA lead to virtually identical results if the translational modes of the solvent molecules are neglected in the former. DMSA has also been used to investigate the dynamics of solvation of a dipolar solute in water. It is found that the dynamics of dipolar solvation exhibit features rather different from those of ion solvation.

  18. Photoelectron Spectroscopy of Rare-Gas Solvated Nucleobase Anions

    NASA Astrophysics Data System (ADS)

    Buonaugurio, Angela M.; Chen, Jing; Bowen, Kit H.

    2012-06-01

    Gas-phase polar molecular anions [uracil (U^-), thymine (T^-), 1-3 dimethyluracil (DMU^-)] solvated by rare gas atoms were studied by means of negative ion photoelectron spectroscopy. The photoelectron spectrum (PES) of U^-, T^-, and DMU^- each exhibit a distinctive dipole-bound (DB) spectral signature. The spectra of U^-, U^- (Ar)_1,2 and U^- (Kr)_1 also only displayed the DB anion feature. Upon the solvation of more rare gas atoms, the spectra of U^- (Ar)_3, U^- (Kr)_2, and U^- (Xe)1-3 not only retained the DB signature but also exhibited the valence anion features. Moreover, the DB and the valence features shifted together to higher electron binding energies (EBEs) with increasing numbers of rare gas solvent atoms. Therefore, the co-existing DB and the valence anions appeared to be strongly coupled with each other, i.e. they effectively form a single state that is a superposition of both DB and valence anion states. For both U^- and T^- series, the ``onset size" of the Xe, Kr, and Ar solvents for the co-existing of the two anionic states was 1, 2, and 3 respectively. In addition, a minimum of 2 methane (CH_4) molecules or 1 ethane (C_2H_6) molecule were required to induce the coupling between the two states in the T^- series. Thus, the nucleobase anion interaction with non-polar solvent atoms tracks as the sum of the solvent polarizabilities. However for the DMU- series, the DB and the valence anions of DMU^-(Xe)_1, DMU^-(Kr)_2, and DMU^-(Ar)_3 were completely absent in both the mass spectra and the PES. Beyond these ``holes", their PES displayed the similar behaviors to the U^- and T^- series. Extrapolated EA values for these missing species were at or very close to zero, which may explain why they were not seen. However, why this was the case is not clear. With better Franck-Condon overlap between the origins of the NB^- (Rg)_n valence anion and the neutral NB(Rg)n than between those of the NB^- (H2O)n valence anion and the neutral NB(H2O)n, extrapolation of

  19. Polar solvation dynamics of polyatomic solutes: Simulation studies in acetonitrile and methanol

    NASA Astrophysics Data System (ADS)

    Kumar, P. V.; Maroncelli, M.

    1995-08-01

    This paper describes results of simulations of solvation dynamics of a variety of solutes in two reference solvents, acetonitrile and methanol. Part of these studies involve attempts to realistically model the solvation dynamics observed experimentally with the fluorescence probe coumarin 153 (C153). After showing that linear response simulations afford a reliable route to the dynamics of interest, experimental and simulation results for C153 are compared. Agreement between the observed and calculated dynamics is found to be satisfactory in the case of acetonitrile but poor in the case of methanol. The latter failure is traced to a lack of realism in the dielectric properties of the methanol model employed. A number of further simulations are then reported for solvation of a number of atomic, diatomic, and benzenelike solutes which are used to elucidate what features of the solute are important for determining the time dependence of the solvation response. As far as large polyatomic solutes like C153 are concerned, the solute attribute of foremost importance is shown to be the ``effective moment'' of its charge distribution (actually the difference between the S1 and S0 charge distributions). This effective moment, determined from consideration of continuum electrostatics, provides a simple measure of how rapidly the solute's electric field varies spatially in the important regions of the solvent. Simulations of fictitious excitations in a benzene solute show that this single quantity is able to correlate the dynamics observed in widely different solutes. Also explored is the effect of solute motion on its solvation dynamics. While of minor relevance for large solutes like C153, in small solutes of the size of benzene, solute motion can dramatically enhance the rate of solvation. A model based on independent solvent dynamics and solute rotational motion is able to account for the bulk of the observed effects. Finally, the influence of solute polarizability on

  20. Thermosolvatochromism of betaine dyes revisited: theoretical calculations of the concentrations of alcohol-water hydrogen-bonded species and application to solvation in aqueous alcohols.

    PubMed

    Bastos, Erick L; Silva, Priscilla L; El Seoud, Omar A

    2006-08-31

    Solvatochromic data of 2,6-diphenyl-4-(2,4,6-triphenylpyridinium-1-yl)phenolate (RB) in aqueous methanol, 1-propanol, 2-propanol, and 2-methyl-2-propanol at 25 degrees C were recalculated by employing a recently introduced model that explicitly considers the presence of 1:1 alcohol-water hydrogen-bonded species, ROH-W, in bulk solution and their exchange equilibria with water and alcohol in the probe solvation microsphere. The thermosolvatochromic behavior of RB in aqueous ethanol was measured in the temperature range from 10 to 60 degrees C; the results thus obtained were treated according to the same model. All calculations require reliable values of Kdissoc, the dissociation constant of the ROH-W species. This was previously calculated from the dependence of the density of the binary solvent mixture on its composition. Through the use of iteration, the volume of the hydrogen-bonded species, VROH-W, and Kdissoc are obtained simultaneously from the same set of experimental data. This approach may be potentially problematic because Kdissoc and VROH-W are highly correlated. Therefore, we introduced the following approach: (i) VROH-W was obtained from ab initio calculations, (ii) these volumes were corrected for the nonideal behavior of the binary solvent mixtures at different temperatures, (iii) corrected VROH-W values were employed as a constant in the equation used to calculate Kdissoc (from density vs binary solvent mixture composition). VROH-W calculated by the COSMO-RS solvation model fitted the density data better than those calculated by the IEFPCM model. In all aqueous alcohols, solvation by ROH-W is favored over that by the two precursor solvents. In aqueous ethanol, a temperature increase resulted in a gradual desolvation of RB, due to a decrease in the hydrogen-bonding of both components of the mixture. The microscopic polarities of ROH-W are much closer to those of the precursor alcohols.

  1. Computational solvation dynamics of oxyquinolinium betaine linked to trehalose

    NASA Astrophysics Data System (ADS)

    Heid, Esther; Schröder, Christian

    2016-10-01

    Studying the changed water dynamics in the hydration layers of biomolecules is an important step towards fuller understanding of their function and mechanisms, but has shown to be quite difficult. The measurement of the time-dependent Stokes shift of a chromophore attached to the biomolecule is a promising method to achieve this goal, as published in Sajadi et al. [J. Phys. Chem. Lett., 5, 1845 (2014).] where trehalose was used as biomolecule, 1-methyl-6-oxyquinolinium betaine as chromophore, and water as solvent. An overall retardation of solvent molecules is then obtained by comparison of the linked system to the same system without trehalose, but contributions from different subgroups of solvent molecules, for example, molecules close to or far from trehalose, are unknown. The difficulty arising from these unknown contributions of retarded and possibly unretarded solvent molecules is overcome in this work by conducting computer simulations on this system and decomposing the overall signal into the contributions from various molecules at different locations. We performed non-equilibrium molecular dynamics simulation using a polarizable water model and a non-polarizable solute model and could reproduce the experimental time-dependent Stokes shift accurately for the linked trehalose-oxyquinolinium and the pure oxyquinolinium over a wide temperature range, indicating the correctness of our employed models. Decomposition of the shift into contributions from different solvent subgroups showed that the amplitude of the measured shift is made up only half by the desired retarded solvent molecules in the hydration layer, but to another half by unretarded bulk water, so that measured relaxation times of the overall Stokes shift are only a lower boundary for the true relaxation times in the hydration layer of trehalose. As a side effect, the results on the effect of trehalose on solvation dynamics contribute to the long standing debate on the range of influence of

  2. 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.

  3. 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.

  4. Energetics of Cyclic Dipeptide Crystal Packing and Solvation

    PubMed Central

    Brady, G. Patrick; Sharp, Kim A.

    1997-01-01

    Calculations of the thermodynamics of transfer of the cyclic alanine-alanine (cAA) and glycine-glycine (cGG) dipeptides between the gas, water, and crystal phases were carried out using a combination of molecular mechanics, normal mode analysis, and continuum electrostatics. The experimental gas-to-water solvation free energy and the enthalpy of gas-to-crystal transfer of cGG are accurately reproduced by the calculations. The enthalpies of cGG and cAA crystal-to-water transfer are also close to the experimental values. A combination of experimental data and normal mode analysis of cGG provides an accurate estimate of the association entropy penalty (loss of rotational and translational entropy and gain in vibrational entropy) for “binding” in the crystalline phase of -14.1 cal/mol/K. This is a smaller number than most previous theoretical estimates, but it is similar to previous experimental estimates. Calculated entropies of the crystal phase under-estimate the experimental entropy by about 15 cal/mol/K because of neglect of longe-range lattice motions. Comparison of the intermolecular interactions in the crystals of cGG and cAA provides a possible explanation of the puzzling decrease in enthalpy, with increasing hydrophobicity seen previously for both cyclic dipeptide dissolution and protein unfolding. This decrease arises from a favorable long-range electrostatic interaction between dipeptide molecules in the crystals, which is attenuated by the more hydrophobic side chains. PMID:9017216

  5. 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.

  6. Solvation pressure as real pressure: I. Ethanol and starch under negative pressure

    NASA Astrophysics Data System (ADS)

    van Uden, N. W. A.; Hubel, H.; Faux, D. A.; Tanczos, A. C.; Howlin, B.; Dunstan, D. J.

    2003-03-01

    The reality of the solvation pressure generated by the cohesive energy density of liquids is demonstrated by three methods. Firstly, the Raman spectrum of ethanol as a function of cohesive energy density (solvation pressure) in ethanol-water and ethanol-chloroform mixtures is compared with the Raman spectrum of pure ethanol under external hydrostatic pressure and the solvation pressure and hydrostatic pressure are found to be equivalent for some transitions. Secondly, the bond lengths of ethanol are calculated by molecular dynamics modelling for liquid ethanol under pressure and for ethanol vapour. The difference in bond lengths between vapour and liquid are found to be equivalent to the solvation pressure for the C-H3, C-H2 and O-H bond lengths, with discrepancies for the C-C and C-O bond lengths. Thirdly, the pressure-induced gelation of potato starch is measured in pure water and in mixtures of water and ethanol. The phase transition pressure varies in accordance with the change in solvation pressure of the solvent. These results demonstrate the reality of 'negative pressures' generated by reductions in the cohesive energy density of solvent mixtures.

  7. Scaling Atomic Partial Charges of Carbonate Solvents for Lithium Ion Solvation and Diffusion

    SciTech Connect

    Chaudhari, Mangesh I.; Nair, Jijeesh R.; Pratt, Lawrence R.; Soto, Fernando A.; Balbuena, Perla B.; Rempe, Susan B.

    2016-10-21

    Lithium-ion solvation and diffusion properties in ethylene carbonate (EC) and propylene carbonate (PC) were studied by molecular simulation, experiments, and electronic structure calculations. Studies carried out in water provide a reference for interpretation. Classical molecular dynamics simulation results are compared to ab initio molecular dynamics to assess nonpolarizable force field parameters for solvation structure of the carbonate solvents. Quasi-chemical theory (QCT) was adapted to take advantage of fourfold occupancy of the near-neighbor solvation structure observed in simulations and used to calculate solvation free energies. The computed free energy for transfer of Li+ to PC from water, based on electronic structure calculations with cluster-QCT, agrees with the experimental value. The simulation-based direct-QCT results with scaled partial charges agree with the electronic structure-based QCT values. The computed Li+/PF6- transference numbers of 0.35/0.65 (EC) and 0.31/0.69 (PC) agree well with NMR experimental values of 0.31/0.69 (EC) and 0.34/0.66 (PC) and similar values obtained here with impedance spectroscopy. These combined results demonstrate that solvent partial charges can be scaled in systems dominated by strong electrostatic interactions to achieve trends in ion solvation and transport properties that are comparable to ab initio and experimental results. Thus, the results support the use of scaled partial charges in simple, nonpolarizable force fields in future studies of these electrolyte solutions.

  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.

  9. 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.

  10. Predicting hydrophobic solvation by molecular simulation: 1. Testing united-atom alkane models.

    PubMed

    Jorge, Miguel; Garrido, Nuno M; Simões, Carlos J V; Silva, Cândida G; Brito, Rui M M

    2017-03-05

    We present a systematic test of the performance of three popular united-atom force fields-OPLS-UA, GROMOS and TraPPE-at predicting hydrophobic solvation, more precisely at describing the solvation of alkanes in alkanes. Gibbs free energies of solvation were calculated for 52 solute/solvent pairs from Molecular Dynamics simulations and thermodynamic integration making use of the IBERCIVIS volunteer computing platform. Our results show that all force fields yield good predictions when both solute and solvent are small linear or branched alkanes (up to pentane). However, as the size of the alkanes increases, all models tend to increasingly deviate from experimental data in a systematic fashion. Furthermore, our results confirm that specific interaction parameters for cyclic alkanes in the united-atom representation are required to account for the additional excluded volume within the ring. Overall, the TraPPE model performs best for all alkanes, but systematically underpredicts the magnitude of solvation free energies by about 6% (RMSD of 1.2 kJ/mol). Conversely, both GROMOS and OPLS-UA systematically overpredict solvation free energies (by ∼13% and 15%, respectively). The systematic trends suggest that all models can be improved by a slight adjustment of their Lennard-Jones parameters. © 2016 Wiley Periodicals, Inc.

  11. Redox entropy of plastocyanin: developing a microscopic view of mesoscopic polar solvation.

    PubMed

    LeBard, David N; Matyushov, Dmitry V

    2008-04-21

    We report applications of analytical formalisms and molecular dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of the theory required to describe polar solvation at the mesoscopic scale. The analytical techniques include a microscopic formalism based on structure factors of the solvent dipolar orientations and density and continuum dielectric theories. The microscopic theory employs the atomistic structure of the protein with force-field atomic charges and solvent structure factors obtained from separate MD simulations of the homogeneous solvent. The MD simulations provide linear response solvation free energies and reorganization energies of electron transfer in the temperature range of 280-310 K. We found that continuum models universally underestimate solvation entropies, and a more favorable agreement is reported between the microscopic calculations and MD simulations. The analysis of simulations also suggests that difficulties of extending standard formalisms to protein solvation are related to the inhomogeneous structure of the solvation shell at the protein-water interface combining islands of highly structured water around ionized residues along with partial dewetting of hydrophobic patches. Quantitative theories of electrostatic protein hydration need to incorporate realistic density profile of water at the protein-water interface.

  12. Toward a Molecular-Based Understanding of High-Temperature Solvation Phenomena in Aqueous Electrolyte Solutions

    SciTech Connect

    Chialvo, A.A.; Cummings, P.T.; Kusalik, P.G.; Simonson, J.M.

    1999-10-30

    The theoretical treatment of the solvation phenomenon of simple ions in aqueous solutions has been rather difficult, despite the apparent simplicity of the system. Long-range solvent-screened electrostatic interactions, coupled to the large variation (with state conditions) of the dielectric permittivity of water, give rise to a variety of rather complex solvation phenomena including dielectric saturation, electrostriction, and ion association. Notably, ion solvation in high-temperature/pressure aqueous solutions plays a leading role in hydrothermal chemistry, such as in the natural formation of ore deposits, the corrosion in boilers and reactors, and in high-temperature microbiology. Tremendous effort has been invested in the study of hydrothermal solutions to determine their thermodynamic, transport, and spectroscopic properties with the goal of elucidating the solute-solvent and solute-solute interactions over a wide range of state conditions. It is precisely at these conditions where our understanding and predictive capabilities are most precarious, in part, as a result of the coexistence of processes with two rather different length scales, i.e., short-ranged (solvation) and long-ranged (compressibility-driven) phenomena (Chialvo and Cummings 1994a). The latter feature makes hydrothermal systems extremely challenging to model, unless we are able to isolate the (compressibility-driven) propagation of the density perturbation from the (solvation-related) finite-density perturbation phenomena (Chialvo and Cummings 1995a).

  13. Understanding Lithium Solvation and Diffusion through Topological Analysis of First-Principles Molecular Dynamics

    SciTech Connect

    Bhatia, Harsh; Gyulassy, Attila; Ong, Mitchell; Lordi, Vincenzo; Draeger, Erik; Pask, John; Pascucci, Valerio; Bremer, Peer -Timo

    2016-09-27

    The performance of lithium-ion batteries is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact, both, the solvation and diffusivity of Li ions. In this work, we present our application of the topological techniques to extract and predict such behavior in the data generated by the first-principles molecular dynamics simulation of Li ions in an important organic solvent -ethylene carbonate. More specifically, we use the scalar topology of the electron charge density field to analyze the evolution of the solvation structures. This allows us to derive a parameter-free bond definition for lithium-oxygen bonds, to provide a quantitative measure for bond strength, and to understand the regions of influence of each atom in the simulation. This has provided new insights into how and under what conditions certain bonds may form and break. As a result, we can identify and, more importantly, predict, unstable configurations in solvation structures. This can be very useful in understanding when small changes to the atoms' movements can cause significantly different bond structures to evolve. Ultimately, this promises to allow scientists to explore lithium ion solvation and diffusion more systematically, with the aim of new insights and potentially accelerating the calculations themselves.

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

    PubMed Central

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

    2016-01-01

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

  15. Study of Microheterogeneity in Acetonitrile-Water Binary Mixtures by using Polarity-Resolved Solvation Dynamics.

    PubMed

    Koley, Somnath; Ghosh, Subhadip

    2015-11-16

    The solvation dynamics of three coumarin dyes with widely varying polarities were studied in acetonitrile-water (ACN-H2O) mixtures across the entire composition range. At low ACN concentrations [ACN mole fractions (X(ACN))≤0.1], the solvation dynamics are fast (<40 ps), indicating a nearly homogeneous environment. This fast region is followed by a sudden retardation of the average solvation time (230-1120 ps) at higher ACN concentrations (X(ACN)≈0.2), thus indicating the onset of nonideality within the mixture that continues until X(ACN)≈0.8. This nonideality regime (X(ACN)≈0.2-0.8) comprises of multiple dye-dependent anomalous regions. At very high ACN concentrations (X(ACN)≈0.8-1), the ACN-H2O mixtures regain homogeneity, with faster solvation times. The source of the inherent nonideality of the ACN-H2O mixtures is a subject of debate. However, a careful examination of the widths of time-resolved emission spectra shows that the origin of the slow dynamics may be due to the diffusion of polar solvent molecules into the first solvation shell of the excited coumarin dipole.

  16. Mapping solvation dynamics at the function site of flavodoxin in three redox states.

    PubMed

    Chang, Chih-Wei; He, Ting-Fang; Guo, Lijun; Stevens, Jeffrey A; Li, Tanping; Wang, Lijuan; Zhong, Dongping

    2010-09-15

    Flavoproteins are unique redox coenzymes, and the dynamic solvation at their function sites is critical to the understanding of their electron-transfer properties. Here, we report our complete characterization of the function-site solvation of holoflavodoxin in three redox states and of the binding-site solvation of apoflavodoxin. Using intrinsic flavin cofactor and tryptophan residue as the local optical probes with two site-specific mutations, we observed distinct ultrafast solvation dynamics at the function site in the three states and at the related recognition site of the cofactor, ranging from a few to hundreds of picoseconds. The initial ultrafast motion in 1-2.6 ps reflects the local water-network relaxation around the shallow, solvent-exposed function site. The second relaxation in 20-40 ps results from the coupled local water-protein fluctuation. The third dynamics in hundreds of picoseconds is from the intrinsic fluctuation of the loose loops flanking the cofactor at the function site. These solvation dynamics with different amplitudes well correlate with the redox states from the oxidized form, to the more rigid semiquinone and to the much looser hydroquinone. This observation of the redox control of local protein conformation plasticity and water network flexibility is significant, and such an intimate relationship is essential to the biological function of interprotein electron transfer.

  17. Scaling Atomic Partial Charges of Carbonate Solvents for Lithium Ion Solvation and Diffusion

    DOE PAGES

    Chaudhari, Mangesh I.; Nair, Jijeesh R.; Pratt, Lawrence R.; ...

    2016-10-21

    Lithium-ion solvation and diffusion properties in ethylene carbonate (EC) and propylene carbonate (PC) were studied by molecular simulation, experiments, and electronic structure calculations. Studies carried out in water provide a reference for interpretation. Classical molecular dynamics simulation results are compared to ab initio molecular dynamics to assess nonpolarizable force field parameters for solvation structure of the carbonate solvents. Quasi-chemical theory (QCT) was adapted to take advantage of fourfold occupancy of the near-neighbor solvation structure observed in simulations and used to calculate solvation free energies. The computed free energy for transfer of Li+ to PC from water, based on electronic structuremore » calculations with cluster-QCT, agrees with the experimental value. The simulation-based direct-QCT results with scaled partial charges agree with the electronic structure-based QCT values. The computed Li+/PF6- transference numbers of 0.35/0.65 (EC) and 0.31/0.69 (PC) agree well with NMR experimental values of 0.31/0.69 (EC) and 0.34/0.66 (PC) and similar values obtained here with impedance spectroscopy. These combined results demonstrate that solvent partial charges can be scaled in systems dominated by strong electrostatic interactions to achieve trends in ion solvation and transport properties that are comparable to ab initio and experimental results. Thus, the results support the use of scaled partial charges in simple, nonpolarizable force fields in future studies of these electrolyte solutions.« less

  18. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  20. Selective photoelectrochemical reduction of aqueous CO₂ to CO by solvated electrons.

    PubMed

    Zhang, Linghong; Zhu, Di; Nathanson, Gilbert M; Hamers, Robert J

    2014-09-08

    Reduction of CO2 by direct one-electron activation is extraordinarily difficult because of the -1.9 V reduction potential of CO2. Demonstrated herein is reduction of aqueous CO2 to CO with greater than 90% product selectivity by direct one-electron reduction to CO2(˙-) by solvated electrons. Illumination of inexpensive diamond substrates with UV light leads to the emission of electrons directly into water, where they form solvated electrons and induce reduction of CO2 to CO2(˙-). Studies using diamond were supported by studies using aqueous iodide ion (I(-)), a chemical source of solvated electrons. Both sources produced CO with high selectivity and minimal formation of H2 . The ability to initiate reduction reactions by emitting electrons directly into solution without surface adsorption enables new pathways which are not accessible using conventional electrochemical or photochemical processes.

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

    NASA Astrophysics Data System (ADS)

    van Driel, Tim B.; Kjær, Kasper S.; Hartsock, Robert W.; Dohn, Asmus O.; Harlang, Tobias; Chollet, Matthieu; Christensen, Morten; Gawelda, Wojciech; Henriksen, Niels E.; Kim, Jong Goo; Haldrup, Kristoffer; Kim, Kyung Hwan; Ihee, Hyotcherl; Kim, Jeongho; Lemke, Henrik; Sun, Zheng; Sundström, Villy; Zhang, Wenkai; Zhu, Diling; Møller, Klaus B.; Nielsen, Martin M.; Gaffney, Kelly J.

    2016-11-01

    The interactions between the reactive excited state of molecular photocatalysts and surrounding solvent dictate reaction mechanisms and pathways, but are not readily accessible to conventional optical spectroscopic techniques. Here we report an investigation of the structural and solvation dynamics following excitation of a model photocatalytic molecular system [Ir2(dimen)4]2+, where dimen is para-diisocyanomenthane. The time-dependent structural changes in this model photocatalyst, as well as the changes in the solvation shell structure, have been measured with ultrafast diffuse X-ray scattering and simulated with Born-Oppenheimer Molecular Dynamics. Both methods provide direct access to the solute-solvent pair distribution function, enabling the solvation dynamics around the catalytically active iridium sites to be robustly characterized. Our results provide evidence for the coordination of the iridium atoms by the acetonitrile solvent and demonstrate the viability of using diffuse X-ray scattering at free-electron laser sources for studying the dynamics of photocatalysis.

  2. Structure of the hydrated and dimethyl sulfoxide solvated rubidium ions in solution.

    PubMed

    D'Angelo, Paola; Persson, Ingmar

    2004-05-31

    The structure of the hydrated and the dimethyl sulfoxide solvated rubidium ions in solution has been determined by means of large-angle X-ray scattering (LAXS) and extended X-ray absorption fine structure (EXAFS) studies. The models of the hydrated and dimethyl sulfoxide solvated rubidium ions fitting the experimental data best are square antiprisms with Rb-O bond distances of 2.98(2) and 2.98(3) A, respectively. The EXAFS data show a significant asymmetry in the Rb-O bond distance distribution with C(3) values of 0.0076 and 0.015 A(3), respectively. No second hydration sphere is observed around the hydrated rubidium ion. The dimethyl sulfoxide solvated rubidium ion displays a Rb-O-S bond angle of ca. 130 degrees, which is typical for a medium hard electron acceptor such as rubidium.

  3. High pressure infrared spectroscopy study on C60∗CS2 solvates

    NASA Astrophysics Data System (ADS)

    Du, Mingrun; Zhou, Miao; Yao, Mingguang; Ge, Peng; Chen, Shuanglong; Yang, Xigui; Liu, Ran; Liu, Bo; Cui, Tian; Sundqvist, Bertil; Liu, Bingbing

    2017-02-01

    High pressure IR study has been carried out on C60∗CS2 solvates up to 34.8 GPa. It is found that the intercalated CS2 molecules significantly affect the transformations of C60 molecules under pressure. As a probe, the intercalated CS2 molecules can well detect the orientational ordering transition and deformation of C60 molecules under pressure. The chemical stability of CS2 molecules under pressure is also dramatically enhanced due to the spacial shielding effet from C60 molecules around in the solvated crystal. These results provide new insight into the effect of interactions between intercalants and fullerenes on the transformations in fullerene solvates under pressure.

  4. 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

  5. Solvation in protein (un)folding of melittin tetramer–monomer transition

    PubMed Central

    Othon, Christina M.; Kwon, Oh-Hoon; Lin, Milo M.; Zewail, Ahmed H.

    2009-01-01

    Protein structural integrity and flexibility are intimately tied to solvation. Here, we examine the effect that changes in bulk and local solvent properties have on protein structure and stability. We observe the change in solvation of an unfolding of the protein model, melittin, in the presence of a denaturant, trifluoroethanol. The peptide system displays a well defined transition in that the tetramer unfolds without disrupting the secondary or tertiary structure. In the absence of local structural perturbation, we are able to reveal exclusively the role of solvation dynamics in protein structure stabilization and the (un)folding pathway. A sudden retardation in solvent dynamics, which is coupled to the change in protein structure, is observed at a critical trifluoroethanol concentration. The large amplitude conformational changes are regulated by the local solvent hydrophobicity and bulk solvent viscosity. PMID:19622745

  6. Solvation in protein (un)folding of melittin tetramer-monomer transition.

    PubMed

    Othon, Christina M; Kwon, Oh-Hoon; Lin, Milo M; Zewail, Ahmed H

    2009-08-04

    Protein structural integrity and flexibility are intimately tied to solvation. Here, we examine the effect that changes in bulk and local solvent properties have on protein structure and stability. We observe the change in solvation of an unfolding of the protein model, melittin, in the presence of a denaturant, trifluoroethanol. The peptide system displays a well defined transition in that the tetramer unfolds without disrupting the secondary or tertiary structure. In the absence of local structural perturbation, we are able to reveal exclusively the role of solvation dynamics in protein structure stabilization and the (un)folding pathway. A sudden retardation in solvent dynamics, which is coupled to the change in protein structure, is observed at a critical trifluoroethanol concentration. The large amplitude conformational changes are regulated by the local solvent hydrophobicity and bulk solvent viscosity.

  7. 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.

  8. Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery

    NASA Astrophysics Data System (ADS)

    Lee, Kyung-Koo; Park, Kwanghee; Lee, Hochan; Noh, Yohan; Kossowska, Dorota; Kwak, Kyungwon; Cho, Minhaeng

    2017-03-01

    Lithium cation is the charge carrier in lithium-ion battery. Electrolyte solution in lithium-ion battery is usually based on mixed solvents consisting of polar carbonates with different aliphatic chains. Despite various experimental evidences indicating that lithium ion forms a rigid and stable solvation sheath through electrostatic interactions with polar carbonates, both the lithium solvation structure and more importantly fluctuation dynamics and functional role of carbonate solvent molecules have not been fully elucidated yet with femtosecond vibrational spectroscopic methods. Here we investigate the ultrafast carbonate solvent exchange dynamics around lithium ions in electrolyte solutions with coherent two-dimensional infrared spectroscopy and find that the time constants of the formation and dissociation of lithium-ion...carbonate complex in solvation sheaths are on a picosecond timescale. We anticipate that such ultrafast microscopic fluxional processes in lithium-solvent complexes could provide an important clue to understanding macroscopic mobility of lithium cation in lithium-ion battery on a molecular level.

  9. Ermod: fast and versatile computation software for solvation free energy with approximate theory of solutions.

    PubMed

    Sakuraba, Shun; Matubayasi, Nobuyuki

    2014-08-05

    ERmod is a software package to efficiently and approximately compute the solvation free energy using the method of energy representation. Molecular simulation is to be conducted at two condensed-phase systems of the solution of interest and the reference solvent with test-particle insertion of the solute. The subprogram ermod in ERmod then provides a set of energy distribution functions from the simulation trajectories, and another subprogram slvfe determines the solvation free energy from the distribution functions through an approximate functional. This article describes the design and implementation of ERmod, and illustrates its performance in solvent water for two organic solutes and two protein solutes. Actually, the free-energy computation with ERmod is not restricted to the solvation in homogeneous medium such as fluid and polymer and can treat the binding into weakly ordered system with nano-inhomogeneity such as micelle and lipid membrane. ERmod is available on web at http://sourceforge.net/projects/ermod.

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

    SciTech Connect

    Lee, J.H.; Brunt, V. van; King, C.J. . Dept. of Chemical Engineering Lawrence Berkeley Lab., CA )

    1994-05-01

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

  11. 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

    2016-08-05

    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.

  12. 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.

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

    PubMed

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

    2011-02-07

    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.

  14. 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.

  15. 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.

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

    PubMed

    Rane, Kaustubh; van der Vegt, Nico F A

    2016-03-21

    This work investigates the question if surface capillary waves (CWs) affect interfacial solvation thermodynamic properties that determine the propensity of small molecules toward the liquid-vapor interface. We focus on (1) the evaluation of these properties from molecular simulations in a practical manner and (2) understanding them from the perspective of theories in solvation thermodynamics, especially solvent reorganization effects. Concerning the former objective, we propose a computational method that exploits the relationship between an external field acting on the liquid-vapor interface and the magnitude of CWs. The system considered contains the solvent, an externally applied field (f) and the solute 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.

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

    SciTech Connect

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

    2014-12-19

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

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

    DOE PAGES

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

    2014-12-19

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

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

    PubMed Central

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

    2008-01-01

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

  20. 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.

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

    PubMed

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

    2015-08-07

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

  2. 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.

  3. 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

  4. Dual sites of solvation for electrons produced by photoionisation in aqueous micellar solutions

    NASA Astrophysics Data System (ADS)

    Ghosh, H. N.; Palit, D. K.; Sapre, A. V.; Rama, K. V. S.; Rao; Mittal, J. P.

    1993-02-01

    Laser flash photolysis of either aqueous micellar solutions of triton X-165 at 248 nm or of a probe phenothiazine (PTH) in triton X-165 or brij-35 micelles at 351 nm gives transient absorption peaks at 630 and 720 nm which are attributed to electrons solvated in the palisade region of the nonionic micelle and to electrons hydrated in bulk water. Picosecond studies show that, at the end of a 35 ps pulse, the electrons are already solvated, a major fraction of which undergo geminate recombination with the sibling cations. After 10 ns, both the 630 and 720 nm peaks are clearly seen.

  5. Solvation structure of coumarin 1 in acetonitrile: role of the electrostatic solute solvent potential

    NASA Astrophysics Data System (ADS)

    Diraison, M.; Millie, P.; Pommeret, S.; Gustavsson, T.; Mialocq, J.-Cl

    1998-01-01

    A molecular dynamics simulation study of a coumarin 1 molecule solvated in acetonitrile, in its S 0 and S 1 electronic states, is presented. Three solute-solvent interaction potentials, all containing the same Lennard-Jones component but different electrostatic interactions, have been considered. The structure of the solvent around the large dye solute strongly depends on the electrostatic solute-solvent potential, illustrating the crucial role of the local electric field. An accurate description of the charge distribution of the solute is therefore necessary to describe correctly the solute-solvent structure and the solvation energy.

  6. Angle-Resolved Photoemission of Solvated Electrons in Sodium-Doped Clusters.

    PubMed

    West, Adam H C; Yoder, Bruce L; Luckhaus, David; Saak, Clara-Magdalena; Doppelbauer, Maximilian; Signorell, Ruth

    2015-04-16

    Angle-resolved photoelectron spectroscopy of the unpaired electron in sodium-doped water, methanol, ammonia, and dimethyl ether clusters is presented. The experimental observations and the complementary calculations are consistent with surface electrons for the cluster size range studied. Evidence against internally solvated electrons is provided by the photoelectron angular distribution. The trends in the ionization energies seem to be mainly determined by the degree of hydrogen bonding in the solvent and the solvation of the ion core. The onset ionization energies of water and methanol clusters do not level off at small cluster sizes but decrease slightly with increasing cluster size.

  7. Systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions

    DOEpatents

    Cooks, Robert Graham; Li, Anyin; Luo, Qingjie

    2017-01-24

    The invention generally relates to systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions. In certain aspects, the invention provides methods that involve providing a metal and a solvent. The methods additionally involve applying voltage to the solvated metal to thereby produce solvent droplets including ions of the metal containing compound, and directing the solvent droplets including the metal ions to a target. In certain embodiments, once at the target, the metal ions can react directly or catalyze reactions.

  8. Crystal structure of olanzapine and its solvates. Part 3. Two and three-component solvates with water, ethanol, butan-2-ol and dichloromethane

    NASA Astrophysics Data System (ADS)

    Wawrzycka-Gorczyca, Irena; Borowski, Piotr; Osypiuk-Tomasik, Joanna; Mazur, Liliana; Koziol, Anna E.

    2007-03-01

    Crystalline solvates of olanzapine ( 1), 2-methyl-4-(4-methyl-1-piperazinyl)-10 H-thieno[2,3- b][1,5]benzodiazepine, have been characterized by an X-ray analysis and thermal (DSC) data. Crystallization of 1 from ethanol gives a solid containing both water and ethanol molecules; the solvate 1 · H 2O · EtOH (2:2:1) is monoclinic with the space group P2 1/ c and the unit-cell volume V = 3752.8(12) Å 3. Butan-2-ol forms with 1 solvate which is also a three-component phase, 1 · H 2O · BuOH, but its stoichiometry is different (1:1:1). The space group for this crystal is P2 1/ c and the unit-cell volume V = 2216.5(7) Å 3. Crystalline olanzapine dichloromethane solvate (2:1), 1 · CH 2Cl 2, is triclinic with the space group P1¯. The characteristic feature of all crystal structures is presence of a pair of olanzapine molecules which form dimer stabilized by multiple weak C-H⋯π interactions between the N-methylpiperazine fragment and the phenyl / thiophene systems. Theoretical calculations have been performed indicating that the total C-H⋯π binding energy is about 8 kcal mol -1. In the crystal structure, the self-assembled olanzapine molecular dimers are arranged into parallel crystal planes. Packing of the layers proceeds in two ways in which structural motives are replicated by (i) perpendicular translation forming columns, and (ii) rotation around the twofold screw axis (parallel to the layer).

  9. Rational design of ion force fields based on thermodynamic solvation properties

    NASA Astrophysics Data System (ADS)

    Horinek, Dominik; Mamatkulov, Shavkat I.; Netz, Roland R.

    2009-03-01

    Most aqueous biological and technological systems contain solvated ions. Atomistic explicit-water simulations of ionic solutions rely crucially on accurate ionic force fields, which contain most commonly two adjustable parameters: the Lennard-Jones diameter and the interaction strength. Assuming these parameters to be properly optimized, the plethora of parameters one finds in the literature for one and the same ion is surprising. In principle, the two parameters should be uniquely determined by matching two ionic properties obtained for a particular water model and within a given simulation protocol with the corresponding experimental observables. Traditionally, ion parameters were chosen in a somewhat unsystematic way to reproduce the solvation free energy and to give the correct ion size when compared with scattering results. Which experimental observable one chooses to reproduce should in principle depend on the context within which the ionic force field is going to be used. In the present work we suggest to use the solvation free energy in conjunction with the solvation entropy to construct thermodynamically sound force fields for the alkali and halide ions for the simulation of ion-specific effects in aqueous environment. To that end we determine the solvation free energy and entropy of both cations and anions in the entire relevant parameter space. As an independent check on the quality of the resulting force fields we also determine the effective ionic radius from the first peak of the radial ion-water distribution function. Several difficulties during parameter optimization are discussed in detail. (i) Single-ion solvation depends decisively on water-air surface properties, which experimentally becomes relevant when introducing extrathermodynamic assumptions on the hydronium (H3O+) solvation energy. Fitting ion pairs circumvents this problem but leaves the parameters of one reference ion (here we choose chloride) undetermined. (ii) For the halides the

  10. 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.

  11. 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).

  12. 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

    2016-02-09

    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.

  13. Collective water dynamics in the first solvation shell drive the NMR relaxation of aqueous quadrupolar cations

    NASA Astrophysics Data System (ADS)

    Carof, Antoine; Salanne, Mathieu; Charpentier, Thibault; Rotenberg, Benjamin

    2016-09-01

    Using molecular simulations, we analyze the microscopic processes driving the Nuclear Magnetic Resonance (NMR) relaxation of quadrupolar cations in water. The fluctuations of the Electric Field Gradient (EFG) experienced by alkaline and magnesium cations, which determine the NMR relaxation time, are mainly due to the dynamics of water molecules in their solvation shell. The dynamics of the ion plays a less important role, with the exception of the short-time dynamics in the lighter Li+ case, for which rattling in the solvent cage results in oscillations of the EFG autocorrelation function (ACF). Several microscopic mechanisms that may a priori contribute to the decay of the EFG-ACF occur in fact over too long time scales: entrance/exit of individual water molecules into/from the solvation shell, rotation of a molecule around the ion, or reorientation of the molecule. In contrast, the fluctuations of the ion-water distance are clearly correlated to that of the EFG. Nevertheless, it is not sufficient to consider a single molecule due to the cancellations arising from the symmetry of the solvation shell. The decay of the EFG-ACF, hence NMR relaxation, is in fact governed by the collective symmetry-breaking fluctuations of water in the first solvation shell.

  14. Solvation dynamics of DCM in a polypeptide-surfactant aggregate: gelatin-sodium dodecyl sulfate.

    PubMed

    Halder, Arnab; Sen, Pratik; Burman, Anupam Das; Bhattacharyya, Kankan

    2004-02-03

    Solvation dynamics of 4-(dicyanomethylidene)-2-[p-(dimethylamino)styryl]-6-methyl-4H-pyran (DCM) is studied in a polypeptide-surfactant aggregate consisting of gelatin and sodium dodecyl sulfate (SDS) in potassium dihydrogen phosphate (KP) buffer. The average solvation time (tauS) in gelatin-SDS aggregate at 45 degrees C is found to be 1780 ps, which is about 13 times slower than that in 15 mM SDS in KP buffer at the same temperature. The fluorescence anisotropy decay in gelatin-SDS aggregate is also different from that in SDS micelles in KP buffer. DCM displays negligible emission in the presence of gelatin in aqueous solution. Thus the solvation dynamics in the presence of gelatin and SDS is exclusively due to the probe (DCM) molecules at the gelatin-micelle interface. The slow solvation dynamics is ascribed to the restrictions imposed on the water molecules trapped between the polypeptide chain and micellar aggregates. The critical association concentration (cac) of SDS for gelatin is determined to be 0.5 +/- 0.1 mM.

  15. Slow solvation dynamics in the microheterogeneous water channels of nafion membranes.

    PubMed

    Burai, Tarak Nath; Datta, Anindya

    2009-12-10

    Solvation dynamics in Nafion membrane is studied using the well-known solvation probe, coumarin 102 (C102). In native Nafion membrane, the fluorescence maximum of C102 occurs at 525 nm. The decays recorded at different wavelengths are superimposable. There is no time-dependent Stokes shift (TDSS) in the time scale of the experiment. This is rationalized in light of the strongly acidic environment in Nafion membrane, which causes the C102 molecules to become protonated. The protonated molecules are bound tightly to the negatively charged sulfonate groups. In Na(+)- and Me(4)N(+)-exchanged Nafion membranes, the fluorescence gets blue-shifted by 65 nm, indicating the deprotonation of the cation and formation of neutral C102 in these membranes. TDSS is observed in the picosecond-nanosecond time scale, in the cation-exchanged Nafion membranes, although the amount of Stokes' shift is rather small, as compared to that observed in organic solvents, indicating that a significant amount of the solvation is ultrafast and is missed in the present experiment. The observed solvation dynamics is bimodal with fast ( approximately 1 ns) and slow (>10 ns) components. The ultraslow component is ascribed to the quasi-static water molecules in the Nafion membrane. The difference in the extents of apparently missing ultrafast components, between Me(4)N(+)- and Na(+)-substituted membranes is rationalized by a model involving the difference in distributions of the cations in the water channel.

  16. 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...

  17. Quantitative Characterization of Local Protein Solvation To Predict Solvent Effects on Protein Structure

    PubMed Central

    Vagenende, Vincent; Trout, Bernhardt L.

    2012-01-01

    Characterization of solvent preferences of proteins is essential to the understanding of solvent effects on protein structure and stability. Although it is generally believed that solvent preferences at distinct loci of a protein surface may differ, quantitative characterization of local protein solvation has remained elusive. In this study, we show that local solvation preferences can be quantified over the entire protein surface from extended molecular dynamics simulations. By subjecting microsecond trajectories of two proteins (lysozyme and antibody fragment D1.3) in 4 M glycerol to rigorous statistical analyses, solvent preferences of individual protein residues are quantified by local preferential interaction coefficients. Local solvent preferences for glycerol vary widely from residue to residue and may change as a result of protein side-chain motions that are slower than the longest intrinsic solvation timescale of ∼10 ns. Differences of local solvent preferences between distinct protein side-chain conformations predict solvent effects on local protein structure in good agreement with experiment. This study extends the application scope of preferential interaction theory and enables molecular understanding of solvent effects on protein structure through comprehensive characterization of local protein solvation. PMID:22995508

  18. 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

    2007-11-08

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    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.

  20. FTIR and DFT studies of LiTFSI solvation in 3-methyl-2-oxazolidinone

    NASA Astrophysics Data System (ADS)

    Jeschke, Steffen; Wiemhöfer, Hans-Dieter

    2016-03-01

    Combined computational/FTIR spectroscopic analyses of 3-methyl-2-oxazolidinone (NMO) solutions with varying molar ratios of lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) are reported. Based on the second derivative spectral profile, overlapping peaks are distinguished as well as assigned to the vibrational modes of implicitly and explicitly interacting NMO molecules. Thereby, the geometry of a monomeric, a dimeric and a simplified solvation structure [Li(NMO)1]+ are optimized with a polarizable continuum model at a B3LYP theoretical level. With increasing contents of LiTFSI, the formation of Li+ solvation structures is scrutinized by semi-quantitative analysis of deconvoluted integral peak areas for three different ring-related vibrations and Cdbnd O-stretch vibration. A discrepancy in the obtained data is observed implying the influence of the TFSI anion the ring-related vibrations are prone to. The solvation number of 4 is determined according to the Cdbnd O-signal in diluted solution, which is proven by the computed Gibbs free energy for solvation of [Li(NMO)4]+ in a NMO medium (- 41.7 kcal mol- 1).

  1. 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.

  2. 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...

  3. Solvation of a Cellulose Microfibril in Imidazolium Acetate Ionic Liquids: Effect of a Cosolvent.

    PubMed

    Velioglu, Sadiye; Yao, Xun; Devémy, Julien; Ahunbay, M Goktug; Tantekin-Ersolmaz, S Birgul; Dequidt, Alain; Costa Gomes, Margarida F; Pádua, Agílio A H

    2014-12-26

    The solvation and the onset of dissolution of a cellulose I(β) microcrystal in ionic liquid media are studied by molecular simulation. Ionic liquids can dissolve large amounts of cellulose, which can later be regenerated from solution, but their high viscosity is an inconvenience. Hydrogen bonding between the anion of the ionic liquid and cellulose is the main aspect determining dissolution. Here we try to elucidate the role of a molecular cosolvent, dimethyl sulfoxide (DMSO), which is an aprotic polar compound, in the system composed of cellulose and the ionic liquid 1-butyl-3-methylimidazolium acetate. We calculated quantities related to specific interactions (mainly hydrogen bonds), conformations, and the structure of local solvation environments, both for a solvated oligomer chain of cellulose and for a model microfibril composed of 36 chains in the I(β) crystal structure. We compare two solvent systems: the pure ionic liquid and a mixed solvent with an equimolar composition in ionic liquid and DMSO. All entities are represented by detailed all-atom, fully flexible force fields. The main conclusions are that DMSO behaves as an "innocent" cosolvent, lowering the viscosity and accelerating mass transport in the system, but without interacting specifically with cellulose or disrupting the interactions between cellulose with the anions of the ionic liquid. An understanding of solvation in mixed solvents composed of ionic liquids and molecular compounds can enable the design of high-performance media for the use of biomass materials.

  4. 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.

  5. 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.

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

    PubMed Central

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

    2016-01-01

    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

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. Abraham Flexner of Kentucky, his report, Medical Education in the United States and Canada, and the historical questions raised by the report.

    PubMed

    Halperin, Edward C; Perman, Jay A; Wilson, Emery A

    2010-02-01

    One hundred years ago, the time was right and the need was critical for medical education reform. Medical education had become a commercial enterprise with proprietary schools of variable quality, lectures delivered in crowded classrooms, and often no laboratory instruction or patient contact. Progress in science, technology, and the quality of medical care, along with political will and philanthropic support, contributed to the circumstances under which Abraham Flexner produced his report. Flexner was dismayed by the quality of many of the medical schools he visited in preparing the report. Many of the recommendations in Medical Education in the United States and Canada are still relevant, especially those concerning the physician as a practitioner whose purpose is more societal and preventive than individual and curative. Flexner helped establish standards for prerequisite education, framed medical school admission criteria, aided in the design of a curriculum introduced by the basic and followed by the clinical sciences, stipulated the resources necessary for medical education, and emphasized medical school affiliation with both a university and a strong clinical system. He proposed integration of basic and clinical sciences leading to contextual learning, active rather than passive learning, and the importance of philanthropy. Flexner's report poses several questions for the historian: How were his views on African American medical education shaped by his post-Civil War upbringing in Louisville? Was the report original or derivative? Why did it have such a large impact? This article describes Flexner's early life and the report's methodology and considers several of the historical questions.

  12. Field-SEA: a model for computing the solvation free energies of nonpolar, polar, and charged solutes in water.

    PubMed

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

    2014-06-19

    Previous work describes a computational solvation model called semi-explicit assembly (SEA). The SEA water model computes the free energies of solvation of nonpolar and polar solutes in water with good efficiency and accuracy. However, SEA gives systematic errors in the solvation free energies of ions and charged solutes. Here, we describe field-SEA, an improved treatment that gives accurate solvation free energies of charged solutes, including monatomic and polyatomic ions and model dipeptides, as well as nonpolar and polar molecules. Field-SEA is computationally inexpensive for a given solute because explicit-solvent model simulations are relegated to a precomputation step and because it represents solvating waters in terms of a solute's free-energy field. In essence, field-SEA approximates the physics of explicit-model simulations within a computationally efficient framework. A key finding is that an atom's solvation shell inherits characteristics of a neighboring atom, especially strongly charged neighbors. Field-SEA may be useful where there is a need for solvation free-energy computations that are faster than explicit-solvent simulations and more accurate than traditional implicit-solvent simulations for a wide range of solutes.

  13. Free energy of solvation from molecular dynamics simulation applying Voronoi-Delaunay triangulation to the cavity creation

    NASA Astrophysics Data System (ADS)

    Goncalves, Paulo F. B.; Stassen, Hubert

    2005-12-01

    The free energy of solvation for a large number of representative solutes in various solvents has been calculated from the polarizable continuum model coupled to molecular dynamics computer simulation. A new algorithm based on the Voronoi-Delaunay triangulation of atom-atom contact points between the solute and the solvent molecules is presented for the estimation of the solvent-accessible surface surrounding the solute. The volume of the inscribed cavity is used to rescale the cavitational contribution to the solvation free energy for each atom of the solute atom within scaled particle theory. The computation of the electrostatic free energy of solvation is performed using the Voronoi-Delaunay surface around the solute as the boundary for the polarizable continuum model. Additional short-range contributions to the solvation free energy are included directly from the solute-solvent force field for the van der Waals-type interactions. Calculated solvation free energies for neutral molecules dissolved in benzene, water, CCl4, and octanol are compared with experimental data. We found an excellent correlation between the experimental and computed free energies of solvation for all the solvents. In addition, the employed algorithm for the cavity creation by Voronoi-Delaunay triangulation is compared with the GEPOL algorithm and is shown to predict more accurate free energies of solvation, especially in solvents composed by molecules with nonspherical molecular shapes.

  14. Towards a critical evaluation of an empirical and volume-based solvation function for ligand docking

    PubMed Central

    Muniz, Heloisa S.

    2017-01-01

    Molecular docking is an important tool for the discovery of new biologically active molecules given that the receptor structure is known. An excellent environment for the development of new methods and improvement of the current methods is being provided by the rapid growth in the number of proteins with known structure. The evaluation of the solvation energies outstands among the challenges for the modeling of the receptor-ligand interactions, especially in the context of molecular docking where a fast, though accurate, evaluation is ought to be achieved. Here we evaluated a variation of the desolvation energy model proposed by Stouten (Stouten P.F.W. et al, Molecular Simulation, 1993, 10: 97–120), or SV model. The SV model showed a linear correlation with experimentally determined solvation energies, as available in the database FreeSolv. However, when used in retrospective docking simulations using the benchmarks DUD, charged-matched DUD and DUD-Enhanced, the SV model resulted in poorer enrichments when compared to a pure force field model with no correction for solvation effects. The data provided here is consistent with other empirical solvation models employed in the context of molecular docking and indicates that a good model to account for solvent effects is still a goal to achieve. On the other hand, despite the inability to improve the enrichment of retrospective simulations, the SV solvation model showed an interesting ability to reduce the number of molecules with net charge -2 and -3 e among the top-scored molecules in a prospective test. PMID:28323889

  15. 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.

  16. Calculation of electron affinities of polycyclic aromatic hydrocarbons and solvation energies of their radical anion.

    PubMed

    Betowski, Leon D; Enlow, Mark; Riddick, Lee; Aue, Donald H

    2006-11-30

    Electron affinities (EAs) and free energies for electron attachment (DeltaGo(a,298K)) have been directly calculated for 45 polynuclear aromatic hydrocarbons (PAHs) and related molecules by a variety of theoretical methods, with standard regression errors of about 0.07 eV (mean unsigned error = 0.05 eV) at the B3LYP/6-31 + G(d,p) level and larger errors with HF or MP2 methods or using Koopmans' Theorem. Comparison of gas-phase free energies with solution-phase reduction potentials provides a measure of solvation energy differences between the radical anion and neutral PAH. A simple Born-charging model approximates the solvation effects on the radical anions, leading to a good correlation with experimental solvation energy differences. This is used to estimate unknown or questionable EAs from reduction potentials. Two independent methods are used to predict DeltaGo(a,298K) values: (1) based upon DFT methods, or (2) based upon reduction potentials and the Born model. They suggest reassignments or a resolution of conflicting experimental EAs for nearly one-half (17 of 38) of the PAH molecules for which experimental EAs have been reported. For the antiaromatic molecules, 1,3,5-tri-tert-butylpentalene and the dithia-substituted cyclobutadiene 1, the reduction potentials lead to estimated EAs close to those expected from DFT calculations and provide a basis for the prediction of the EAs and reduction potentials of pentalene and cyclobutadiene. The Born model has been used to relate the electrostatic solvation energies of PAH and hydrocarbon radical anions, and spherical halide anions, alkali metal cations, and ammonium ions to effective ionic radii from DFT electron-density envelopes. The Born model used for PAHs has been successfully extended here to quantitatively explain the solvation energy of the C60 radical anion.

  17. 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.

  18. Pyridine and 3-methylpyridine solvates of the triple sulfa drug constitutent sulfamethazine.

    PubMed

    Patel, Urmila H; Purohit, Ketankumar P

    2017-01-01

    Sulfonamides display a wide variety of pharmacological activities. Sulfamethazine [abbreviated as SMZ; systematic name 4-amino-N-(4,6-dimethylpyrimidin-2-yl)benzenesulfonamide], one of the constitutents of the triple sulfa drugs, has wide clinical use. Pharmaceutical solvates are crystalline solids of active pharmaceutical ingredients (APIs) incorporating one or more solvent molecules in the crystal lattice, and these have received special attention, as the solvent molecule can impart characteristic physicochemical properties to APIs and solvates, therefore playing a significant role in drug development. The ability of SMZ to form solvates has been investigated. Both pyridine and 3-methylpyridine form solvates with SMZ in 1:1 molar ratios. The pyridine monosolvate, C12H14N4O2S·C5H5N, crystallizes in the orthorhombic space group Pna21, with Z = 8 and two molecules per assymetric unit, whereas the 3-methylpyridine monosolvate, C12H14N4O2S·C6H7N, crystallizes in the orthorhombic space group P212121, with Z = 4. Crystal structure analysis reveals intramolecular N-H...N hydrogen bonds between the molecules of SMZ and the pyridine solvent molecules. The solvent molecules in both structures play an active part in strong intermolecular interactions, thereby contributing significantly to the stability of both structures. Three-dimensional hydrogen-bonding networks exist in both structures involving at least one sulfonyl O atom and the amine N atom. In the pyridine solvate, there is a short π-π interaction [centroid-centroid distance = 3.926 (3) Å] involving the centroids of the pyridine rings of two solvent molecules and a weak intermolecular C-H...π interaction also contributes to the stability of the crystal packing.

  19. Solvated water molecules and hydrogen-bridged networks in liquid water

    NASA Astrophysics Data System (ADS)

    Corongiu, Giorgina; Clementi, Enrico

    1993-02-01

    We have analyzed the molecular-dynamics (MD) trajectories for the oxygen and hydrogen atoms of liquid water, at six temperatures (from hot, T=361 K, to supercooled water, T=242 K); in the MD simulations the Nieser-Corongiu-Clementi ab initio potential has been used, since it yields reliable x-ray and neutron-diffraction data as well as infrared, Raman, and neutron-scattering spectra. Our analysis leads to two complementary models where we can consider each water as a solvated molecule (placed at the center of a solvation shell) or as a component of a cyclic polymer, a substructure of the hydrogen-bonded network. In the first solvation shell all water molecules are solvated with coordination values in the range 2-8. The most probable solvation number is four, at low temperature, and five at high temperature considering oxygen-oxygen pairs; however, the coordination number is four at all the temperatures if we consider oxygen-hydrogen pairs. The lifetime of the tetra coordinated complexes is the largest one and increases as temperature decreases. The computed population of cyclic polymers is highest for the pentameters in the studied temperature range, the second most probable cyclic structure is for hexamers. The average O-O distances in the liquid are temperature dependent and shorter than those in the gas phase, approaching ice values at low temperature (except for cyclic trimers, for which the O-O distance is nearly temperature independent). As a preliminary result, the lifetime of the polygons is estimated to be around 0.01 ps.

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

    PubMed Central

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

    2015-01-01

    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 toward 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 toward the ground state and subsequent relaxation back to the FC region. PMID:25941671

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

    DOE PAGES

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

    2015-11-17

    The composition of the lithium cation (Li+) solvation shell in mixed linear and cyclic carbonate-based electrolytes has been re-examined using Born–Oppenheimer molecular dynamics (BOMD) as a function of salt concentration and cluster calculations with ethylene carbonate:dimethyl carbonate (EC:DMC)–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

  2. IR spectroscopy of aqueous alkali halide solutions: Pure salt-solvated water spectra and hydration numbers

    NASA Astrophysics Data System (ADS)

    Max, Jean-Joseph; Chapados, Camille

    2001-08-01

    Extrapolation techniques were used to obtain pure salt-solvated water spectra from the attenuated total reflection infrared spectra (ATR-IR) of aqueous solutions of the nine alkali halide salts LiCl, NaCl, KCl, CsCl, NaBr, KBr, NaI, KI, and CsI and the alkaline-earth chloride salt MgCl2. These salts ionize completely in water. The ions by themselves do not absorb in the IR, but their interactions with water can be observed and analyzed. A pure salt-solvated water spectrum is easier to analyze than that of a combined solution of pure water and salt-solvated water. Although the salt-solvated water spectra examined have distinctive signatures, they can be classified in three categories: those similar to NaCl; those not similar to NaCl; and MgCl2, in a class by itself. Each of the pure salt-solvated water spectra differs from that of liquid water, though the number of bands is the same. From the Gaussian band fitting, we found that the positions of the bands were fairly constant, whereas their intensities differed. The salt hydration numbers were determined: for NaCl, KCl, NaBr, KBr, and CsI solutions it is 5; for KI and MgCL2 it is 4; for NaI it is 3.5; for CsCl it is 3; and for LiCl it is 2. From these results we found that each pair of ions (monoatomic ions) of the ten salt solutions studied are close bound and form a complex in a cluster organization with a fixed number of water molecules.

  3. Competitive Lithium Solvation of Linear and Cyclic Carbonates from Quantum Chemistry

    SciTech Connect

    Borodin, Oleg; Olguin, Marco; Ganesh, P.; Kent, Paul; Allen, Joshua S.; 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 with ethylene carbonate:dimethyl carbonate (EC:DMC)-LiPF6 as a model system. A slight 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 (EC:DMC)LiPF6 mixed solvent electrolyte was studied using the BOMD simulations.

  4. 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.

  5. Thermodynamic study of the binding of calcium and magnesium ions with myelin basic protein using the extended solvation theory.

    PubMed

    Behbehani, G Rezaei; Saboury, A A; Divsalar, A

    2008-11-01

    The interaction of myelin basic protein (MBP) from the bovine central nervous system with Ca2+ and Mg2+ ions, named as M2+, was studied by isothermal titration calorimetry at 27 degrees C in aqueous solution. The extended solvation model was used to reproduce the enthalpies of MBP+M2+ interactions. The solvation parameters recovered from the extended solvation model were attributed to the structural change of MBP due to the metal ion interaction. It was found that there is a set of two identical and noninteracting binding sites for Ca2+ and Mg2+ ions.

  6. Ligand and solvation effects on the electronic properties of Au55 clusters: a density functional theory study.

    PubMed

    Periyasamy, Ganga; Remacle, F

    2009-08-01

    The electronic properties of the neutral, positively and negatively charged bare Au(55), passivated Au(55)(PH(3))(12), Au(55)(PH(3))(12)Cl(6), and solvated Au(55)(PH(3))(12)Cl(6) 54 H(2)O clusters are studied using density functional theory. The presence of Cl atoms in the ligand shell favors a nonmetallic behavior while a more metallic behavior is induced by explicit solvation of Au(55)(PH(3))(12)Cl(6) with water molecules. The trends observed in the electronic properties upon ligation and solvation are in agreement with experimental studies.

  7. Coordination chemistry study of hydrated and solvated lead(II) ions in solution and solid state.

    PubMed

    Persson, Ingmar; Lyczko, Krzysztof; Lundberg, Daniel; Eriksson, Lars; Płaczek, Anna

    2011-02-07

    The coordination chemistry of lead(II) in the oxygen donor solvents water, dimethylsulfoxide (dmso, Me(2)SO), N,N-dimethylformamide (dmf), N,N-dimethylacetamide (dma), N,N'-dimethylpropyleneurea (dmpu), and 1,1,3,3-tetramethylurea (tmu), as well as in the sulfur donor solvent N,N-dimethylthioformamide (dmtf), has been investigated by extended X-ray absorption fine structure (EXAFS) and/or large angle X-ray scattering (LAXS) in solution, and by single crystal X-ray diffraction and/or EXAFS of solid hydrates and solvates. Lead(II) may either form hemidirected complexes with large bond distance distribution and an apparent gap for excess electron density, or holodirected ones with a symmetric coordination sphere with normal bond distance distribution, depending on the strength of antibonding lead 6s/ligand np molecular orbital interactions and ligand-ligand interactions. The crystallographic data show that the solid lead(II) perchlorate and trifluoromethanesulfonate hydrate structures are hemidirected, while the solid lead(II) solvates of dma and dmpu have regular octahedral configuration with holodirected geometry and mean Pb-O bond distances in the range 2.50-2.52 Å. EXAFS data on the hydrated lead(II) ion in aqueous solution show broad bond distance distribution and a lack of inner-core multiple scattering contributions strongly indicating a hemidirected structure. The Pb-O bond distances found both by EXAFS and LAXS, 2.54(1) Å, point to a six-coordinate hydrated lead(II) ion in hemidirected fashion with an unevenly distributed electron density. The results obtained for the dmso solvated lead(II) ion in solution are ambiguous, but for the most part support a six-coordinate hemidirected complex. The mean Pb-O bond distances determined in dmf and dma solution by LAXS, 2.55(1) and 2.48(1) Å, respectively, indicate that in both solvate complexes lead(II) binds six solvent molecules with the former complex being hemidirected whereas the latter is holodirected. The

  8. Preferential solvation of thiophene and furan-2-carboxaldehyde phenylhydrazone derivatives in DMSO-water and DMSO-n-octanol mixtures.

    PubMed

    Alvarado, Ysaías J; Ballestas-Barrientos, Alfonso; Cubillán, Néstor; Morales-Toyo, Miguel; Restrepo, Jelem; Ferrer-Amado, Gladys

    2013-02-15

    The preferential solvation of thiophene- and furan-2-carboxaldehyde phenylhydrazone derivatives in DMSO-water and DMSO-n-octanol mixtures has been studied using visible absorption spectroscopy with a previous characterization of the electronic transitions by Time-Dependent Density Functional Theory (TDDFT) and solvatochromic study in several solvents with different hydrogen-bond donor capacity. The results indicate that the phenylhydrazones are preferentially solvated by clusters of DMSO-water existing in the solvent mixture and the dielectric enrichment as preferential solvation mechanism was discarded. A relation between local DMSO concentration with nitro groups and the electronegativity of the heteroatom of the five-membered ring was found. For DMSO-1-octanol mixtures, the results showed no preferential solvation.

  9. Preferential solvation of thiophene and furan-2-carboxaldehyde phenylhydrazone derivatives in DMSO-water and DMSO-n-octanol mixtures

    NASA Astrophysics Data System (ADS)

    Alvarado, Ysaías J.; Ballestas-Barrientos, Alfonso; Cubillán, Néstor; Morales-Toyo, Miguel; Restrepo, Jelem; Ferrer-Amado, Gladys

    2013-02-01

    The preferential solvation of thiophene- and furan-2-carboxaldehyde phenylhydrazone derivatives in DMSO-water and DMSO-n-octanol mixtures has been studied using visible absorption spectroscopy with a previous characterization of the electronic transitions by Time-Dependent Density Functional Theory (TDDFT) and solvatochromic study in several solvents with different hydrogen-bond donor capacity. The results indicate that the phenylhydrazones are preferentially solvated by clusters of DMSO-water existing in the solvent mixture and the dielectric enrichment as preferential solvation mechanism was discarded. A relation between local DMSO concentration with nitro groups and the electronegativity of the heteroatom of the five-membered ring was found. For DMSO-1-octanol mixtures, the results showed no preferential solvation.

  10. Formation of solvated ions in the atmospheric interface of an electrospray ionization triple-quadrupole mass spectrometer.

    PubMed

    Schlosser, Gitta; Takáts, Zoltán; Vékey, Károly

    2003-12-01

    A simple method capable of generating and investigating various solvent clusters and solvated ions was developed. The technique opens a door to studying these complexes on commercially available instruments. Formation of the desired solvated ion in the gas phase was achieved by introducing the appropriate volatile solvent vapour into the curtain gas stream. Capabilities of the technique are illustrated by generating alkali, alkaline earth and transition metal cations solvated by various volatile compounds such as water, methanol and acetonitrile. Depending on the ligands and on the experimental conditions, clusters of 2-100 molecules may be observed. Isotope labelling suggests that these are formed by a re-solvation process in the curtain gas region.

  11. On-line preferential solvation studies of polymers by coupled chromatographic-Fourier transform infrared spectroscopic flow-cell technique.

    PubMed

    Malanin, M; Eichhorn, K-J; Lederer, A; Treppe, P; Adam, G; Fischer, D; Voigt, D

    2009-12-18

    Qualitative and quantitative comparison between liquid chromatography (LC) and LC coupled with Fourier transform infrared spectroscopy (LC-FTIR) to evaluate preferential solvation phenomenon of polymers in a mixed solvent has been performed. These studies show that LC-FTIR technique leads to detailed structural information without the requirement for determination of additional parameters for quantitative analysis except calibration. Appropriate experimental conditions for preferential solvation study have been established by variation of polymer concentration, molar mass and eluent content.

  12. A Seamless Grid-Based Interface for Mean-Field QM/MM Coupled with Efficient Solvation Free Energy Calculations.

    PubMed

    Lim, Hyung-Kyu; Lee, Hankyul; Kim, Hyungjun

    2016-10-11

    Among various models that incorporate solvation effects into first-principles-based electronic structure theory such as density functional theory (DFT), the average solvent electrostatic potential/molecular dynamics (ASEP/MD) method is particularly advantageous. This method explicitly includes the nature of complicated solvent structures that is absent in implicit solvation methods. Because the ASEP/MD method treats only solvent molecule dynamics, it requires less computational cost than the conventional quantum mechanics/molecular mechanics (QM/MM) approaches. Herein, we present a real-space rectangular grid-based method to implement the mean-field QM/MM idea of ASEP/MD to plane-wave DFT, which is termed "DFT in classical explicit solvents", or DFT-CES. By employing a three-dimensional real-space grid as a communication medium, we can treat the electrostatic interactions between the DFT solute and the ASEP sampled from MD simulations in a seamless and straightforward manner. Moreover, we couple a fast and efficient free energy calculation method based on the two-phase thermodynamic (2PT) model with our DFT-CES method, which enables direct and simultaneous computation of the solvation free energies as well as the geometric and electronic responses of a solute of interest under the solvation effect. With the aid of DFT-CES/2PT, we investigate the solvation free energies and detailed solvation thermodynamics for 17 types of organic molecules, which show good agreement with the experimental data. We further compare our simulation results with previous theoretical models and assumptions made for the development of implicit solvation models. We anticipate that our proposed method, DFT-CES/2PT, will enable vast utilization of the ASEP/MD method for investigating solvation properties of materials by using periodic DFT calculations in the future.

  13. 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.

  14. Evaluating continuum solvation models for the electrode-electrolyte interface: Challenges and strategies for improvement

    NASA Astrophysics Data System (ADS)

    Sundararaman, Ravishankar; Schwarz, Kathleen

    2017-02-01

    Ab initio modeling of electrochemical systems is becoming a key tool for understanding and predicting electrochemical behavior. Development and careful benchmarking of computational electrochemical methods are essential to ensure their accuracy. Here, using charging curves for an electrode in the presence of an inert aqueous electrolyte, we demonstrate that most continuum models, which are parameterized and benchmarked for molecules, anions, and cations in solution, undersolvate metal surfaces, and underestimate the surface charge as a function of applied potential. We examine features of the electrolyte and interface that are captured by these models and identify improvements necessary for realistic electrochemical calculations of metal surfaces. Finally, we reparameterize popular solvation models using the surface charge of Ag(100) as a function of voltage to find improved accuracy for metal surfaces without significant change in utility for molecular and ionic solvation.

  15. 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.

  16. 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.

  17. 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

  18. Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen-Hydrogen Correlations.

    PubMed

    Velez-Vega, Camilo; McKay, Daniel J J; Kurtzman, Tom; Aravamuthan, Vibhas; Pearlstein, Robert A; Duca, José S

    2015-11-10

    A statistical-mechanical framework for estimation of solvation entropies and enthalpies is proposed, which is based on the analysis of water as a mixture of correlated water oxygens and water hydrogens. Entropic contributions of increasing order are cast in terms of a Mutual Information Expansion that is evaluated to pairwise interactions. In turn, the enthalpy is computed directly from a distance-based hydrogen bonding energy algorithm. The resulting expressions are employed for grid-based analyses of Molecular Dynamics simulations. In this first assessment of the methodology, we obtained global estimates of the excess entropy and enthalpy of water that are in good agreement with experiment and examined the method's ability to enable detailed elucidation of solvation thermodynamic structures, which can provide valuable knowledge toward molecular design.

  19. 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.

  20. Solvation Dynamics and Adsorption on Ag Hydrosols of Oxazole: A Raman and Computational Study

    NASA Astrophysics Data System (ADS)

    Pagliai, Marco; Muniz-Miranda, Maurizio; Cardini, Gianni; Schettino, Vincenzo

    2009-09-01

    The interactions between oxazole and water or silver nanoparticles in aqueous dispersions have been studied with a computational approach based on ab initio molecular dynamics simulations, with the Car-Parrinello method, and density functional calculations in combination with Raman and surface enhanced Raman scattering (SERS) experiments. The solvation dynamics of oxazole in water allowed for the characterization of the hydrogen bond between water and solute, which has been shown to occur essentially through the nitrogen atom of the heterocyclic molecule. To mimic the solvation process or the adsorption on silver and interpreting the corresponding Raman and SERS spectra in aqueous solution or in Ag hydrosols, density functional calculations have been carried out on model systems made up by oxazole bound to water molecules or to positively charged silver clusters. Also, the chemisorption on Ag nanoparticles is found to occur by means of the nitrogen atom of oxazole interacting with the metal substrate.

  1. Sparingly solvating electrolytes for high energy density Lithium–sulfur batteries

    SciTech Connect

    Cheng, Lei; Curtiss, Larry A.; Zavadil, Kevin R.; Gewirth, Andrew A.; Shao, Yuyan; Gallagher, Kevin G.

    2016-07-11

    Moving to lighter and less expensive battery chemistries compared to lithium-ion requires the control of energy storage mechanisms based on chemical transformations rather than intercalation. Lithium sulfur (Li/S) has tremendous theoretical specific energy, but contemporary approaches to control this solution-mediated, precipitation-dissolution chemistry requires using large excesses of electrolyte to fully solubilize the polysulfide intermediate. Achieving reversible electrochemistry under lean electrolyte operation is the only path for Li/S to move beyond niche applications to potentially transformational performance. An emerging topic for Li/S research is the use of sparingly solvating electrolytes and the creation of design rules for discovering new electrolyte systems that fundamentally decouple electrolyte volume from reaction mechanism. Furthermore, this perspective presents an outlook for sparingly solvating electrolytes as the key path forward for longer-lived, high-energy density Li/S batteries including an overview of this promising new concept and some strategies for accomplishing it.

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

    PubMed

    Delgado, Eduardo J; Jaña, Gonzalo A

    2009-03-01

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

  3. Dynamics of electrons in ammonia cages: the discovery system of solvation.

    PubMed

    Lee, I-Ren; Lee, Wonchul; Zewail, Ahmed H

    2008-01-11

    Two centuries ago solvated electrons were discovered in liquid ammonia and a century later the concept of the solvent cage was introduced. Here, we report a real time study of the dynamics of size-selected clusters, n=20 to 60, of electrons in ammonia, and, for comparison, that of electrons in water cages. Unlike the water case, the observed dynamics for ammonia indicates the formation, through a 100 fs temperature jump, of a solvent collective motion in a 500 fs relaxation process. The agreement of the experimental results-obtained for a well-defined n, gated electron kinetic energy, and time delay-with molecular dynamics theory suggests the critical and different role of the kinetic energy and the librational motions involved in solvation.

  4. Excited-state solvation and proton transfer dynamics of DAPI in biomimetics and genomic DNA.

    PubMed

    Banerjee, Debapriya; Pal, Samir Kumar

    2008-08-14

    The fluorescent probe DAPI (4',6-diamidino-2-phenylindole) is an efficient DNA binder. Studies on the DAPI-DNA complexes show that the probe exhibits a wide variety of interactions of different strengths and specificities with DNA. Recently the probe has been used to report the environmental dynamics of a DNA minor groove. However, the use of the probe as a solvation reporter in restricted environments is not straightforward. This is due to the presence of two competing relaxation processes (intramolecular proton transfer and solvation stabilization) in the excited state, which can lead to erroneous interpretation of the observed excited-state dynamics. In this study, the possibility of using DAPI to unambiguously report the environmental dynamics in restricted environments including DNA is explored. The dynamics of the probe is studied in bulk solvents, biomimetics like micelles and reverse micelles, and genomic DNA using steady-state and picosecond-resolved fluorescence spectroscopies.

  5. Sparingly Solvating Electrolytes for High Energy Density Lithium-Sulfur Batteries

    SciTech Connect

    Cheng, Lei; Curtiss, Larry A.; Zavadil, Kevin R.; Gewirth, Andrew A.; Shao, Yuyan; Gallagher, Kevin

    2016-07-11

    Moving to lighter and less expensive battery chemistries compared to lithium-ion requires the control of energy storage mechanisms based on chemical transformations rather than intercalation. Lithium sulfur (Li/S) has tremendous theoretical specific energy, but contemporary approaches to control this solution-mediated, precipitation-dissolution chemistry requires using large excesses of electrolyte to fully solubilize the polysulfide intermediate. Achieving reversible electrochemistry under lean electrolyte operation is the only path for Li/S to move beyond niche applications to potentially transformational performance. An emerging topic for Li/S research is the use of sparingly solvating electrolytes and the creation of design rules for discovering new electrolyte systems that fundamentally decouple electrolyte volume from reaction mechanism. This perspective presents an outlook for sparingly solvating electrolytes as the key path forward for longer-lived, high-energy density Li/S batteries including an overview of this promising new concept and some strategies for accomplishing it.

  6. 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.

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

    PubMed

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

    2011-06-06

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

  8. 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

  9. Hybrid Perovskite Thin-Film Photovoltaics: In Situ Diagnostics and Importance of the Precursor Solvate Phases.

    PubMed

    Munir, Rahim; Sheikh, Arif D; Abdelsamie, Maged; Hu, Hanlin; Yu, Liyang; Zhao, Kui; Kim, Taesoo; Tall, Omar El; Li, Ruipeng; Smilgies, Detlef-M; Amassian, Aram

    2017-01-01

    Solution-processed hybrid perovskite semiconductors attract a great deal of attention, but little is known about their formation process. The one-step spin-coating process of perovskites is investigated in situ, revealing that thin-film formation is mediated by solid-state precursor solvates and their nature. The stability of these intermediate phases directly impacts the quality and reproducibility of thermally converted perovskite films and their photovoltaic performance.

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

    PubMed

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

    2016-12-21

    Sodium ion batteries are on the cusp of being a commercially available technology. Compared to lithium ion batteries, sodium ion batteries can potentially offer an attractive dollar-per-kilowatt-hour value, though at the penalty of reduced energy density. As a materials system, sodium ion batteries present a unique opportunity to apply lessons learned in the study of electrolytes for lithium ion batteries; specifically, the behavior of the sodium ion in an organic carbonate solution and the relationship of ion solvation with electrode surface passivation. In this work the Li(+) and Na(+)-based solvates were characterized using electrospray mass spectrometry, infrared and Raman spectroscopy, (17)O, (23)Na and pulse field gradient double-stimulated-echo pulse sequence nuclear magnetic resonance (NMR), and conductivity measurements. Spectroscopic evidence demonstrate that the Li(+) and Na(+) cations share a number of similar ion-solvent interaction trends, such as a preference in the gas and liquid phase for a solvation shell rich in cyclic carbonates over linear carbonates and fluorinated carbonates. However, quite different IR spectra due to the PF6(-) anion interactions with the Na(+) and Li(+) cations were observed and were rationalized with the help of density functional theory (DFT) calculations that were also used to examine the relative free energies of solvates using cluster - continuum models. Ion-solvent distances for Na(+) were longer than Li(+), and Na(+) had a greater tendency towards forming contact pairs compared to Li(+) in linear carbonate solvents. In tests of hard carbon Na-ion batteries, performance was not well correlated to Na(+) solvent preference, leading to the possibility that Na(+) solvent preference may play a reduced role in the passivation of anode surfaces and overall Na-ion battery performance.

  11. Amino-acid solvation structure in transmembrane helices from molecular dynamics simulations.

    PubMed

    Johansson, Anna C V; Lindahl, Erik

    2006-12-15

    Understanding the solvation of amino acids in biomembranes is an important step to better explain membrane protein folding. Several experimental studies have shown that polar residues are both common and important in transmembrane segments, which means they have to be solvated in the hydrophobic membrane, at least until helices have aggregated to form integral proteins. In this work, we have used computer simulations to unravel these interactions on the atomic level, and classify intramembrane solvation properties of amino acids. Simulations have been performed for systematic mutations in poly-Leu helices, including not only each amino acid type, but also every z-position in a model helix. Interestingly, many polar or charged residues do not desolvate completely, but rather retain hydration by snorkeling or pulling in water/headgroups--even to the extent where many of them exist in a microscopic polar environment, with hydration levels corresponding well to experimental hydrophobicity scales. This suggests that even for polar/charged residues a large part of solvation cost is due to entropy, not enthalpy loss. Both hydration level and hydrogen bonding exhibit clear position-dependence. Basic side chains cause much less membrane distortion than acidic, since they are able to form hydrogen bonds with carbonyl groups instead of water or headgroups. This preference is supported by sequence statistics, where basic residues have increased relative occurrence at carbonyl z-coordinates. Snorkeling effects and N-/C-terminal orientation bias are directly observed, which significantly reduces the effective thickness of the hydrophobic core. Aromatic side chains intercalate efficiently with lipid chains (improving Trp/Tyr anchoring to the interface) and Ser/Thr residues are stabilized by hydroxyl groups sharing hydrogen bonds to backbone oxygens.

  12. 4-Benzyl­piperazin-1-ium chloride chloro­form solvate

    PubMed Central

    Nema, Mihai G.; Varga, Richard A.; Silvestru, Cristian; Breunig, Hans J.

    2008-01-01

    The ions of the title chloro­form-solvated salt, C11H17N2 +·Cl−·CHCl3, are linked by a strong N—H⋯Cl hydrogen bond; the solvent mol­ecule also inter­acts with the chloride ion through a C—H⋯Cl hydrogen bond. Additionally, neighboring cations form weak hydrogen bonds to the anion, resulting in a supra­molecular ribbon that runs along the a axis. PMID:21203283

  13. Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber

    SciTech Connect

    Luchko, T.; Simmerling, C.; Gusarov, S.; Roe, D.R., Case, D.A.; Tuszynski, J.; Kovalenko, A.

    2010-02-01

    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 multiple 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.

  14. Using the theoretical linear energy solvation energy relationship to correlate and predict nasal pungency thresholds.

    PubMed

    Famini, George R; Aguiar, Denise; Payne, Marvin A; Rodriquez, Ryan; Wilson, Leland Y

    2002-01-01

    The theoretical linear solvation energy relationship (TLSER) has been used to correlate and characterize 44 nasal pungency threshold (NPT) values in man with parameters derived from semi-empirical molecular orbital theory. The resulting relationship provides good correlative (R2 > 0.92) and predictive (R2cy > 0.88) capability. In addition, the TLSER parameters are used as a molecular probe to attempt to understand the fundamental properties influencing nasal pungency.

  15. Nanocalorimetry in mass spectrometry: a route to understanding ion and electron solvation.

    PubMed

    Donald, William A; Leib, Ryan D; O'Brien, Jeremy T; Holm, Anne I S; Williams, Evan R

    2008-11-25

    A gaseous nanocalorimetry approach is used to investigate effects of hydration and ion identity on the energy resulting from ion-electron recombination. Capture of a thermally generated electron by a hydrated multivalent ion results in either loss of a H atom accompanied by water loss or exclusively loss of water. The energy resulting from electron capture by the precursor is obtained from the extent of water loss. Results for large-size-selected clusters of Co(NH(3))(6)(H(2)O)(n3)(+) and Cu(H(2)O)(n2)(+) indicate that the ion in the cluster is reduced on electron capture. The trend in the data for Co(NH(3))(6)(H(2)O)(n3)(+) over the largest sizes (n >/= 50) can be fit to that predicted by the Born solvation model. This agreement indicates that the decrease in water loss for these larger clusters is predominantly due to ion solvation that can be accounted for by using a model with bulk properties. In contrast, results for Ca(H(2)O)(n2)(+) indicate that an ion-electron pair is formed when clusters with more than approximately 20 water molecules are reduced. For clusters with n = approximately 20-47, these results suggest that the electron is located near the surface, but a structural transition to a more highly solvated electron is indicated for n = 47-62 by the constant recombination energy. These results suggest that an estimate of the adiabatic electron affinity of water could be obtained from measurements of even larger clusters in which an electron is fully solvated.

  16. Solvent Acidity and Basicity in Polar Media and their Role in Solvation

    DTIC Science & Technology

    1994-04-20

    accept a pair of electrons or as its ability to donate a hydrogen bond . In the case of protic solvents, the latter function is generally considered...obtained for protic solvents which are highly structured because of hydrogen bonding . However. on the basis of the polar basicity scale estimated from...for ionic solvation which are based on continuum concepts have been presented 161, but they are not popular because they neglect the molecular nature

  17. 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.

  18. A highly concentrated catholyte based on a solvate ionic liquid for rechargeable flow batteries.

    PubMed

    Takechi, Kensuke; Kato, Yuichi; Hase, Yoko

    2015-04-17

    A redox-active supercooled liquid is obtained by forming a "solvate ionic liquid" from a mixture of a stabilized organic radical and a specific Li salt and stabilizing the mixture further below their melting points. As a catholyte, the addition of an appropriate amount of water helps to enhance the electrochemical advantage while maintaining its supercooled nature and the liquid shows a high energy density of 200 W h L(-1) with reversible charge/discharge.

  19. Electrolytes in a nanometer slab-confinement: ion-specific structure and solvation forces.

    PubMed

    Kalcher, Immanuel; Schulz, Julius C F; Dzubiella, Joachim

    2010-10-28

    We study the liquid structure and solvation forces of dense monovalent electrolytes (LiCl, NaCl, CsCl, and NaI) in a nanometer slab-confinement by explicit-water molecular dynamics (MD) simulations, implicit-water Monte Carlo (MC) simulations, and modified Poisson-Boltzmann (PB) theories. In order to consistently coarse-grain and to account for specific hydration effects in the implicit methods, realistic ion-ion and ion-surface pair potentials have been derived from infinite-dilution MD simulations. The electrolyte structure calculated from MC simulations is in good agreement with the corresponding MD simulations, thereby validating the coarse-graining approach. The agreement improves if a realistic, MD-derived dielectric constant is employed, which partially corrects for (water-mediated) many-body effects. Further analysis of the ionic structure and solvation pressure demonstrates that nonlocal extensions to PB (NPB) perform well for a wide parameter range when compared to MC simulations, whereas all local extensions mostly fail. A Barker-Henderson mapping of the ions onto a charged, asymmetric, and nonadditive binary hard-sphere mixture shows that the strength of structural correlations is strongly related to the magnitude and sign of the salt-specific nonadditivity. Furthermore, a grand canonical NPB analysis shows that the Donnan effect is dominated by steric correlations, whereas solvation forces and overcharging effects are mainly governed by ion-surface interactions. However, steric corrections to solvation forces are strongly repulsive for high concentrations and low surface charges, while overcharging can also be triggered by steric interactions in strongly correlated systems. Generally, we find that ion-surface and ion-ion correlations are strongly coupled and that coarse-grained methods should include both, the latter nonlocally and nonadditive (as given by our specific ionic diameters), when studying electrolytes in highly inhomogeneous situations.

  20. Ultrafast 2D-IR and simulation investigations of preferential solvation and cosolvent exchange dynamics.

    PubMed

    Dunbar, Josef A; Arthur, Evan J; White, Aaron M; Kubarych, Kevin J

    2015-05-21

    Using a derivative of the vitamin biotin labeled with a transition-metal carbonyl vibrational probe in a series of aqueous N,N-dimethylformamide (DMF) solutions, we observe a striking slowdown in spectral diffusion dynamics with decreased DMF concentration. Equilibrium solvation dynamics, measured with the rapidly acquired spectral diffusion (RASD) technique, a variant of heterodyne-detected photon-echo peak shift experiments, range from 1 ps in neat DMF to ∼3 ps in 0.07 mole fraction DMF/water solution. Molecular dynamics simulations of the biotin-metal carbonyl solute in explicit aqueous DMF solutions show marked preferential solvation by DMF, which becomes more pronounced at lower DMF concentrations. The simulations and the experimental data are consistent with an interpretation where the slowdown in spectral diffusion is due to solvent exchange involving distinct cosolvent species. A simple two-component model reproduces the observed spectral dynamics as well as the DMF concentration dependence, enabling the extraction of the solvent exchange time scale of 8 ps. This time scale corresponds to the diffusive motion of a few Å, consistent with a solvent-exchange mechanism. Unlike most previous studies of solvation dynamics in binary mixtures of polar solvents, our work highlights the ability of vibrational probes to sense solvent exchange as a new, slow component in the spectral diffusion dynamics.

  1. 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.

  2. 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.

  3. Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery.

    PubMed

    Lee, Kyung-Koo; Park, Kwanghee; Lee, Hochan; Noh, Yohan; Kossowska, Dorota; Kwak, Kyungwon; Cho, Minhaeng

    2017-03-08

    Lithium cation is the charge carrier in lithium-ion battery. Electrolyte solution in lithium-ion battery is usually based on mixed solvents consisting of polar carbonates with different aliphatic chains. Despite various experimental evidences indicating that lithium ion forms a rigid and stable solvation sheath through electrostatic interactions with polar carbonates, both the lithium solvation structure and more importantly fluctuation dynamics and functional role of carbonate solvent molecules have not been fully elucidated yet with femtosecond vibrational spectroscopic methods. Here we investigate the ultrafast carbonate solvent exchange dynamics around lithium ions in electrolyte solutions with coherent two-dimensional infrared spectroscopy and find that the time constants of the formation and dissociation of lithium-ion···carbonate complex in solvation sheaths are on a picosecond timescale. We anticipate that such ultrafast microscopic fluxional processes in lithium-solvent complexes could provide an important clue to understanding macroscopic mobility of lithium cation in lithium-ion battery on a molecular level.

  4. Enabling forbidden processes: quantum and solvation enhancement of nitrate anion UV absorption.

    PubMed

    Svoboda, Ondřej; Kubelová, Lucie; Slavíček, Petr

    2013-12-05

    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.

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

    SciTech Connect

    Wu, Qin; Zaikowski, Lori; Kaur, Parmeet; Asaoka, Sadayuki; Gelfond, Claudia; Miller, John R.

    2016-07-01

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

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

    DOE PAGES

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

    2016-07-01

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

  7. A femtosecond study of excitation-wavelength dependence of solvation dynamics in a vesicle.

    PubMed

    Sen, Pratik; Ghosh, Subhadip; Mondal, Sudip Kumar; Sahu, Kalyanasis; Roy, Durba; Bhattacharyya, Kankan; Tominaga, Keisuke

    2006-07-17

    The dependence of fluorescence and solvation dynamics of coumarin 480 (C480) in a dimyristoyl-phosphatidylcholine (DMPC) vesicle on excitation wavelength (lambda(ex)) was studied with femtosecond fluorescence upconversion. The study revealed an ultrafast 1.5-ps component of solvation that was not detected earlier. C480 exhibits pronounced red-edge excitation shift (REES) by 10 nm in a DMPC vesicle. This is due to the microheterogeneity of the lipid vesicle. In lipids, the probe is distributed in different locations with varying static and dynamic electrostatic responses. Solvent relaxation becomes faster and the amount of dynamic Stokes shift decreases with increasing lambda(ex). For excitation at the red end (lambda(ex) = 430 nm), the solvation time was found to be 1.5 ps. However, for excitation at the blue end, (lambda(ex) = 390 nm), there are two substantially slower components of 250 and 2000 ps. It seems that for lambda(ex) = 390 nm, the major contribution to total emission is due to the probe (C480) molecules in the hydrophobic and restricted locations inside the lipid bilayer. Excitation at 430 nm preferentially selects the probe molecules in a highly mobile environment (water pool of the lipid).

  8. 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.

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

    DOE PAGES

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

    2016-11-28

    The interactions between the reactive excited state of molecular photocatalysts and surrounding solvent dictate reaction mechanisms and pathways, but are not readily accessible to conventional optical spectroscopic techniques. Here we report an investigation of the structural and solvation dynamics following excitation of a model photocatalytic molecular system [Ir2(dimen)4]2+, where dimen is para-diisocyanomenthane. The time-dependent structural changes in this model photocatalyst, as well as the changes in the solvation shell structure, have been measured with ultrafast diffuse X-ray scattering and simulated with Born-Oppenheimer Molecular Dynamics. Both methods provide direct access to the solute–solvent pair distribution function, enabling the solvation dynamics aroundmore » the catalytically active iridium sites to be robustly characterized. Our results provide evidence for the coordination of the iridium atoms by the acetonitrile solvent and demonstrate the viability of using diffuse X-ray scattering at free-electron laser sources for studying the dynamics of photocatalysis.« less

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

    SciTech Connect

    van Driel, Tim B.; Kjær, Kasper S.; Hartsock, Robert W.; Dohn, Asmus O.; Harlang, Tobias; Chollet, Matthieu; Christensen, Morten; Gawelda, Wojciech; Henriksen, Niels E.; Kim, Jong Goo; Haldrup, Kristoffer; Kim, Kyung Hwan; Ihee, Hyotcherl; Kim, Jeongho; Lemke, Henrik; Sun, Zheng; Sundström, Villy; Zhang, Wenkai; Zhu, Diling; Møller, Klaus B.; Nielsen, Martin M.; Gaffney, Kelly J.

    2016-11-28

    The interactions between the reactive excited state of molecular photocatalysts and surrounding solvent dictate reaction mechanisms and pathways, but are not readily accessible to conventional optical spectroscopic techniques. Here we report an investigation of the structural and solvation dynamics following excitation of a model photocatalytic molecular system [Ir2(dimen)4]2+, where dimen is para-diisocyanomenthane. The time-dependent structural changes in this model photocatalyst, as well as the changes in the solvation shell structure, have been measured with ultrafast diffuse X-ray scattering and simulated with Born-Oppenheimer Molecular Dynamics. Both methods provide direct access to the solute–solvent pair distribution function, enabling the solvation dynamics around the catalytically active iridium sites to be robustly characterized. Our results provide evidence for the coordination of the iridium atoms by the acetonitrile solvent and demonstrate the viability of using diffuse X-ray scattering at free-electron laser sources for studying the dynamics of photocatalysis.

  11. Strategy using three layers of surface charge for computing solvation free energy of ions.

    PubMed

    Yang, Pei-Kun

    2013-12-31

    Continuum solvent model is the common used strategy for computing the solvation free energy. However, the dielectric polarization from Gauss's law differs from that obtained from molecular dynamics simulations. To mimic the dielectric polarization surrounding a solute in molecular dynamics simulations, the first-shell water molecule was modeled using a charge distribution of TIP4P molecule in a hard sphere. The dielectric polarization of the first-shell water was modeled as a pair of surface charge layers with a fixed distance between them, but with variable, equal, and opposite charge magnitudes that respond to the electric field on the first-shell water. The water outside the first shell water is treated as a bulk solvent, and the electric effect of the bulk solvent can be modeled as a surface charge. Based on this strategy, the analytical solution describing the solvation free energy of ions was derived, and the values of computed solvation free energy were compared to the values of experiments.

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  13. Solvation of Na2+ in Arn clusters. I. Structures and spectroscopic properties

    NASA Astrophysics Data System (ADS)

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

    2008-11-01

    We present a theoretical study of Na2+ solvation in an argon matrix Arn for n =1 to a few tens. We use a model based on an explicit description of valence electron interaction with Na+ and Ar cores by means of core polarization pseudopotential. The electronic structure determination is thus reduced to a one-electron problem, which can be handled efficiently. We investigate the ground state geometry and related optical absorption of Na2+Arn clusters. For n ⩽5, the lowest energy isomers are obtained by aggregation of Ar atoms at one single extremity of Na2+, leading to moderate perturbation of the optical transition. For 6⩽n⩽15, the Ar atoms aggregate at both extremities. This structural change is associated with a strong blueshift of the first optical transition (XΣg+2→AΣu+2), which reveals the confinement of the excited AΣu +2 state. The Na2+ energy spectrum is so strongly perturbed that the AΣu +2 state becomes higher than the BΠu +2 states. The closure of the first solvation shell is observed at n =17. Above this size, the second solvation shell develops. Its structure is dominated by a pentagonal organization around the Na2+ molecular axis. The optical transitions vary smoothly with n and the AΣu +2 and BΠu2 states are no longer inverted, though the first optical transition remains strongly blueshifted.

  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.

  15. Influence of silane and solvated bonding agents on the bond strength to glass-fibre posts.

    PubMed

    Oliveira, Aline S; Ramalho, Elisa S; Spazzin, Aloísio O; Naves, Lucas Z; Moraes, Rafael R

    2013-12-01

    The combined use of silane and solvated bonding agents on the bond strength to glass-fibre posts was investigated. A model Bis-GMA/HEMA adhesive was formulated with no solvent, 30% of ethanol or 80% of acetone. The surfaces of rectangular-shaped posts were silanated or not and one of the agents was applied, except for the control group. Cylinders of resin cement (RelyX ARC, 3M ESPE, Saint Paul, MN, USA) were built-up on the surfaces (n = 20) and submitted to shear testing. All groups showed higher bond strengths when the surfaces were silanated. When no silanization was carried out, the use of bonding agents, either solvated or non-solvated, increased the bond strengths. All groups treated with both silane and bonding agent showed higher bond strengths than the group that was only silanated. Control and ethanol-based adhesives were similar, whereas the acetone-based agent yielded higher bond strengths. Adhesive failures were predominant. Combination of silane and adhesive enhanced the bond to fibre posts.

  16. Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery

    PubMed Central

    Lee, Kyung-Koo; Park, Kwanghee; Lee, Hochan; Noh, Yohan; Kossowska, Dorota; Kwak, Kyungwon; Cho, Minhaeng

    2017-01-01

    Lithium cation is the charge carrier in lithium-ion battery. Electrolyte solution in lithium-ion battery is usually based on mixed solvents consisting of polar carbonates with different aliphatic chains. Despite various experimental evidences indicating that lithium ion forms a rigid and stable solvation sheath through electrostatic interactions with polar carbonates, both the lithium solvation structure and more importantly fluctuation dynamics and functional role of carbonate solvent molecules have not been fully elucidated yet with femtosecond vibrational spectroscopic methods. Here we investigate the ultrafast carbonate solvent exchange dynamics around lithium ions in electrolyte solutions with coherent two-dimensional infrared spectroscopy and find that the time constants of the formation and dissociation of lithium-ion···carbonate complex in solvation sheaths are on a picosecond timescale. We anticipate that such ultrafast microscopic fluxional processes in lithium-solvent complexes could provide an important clue to understanding macroscopic mobility of lithium cation in lithium-ion battery on a molecular level. PMID:28272396

  17. Solvation free energies of aqueous mixtures in a ``truly'' open boundary simulation

    NASA Astrophysics Data System (ADS)

    Mukherji, Debashish; Kremer, Kurt

    2013-03-01

    (Bio)macromolecular solvation in water cosolvent mixtures are dictated by the preferential interaction of cosolvents with the proteins. The numerical studies in the field are limited to the closed boundary schemes, which, however, suffers from severe system size effects. More specifically, when the conformational transitions are intimately linked to the large concentration fluctuations, the excess of cosolvents near a protein lead to depletion elsewhere in a small-sized closed boundary setup. This disturbs solvent equilibrium within the bulk solution. Therefore, by combining the adaptive resolution scheme (AdResS) with a metropolis particle exchange criterion, we propose a ``truly'' open boundary method that heals the particle depletion in a closed boundary setup. In AdResS, an all-atom region, containing protein, is coupled to a coarse-grained (CG) reservoir. Particle exchange is performed in the CG region, which otherwise would be impossible in an all-atom setup of dense fluids. We calculate solvation free energies within the all-atom region using Kirkwood-Buff theory. Our method produces well converged solvation energies that are impossible in a brute force all-atom MD of small system sizes. We will discuss two cases of triglycine in aqueous urea and PNIPAm in aqueous methanol.

  18. Valence-bond non-equilibrium solvation model for a twisting monomethine cyanine.

    PubMed

    McConnell, Sean; McKenzie, Ross H; Olsen, Seth

    2015-02-28

    We propose and analyze a two-state valence-bond model of non-equilibrium solvation effects on the excited-state twisting reaction of monomethine cyanines. Suppression of this reaction is thought responsible for environment-dependent fluorescence yield enhancement in these dyes. Fluorescence is quenched because twisting is accompanied via the formation of dark twisted intramolecular charge-transfer (TICT) states. For monomethine cyanines, where the ground state is a superposition of structures with different bond and charge localizations, there are two possible twisting pathways with different charge localizations in the excited state. For parameters corresponding to symmetric monomethines, the model predicts two low-energy twisting channels on the excited-state surface, which leads to a manifold of TICT states. For typical monomethines, twisting on the excited state surface will occur with a small barrier or no barrier. Changes in the solvation configuration can differentially stabilize TICT states in channels corresponding to different bonds, and that the position of a conical intersection between adiabatic states moves in response to solvation to stabilize either one channel or the other. There is a conical intersection seam that grows along the bottom of the excited-state potential with increasing solvent polarity. For monomethine cyanines with modest-sized terminal groups in moderately polar solution, the bottom of the excited-state potential surface is completely spanned by a conical intersection seam.

  19. Valence-bond non-equilibrium solvation model for a twisting monomethine cyanine

    NASA Astrophysics Data System (ADS)

    McConnell, Sean; McKenzie, Ross H.; Olsen, Seth

    2015-02-01

    We propose and analyze a two-state valence-bond model of non-equilibrium solvation effects on the excited-state twisting reaction of monomethine cyanines. Suppression of this reaction is thought responsible for environment-dependent fluorescence yield enhancement in these dyes. Fluorescence is quenched because twisting is accompanied via the formation of dark twisted intramolecular charge-transfer (TICT) states. For monomethine cyanines, where the ground state is a superposition of structures with different bond and charge localizations, there are two possible twisting pathways with different charge localizations in the excited state. For parameters corresponding to symmetric monomethines, the model predicts two low-energy twisting channels on the excited-state surface, which leads to a manifold of TICT states. For typical monomethines, twisting on the excited state surface will occur with a small barrier or no barrier. Changes in the solvation configuration can differentially stabilize TICT states in channels corresponding to different bonds, and that the position of a conical intersection between adiabatic states moves in response to solvation to stabilize either one channel or the other. There is a conical intersection seam that grows along the bottom of the excited-state potential with increasing solvent polarity. For monomethine cyanines with modest-sized terminal groups in moderately polar solution, the bottom of the excited-state potential surface is completely spanned by a conical intersection seam.

  20. UV resonance Raman investigation of the aqueous solvation dependence of primary amide vibrations.

    PubMed

    Punihaole, David; Jakubek, Ryan S; Dahlburg, Elizabeth M; Hong, Zhenmin; Myshakina, Nataliya S; Geib, Steven; Asher, Sanford A

    2015-03-12

    We investigated the normal mode composition and the aqueous solvation dependence of the primary amide vibrations of propanamide. Infrared, normal Raman, and UV resonance Raman (UVRR) spectroscopy were applied in conjunction with density functional theory (DFT) to assign the vibrations of crystalline propanamide. We examined the aqueous solvation dependence of the primary amide UVRR bands by measuring spectra in different acetonitrile/water mixtures. As previously observed in the UVRR spectra of N-methylacetamide, all of the resonance enhanced primary amide bands, except for the Amide I (AmI), show increased UVRR cross sections as the solvent becomes water-rich. These spectral trends are rationalized by a model wherein the hydrogen bonding and the high dielectric constant of water stabilizes the ground state dipolar (-)O-C═NH2(+) resonance structure over the neutral O═C-NH2 resonance structure. Thus, vibrations with large C-N stretching show increased UVRR cross sections because the C-N displacement between the electronic ground and excited state increases along the C-N bond. In contrast, vibrations dominated by C═O stretching, such as the AmI, show a decreased displacement between the electronic ground and excited state, which result in a decreased UVRR cross section upon aqueous solvation. The UVRR primary amide vibrations can be used as sensitive spectroscopic markers to study the local dielectric constant and hydrogen bonding environments of the primary amide side chains of glutamine (Gln) and asparagine (Asn).

  1. Prediction of Solvation Free Energies with Thermodynamic Integration Using the General Amber Force Field.

    PubMed

    Martins, Silvia A; Sousa, Sergio F; Ramos, Maria João; Fernandes, Pedro A

    2014-08-12

    Computer-aided drug design (CADD) techniques can be very effective in reducing costs and speeding up drug discovery. The determination of binding and solvation free energies is pivotal for this process and is, therefore, the subject of many studies. In this work, the solvation free energy change (ΔΔGsolv) for a total of 92 transformations in small molecules was predicted using Thermodynamic Integration (TI). It was our aim to compare experimental and calculated solvation free energies for typical and prime additions considered in drug optimizations, analyzing trends, and optimizing a TI protocol. The results showed a good agreement between experimental and predicted values, with an overestimation of the predicted values for CH3, halogens, and NH2, as well as an underestimation for CONH2, but all fall within ±1 kcal/mol. NO2 addition showed a larger and systematic underestimation of the predicted ΔΔGsolv, indicating the need for special attention in these cases. For small molecules, if no experimental data is available, using TI as a theoretical strategy thus appears to be a suitable choice in CADD. It provides a good compromise between time and accuracy.

  2. Real-Time Quantum Dynamics Reveals Complex, Many-Body Interactions in Solvated Nanodroplets.

    PubMed

    Oviedo, M Belén; Wong, Bryan M

    2016-04-12

    Electronic excitations in the liquid phase are surprisingly rich and considerably more complex than either gas-phase or solid-state systems. While the majority of physical and biological processes take place in solvent, our understanding of nonequilibrium excited-state processes in these condensed phase environments remains far from complete. A central and long-standing issue in these solvated environments is the assessment of many-body interactions, particularly when the entire system is out of equilibrium and many quantum states participate in the overall process. Here we present a microscopic picture of solute-solvent electron dynamics and solvatochromic effects, which we uncover using a new real-time quantum dynamics approach for extremely large solvated nanodroplets. In particular, we find that a complex interplay of quantum interactions underlies our observations of solute-solvent effects, and simple macroscopic solvatochromic shifts can even be qualitatively different at the microscopic molecular level in these systems. By treating both the solvent and the solute on the same footing at a quantum-mechanical level, we demonstrate that the electron dynamics in these systems are surprisingly complex, and the emergence of many-body interactions underlies the dynamics in these solvated systems.

  3. Resonance Raman spectrum of the solvated electron in methanol: simulation within a cluster model.

    PubMed

    Neumann, Stefanie; Eisfeld, Wolfgang; Sobolewski, Andrzej L; Domcke, Wolfgang

    2006-05-04

    The microsolvation of the CH(3)OH(2) hypervalent radical in methanol clusters has been investigated by density functional theory. It is shown that the CH(3)OH(2) radical spontaneously decomposes within methanol clusters into protonated methanol and a localized solvated electron cloud. The geometric and electronic structures of these clusters as well as their vibrational frequencies have been characterized. Resonance Raman intensities, associated with the s --> p transition of the unpaired electron, have been estimated for CH(3)OH(2)M(n) (M = CH(3)OH, n = 1-3) clusters. It is shown that with increasing cluster size the simulated spectra converge toward the resonance Raman spectrum of the solvated electron in methanol measured recently by Tauber and Mathies (J. Am. Chem. Soc. 2004, 126, 3414). The results suggest that CH(3)OH(2)M(n) clusters are useful finite-size model systems for the computational investigation of the spectroscopic properties of the solvated electron in liquid methanol.

  4. Photoinduced electron transfer and solvation in iodide-doped acetonitrile clusters.

    PubMed

    Ehrler, Oli T; Griffin, Graham B; Young, Ryan M; Neumark, Daniel M

    2009-04-02

    We have used ultrafast time-resolved photoelectron imaging to measure charge transfer dynamics in iodide-doped acetonitrile clusters I(-)(CH(3)CN)(n) with n = 5-10. Strong modulations of vertical detachment energies were observed following charge transfer from the halide, allowing interpretation of the ongoing dynamics. We observe a sharp drop in the vertical detachment energy (VDE) within 300-400 fs, followed by a biexponential increase that is complete by approximately 10 ps. Comparison to theory suggests that the iodide is internally solvated and that photodetachment results in formation of a diffuse electron cloud in a confined cavity. We interpret the initial drop in VDE as a combination of expansion of the cavity and localization of the excess electron on one or two solvent molecules. The subsequent increase in VDE is attributed to a combination of the I atom leaving the cavity and rearrangement of the acetonitrile molecules to solvate the electron. The n = 5-8 clusters then show a drop in VDE of around 50 meV on a much longer time scale. The long-time VDEs are consistent with those of (CH(3)CN)(n)(-) clusters with internally solvated electrons. Although the excited-state created by the pump pulse decays by emission of a slow electron, no such decay is seen by 200 ps.

  5. Subtle solvation behaviour of a biofuel additive: the methanol complex with 2,5-dimethylfuran.

    PubMed

    Poblotzki, Anja; Altnöder, Jonas; Suhm, Martin A

    2016-10-05

    Methanol is shown to engage two nearly equivalent solvation sites in 2,5-dimethylfuran, the electron-rich π cloud and the electron-deficient oxygen site. The latter only wins by a slight margin, thanks to the methyl group undergoing secondary interactions with the ring. These secondary attractions reduce the hydrogen bond-induced OH frequency shift of the OH-O contact, whereas the π cloud allows for a combined action of both binding mechanisms in the OH-π arrangement. In total, the hydrophobic character of 2,5-dimethylfuran is well reflected in the weak pair interactions, as judged by the small solvation shifts. Methanol solvation of 2,3-benzofuran is revisited and shown to be more ambiguous than previously thought, involving competition between five- and six-ring π clouds and the oxygen site for the OH group. The six-ring π cloud is slightly preferred. FTIR spectroscopy in supersonic jets is in systematic agreement with dispersion-corrected harmonic B3LYP and also B2PLYP predictions for these competing furan docking sites. Deuteration of the OH group helps to identify the docking sites because of its attenuated zero-point energy weakening effect on localized hydrogen bonds. Extension to less methylated furans is proposed in the context of a future forecasting competition for the performance of quantum chemical methods for intermolecular interactions.

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

    PubMed Central

    van Driel, Tim B.; Kjær, Kasper S.; Hartsock, Robert W.; Dohn, Asmus O.; Harlang, Tobias; Chollet, Matthieu; Christensen, Morten; Gawelda, Wojciech; Henriksen, Niels E.; Kim, Jong Goo; Haldrup, Kristoffer; Kim, Kyung Hwan; Ihee, Hyotcherl; Kim, Jeongho; Lemke, Henrik; Sun, Zheng; Sundström, Villy; Zhang, Wenkai; Zhu, Diling; Møller, Klaus B.; Nielsen, Martin M.; Gaffney, Kelly J.

    2016-01-01

    The interactions between the reactive excited state of molecular photocatalysts and surrounding solvent dictate reaction mechanisms and pathways, but are not readily accessible to conventional optical spectroscopic techniques. Here we report an investigation of the structural and solvation dynamics following excitation of a model photocatalytic molecular system [Ir2(dimen)4]2+, where dimen is para-diisocyanomenthane. The time-dependent structural changes in this model photocatalyst, as well as the changes in the solvation shell structure, have been measured with ultrafast diffuse X-ray scattering and simulated with Born-Oppenheimer Molecular Dynamics. Both methods provide direct access to the solute–solvent pair distribution function, enabling the solvation dynamics around the catalytically active iridium sites to be robustly characterized. Our results provide evidence for the coordination of the iridium atoms by the acetonitrile solvent and demonstrate the viability of using diffuse X-ray scattering at free-electron laser sources for studying the dynamics of photocatalysis. PMID:27892472

  7. Anharmonicity, solvation forces, and resolution in atomic force microscopy at the solid-liquid interface

    NASA Astrophysics Data System (ADS)

    Voïtchovsky, Kislon

    2013-08-01

    Solid-liquid interfaces are central to nanoscale science and technology and control processes as diverse as self-assembly, heterogeneous catalysis, wetting, electrochemistry, or protein function. Experimentally, measuring the structure and dynamics of solid-liquid interfaces with molecular resolution remains a challenge. This task can, in principle, be achieved with atomic force microscopy (AFM), which functions locally, and with nanometer precision. When operated dynamically and at small amplitudes, AFM can provide molecular-level images of the liquid solvation layers at the interfaces. At larger amplitudes, results in the field of multifrequency AFM have shown that anharmonicities in the tip motion can provide quantitative information about the solid's mechanical properties. The two approaches probe opposite aspects of the interface and are generally seen as distinct. Here it is shown that, for amplitudes Asolvation region, the tip mainly probes the interfacial liquid, and subnanometer resolution can be achieved through solvation forces. For A>d, the tip trajectory becomes rapidly anharmonic due to the tip tapping the solid, and the resolution decreases. A nonlinear transition between the two regimes occurs for A˜d and can be quantified with the second harmonic of the tip oscillation. These results, confirmed by computer simulations, remain valid in most experimental conditions. Significantly, they provide an objective criterion to enhance resolution and to decide whether the results are dominated by the properties of the solid or of the liquid.

  8. Interaction Mechanism Insights on the Solvation of Fullerene B(80)with Choline-based Ionic Liquids.

    PubMed

    García, Gregorio; Atilhan, Mert; Aparicio, Santiago

    2015-09-24

    Beyond carbon allotropes, other nanostructures such as fullerene B80 are attracting a growing interest due to their potential applications. The use of new materials based on fullerene B80 is still in a premature stage; however many of these applications would require the use of B80 in solution. This paper reports an unprecedented density functional theory (DFT) analysis on the interaction mechanism between B80 and two choline-based ionic liquids as a first insight for the fullerene B80 solvation by ionic liquids. The analysis of properties such as binding energies, charge distributions or intermolecular interactions shed light on the main features, which should govern interaction between ionic liquids and fullerene B80. In addition, the optimization of systems composed by six ionic pairs around a fullerene B80 has supplied some information about the first solvation shell at the molecular level. As a summary, this paper provides the first insights in the rational design of ionic liquids with suitable properties for the solvation of B80.

  9. Kinetic solvation pressure: a measure of environmental effects on reaction rates. 1. Application to hydrophobic systems

    SciTech Connect

    Mata-Segreda, J.F.

    1988-08-31

    A quantity termed kinetic solvation pressure is defined as (/partial derivative//Delta/G/sup /double dagger////partial derivative//anti/V)/sub T/, where /anti/V is the reactant molar volume. It is identified with the difference in the amount of isothermal work, per unit volume expansion necessary to create a solvation cavity in a particular medium, upon transition-state complex formation. The quantity was evaluated for the hydrolysis of carboxylic esters mediated by different hydrophobic catalysts and was found to be equal to +26 J cm/sup /minus/3/ for the acid-catalyzed hydrolysis of n-alkyl acetates in water solvent; but it becomes negative when macro- or supramolecular acids were used as catalysts: /minus/16 J cm/sup /minus/3/ for Dowex 50W-X2, /minus/43J cm/sup /minus/3/ for poly(styrenesulfonic acid), /minus/64 J cm/sup /minus/3/ for dodecylsulfuric acid micelles. These results suggest the action of hydrophobic forces in enhancing the catalytic power of the supermolecules, relative to aqueous hydrogen ion. No such effect is seen in aqueous acetone or when more hydrophilic acetates are used as substrates. Kinetic solvation pressure for enzyme-catalyzed ester hydrolysis is five times more negative than for the resin system, indicating the full action of hydrophobic forces in the catalytic process.

  10. 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

  11. 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

  12. Linear-scaling density functional simulations of the effect of crystallographic structure on the electronic and optical properties of fullerene solvates.

    PubMed

    Xue, Hong-Tao; Boschetto, Gabriele; Krompiec, Michal; Morse, Graham E; Tang, Fu-Ling; Skylaris, Chris-Kriton

    2017-02-15

    In this work, the crystal properties, HOMO and LUMO energies, band gaps, density of states, as well as the optical absorption spectra of fullerene C60 and its derivative phenyl-C61-butyric-acid-methyl-ester (PCBM) co-crystallised with various solvents such as benzene, biphenyl, cyclohexane, and chlorobenzene were investigated computationally using linear-scaling density functional theory with plane waves as implemented in the ONETEP program. Such solvates are useful materials as electron acceptors for organic photovoltaic (OPV) devices. We found that the fullerene parts contained in the solvates are unstable without solvents, and the interactions between fullerene and solvent molecules in C60 and PCBM solvates make a significant contribution to the cohesive energies of solvates, indicating that solvent molecules are essential to keep C60 and PCBM solvates stable. Both the band gap (Eg) and the HOMO and LUMO states of C60 and PCBM solvates are mainly determined by the fullerene parts contained in solvates. Chlorobenzene- and ortho-dichlorobenzene-solvated PCBM are the most promising electron-accepting materials among these solvates for increasing the driving force for charge separation in OPVs due to their relatively high LUMO energies. The UV-Vis absorption spectra of solvent-free C60 and PCBM crystals in the present work are similar to those of C60 and PCBM thin films shown in the literature. Changes in the absorption spectra of C60 solvates relative to the solvent-free C60 crystal are more significant than those of PCBM solvates due to the weaker effect of solvents on the π-stacking interactions between fullerene molecules in the latter solvates. The main absorptions for all C60 and PCBM crystals are located in the ultraviolet (UV) region.

  13. 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.

  14. Predicting retention in reverse-phase liquid chromatography at different mobile phase compositions and temperatures by using the solvation parameter model.

    PubMed

    Gotta, Javier; Keunchkarian, Sonia; Castells, Cecilia; Reta, Mario

    2012-10-01

    The prediction capability of the solvation parameter model in reverse-phase liquid chromatography at different methanol-water mobile phase compositions and temperatures was investigated. By using a carefully selected set of solutes, the training set, linear relationships were established through regression equations between the logarithm of the solute retention factor, logk, and different solute parameters. The coefficients obtained in the regressions were used to create a general retention model able to predict retention in an octadecylsilica stationary phase at any temperature and methanol-water composition. The validity of the model was evaluated by using a different set (the test set) of 30 solutes of very diverse chemical nature. Predictions of logk values were obtained at two different combinations of temperature and mobile phase composition by using two different procedures: (i) by calculating the coefficients through a mathematical linear relationship in which the mobile phase composition and temperature are involved; (ii) by using a general equation, obtained by considering the previous results, in which only the experimental values of temperature and mobile phase composition are required. Predicted logk values were critically compared with the experimental values. Excellent results were obtained considering the diversity of the test set.

  15. Octanol-Water Partition Coefficient from 3D-RISM-KH Molecular Theory of Solvation with Partial Molar Volume Correction.

    PubMed

    Huang, WenJuan; Blinov, Nikolay; Kovalenko, Andriy

    2015-04-30

    The octanol-water partition coefficient is an important physical-chemical characteristic widely used to describe hydrophobic/hydrophilic properties of chemical compounds. The partition coefficient is related to the transfer free energy of a compound from water to octanol. Here, we introduce a new protocol for prediction of the partition coefficient based on the statistical-mechanical, 3D-RISM-KH molecular theory of solvation. It was shown recently that with the compound-solvent correlation functions obtained from the 3D-RISM-KH molecular theory of solvation, the free energy functional supplemented with the correction linearly related to the partial molar volume obtained from the Kirkwood-Buff/3D-RISM theory, also called the "universal correction" (UC), provides accurate prediction of the hydration free energy of small compounds, compared to explicit solvent molecular dynamics [ Palmer , D. S. ; J. Phys.: Condens. Matter 2010 , 22 , 492101 ]. Here we report that with the UC reparametrized accordingly this theory also provides an excellent agreement with the experimental data for the solvation free energy in nonpolar solvent (1-octanol) and so accurately predicts the octanol-water partition coefficient. The performance of the Kovalenko-Hirata (KH) and Gaussian fluctuation (GF) functionals of the solvation free energy, with and without UC, is tested on a large library of small compounds with diverse functional groups. The best agreement with the experimental data for octanol-water partition coefficients is obtained with the KH-UC solvation free energy functional.

  16. The Solvation Structure of Lithium Ions in an Ether Based Electrolyte Solution from First-Principles Molecular Dynamics.

    PubMed

    Callsen, Martin; Sodeyama, Keitaro; Futera, Zdeněk; Tateyama, Yoshitaka; Hamada, Ikutaro

    2017-01-12

    The solvation and desolvation of the Li ion play a crucial role in the electrolytes of Li based secondary batteries, and their understanding at the microscopic level is of great importance. Oligoether (glyme) based electrolytes have attracted much attention as electrolytes used in Li based secondary batteries, such as Li-ion, Li-S, and Li-O2 batteries. However, the solvation structure of the Li ion in glyme based electrolytes has not been fully clarified yet. We present a computational study on the solvation structure of lithium ions in the mixture of triglyme and lithium bis(trifluoromethylsulfonyl)-amide (LiTFSA) by means of molecular orbital and molecular dynamics calculations based on density functional theory. We found that, in the electrolyte solution composed of the equimolar mixture of triglyme and LiTFSA, lithium ions are solvated mainly by crown-ether-like curled triglyme molecules and in direct contact with an TFSA anion. We also found the aggregate formed with Li ion and TFSA anions and/or triglyme molecule(s) is equally stable, which has not been reported in the previous classical molecular dynamics simulations, suggesting that in reality a small fraction of Li ions form aggregates and they might have a significant impact on the Li ion transport. Our results demonstrate the importance of performing electronic structure based molecular dynamics of electrolyte solution to clarify the detailed solvation structure of the Li ion.

  17. Dielectric relaxation and solvation dynamics in a prototypical ionic liquid + dipolar protic liquid mixture: 1-butyl-3-methylimidazolium tetrafluoroborate + water.

    PubMed

    Zhang, Xin-Xing; Liang, Min; Hunger, Johannes; Buchner, Richard; Maroncelli, Mark

    2013-12-12

    Dielectric and solvation data on mixtures of 1-butyl-3-methylimidazilium tetrafluoroborate ([Im41][BF4]) + water are reported and used to examine the utility of dielectric solvation models. Dielectric permittivity and loss spectra (25 °C) were recorded over the frequency range 200 MHz to 89 GHz at 17 compositions and fit to a 4-Debye form. Dynamic Stokes shift measurements on the solute coumarin 153 (C153), made by combining fluorescence upconversion (80 fs resolution) and time-correlated single photon counting data (20 ns range), were used to determine the solvation response at 7 compositions (20.5 °C). All properties measured here were found to depend upon mixture composition in a simple continuous manner, especially when viewed in terms of volume fraction. Solvation response functions predicted by a simple dielectric continuum model are similar to but ∼7-fold faster than the spectral response functions measured with C153. The solvation data are in better agreement with the recently published predictions of a semimolecular model of Biswas and co-workers [J. Phys. Chem. B 2011, 115, 4011], but these latter predictions are systematically slow by a factor of ∼3.

  18. Predicting hydrophobic solvation by molecular simulation: 2. New united-atom model for alkanes, alkenes, and alkynes.

    PubMed

    Jorge, Miguel

    2017-03-05

    Existing united-atom models for non-polar hydrocarbons lead to systematic deviations in predicted solvation free energies in hydrophobic solvents. In this article, an improved set of parameters is proposed for alkane molecules that corrects this systematic deviation and accurately predicts solvation free energies in hydrophobic media, while simultaneously providing a very good description of pure liquid densities. The model is then extended to alkenes and alkynes, again yielding very accurate predictions of solvation free energies and densities for these classes of compounds. For alkynes in particular, this work represents the first attempt at a systematic parameterization using the united-atom approach. Averaging over all 95 solute/solvent pairs tested, the mean signed deviation from experimental data is very close to zero, indicating no systematic error in the predictions. The fact that predictions are robust even for relatively large molecules suggests that the new model may be applicable to solvation of non-polar macromolecules without accumulation of errors. The root mean squared deviation of the simulations is only 0.6 kJ/mol, which is lower than the estimated uncertainty in the experimental measurements. This excellent performance constitutes a solid basis on which a more general model can be parameterized to describe solvation in both polar and non-polar environments. © 2016 Wiley Periodicals, Inc.

  19. Solvation Energy of Ions in Polymers: Effects of Chain Length and Connectivity on Saturated Dipoles near Ions.

    PubMed

    Liu, Lijun; Nakamura, Issei

    2017-04-03

    We illustrate the effects of chain connectivity on the solvation energy of ions immersed in polymer liquids by developing a new coarse-grained molecular dynamics simulation. Our theory accounts for the dielectric response of the polymers through the connection of dipolar, monomeric units with nonlinear springs. In stark contrast to the standard Born solvation energy of ions, our results depend substantially on the chain length of the polymers. We also demonstrate the marked difference in the solvation energies of the ions immersed in non-polymeric particle mixtures, single-component polymers, polymer blends, and block copolymers. Thus, we suggest that the chain architecture of polymers is a key factor in ion solvation, whereas this feature is often inadequately considered in main theory and simulation literature. Our results are consistent with those predicted by previous coarse-grained mean-field theories when the dipole moment of the polymer compositions is relatively small. However, we also demonstrate that the strong ion-dipole and dipole-dipole interactions cause the chain-like association of the monomeric units, resulting in a qualitative discrepancy between the mean-field theory and simulation. Such a strong electrostatic correlation may reverse the dependence of the chain length on the solvation energy of the ions in the polymers.

  20. Solvation and hydrogen bonding in alanine- and glycine-containing dipeptides probed using solution- and solid-state NMR spectroscopy.

    PubMed

    Bhate, Manasi P; Woodard, Jaie C; Mehta, Manish A

    2009-07-15

    The NMR chemical shift is a sensitive reporter of peptide secondary structure and its solvation environment, and it is potentially rich with information about both backbone dihedral angles and hydrogen bonding. We report results from solution- and solid-state (13)C and (15)N NMR studies of four zwitterionic model dipeptides, L-alanyl-L-alanine, L-alanyl-glycine, glycyl-L-alanine, and glycyl-glycine, in which we attempt to isolate structural and environmental contributions to the chemical shift. We have mapped hydrogen-bonding patterns in the crystalline states of these dipeptides using the published crystal structures and correlated them with (13)C and (15)N magic angle spinning chemical shift data. To aid in the interpretation of the solvated chemical shifts, we performed ab initio quantum chemical calculations to determine the low-energy conformers and their chemical shifts. Assuming low energy barriers to interconversion between thermally accessible conformers, we compare the Boltzmann-averaged chemical shifts with the experimentally determined solvated-state shifts. The results allow us to correlate the observed differences in chemical shifts between the crystalline and solvated states to changes in conformation and hydrogen bonding that occur upon solvation.

  1. 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.

  2. 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)

  3. Probing the transition from hydrophilic to hydrophobic solvation with atomic scale resolution.

    PubMed

    Pham, Van-Thai; Penfold, Thomas J; van der Veen, Renske M; Lima, Frederico; El Nahhas, Amal; Johnson, Steve L; Beaud, Paul; Abela, Rafael; Bressler, Christian; Tavernelli, Ivano; Milne, Christopher J; Chergui, Majed

    2011-08-17

    Picosecond and femtosecond X-ray absorption spectroscopy is used to probe the changes of the solvent shell structure upon electron abstraction of aqueous iodide using an ultrashort laser pulse. The transient L(1,3) edge EXAFS at 50 ps time delay points to the formation of an expanded water cavity around the iodine atom, in good agreement with classical and quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. These also show that while the hydrogen atoms pointed toward iodide, they predominantly point toward the bulk solvent in the case of iodine, suggesting a hydrophobic behavior. This is further confirmed by quantum chemical (QC) calculations of I(-)/I(0)(H(2)O)(n=1-4) clusters. The L(1) edge sub-picosecond spectra point to the existence of a transient species that is not present at 50 ps. The QC calculations and the QM/MM MD simulations identify this transient species as an I(0)(OH(2)) complex inside the cavity. The simulations show that upon electron abstraction most of the water molecules move away from iodine, while one comes closer to form the complex that lives for 3-4 ps. This time is governed by the reorganization of the main solvation shell, basically the time it takes for the water molecules to reform an H-bond network. Only then is the interaction with the solvation shell strong enough to pull the water molecule of the complex toward the bulk solvent. Overall, much of the behavior at early times is determined by the reorientational dynamics of water molecules and the formation of a complete network of hydrogen bonded molecules in the first solvation shell.

  4. Photoelectron imaging and density-functional investigation of bismuth and lead anions solvated in ammonia clusters.

    PubMed

    Sobhy, Mohamed A; Casalenuovo, K; Reveles, J Ulises; Gupta, Ujjwal; Khanna, Shiv N; Castleman, A W

    2010-10-28

    We present the results of photoelectron velocity-map imaging experiments for the photodetachment of small negatively charged ammonia solvated Bi(n) and Pb(n) (n = 1, 2) clusters at 527 nm. The vertical detachment energies of the observed multiple electronic bands and their respective anisotropy parameters for the solvated Bi and Pb anions and clusters derived from the photoelectron images are reported. The electronic bands of Bi(NH(3))(n=1,2) are distinct from the Bi metal ion in exhibiting a perpendicular distribution whereas the electronic bands in Pb(NH(3))(n=1,2), unlike the Pb anion, show an isotropic distribution with respect to the laser polarization. Density-functional theory calculations with a generalized gradient approximation for the exchange-correlation potential were performed on these clusters to determine their atomic and electronic structures. Calculated geometries show a dramatic change between anionic and neutral ammonia solvated Bi and Pb species. Anionic clusters exhibit van der Waals interactions between the hydrogen atoms of ammonia and the metal core, where it was determined that the negative charge is localized. Neutral clusters, on the other hand, present a covalent bond between the nitrogen atom of ammonia and the metal core. Calculated binding energies show an enhancement in the bonding of the (NH(3))(2) dimer in the presence of the anionic Bi(1,2)(-) and Pb(1,2)(-) metal ions. This is rationalized by the electrostatic interaction between the negative charged metal core and the hydrogen atoms of the ammonia molecule.

  5. Local Aqueous Solvation Structure Around Ca2+ During Ca2+---Cl– Pair Formation

    SciTech Connect

    Baer, Marcel D.; Mundy, Christopher J.

    2016-03-03

    The molecular details of single ion solvation around Ca2+ and ion-pairing of Ca2--Cl- are investigated using ab initio molecular dynamics. The use of empirical dispersion corrections to the BLYP functional are investigated by comparison to experimentally available extended X-ray absorption fine structure (EXAFS) measurements, which probes the first solvation shell in great detail. Besides finding differences in the free-energy for both ion-pairing and the coordination number of ion solvation between the quantum and classical descriptions of interaction, there were important differences found between dispersion corrected and uncorrected density functional theory (DFT). Specifically, we show significantly different free-energy landscapes for both coordination number of Ca2+ and its ion-pairing with Cl- depending on the DFT simulation protocol. Our findings produce a self-consistent treatment of short-range solvent response to the ion and the intermediate to long-range collective response of the electrostatics of the ion-ion interaction to produce a detailed picture of ion-pairing that is consistent with experiment. MDB is supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative at Pacific Northwest National Laboratory. It was conducted under the Laboratory Directed Research and Development Program at PNNL, a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy. CJM acknowledges support from US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. This research used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Additional computing resources were generously allocated by PNNL's Institutional Computing program. The authors thank Prof. Tom Beck for discussions regarding

  6. Solvation enthalpies of free radicals: O-O bond strength in di-tert-butylperoxide.

    PubMed

    Borges Dos Santos, R M; Muralha, V S; Correia, C F; Martinho Simões, J A

    2001-12-19

    The photolysis reaction of di-tert-butylperoxide was studied in various solvents by photoacoustic calorimetry (PAC). This technique allows the determination of the enthalpy of this homolysis reaction, which by definition corresponds to the O-O bond dissociation enthalpy of the peroxide in solution, DHsin(degrees)(O-O). The derived value from these experiments in benzene, 156.7 +/- 9.9 kJ mol(-1), is very similar to a widely accepted value for the gas-phase bond dissociation enthalpy, DH(degrees)(O-O) = 159.0 +/- 2.1 kJ mol(-1). However, when the PAC-based value is used together with auxiliary experimental data and Drago's ECW model to estimate the required solvation terms, it leads to 172.3 +/- 10.2 kJ mol(-1) for the gas-phase bond dissociation enthalpy. This result, significantly higher than the early literature value, is however in excellent agreement with a recent gas-phase determination of 172.5 +/- 6.6 kJ mol(-1). The procedure to derive the gas-phase DH(degrees)(O-O) was tested by repeating the PAC experiments in carbon tetrachloride and acetonitrile. The average of the values thus obtained was DH(degrees)(O-O) = 179.6 +/- 4.5 kJ mol(-1), confirming that the early gas-phase result is a lower limit. More importantly, the present study questions the usual assumption that the solvation terms of homolysis reactions producing free radicals in solution should cancel, and suggests a methodology to estimate solvation enthalpies of free radicals.

  7. Gating mechanism of mechanosensitive channel of large conductance: a coupled continuum mechanical-continuum solvation approach.

    PubMed

    Zhu, Liangliang; Wu, Jiazhong; Liu, Ling; Liu, Yilun; Yan, Yuan; Cui, Qiang; Chen, Xi

    2016-12-01

    Gating transition of the mechanosensitive channel of large conductance (MscL) represents a good example of important biological processes that are difficult to describe using atomistic simulations due to the large (submicron) length scale and long (millisecond) time scale. Here we develop a novel computational framework that tightly couples continuum mechanics with continuum solvation models to study the detailed gating behavior of E. coli-MscL. The components of protein molecules are modeled by continuum elements that properly describe their shape, material properties and physicochemical features (e.g., charge distribution). The lipid membrane is modeled as a three-layer material in which the lipid head group and tail regions are treated separately, taking into account the fact that fluidic lipid bilayers do not bear shear stress. Coupling between mechanical and chemical responses of the channel is realized by an iterative integration of continuum mechanics (CM) modeling and continuum solvation (CS) computation. Compared to previous continuum mechanics studies, the present model is capable of capturing the most essential features of the gating process in a much more realistic fashion: due mainly to the apolar solvation contribution, the membrane tension for full opening of MscL is reduced substantially to the experimental measured range. Moreover, the pore size stabilizes constantly during gating because of the intricate interactions of the multiple components of the system, implying the mechanism for sub-conducting states of MscL gating. A significant fraction ([Formula: see text]2/3) of the gating membrane strain is required to reach the first sub-conducting state of our model, which is featured with a relative conductance of 0.115 to the fully opened state. These trends agree well with experimental observations. We anticipate that the coupled CM/CS modeling framework is uniquely suited for the analysis of many biomolecules and their assemblies under external

  8. 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

  9. Solvation of coumarin6 studied by vibrational spectroscopy and density functional theory

    NASA Astrophysics Data System (ADS)

    Singh, Randhir; Sathe, Vasant; Sharma, Amit; Kaur, Sarvpreet; Saini, G. S. S.

    2016-02-01

    Effect of solvation on coumarin6 dye has been studied with density functional theory (DFT). Optimized structure of the dye has been obtained in various solvents and frequencies of various vibrational bands have been calculated in these solvents. Calculations predict shift in the frequency of certain bands in the solvents. Similar shifts have been observed experimentally in the vibrational spectra of the dye in solvents. In order to ascertain the origin of these shifts, the interactions of solvent molecules with the coumarin6 molecule have been studied using various tools of DFT like donor-acceptor interactions, Molecular Electrostatic potential (MEP) and HOMO-LUMO analysis etc.

  10. 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

  11. 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

  12. Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field.

    PubMed

    Shivakumar, Devleena; Harder, Edward; Damm, Wolfgang; Friesner, Richard A; Sherman, Woody

    2012-08-14

    Explicit solvent molecular dynamics free energy perturbation simulations were performed to predict absolute solvation free energies of 239 diverse small molecules. We use OPLS2.0, the next generation OPLS force field, and compare the results with popular small molecule force fields-OPLS_2005, GAFF, and CHARMm-MSI. OPLS2.0 produces the best correlation with experimental data (R(2) = 0.95, slope = 0.96) and the lowest average unsigned errors (0.7 kcal/mol). Important classes of compounds that performed suboptimally with OPLS_2005 show significant improvements.

  13. Local, solvation pressures and conformational changes in ethylenediamine aqueous solutions probed using Raman spectroscopy.

    PubMed

    Cáceres, Mercedes; Lobato, Alvaro; Mendoza, Nubia J; Bonales, Laura J; Baonza, Valentín G

    2016-09-21

    Raman spectra of 1,2-ethylenediamine (EDA) in aqueous solutions are used to demonstrate that EDA molecules experience an anti-gauche conformational change resulting from the interactions with water. The observed Raman shift reveals a compressive (hydrophobic) effect of water on both methylene and amino groups of EDA. Raman spectra of EDA at high pressures are used as reference to quantify the intermolecular EDA-H2O interactions in terms of local pressures. These results are compared with macroscopic solvation pressures calculated from the cohesive energy parameter. We compare and discuss all our observations with available computational and experimental studies.

  14. 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

  15. A study of solvation of benzaldehyde and cinnamaldehyde in CO 2 by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Wang, Jinyao; Zhao, Fengyu; Wu, Zhijian

    2010-05-01

    The solvation of benzaldehyde and cinnamaldehyde in CO 2 was simulated at 323 K at a density range from 0.135 to 0.807 g/cm 3. It was observed that the spatial distribution of CO 2 molecules around solutes closely follows the negative electrostatic potential in the solute molecules. The solvent density distribution maps and radial distribution maps at different densities provided the details of the local solvent density augmentation around each solute. In order to understand the difference of the local density augmentation, the interaction energies between CO 2 molecules and solutes were discussed.

  16. Resolving solvophobic interactions inferred from experimental solvation free energies and evaluated from molecular simulations

    NASA Astrophysics Data System (ADS)

    Barnett, J. Wesley; Bhutta, Amna; Bierbrier, Sarah C.; da Silva Moura, Natalia; Ashbaugh, Henry S.

    2017-01-01

    Ben-Naim estimated the solvent-mediated interaction between methanes based on experimental solvation free energy differences between chemically similar hydrocarbons. Interactions were predicted to be strongest in water, dominated by characteristic entropic gains. We use molecular simulations in combination with an empirical interpolation procedure that bridges interactions from outside methane's excluded volume down to overlap to test Ben-Naim's estimates. While Ben-Naim's approach captures many distinctive trends, the alchemical differences between methane and a methyl unit play a non-trivial role on the predicted association strength and the sign of enthalpic and entropic components of the interaction free energy in water and ethanol.

  17. Identification, preparation, and characterization of several polymorphs and solvates of terazosin hydrochloride.

    PubMed

    Bauer, J; Morley, J; Spanton, S; Leusen, F J J; Henry, R; Hollis, S; Heitmann, W; Mannino, A; Quick, J; Dziki, W

    2006-04-01

    The phenomenon of polymorphism is prevalent in pharmaceuticals, yet it is unusual to identify more than three or four forms for any particular drug. Terazosin hydrochloride has been found to exist at room temperature in four solvent-free forms that can be isolated directly, one solvent-free form that can be prepared by desolvation of a methanolate, a methanol solvate, and a dihydrate. This study presents characterization and methods for preparation of each of these forms. Data are also presented demonstrating the relative stability of these forms.

  18. 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

  19. Photo-illuminated diamond as a solid-state source of solvated electrons in water for nitrogen reduction.

    PubMed

    Zhu, Di; Zhang, Linghong; Ruther, Rose E; Hamers, Robert J

    2013-09-01

    The photocatalytic reduction of N₂ to NH₃ is typically hampered by poor binding of N₂ to catalytic materials and by the very high energy of the intermediates involved in this reaction. Solvated electrons directly introduced into the reactant solution can provide an alternative pathway to overcome such limitations. Here we demonstrate that illuminated hydrogen-terminated diamond yields facile electron emission into water, thus inducing reduction of N₂ to NH₃ at ambient temperature and pressure. Transient absorption measurements at 632 nm reveal the presence of solvated electrons adjacent to the diamond after photoexcitation. Experiments using inexpensive synthetic diamond samples and diamond powder show that photocatalytic activity is strongly dependent on the surface termination and correlates with the production of solvated electrons. The use of diamond to eject electrons into a reactant liquid represents a new paradigm for photocatalytic reduction, bringing electrons directly to reactants without requiring molecular adsorption to the surface.

  20. 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

    2011-01-07

    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.

  1. Solvation structure and dynamics of K+ in aqueous ammonia solution: Insights from an ONIOM-XS MD simulation

    NASA Astrophysics Data System (ADS)

    Kabbalee, Pilailuk; Sripa, Pattrawan; Tongraar, Anan; Kerdcharoen, Teerakiat

    2015-07-01

    An ONIOM-XS MD simulation has been performed to investigate the solvation structure and dynamics of K+ in aqueous ammonia solution. Detailed analyses on the ONIOM-XS MD trajectories clearly reveal that the K+ solvation is rather flexible, forming numerous possible K+-ligand species, ranging from 4- to 10-fold coordinated complexes. The average coordination number of K+ in such a solvent mixture is predicted to be 7.0, consisting of 4.8 water and 2.2 ammonia molecules. The results obtained by the ONIOM-XS MD simulation have provided more insights into the characteristics of this solvated ion, i.e., when compared to the previous QM/MM MD study.

  2. 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.

  3. Between-species variation in the kinetic stability of TIM proteins linked to solvation-barrier free energies.

    PubMed

    Costas, Miguel; Rodríguez-Larrea, David; De Maria, Leonardo; Borchert, Torben V; Gómez-Puyou, Armando; Sanchez-Ruiz, Jose M

    2009-01-23

    Theoretical, computational, and experimental studies have suggested the existence of solvation barriers in protein unfolding and denaturation processes. These barriers are related to the finite size of water molecules and can be envisioned as arising from the asynchrony between water penetration and breakup of internal interactions. Solvation barriers have been proposed to play roles in protein cooperativity and kinetic stability; therefore, they may be expected to be subject to natural selection. We study the thermal denaturation, in the presence and in the absence of chemical denaturants, of triosephosphate isomerases (TIMs) from three different species: Trypanosoma cruzi, Trypanosoma brucei, and Leishmania mexicana. In all cases, denaturation was irreversible and kinetically controlled. Surprisingly, however, we found large differences between the kinetic denaturation parameters, with T. cruzi TIM showing a much larger activation energy value (and, consequently, much lower room-temperature, extrapolated denaturation rates). This disparity cannot be accounted for by variations in the degree of exposure to solvent in transition states (as measured by kinetic urea m values) and is, therefore, to be attributed mainly to differences in solvation-barrier contributions. This was supported by structure-energetics analyses of the transition states and by application of a novel procedure to estimate from experimental data the solvation-barrier impact at the entropy and free-energy levels. These analyses were actually performed with an extended protein set (including six small proteins plus seven variants of lipase from Thermomyces lanuginosus and spanning a wide range of activation parameters), allowing us to delineate the general trends of the solvation-barrier contributions. Overall, this work supports that proteins sharing the same structure and function but belonging to different organisms may show widely different solvation barriers, possibly as a result of different

  4. Improving the Catalytic Performance of (S)-Proline as Organocatalyst in Asymmetric Aldol Reactions in the Presence of Solvate Ionic Liquids: Involvement of a Supramolecular Aggregate.

    PubMed

    Obregón-Zúñiga, Arturo; Milán, Mario; Juaristi, Eusebio

    2017-03-03

    For the first time, a highly efficient and stereoselective asymmetric aldol reaction employing (S)-proline in the presence of solvate ionic liquids is reported. The reaction seems to proceed via a supramolecular aggregate of (S)-proline, the solvate ionic liquid, and water, affording high yields and excellent stereoselectivities with low catalyst loadings.

  5. 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 ...

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

    PubMed Central

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

    2011-01-01

    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), C11H11N3O2S, (1), 4-amino-N-(1,2-dihydro­pyri­din-2-yl­idene)benzene­sulfonamide 1,3-dioxane monosolvate, C11H11N3O2S·C4H8O2, (2), and 4-amino-N-(1,2-dihydro­pyri­din-2-yl­idene)benzene­sulfonamide tetra­hydro­furan monosolvate, C11H11N3O2S·C4H8O, (3), crystallized as the imide form, while piperidin-1-ium 4-amino-N-(pyridin-2-yl)benzene­sul­fon­amidate, C5H12N+·C11H10N3O2S−, (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

  7. Variational Derivation of Dissipative Equations

    NASA Astrophysics Data System (ADS)

    Sogo, Kiyoshi

    2017-03-01

    A new variational principle is formulated to derive various dissipative equations. Model equations considered are the damping equation, Bloch equation, diffusion equation, Fokker-Planck equation, Kramers equation and Smoluchowski equation. Each equation and its time reversal equation are simultaneously obtained in our variational principle.

  8. 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

  9. An extended aqueous solvation model based on atom-weighted solvent accessible surface areas: SAWSA v2.0 model.

    PubMed

    Hou, Tingjun; Zhang, Wei; Huang, Qin; Xu, Xiaojie

    2005-02-01

    A new method is proposed for calculating aqueous solvation free energy based on atom-weighted solvent accessible surface areas. The method, SAWSA v2.0, gives the aqueous solvation free energy by summing the contributions of component atoms and a correction factor. We applied two different sets of atom typing rules and fitting processes for small organic molecules and proteins, respectively. For small organic molecules, the model classified the atoms in organic molecules into 65 basic types and additionally. For small organic molecules we proposed a correction factor of "hydrophobic carbon" to account for the aggregation of hydrocarbons and compounds with long hydrophobic aliphatic chains. The contributions for each atom type and correction factor were derived by multivariate regression analysis of 379 neutral molecules and 39 ions with known experimental aqueous solvation free energies. Based on the new atom typing rules, the correlation coefficient (r) for fitting the whole neutral organic molecules is 0.984, and the absolute mean error is 0.40 kcal mol(-1), which is much better than those of the model proposed by Wang et al. and the SAWSA model previously proposed by us. Furthermore, the SAWSA v2.0 model was compared with the simple atom-additive model based on the number of atom types (NA). The calculated results show that for small organic molecules, the predictions from the SAWSA v2.0 model are slightly better than those from the atom-additive model based on NA. However, for macromolecules such as proteins, due to the connection between their molecular conformation and their molecular surface area, the atom-additive model based on the number of atom types has little predictive power. In order to investigate the predictive power of our model, a systematic comparison was performed on seven solvation models including SAWSA v2.0, GB/SA_1, GB/SA_2, PB/SA_1, PB/SA_2, AM1/SM5.2R and SM5.0R. The results showed that for organic molecules the SAWSA v2.0 model is better

  10. Molecular thermodynamics of trifluoroethanol-induced helix formation: analysis of the solvation structure and free energy by the 3D-RISM theory.

    PubMed

    Imai, Takashi; Kovalenko, Andriy; Hirata, Fumio; Kidera, Akinori

    2009-06-01

    It has been shown that trifluoroethanol (TFE) induces helical structure in peptides and proteins. The molecular mechanism is, however, still not completely elucidated. In this study, the TFE effects on the solvation structure and on the free energy change associated with the helix-coil transition of a polypeptide are analyzed by using the three-dimensional reference interaction site model (3D-RISM) molecular theory of solvation. The theoretical result shows that TFE preferentially solvates at low concentrations around 30 vol% both for the helix and coil structures. However, the characteristic preferential solvation is not as significant in the TFE-induced helix stabilization as generally considered. It is also found that the overall energy contributes to the free energy difference more substantially than the solvation entropy.

  11. Level-Set Minimization of Potential Controlled Hadwiger Valuations for Molecular Solvation

    PubMed Central

    Cheng, Li-Tien; Li, Bo; Wang, Zhongming

    2012-01-01

    A level-set method is developed for the numerical minimization of a class of Had-wiger valuations with a potential on a set of three-dimensional bodies. Such valuations are linear combinations of the volume, surface area, and surface integral of mean curvature. The potential increases rapidly as the body shrinks beyond a critical size. The combination of the Hadwiger valuation and the potential is the mean-field free-energy functional of the solvation of non-polar molecules in the recently developed variational implicit-solvent model. This functional of surfaces is minimized by the level-set evolution in the steepest decent of the free energy. The normal velocity of this surface evolution consists of both the mean and Gaussian curvatures, and a lower-order, “forcing” term arising from the potential. The forward Euler method is used to discretize the time derivative with a dynamic time stepping that satisfies a CFL condition. The normal velocity is decomposed into two parts. The first part consists of both the mean and Gaussian curvature terms. It is of parabolic type with parameter correction, and is discretized by central differencing. The second part has all the lower-order terms. It is of hyperbolic type, and is discretized by an upwinding scheme. New techniques of local level-set method and numerical integration are developed. Numerical tests demonstrate a second-order convergence of the method. Examples of application to the modeling of molecular solvation are presented. PMID:22323839

  12. Implementation of the SM12 Solvation Model into ADF and Comparison with COSMO.

    PubMed

    Peeples, Craig A; Schreckenbach, Georg

    2016-08-09

    In this article, an implementation of the newest iteration of the Minnesota solvation model, SM12, into the Amsterdam density functional (ADF) computational package is presented. ADF makes exclusive use of Slater-type orbitals (STO), which correctly represent the true atomic orbitals for atoms, whereas SM12 and the underlying charge model 5 (CM5) have previously only been tested on Gaussian-type orbitals (GTO). This new implementation is used to prove the basis set independence of both CM5 and SM12. A detailed comparison of the SM12 and COSMO solvation models, as implemented in ADF, is also presented. We show that this new implementation of SM12 has a mean unsigned error (MUE) of 0.68 kcal/mol for 272 molecules in water solvent, 4.10 kcal/mol MUE for 112 charged ions in water, and 0.92 kcal/mol MUE for 197 solvent calculations of various molecules. SM12 outperforms COSMO for all neutral molecules and performs as well as COSMO for cationic molecules, only falling short when anionic molecules are taken into consideration, likely due to CM5's use of Hirshfeld charges and their poor description of anionic molecules, though CM5 seems to improve upon this discrepancy.

  13. 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.

  14. Acetonitrile cluster solvation in a cryogenic ethane-methane-propane liquid: Implications for Titan lake chemistry.

    PubMed

    Corrales, L René; Yi, Thomas D; Trumbo, Samantha K; Shalloway, David; Lunine, Jonathan I; Usher, David A

    2017-03-14

    The atmosphere of Titan, Saturn's largest moon, exhibits interesting UV- and radiation-driven chemistry between nitrogen and methane, resulting in dipolar, nitrile-containing molecules. The assembly and subsequent solvation of such molecules in the alkane lakes and seas found on the moon's surface are of particular interest for investigating the possibility of prebiotic chemistry in Titan's hydrophobic seas. Here we characterize the solvation of acetonitrile, a product of Titan's atmospheric radiation chemistry tentatively detected on Titan's surface [H. B. Niemann et al., Nature 438, 779-784 (2005)], in an alkane mixture estimated to match a postulated composition of the smaller lakes during cycles of active drying and rewetting. Molecular dynamics simulations are employed to determine the potential of mean force of acetonitrile (CH3CN) clusters moving from the alkane vapor into the bulk liquid. We find that the clusters prefer the alkane liquid to the vapor and do not dissociate in the bulk liquid. This opens up the possibility that acetonitrile-based microscopic polar chemistry may be possible in the otherwise nonpolar Titan lakes.

  15. Theoretical study of the preferential solvation effect on the solvatochromic shifts of para-nitroaniline.

    PubMed

    Frutos-Puerto, Samuel; Aguilar, Manuel A; Fdez Galván, Ignacio

    2013-02-28

    The origin of the nonlinear solvatochromic shift of para-nitroaniline was investigated using a mean-field sequential QM/MM method, with electron transitions computed at the CASPT2/cc-pVDZ level. Experimental data shows that the solvatochromic shift has a strong nonlinear behavior in certain solvent mixtures. We studied the case of cyclohexane-triethylamine mixtures. The results are in good agreement with the experiments and correctly reproduce the nonlinear variation of the solvent shift. Preferential solvation is clearly observed, where the local solvent composition in the neighborhood of the solute is significantly different from the bulk. It is found that even at low triethylamine concentrations a strong hydrogen bond is formed between para-nitroaniline and triethylamine, and cyclohexane is practically absent from the first solvation layer already at a molar fraction of 0.6 in triethylamine. The hydrogen bond formed is sufficiently long-lived to determine an asymmetric environment around the solute molecule. The resulting nonlinear solvent effect is mainly due to this hydrogen bond influence, although there is also a small contribution from dielectric enrichment.

  16. Modeling solvation effects in real-space and real-time within density functional approaches.

    PubMed

    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.

  17. Solvation dynamics of an ionic probe in choline chloride-based deep eutectic solvents.

    PubMed

    Cui, Y; Fulfer, K D; Ma, J; Weldeghiorghis, T K; Kuroda, D G

    2016-11-23

    Solvation of the thiocyanate ion in three different deep eutectic solvents (DES) was investigated by linear FTIR spectroscopy, and Two Dimensional IR spectroscopy. Linear infrared spectroscopy reveals that the thiocyanate ion forms a hydrogen bond through its sulphur atom, while its nitrile end remains free. Photon-echo vibrational spectroscopy shows that the thiocyanate has a frequency-frequency correlation function (FFCF) with two distinct dynamics occurring on the picosecond time scale in all of the studied solvents. The observed dynamics is assigned to in-place and diffusional motions of the components within the thiocyanate solvation shell. Molecular dynamics simulations and ab initio calculations confirm the experimental findings and their molecular interpretation. In addition, theoretical modeling of the thiocyanate nitrile stretch lineshape suggests that alcohol-based DES are more structurally disorganized than the amide-based analogue. However, the organization observed in the different DES is not sufficient to explain physical properties, such as density, indicating that the amount of defects (i.e., hole theory) is not sufficient to fully describe the properties of DES.

  18. Hydrogen-bonding molecular ruler surfactants as probes of specific solvation at liquid/liquid interfaces.

    PubMed

    Siler, A Renee; Brindza, Michael R; Walker, Robert A

    2009-10-01

    Resonance-enhanced, second harmonic generation (SHG) is used to measure the electronic structure of solutes sensitive to specific solvation adsorbed to liquid/liquid and liquid/solid interfaces. Here, specific solvation refers to solvent-solute interactions that are directional and localized. N-methyl-p-methoxyaniline (NMMA) is a solute whose first allowed electronic transition wavelength remains almost constant (approximately 315 nm) in non-hydrogen-bonding solvents regardless of solvent polarity. However, in hydrogen-bond-accepting solvents such as dimethylsulfoxide, NMMA's absorbance shifts to longer wavelengths (320 nm), whereas in hydrogen-bond-donating solvents (e.g., water), the absorbance shifts to shorter wavelengths (approximately 300 nm). SHG experiments show that at alkane/silica interfaces, surface silanol groups serve as moderately strong hydrogen-bond donors as evidenced by NMMA's absorbance of 307 nm. At the carbon tetrachloride/water interface, NMMA absorbance also shifts to slightly shorter wavelengths (298 nm) implying that water molecules at this liquid/liquid interface are donating strong hydrogen bonds to the adsorbed NMMA solutes. In contrast, experiments using newly developed molecular ruler surfactants with NMMA as a model hydrophobic solute and a hydrophilic, cationic headgroup imply that, as NMMA migrates across an aqueous/alkane interface, it carries with it water that functions as a hydrogen-bond-accepting partner.

  19. Atmospheric Implications of Aqueous Solvation on the Photochemistry of Pyruvic Acid

    NASA Astrophysics Data System (ADS)

    Reed Harris, A. E.; Ervens, B.; Shoemaker, R.; Kroll, J. A.; Rapf, R.; Griffith, E. C.; Monod, A.; Vaida, V.

    2014-12-01

    Formation of aerosol from organic compounds is under investigation in order to better predict the overall radiative forcing from atmospheric aerosols and their influence on global climate. One possible formation pathway for secondary organic aerosol (SOA), which is now becoming more widely accepted, is from bulk aqueous photoreactions in atmospheric particles that create low volatility compounds. These products may remain particulate upon droplet evaporation, increasing SOA mass in the atmosphere. SOA formed in this manner may account for some of the discrepancy between measured and predicted amounts of SOA. This presentation will describe the photochemistry of pyruvic acid, an α-keto acid found in the atmosphere, in aqueous solutions representative of solutes in fogs, clouds, and wet aerosols. Solvation of pyruvic acid in water changes the photodissociation mechanism and products from that of the gas phase. The photoproducts from the aqueous phase are higher in molecular weight and therefore possible SOA precursors. Further, these polymers partition to the surface of water and are expected to modify the the surface properties of atmospheric aerosols that determine the kinetics of water uptake. The reaction mechanism of pyruvic acid as a function of its environment and concentration will be presented along with the kinetics obtained for the photochemistry in aqueous solution. These results are used as input in an atmospheric model to evaluate the atmospheric consequences of solvation of pyruvic acid on its atmospheric reactivity and its role as a global sink.

  20. Phase behavior and second osmotic virial coefficient for competitive polymer solvation in mixed solvent solutions.

    PubMed

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

    2015-11-21

    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 B2) 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 B2, and the relation between the positions of the spinodal curves and the theta temperatures at which B2 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 B2 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.

  1. 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.

  2. 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.

  3. Dansylated aminopropyl controlled pore glass: a model for silica-liquid solvation.

    PubMed

    Page, Phillip M; Munson, Chase A; Bright, Frank V

    2004-11-23

    We have prepared a series of aminopropyl controlled pore glass (CPG) particles that have been labeled with a solvatochromic fluorescent probe molecule (dansyl). We report on the behavior of the attached dansyl reporter as a function of dansyl-to-amine molar ratio (i.e., dansyl loading), solvent dipolarity, and surface-residue end capping. In these experiments, we systematically adjust the dansyl loading by 10(5); a range much larger than ever explored. The dansylated CPG particles were also end capped with trimethylchlorosilane to derivatize most of the residual silanol and/or aminopropyl groups. The attached dansyl molecules can be surrounded by other dansyl molecules; they can be distributed within an ensemble of sites with differing physicochemical properties, and/or they can be distributed in sites that are restrictive to dansyl motion and/or solvent inaccessible. At high dansyl loadings, the majority of the dansyl groups are solvated by other dansyl moieties and solvent does not significantly alter the local microenvironment surrounding the average dansyl molecule (i.e., the cybotactic region) to any significant level. At intermediate dansyl loadings, the average distance between the dansyl groups increases and solvent is able to access/solvate/wet the dansyl groups and alter their cybotactic region to a greater extent. At the lowest dansyl loadings studied, the results suggest that these dansyl moieties are localized within solvent inaccessible/restrictive SiO2 sites (e.g., small pores).

  4. Sparingly solvating electrolytes for high energy density Lithium–sulfur batteries

    DOE PAGES

    Cheng, Lei; Curtiss, Larry A.; Zavadil, Kevin R.; ...

    2016-07-11

    Moving to lighter and less expensive battery chemistries compared to lithium-ion requires the control of energy storage mechanisms based on chemical transformations rather than intercalation. Lithium sulfur (Li/S) has tremendous theoretical specific energy, but contemporary approaches to control this solution-mediated, precipitation-dissolution chemistry requires using large excesses of electrolyte to fully solubilize the polysulfide intermediate. Achieving reversible electrochemistry under lean electrolyte operation is the only path for Li/S to move beyond niche applications to potentially transformational performance. An emerging topic for Li/S research is the use of sparingly solvating electrolytes and the creation of design rules for discovering new electrolyte systemsmore » that fundamentally decouple electrolyte volume from reaction mechanism. Furthermore, this perspective presents an outlook for sparingly solvating electrolytes as the key path forward for longer-lived, high-energy density Li/S batteries including an overview of this promising new concept and some strategies for accomplishing it.« less

  5. 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.

  6. Excess electron interactions with solvated DNA nucleotides: strand breaks possible at room temperature.

    PubMed

    Smyth, Maeve; Kohanoff, Jorge

    2012-06-06

    When biological matter is subjected to ionizing radiation, a wealth of secondary low-energy (<20 eV) electrons are produced. These electrons propagate inelastically, losing energy to the medium until they reach energies low enough to localize in regions of high electron affinity. We have recently shown that in fully solvated DNA fragments, nucleobases are particularly attractive for such excess electrons. The next question is what is their longer-term effect on DNA. It has been advocated that they can lead to strand breaks by cleavage of the phosphodiester C(3')-O(3') bond. Here we present a first-principles study of free energy barriers for the cleavage of this bond in fully solvated nucleotides. We have found that except for dAMP, the barriers are on the order of 6 kcal/mol, suggesting that bond cleavage is a regular feature at 300 K. Such low barriers are possible only as a result of solvent and thermal fluctuations. These findings support the notion that low-energy electrons can indeed lead to strand breaks in DNA.

  7. 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.

  8. 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.

  9. Modeling solvation effects in real-space and real-time within density functional approaches

    NASA Astrophysics Data System (ADS)

    Delgado, Alain; Corni, Stefano; Pittalis, Stefano; Rozzi, Carlo Andrea

    2015-10-01

    The Polarizable Continuum Model (PCM) can be used in conjunction with Density Functional Theory (DFT) and its time-dependent extension (TDDFT) to simulate the electronic and optical properties of molecules and nanoparticles immersed in a dielectric environment, typically liquid solvents. In this contribution, we develop a methodology to account for solvation effects in real-space (and real-time) (TD)DFT calculations. The boundary elements method is used to calculate the solvent reaction potential in terms of the apparent charges that spread over the van der Waals solute surface. In a real-space representation, this potential may exhibit a Coulomb singularity at grid points that are close to the cavity surface. We propose a simple approach to regularize such singularity by using a set of spherical Gaussian functions to distribute the apparent charges. We have implemented the proposed method in the Octopus code and present results for the solvation free energies and solvatochromic shifts for a representative set of organic molecules in water.

  10. Mutagenicity of six DMSO and Tween 80-solvated mild gasification products in Salmonella typhimurium

    SciTech Connect

    Stamm, S.C.; Zhong, B.Z.; Bryant, E.D.; Ong, T. . Div. of Respiratory Disease Studies); Johnson, R.; Sharp, S. )

    1992-01-01

    gasification is an emerging coal-conversion process that is being developed by the United States Department of Energy and private industry to meet future energy needs. Products of this process are being submitted to NIOSH in Morgantown, WV, for the evaluation of their genotoxic activity. Six mild gasification products, solvated in both DMSO and Tween 80, have been assayed for mutagenic activity in the preincubation modification of the Ames Salmonella assay system using tester strains TA98 and TA1OO with and without S9 metabolic acbvation. No significant mutagenic activity was detected in these samples when DMSO was used as the solvent vehicle; however, two of the six samples indicated positive mutagenic activity on tester strain TA98 with S9 when solvated in Tween 80. The positive control 2-aminoanthracene, an aromatic amine, demonstrated a significant increase in response when assayed using Tween 80 as a solvent as compared to DMSO. These results suggest that mutagen/solvent interactons may be occurring in the testing of these coal-derived samples and the positive control in the Ames assay. Since past studies have indicated that aromatic amines account for a large percentage of the mutagenic activity of coal-derived materials, the solitary use of DMSO as a solvent for mutagenicity determination must be questioned for these and other chemically related materials.

  11. Mutagenicity of six DMSO and Tween 80-solvated mild gasification products in Salmonella typhimurium

    SciTech Connect

    Stamm, S.C.; Zhong, B.Z.; Bryant, E.D.; Ong, T.; Johnson, R.; Sharp, S.

    1992-12-31

    Mild gasification is an emerging coal-conversion process that is being developed by the United States Department of Energy and private industry to meet future energy needs. Products of this process are being submitted to NIOSH in Morgantown, WV, for the evaluation of their genotoxic activity. Six mild gasification products, solvated in both DMSO and Tween 80, have been assayed for mutagenic activity in the preincubation modification of the Ames Salmonella assay system using tester strains TA98 and TA1OO with and without S9 metabolic acbvation. No significant mutagenic activity was detected in these samples when DMSO was used as the solvent vehicle; however, two of the six samples indicated positive mutagenic activity on tester strain TA98 with S9 when solvated in Tween 80. The positive control 2-aminoanthracene, an aromatic amine, demonstrated a significant increase in response when assayed using Tween 80 as a solvent as compared to DMSO. These results suggest that mutagen/solvent interactons may be occurring in the testing of these coal-derived samples and the positive control in the Ames assay. Since past studies have indicated that aromatic amines account for a large percentage of the mutagenic activity of coal-derived materials, the solitary use of DMSO as a solvent for mutagenicity determination must be questioned for these and other chemically related materials.

  12. Solid-State Characterization of Novel Propylene Glycol Ester Solvates Isolated from Lipid Formulations.

    PubMed

    Chakravarty, Paroma; Kothari, Sanjeev; Deese, Alan; Lubach, Joseph W

    2015-07-06

    The purpose of this study was to identify and characterize precipitates obtained from a liquid formulation of GNE068.HCl, a Genentech developmental compound, and lipophilic excipients, such as propylene glycol monocaprylate, and monolaurate. Precipitates were characterized using powder X-ray diffractometry (PXRD), differential scanning calorimetry, thermogravimetry, microscopy, nuclear magnetic resonance spectroscopy (NMR; solution and solid-state) and water sorption analysis. PXRD and NMR revealed the precipitates to be crystalline solvates of propylene glycol esters. The solvates (capryolate and lauroglycolate) were isomorphic and stable up to 70 °C, beyond which melting of the lattice occurred with subsequent dissolution of the active ingredient in the melt (microscopy and variable temperature PXRD). They were found to be mechanically stable (no change in PXRD pattern upon compression) and were nonhygroscopic up to ∼70% RH (25 °C). Our results highlight the outcome of inadvertent drug-excipient interactions in two separate lipid solution formulations with good solid-state properties and, thus, potential for further development.

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

    PubMed Central

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

    2016-01-01

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

  14. Comparison Study on the Effect of Interlayer Hydration and Solvation on Montmorillonite Delamination

    NASA Astrophysics Data System (ADS)

    Li, Hongliang; Song, Shaoxian; Zhao, Yunliang; Nahmad, Yuri; Chen, Tianxing

    2017-02-01

    The effect of water and isopropanol intercalation on montmorillonite (MMT) delamination was investigated in order to compare the roles of hydration and solvation in the delamination. Transmittance results showed that water has a significant effect on the delamination of MMT compared with isopropanol. This observation was attributed to the difference of the intercalation of water and isopropanol. Thermogravimetric (TG) results illustrate that the intercalation mass of water was greater than that of isopropanol when the pressure remained constant. Weighing test results show that the intercalation mass of water was smaller than that of isopropanol when the volume of MMT remained constant. Molecule dynamic simulation results show that the water and isopropanol molecules were interacting with Na+ and siloxane surface of MMT, respectively. It was demonstrated that the hydration of the MMT interlayer followed two steps: in step 1, the Na+ in the interlayer was hydrated, thereby expanding the interlayer spacing; in step 2, additional water molecules were absorbed into the expanded interlayer space. It was found that step 2 could not be actuated until the completion of step 1. For the solvation of the MMT interlayer with isopropanol, however, only one step was required, in which isopropanol was absorbed onto the siloxane sites of the interlayer while maintaining the interlayer spacing.

  15. Insights into the crystallisation process from anhydrous, hydrated and solvated crystal forms of diatrizoic acid.

    PubMed

    Fucke, Katharina; McIntyre, Garry J; Lemée-Cailleau, Marie-Hélène; Wilkinson, Clive; Edwards, Alison J; Howard, Judith A K; Steed, Jonathan W

    2015-01-12

    Diatrizoic acid (DTA), a clinically used X-ray contrast agent, crystallises in two hydrated, three anhydrous and nine solvated solid forms, all of which have been characterised by X-ray crystallography. Single-crystal neutron structures of DTA dihydrate and monosodium DTA tetrahydrate have been determined. All of the solid-state structures have been analysed using partial atomic charges and hardness algorithm (PACHA) calculations. Even though in general all DTA crystal forms reveal similar intermolecular interactions, the overall crystal packing differs considerably from form to form. The water of the dihydrate is encapsulated between a pair of host molecules, which calculations reveal to be an extraordinarily stable motif. DTA presents functionalities that enable hydrogen and halogen bonding, and whilst an extended hydrogen-bonding network is realised in all crystal forms, halogen bonding is not present in the hydrated crystal forms. This is due to the formation of a hydrogen-bonding network based on individual enclosed water squares, which is not amenable to the concomitant formation of halogen bonds. The main interaction in the solvates involves the carboxylic acid, which corroborates the hypothesis that this strong interaction is the last one to be broken during the crystal desolvation and nucleation process.

  16. 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.

  17. Solvation dynamics and the dielectric response in a glass-forming solvent: from picoseconds to seconds

    NASA Astrophysics Data System (ADS)

    Richert, R.; Stickel, F.; Fee, R. S.; Maroncelli, M.

    1994-10-01

    We have measured the response times of solvation dynamics in the range 100 ps to 100 s and the dielectric relaxation covering 10 decades in frequency for the glass-forming solvent 2-methyltetrahydrofuran. In this wide range of solvent viscosities, from the glass transition to beyond the melting point, the mean relaxation times for the two techniques which monitor dipolar orientation are identical within our resolution. For two characteristic decay traces recorded on the time scales of 10 ns and 1 s we compare the observed Stokes-shift dynamics with various theoretical approaches. The decay pattern is reproduced by the dipolar dynamic-mean-spherical-approximation, whereas the absolute time scale of the solvation is mapped by the dielectric polarization itself. For the solvent under study we find almost perfect agreement between experiment and the dipolar dMSA theory if the time scale of the predicted curve is rescaled by a factor of (epsilon(sub infinity)/epsilon(sub s))(exp 1/2).

  18. Acetonitrile cluster solvation in a cryogenic ethane-methane-propane liquid: Implications for Titan lake chemistry

    NASA Astrophysics Data System (ADS)

    Corrales, L. René; Yi, Thomas D.; Trumbo, Samantha K.; Shalloway, David; Lunine, Jonathan I.; Usher, David A.

    2017-03-01

    The atmosphere of Titan, Saturn's largest moon, exhibits interesting UV- and radiation-driven chemistry between nitrogen and methane, resulting in dipolar, nitrile-containing molecules. The assembly and subsequent solvation of such molecules in the alkane lakes and seas found on the moon's surface are of particular interest for investigating the possibility of prebiotic chemistry in Titan's hydrophobic seas. Here we characterize the solvation of acetonitrile, a product of Titan's atmospheric radiation chemistry tentatively detected on Titan's surface [H. B. Niemann et al., Nature 438, 779-784 (2005)], in an alkane mixture estimated to match a postulated composition of the smaller lakes during cycles of active drying and rewetting. Molecular dynamics simulations are employed to determine the potential of mean force of acetonitrile (CH3CN) clusters moving from the alkane vapor into the bulk liquid. We find that the clusters prefer the alkane liquid to the vapor and do not dissociate in the bulk liquid. This opens up the possibility that acetonitrile-based microscopic polar chemistry may be possible in the otherwise nonpolar Titan lakes.

  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. 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.