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Sample records for explicit solvation effects

  1. 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...

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

    NASA Astrophysics Data System (ADS)

    Williams, Michael; Schwartz, Steven

    2015-03-01

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

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

    PubMed

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

    2015-11-28

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

  4. 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.

  5. 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

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

    PubMed Central

    2012-01-01

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

  7. 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.

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

    NASA Astrophysics Data System (ADS)

    Arias, Tomas

    2015-03-01

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

  9. Solvation!

    SciTech Connect

    Ivana Adamovic

    2004-12-19

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

  10. Computations of absolute solvation free energies of small molecules using explicit and implicit solvent model.

    SciTech Connect

    Shivakumar, D.; Deng, Y.; Roux, B.; Biosciences Division; Univ. of Chicago

    2009-01-01

    Accurate determination of absolute solvation free energy plays a critical role in numerous areas of biomolecular modeling and drug discovery. A quantitative representation of ligand and receptor desolvation, in particular, is an essential component of current docking and scoring methods. Furthermore, the partitioning of a drug between aqueous and nonpolar solvents is one of the important factors considered in pharmacokinetics. In this study, the absolute hydration free energy for a set of 239 neutral ligands spanning diverse chemical functional groups commonly found in drugs and drug-like candidates is calculated using the molecular dynamics free energy perturbation method (FEP/MD) with explicit water molecules, and compared to experimental data as well as its counterparts obtained using implicit solvent models. The hydration free energies are calculated from explicit solvent simulations using a staged FEP procedure permitting a separation of the total free energy into polar and nonpolar contributions. The nonpolar component is further decomposed into attractive (dispersive) and repulsive (cavity) components using the Weeks-Chandler-Anderson (WCA) separation scheme. To increase the computational efficiency, all of the FEP/MD simulations are generated using a mixed explicit/implicit solvent scheme with a relatively small number of explicit TIP3P water molecules, in which the influence of the remaining bulk is incorporated via the spherical solvent boundary potential (SSBP). The performances of two fixed-charge force fields designed for small organic molecules, the General Amber force field (GAFF), and the all-atom CHARMm-MSI, are compared. Because of the crucial role of electrostatics in solvation free energy, the results from various commonly used charge generation models based on the semiempirical (AM1-BCC) and QM calculations [charge fitting using ChelpG and RESP] are compared. In addition, the solvation free energies of the test set are also calculated using

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

    PubMed

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

    2015-06-01

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

  12. 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...

  13. Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation.

    PubMed

    Izadi, Saeed; Aguilar, Boris; Onufriev, Alexey V

    2015-09-01

    Accurate yet efficient computational models of solvent environment are central for most calculations that rely on atomistic modeling, such as prediction of protein-ligand binding affinities. In this study, we evaluate the accuracy of a recently developed generalized Born implicit solvent model, GBNSR6 (Aguilar et al. J. Chem. Theory Comput. 2010, 6, 3613-3639), in estimating the electrostatic solvation free energies (ΔG(pol)) and binding free energies (ΔΔG(pol)) for small protein-ligand complexes. We also compare estimates based on three different explicit solvent models (TIP3P, TIP4PEw, and OPC). The two main findings are as follows. First, the deviation (RMSD = 7.04 kcal/mol) of GBNSR6 binding affinities from commonly used TIP3P reference values is comparable to the deviations between explicit models themselves, e.g. TIP4PEw vs TIP3P (RMSD = 5.30 kcal/mol). A simple uniform adjustment of the atomic radii by a single scaling factor reduces the RMS deviation of GBNSR6 from TIP3P to within the above "error margin" - differences between ΔΔG(pol) estimated by different common explicit solvent models. The simple radii scaling virtually eliminates the systematic deviation (ΔΔG(pol)) between GBNSR6 and two out of the three explicit water models and significantly reduces the deviation from the third explicit model. Second, the differences between electrostatic binding energy estimates from different explicit models is disturbingly large; for example, the deviation between TIP4PEw and TIP3P estimates of ΔΔG(pol) values can be up to ∼50% or ∼9 kcal/mol, which is significantly larger than the "chemical accuracy" goal of ∼1 kcal/mol. The absolute ΔG(pol) calculated with different explicit models could differ by tens of kcal/mol. These discrepancies point to unacceptably high sensitivity of binding affinity estimates to the choice of common explicit water models. The absence of a clear "gold standard" among these models strengthens the case for the use of

  14. 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

    steered by effective solvation forces allows huge outer time steps up to tens of picoseconds without affecting the equilibrium and conformational properties, and thus provides a 100- to 500-fold effective speedup in comparison to conventional MD with explicit solvent. With the statistical-mechanical 3D-RISM-KH account for effective solvation forces, the method provides efficient sampling of biomolecular processes with slow and/or rare solvation events such as conformational transitions of hydrated alanine dipeptide with the mean life times ranging from 30 ps up to 10 ns for “flip-flop” conformations, and is particularly beneficial for biomolecular systems with exchange and localization of solvent and ions, ligand binding, and molecular recognition.

  15. 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

    steered by effective solvation forces allows huge outer time steps up to tens of picoseconds without affecting the equilibrium and conformational properties, and thus provides a 100- to 500-fold effective speedup in comparison to conventional MD with explicit solvent. With the statistical-mechanical 3D-RISM-KH account for effective solvation forces, the method provides efficient sampling of biomolecular processes with slow and/or rare solvation events such as conformational transitions of hydrated alanine dipeptide with the mean life times ranging from 30 ps up to 10 ns for "flip-flop" conformations, and is particularly beneficial for biomolecular systems with exchange and localization of solvent and ions, ligand binding, and molecular recognition.

  16. Solvent effects on the electronic absorption spectrum of camphor using continuum, discrete or explicit approaches

    NASA Astrophysics Data System (ADS)

    Kongsted, Jacob; Mennucci, Benedetta; Coutinho, Kaline; Canuto, Sylvio

    2010-01-01

    We address the effect of solvation on the lowest electronic excitation energy of camphor. The solvents considered represent a large variation in-solvent polarity. We consider three conceptually different ways of accounting for the solvent using either an implicit, a discrete or an explicit solvation model. The solvatochromic shifts in polar solvents are found to be in good agreement with the experimental data for all three solvent models. However, both the implicit and discrete solvation models are less successful in predicting solvatochromic shifts for solvents of low polarity. The results presented suggest the importance of using explicit solvent molecules in the case of nonpolar solvents.

  17. Accurate calculation of conformational free energy differences in explicit water: the confinement-solvation free energy approach.

    PubMed

    Esque, Jeremy; Cecchini, Marco

    2015-04-23

    The calculation of the free energy of conformation is key to understanding the function of biomolecules and has attracted significant interest in recent years. Here, we present an improvement of the confinement method that was designed for use in the context of explicit solvent MD simulations. The development involves an additional step in which the solvation free energy of the harmonically restrained conformers is accurately determined by multistage free energy perturbation simulations. As a test-case application, the newly introduced confinement/solvation free energy (CSF) approach was used to compute differences in free energy between conformers of the alanine dipeptide in explicit water. The results are in excellent agreement with reference calculations based on both converged molecular dynamics and umbrella sampling. To illustrate the general applicability of the method, conformational equilibria of met-enkephalin (5 aa) and deca-alanine (10 aa) in solution were also analyzed. In both cases, smoothly converged free-energy results were obtained in agreement with equilibrium sampling or literature calculations. These results demonstrate that the CSF method may provide conformational free-energy differences of biomolecules with small statistical errors (below 0.5 kcal/mol) and at a moderate computational cost even with a full representation of the solvent.

  18. Free Energies of Solvation with Surface, Volume, and Local Electrostatic Effects and Atomic Surface Tensions to Represent the First Solvation Shell.

    PubMed

    Liu, Junjun; Kelly, Casey P; Goren, Alan C; Marenich, Aleksandr V; Cramer, Christopher J; Truhlar, Donald G; Zhan, Chang-Guo

    2010-03-01

    Building on the SVPE (surface and volume polarization for electrostatics) model for electrostatic contributions to the free energy of solvation with explicit consideration of both surface and volume polarization effects, on the SMx approach to including first-solvation-shell contributions, and on the linear relationship between the electric field and short-range electrostatic contributions found by Chipman, we have developed a new method for computing absolute aqueous solvation free energies by combining the SVPE method with semiempirical terms that account for effects beyond bulk electrostatics. The new method is called SMVLE, and the elements it contains are denoted by SVPE-CDSL where SVPE denotes accounting for bulk electrostatic interactions between solute and solvent with both surface and volume contributions, CDS denotes the inclusion of solvent cavitation, changes in dispersion energy, and possible changes in local solvent structure by a semiempirical term utilizing geometry-dependent atomic surface tensions as implemented in SMx models, and L represents the local electrostatic effect derived from the outward-directed normal electric field on the cavity surface. The semiempirical CDS and L terms together represent the deviation of short-range contributions to the free energy of solvation from those accounted for by the SVPE term based on the bulk solvent dielectric constant. A solute training set containing a broad range of molecules used previously in the development of SM6 is used here for SMVLE model calibration. The aqueous solvation free energies predicted by the parameterized SMVLE model correlate exceedingly well with experimental values. The square of the correlation coefficient is 0.9949 and the slope is 1.0079. Comparison of the final SMVLE model against the earlier SMx solvation model shows that the parameterized SMVLE model not only yields good accuracy for neutrals but also significantly increases the accuracy for ions, making it the best

  19. Ab Initio and Density Functional Theory Modeling of the Chiroptical Response of Glycine and Alanine in Solution Using Explicit Solvation and Molecular Dynamics.

    PubMed

    Kundrat, Matthew D; Autschbach, Jochen

    2008-11-11

    We investigate ways in which simple point charge (SPC) water models can be used in place of more expensive quantum mechanical water molecules to efficiently model the solvent effect on a solute molecule's chiroptical responses. The effect that SPC waters have on the computed circular dichroism of a solvated glycine molecule are comparable to, albeit somewhat weaker than, that of quantum mechanical waters at the coupled cluster CC2 level of theory. The effects of SPC waters in fact correlate better with QM-CC2 waters than quantum mechanical waters computed with density functional theory (DFT) methods, since they do not promote spurious charge transfer excitations that are a known deficiency with most popular density functionals. Furthermore, the near zero order scaling of point charge waters allows multiple layers of explicit solvation to be modeled with negligible computational cost, which is not practical with CC2 or DFT levels. As a practical example, we model the molar rotations of glycine and alanine, and track their convergence.

  20. Conformation of a flexible chain in explicit solvent: exact solvation potentials for short Lennard-Jones chains.

    PubMed

    Taylor, Mark P; Adhikari, Shishir R

    2011-07-28

    The average conformation of a flexible chain molecule in solution is coupled to the local solvent structure. In a dense solvent, local chain structure often mirrors the pure solvent structure, whereas, in a dilute solvent, the chain can strongly perturb the solvent structure which, in turn, can lead to either chain expansion or compression. Here we use Monte Carlo (MC) simulation to study such solvent effects for a short Lennard-Lones (LJ) chain in monomeric LJ solvent. For an n-site chain molecule in solution these many-body solvent effects can be formally mapped to an n-body solvation potential. We have previously shown that for hard-sphere and square-well chain-in-solvent systems this n-body potential can be decomposed into a set of two-body potentials. Here, we show that this decomposition is also valid for the LJ system. Starting from high precision MC results for the n = 5 LJ chain-in-solvent system, we use a Boltzmann inversion technique to compute numerically exact sets of two-body solvation potentials which map the many-body chain-in-solvent problem to a few-body single-chain problem. We have carried out this mapping across the full solvent phase diagram including the dilute vapor, dense liquid, and supercritical regions and find that these sets of solvation potentials are able to encode the complete range of solvent effects found in the LJ chain-in-solvent system. We also show that these two-site solvation potentials can be used to obtain accurate multi-site intramolecular distribution functions and we discuss the application of these exact short chain potentials to the study of longer chains in solvent. PMID:21806157

  1. Surface Protonation at the Rutile (110) Interface: Explicit Incorporation of Solvation Structure within the Refined MUSIC Model Framework

    SciTech Connect

    Machesky, Michael L.; Predota, M.; Wesolowski, David J

    2008-11-01

    The detailed solvation structure at the (110) surface of rutile ({alpha}-TiO{sub 2}) in contact with bulk liquid water has been obtained primarily from experimentally verified classical molecular dynamics (CMD) simulations of the ab initio-optimized surface in contact with SPC/E water. The results are used to explicitly quantify H-bonding interactions, which are then used within the refined MUSIC model framework to predict surface oxygen protonation constants. Quantum mechanical molecular dynamics (QMD) simulations in the presence of freely dissociable water molecules produced H-bond distributions around deprotonated surface oxygens very similar to those obtained by CMD with nondissociable SPC/E water, thereby confirming that the less computationally intensive CMD simulations provide accurate H-bond information. Utilizing this H-bond information within the refined MUSIC model, along with manually adjusted Ti-O surface bond lengths that are nonetheless within 0.05 {angstrom} of those obtained from static density functional theory (DFT) calculations and measured in X-ray reflectivity experiments (as well as bulk crystal values), give surface protonation constants that result in a calculated zero net proton charge pH value (pHznpc) at 25 C that agrees quantitatively with the experimentally determined value (5.4 {+-} 0.2) for a specific rutile powder dominated by the (110) crystal face. Moreover, the predicted pH{sub znpc} values agree to within 0.1 pH unit with those measured at all temperatures between 10 and 250 C. A slightly smaller manual adjustment of the DFT-derived Ti-O surface bond lengths was sufficient to bring the predicted pH{sub znpc} value of the rutile (110) surface at 25 C into quantitative agreement with the experimental value (4.8 {+-} 0.3) obtained from a polished and annealed rutile (110) single crystal surface in contact with dilute sodium nitrate solutions using second harmonic generation (SHG) intensity measurements as a function of ionic

  2. 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

  3. Toward accurate microscopic calculation of solvation entropies: extending the restraint release approach to studies of solvation effects.

    PubMed

    Singh, Nidhi; Warshel, Arieh

    2009-05-21

    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, whereas 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 of 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 general 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

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

    PubMed

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

    2015-01-29

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

  5. Theoretical study of the formation of mercury (Hg2+) complexes in solution using an explicit solvation shell in implicit solvent calculations.

    PubMed

    Afaneh, Akef T; Schreckenbach, Georg; Wang, Feiyue

    2014-09-25

    The structures and harmonic vibrational frequencies of water clusters (H2O)n, n = 1-10, have been computed using the M06-L/, B3LYP/, and CAM-BLYP/cc-pVTZ levels of theories. On the basis of the literature and our results, we use three hexamer structures of the water molecules to calculate an estimated "experimental" average solvation free energy of [Hg(H2O)6](2+). Aqueous formation constants (log K) for Hg(2+) complexes, [Hg(L)m(H2O)n](2-mq), L = Cl(-), HO(-), HS(-), and S(2-), are calculated using a combination of experimental (solvation free energies of ligands and Hg(2+)) and calculated gas- and liquid-phase free energies. A combined approach has been used that involves attaching n explicit water molecules to the Hg(2+) complexes such that the first coordination sphere is complete, then surrounding the resulting (Hg(2+)-Lm)-(OH2)n cluster by a dielectric continuum, and using suitable thermodynamic cycles. This procedure significantly improves the agreement between the calculated log K values and experiment. Thus, for some neutral and anionic Hg(II) complexes, particularly Hg(II) metal ion surrounded with homo- or heteroatoms, augmenting implicit solvent calculations with sufficient explicit water molecules to complete the first coordination sphere is required-and adequate-to account for strong short-range hydrogen bonding interactions between the anion and the solvent. Calculated values for formation constants of Hg(2+) complexes with S(2-) and SH(-) are proposed. Experimental measurements of these log K values have been lacking or controversial.

  6. Explicit Form Focus Instruction: The Effects on Implicit and Explicit Knowledge of ESL Learners

    ERIC Educational Resources Information Center

    Ebadi, Mandana Rohollahzadeh; Saad, Mohd Rashid Mohd; Abedalaziz, Nabil

    2014-01-01

    The study examines the effect of explicit form focus instruction and specifically metalinguistic information feedback on the development of both implicit and explicit knowledge of adult English as a Second Language (ESL) learners. Ninety-one subjects at the lower intermediate level were carefully selected through placement test at one of the…

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

    PubMed

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

    2015-11-11

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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

    Liu, Lijun; Nakamura, Issei

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

  10. Solvation Effects on Counterion Transport in Single-Ion Conducting Ionomers

    NASA Astrophysics Data System (ADS)

    Wang, Jing-Han Helen; Colby, Ralph

    2012-02-01

    Ionomers with short ethylene oxide side chains are synthesized by free radical polymerization, to systematically test effects of solvating anion and cation, including directly substituting the ion attached to the polymer with its counterion. Dielectric relaxation spectroscopy is used to measure the conductivity, dielectric constant and segmental relaxations in these ionomers and the electrode polarization at very low frequencies is used to assess the number density of simultaneously conducting ions and their mobility. Conductivity and conducting ion content are larger for polyanions than their corresponding polycation because the counterion can be more effectively solvated by the ether oxygens. Changing ester linkages to amide linkages in polycations boosts conductivity and conducting ion content by solvating the anionic counterion. Such findings point a clear path toward design of superior single-ion conductors.

  11. 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

  12. 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.

  13. 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.

  14. The Effectiveness of Explicit Attention to Form in Language Learning

    ERIC Educational Resources Information Center

    Radwan, Adel Abu

    2005-01-01

    This paper explores the facilitative effects of various types of attention-drawing instructional conditions (explicit and implicit) on the acquisition of English dative alternation. Specifically, the study addresses: (a) whether differences in the degree of explicitness manipulated in various instructional conditions differently affect the…

  15. Effects of Explicit Instructions, Metacognition, and Motivation on Creative Performance

    ERIC Educational Resources Information Center

    Hong, Eunsook; O'Neil, Harold F.; Peng, Yun

    2016-01-01

    Effects of explicit instructions, metacognition, and intrinsic motivation on creative homework performance were examined in 303 Chinese 10th-grade students. Models that represent hypothesized relations among these constructs and trait covariates were tested using structural equation modelling. Explicit instructions geared to originality were…

  16. Serial position effects in implicit and explicit tests of memory.

    PubMed

    Gershberg, F B; Shimamura, A P

    1994-11-01

    The effects of serial position at study on implicit and explicit tests of memory were investigated. Both primary and recency effects were observed in implicit tests of word-stem completion. These effects, however, were transient. No serial position effects were found in the second half of testing (Experiments 1 and 3) or when testing followed a 1-min, filled delay (Experiment 2). Serial position effects were also examined in explicit tests of cued recall. When performance on explicit cued recall was below ceiling levels, a primacy effect persisted throughout testing (Experiment 3). Similarly, in explicit tests of free recall, primacy effects were consistently observed, both with immediate testing (Experiments 1 and 3) and when testing followed a filled delay (Experiment 2).

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

    PubMed

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

    2016-08-23

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

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

    NASA Astrophysics Data System (ADS)

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

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

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

    SciTech Connect

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

    1998-03-01

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

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

    PubMed

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

    2015-04-01

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

  2. A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects.

    PubMed

    Zgarbová, Marie; Luque, F Javier; Šponer, Jiří; Otyepka, Michal; Jurečka, Petr

    2012-09-11

    A procedure for deriving force field torsion parameters including certain previously neglected solvation effects is suggested. In contrast to the conventional in vacuo approaches, the dihedral parameters are obtained from the difference between the quantum-mechanical self-consistent reaction field and Poisson-Boltzmann continuum solvation models. An analysis of the solvation contributions shows that two major effects neglected when torsion parameters are derived in vacuo are (i) conformation-dependent solute polarization and (ii) solvation of conformation-dependent charge distribution. Using the glycosidic torsion as an example, we demonstrate that the corresponding correction for the torsion potential is substantial and important. Our approach avoids double counting of solvation effects and provides parameters that may be used in combination with any of the widely used nonpolarizable discrete solvent models, such as TIPnP or SPC/E, or with continuum solvent models. Differences between our model and the previously suggested solvation models are discussed. Improvements were demonstrated for the latest AMBER RNA χOL3 parameters derived with inclusion of solvent effects in a previous publication (Zgarbova et al. J. Chem. Theory Comput.2011, 7, 2886). The described procedure may help to provide consistently better force field parameters than the currently used parametrization approaches.

  3. Olanzapine solvates.

    PubMed

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

    2013-11-01

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

  4. 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.

  5. Explicit-water theory for the salt-specific effects and Hofmeister series in protein solutions

    NASA Astrophysics Data System (ADS)

    Kalyuzhnyi, Yuriy V.; Vlachy, Vojko

    2016-06-01

    Effects of addition of salts on stability of aqueous protein solutions are studied theoretically and the results are compared with experimental data. In our approach, all the interacting species, proteins, ions, and water molecules, are accounted for explicitly. Water molecules are modeled as hard spheres with four off-center attractive square-well sites. These sites serve to bind either another water or to solvate the ions or protein charges. The ions are represented as charged hard spheres, and decorated by attractive sites to allow solvation. Spherical proteins simultaneously possess positive and negative groups, represented by charged hard spheres, attached to the surface of the protein. The attractive square-well sites, mimicking the protein-protein van der Waals interaction, are located on the surface of the protein. To obtain numerical results, we utilized the energy route of Wertheim's associative mean spherical approximation. From measurable properties, we choose to calculate the second virial coefficient B2, which is closely related to the tendency of proteins to aggregate and eventually crystalize. Calculations are in agreement with experimental trends: (i) For low concentration of added salt, the alkali halide salts follow the inverse Hofmeister series. (ii) At higher concentration of added salt, the trend is reversed. (iii) When cations are varied, the salts follow the direct Hofmeister series. (iv) In contrast to the colloidal theories, our approach correctly predicts the non-monotonic behavior of B2 upon addition of salts. (v) With respect to anions, the theory predicts for the B2 values to follow different sequences below and above the iso-ionic point, as also confirmed experimentally. (vi) A semi-quantitative agreement between measured and calculated values for the second virial coefficient, as functions of pH of solution and added salt type and concentration, is obtained.

  6. Solvation effects on reactions of triplet benzophenone in supercritical fluids

    SciTech Connect

    Roberts, C.B.; Brennecke, J.F.; Chateauneuf, J.E.

    1995-05-01

    Laser flash photolysis of the hydrogen abstraction reaction of triplet benzophenone ({sup 3}BP) from 2-propanol and 1,4-cyclohexadiene in supercritical ethane and fluoroform was investigated. Bimolecular rate constants based on bulk concentrations decrease with an increase in pressure along both isotherms studied. These results corroborate previous studies in CO{sub 2} that show increased reaction rates due to enhanced local compositions of cosolvent around the {sup 3}BP solute. Analysis of the results includes prediction of the thermodynamic pressure effect on the rate constant, which suggests an increase in the rate constant with pressure, as well as the effects of increased local cosolvent concentrations about {sup 3}BP. Spectroscopic measurements of the local composition of 2-propanol about a solute in supercritical CO{sub 2} are used to explain the apparent discrepancy between experiment and prediction, providing reasonable evidence that the local environment can influence kinetically controlled reactions in supercritical fluids.

  7. 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

  8. Effect of explicit dimensional instruction on speech category learning.

    PubMed

    Chandrasekaran, Bharath; Yi, Han-Gyol; Smayda, Kirsten E; Maddox, W Todd

    2016-02-01

    Learning nonnative speech categories is often considered a challenging task in adulthood. This difficulty is driven by cross-language differences in weighting critical auditory dimensions that differentiate speech categories. For example, previous studies have shown that differentiating Mandarin tonal categories requires attending to dimensions related to pitch height and direction. Relative to native speakers of Mandarin, the pitch direction dimension is underweighted by native English speakers. In the current study, we examined the effect of explicit instructions (dimension instruction) on native English speakers' Mandarin tone category learning within the framework of a dual-learning systems (DLS) model. This model predicts that successful speech category learning is initially mediated by an explicit, reflective learning system that frequently utilizes unidimensional rules, with an eventual switch to a more implicit, reflexive learning system that utilizes multidimensional rules. Participants were explicitly instructed to focus and/or ignore the pitch height dimension, the pitch direction dimension, or were given no explicit prime. Our results show that instruction instructing participants to focus on pitch direction, and instruction diverting attention away from pitch height, resulted in enhanced tone categorization. Computational modeling of participant responses suggested that instruction related to pitch direction led to faster and more frequent use of multidimensional reflexive strategies and enhanced perceptual selectivity along the previously underweighted pitch direction dimension.

  9. Effect of explicit dimension instruction on speech category learning

    PubMed Central

    Chandrasekaran, Bharath; Yi, Han-Gyol; Smayda, Kirsten E.; Maddox, W. Todd

    2015-01-01

    Learning non-native speech categories is often considered a challenging task in adulthood. This difficulty is driven by cross-language differences in weighting critical auditory dimensions that differentiate speech categories. For example, previous studies have shown that differentiating Mandarin tonal categories requires attending to dimensions related to pitch height and direction. Relative to native speakers of Mandarin, the pitch direction dimension is under-weighted by native English speakers. In the current study, we examined the effect of explicit instructions (dimension instruction) on native English speakers' Mandarin tone category learning within the framework of a dual-learning systems (DLS) model. This model predicts that successful speech category learning is initially mediated by an explicit, reflective learning system that frequently utilizes unidimensional rules, with an eventual switch to a more implicit, reflexive learning system that utilizes multidimensional rules. Participants were explicitly instructed to focus and/or ignore the pitch height dimension, the pitch direction dimension, or were given no explicit prime. Our results show that instruction instructing participants to focus on pitch direction, and instruction diverting attention away from pitch height resulted in enhanced tone categorization. Computational modeling of participant responses suggested that instruction related to pitch direction led to faster and more frequent use of multidimensional reflexive strategies, and enhanced perceptual selectivity along the previously underweighted pitch direction dimension. PMID:26542400

  10. Deuterium isotope effect on femtosecond solvation dynamics in an ionic liquid microemulsion: an excitation wavelength dependence study.

    PubMed

    Sasmal, Dibyendu Kumar; Mojumdar, Supratik Sen; Adhikari, Aniruddha; Bhattacharyya, Kankan

    2010-04-01

    The deuterium isotope effect on the solvation dynamics and the anisotropy decay of coumarin 480 (C480) in a room temperature ionic liquid (RTIL) microemulsion is studied by femtosecond up-conversion. The microemulsion consists of the RTIL 1-pentyl-3-methyl-imidazolium tetra-fluoroborate ([pmim][BF(4)]) in triton X-100 (TX-100)/benzene. Replacement of H(2)O by D(2)O in the microemulsion causes retardation of solvation dynamics. The average solvation time of C480 (tau(s)) in RTIL microemulsion with 5 wt % D(2)O is approximately 1.5-1.7 times slower compared to that in the H(2)O containing RTIL microemulsion. This suggests that the main species in the microemulsion responsible for solvation is the water molecules. In both D(2)O and H(2)O containing RTIL microemulsion, the solvation dynamics exhibits marked dependence on the excitation wavelength (lambda(ex)) and becomes about 15 times faster as lambda(ex) increases from 375 to 435 nm. This is ascribed to the structural heterogeneity in the RTIL microemulsion. For lambda(ex) = 375 nm, the region near the TX-100 surfactant is probed where bound water molecules cause slow solvation dynamics. At 435 nm, the RTIL pool is selected where the water molecules are more mobile and hence gives rise to faster solvation. The average time constant of anisotropy decay shows opposite dependence on lambda(ex) and increases about 2.5-fold from 180 ps at lambda(ex) = 375 nm to 500 ps at lambda(ex) = 435 nm for D(2)O containing RTIL microemulsion. The slower anisotropy decay at lambda(ex) = 435 nm is ascribed to the higher viscosity of RTIL which causes greater friction at the core. PMID:20235504

  11. SASSIM: a method for calculating small-angle X-ray and neutron scattering and the associated molecular envelope from explicit-atom models of solvated proteins.

    PubMed

    Merzel, Franci; Smith, Jeremy C

    2002-02-01

    A method is presented to calculate efficiently small-angle neutron and X-ray solution scattering intensities from explicit-atom models of macromolecules and the surrounding solvent. The method is based on a multipole expansion of the scattering amplitude. It is particularly appropriate for extensive configurational averaging, as is required for calculations based on computer-simulation results. In test calculations, excellent agreement with experiment is found between neutron and X-ray scattering profiles calculated from a molecular-dynamics simulation of lysozyme in water. The question of definition of the protein surface is also addressed. For comparison with the continuum model, an analytical envelope around the protein is defined in terms of spherical harmonics and is calculated using a Lebedev grid. The analytical surface thus defined is shown to reproduce well the scattering profile calculated from the explicit-atom model of the protein.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  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. PMID:26472367

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

    PubMed

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

    2016-09-01

    The effects of hydration on the solvation, diffusivity, solubility, and permeability of oxygen molecules in sustainable, biodegradable chitosan/chitin food packaging films were studied via molecular dynamics and confined random walk simulations. With increasing hydration, the membrane has a more homogeneous water distribution with the polymer chains being fully solvated. The diffusivity increased by a factor of 4 for oxygen molecules and by an order of magnitude for water with increasing the humidity. To calculate the Henry's constant and solubility of oxygen in the membranes with changing hydration, the excess chemical potential was calculated via free energy perturbation, thermodynamic integration and direct particle deletion methods. The simulations predicted a higher solubility and permeability for the lower humidity, in contradiction to experimental results. All three methods for calculating the solubility were in good agreement. It was found that the Coulombic interactions in the potential caused the oxygen to bind too strongly to the protonated amine group. Insight from this work will help guide molecular modeling of chitosan/chitin membranes, specifically permeability measurements for small solute molecules. Efforts to chemically tailor chitosan/chitin membranes to favor discrete as opposed to continuous aqueous domains could reduce oxygen permeability. PMID:27487964

  18. A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model.

    PubMed

    Yamagishi, Junya; Okimoto, Noriaki; Morimoto, Gentaro; Taiji, Makoto

    2014-11-01

    The Poisson-Boltzmann implicit solvent (PB) is widely used to estimate the solvation free energies of biomolecules in molecular simulations. An optimized set of atomic radii (PB radii) is an important parameter for PB calculations, which determines the distribution of dielectric constants around the solute. We here present new PB radii for the AMBER protein force field to accurately reproduce the solvation free energies obtained from explicit solvent simulations. The presented PB radii were optimized using results from explicit solvent simulations of the large systems. In addition, we discriminated PB radii for N- and C-terminal residues from those for nonterminal residues. The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment. The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules.

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

    PubMed

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

    2016-09-14

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

  20. Effects of explicit atmospheric convection at high CO2.

    PubMed

    Arnold, Nathan P; Branson, Mark; Burt, Melissa A; Abbot, Dorian S; Kuang, Zhiming; Randall, David A; Tziperman, Eli

    2014-07-29

    The effect of clouds on climate remains the largest uncertainty in climate change predictions, due to the inability of global climate models (GCMs) to resolve essential small-scale cloud and convection processes. We compare preindustrial and quadrupled CO2 simulations between a conventional GCM in which convection is parameterized and a "superparameterized" model in which convection is explicitly simulated with a cloud-permitting model in each grid cell. We find that the global responses of the two models to increased CO2 are broadly similar: both simulate ice-free Arctic summers, wintertime Arctic convection, and enhanced Madden-Julian oscillation (MJO) activity. Superparameterization produces significant differences at both CO2 levels, including greater Arctic cloud cover, further reduced sea ice area at high CO2, and a stronger increase with CO2 of the MJO.

  1. Effects of explicit atmospheric convection at high CO2

    PubMed Central

    Arnold, Nathan P.; Branson, Mark; Burt, Melissa A.; Abbot, Dorian S.; Kuang, Zhiming; Randall, David A.; Tziperman, Eli

    2014-01-01

    The effect of clouds on climate remains the largest uncertainty in climate change predictions, due to the inability of global climate models (GCMs) to resolve essential small-scale cloud and convection processes. We compare preindustrial and quadrupled CO2 simulations between a conventional GCM in which convection is parameterized and a “superparameterized” model in which convection is explicitly simulated with a cloud-permitting model in each grid cell. We find that the global responses of the two models to increased CO2 are broadly similar: both simulate ice-free Arctic summers, wintertime Arctic convection, and enhanced Madden–Julian oscillation (MJO) activity. Superparameterization produces significant differences at both CO2 levels, including greater Arctic cloud cover, further reduced sea ice area at high CO2, and a stronger increase with CO2 of the MJO. PMID:25024204

  2. Effect of Solvation on Electron Detachment and Excitation Energies of a Green Fluorescent Protein Chromophore Variant.

    PubMed

    Bose, Samik; Chakrabarty, Suman; Ghosh, Debashree

    2016-05-19

    Hybrid quantum mechanics/molecular mechanics (QM/MM) is applied to the fluorinated green fluorescent protein (GFP) chromophore (DFHBDI) in its deprotonated form to understand the solvatochromic shifts in its vertical detachment energy (VDE) and vertical excitation energy (VEE). This variant of the GFP chromophore becomes fluorescent in an RNA environment and has a wide range of applications in biomedical and biochemical fields. From microsolvation studies, we benchmark (with respect to full QM) the accuracy of our QM/MM calculations with effective fragment potential (EFP) as the MM method of choice. We show that while the solvatochromic shift in the VEE is minimal (0.1 eV blue shift) and its polarization component is only 0.03 eV, the effect of the solvent on the VDE is quite large (3.85 eV). We also show by accurate calculations on the solvatochromic shift of the VDE that polarization accounts for ∼0.23 eV and therefore cannot be neglected. The effect of the counterions on the VDE of the deprotonated chromophore in solvation is studied in detail, and a charge-smearing scheme is suggested for charged chromophores. PMID:27116477

  3. Solvation effect on conformations of 1,2:Dimethoxyethane: Charge dependent nonlinear response in implicit solvent models

    PubMed Central

    Jha, Abhishek K; Freed, Karl F

    2009-01-01

    We provide an improvement in the Langevin-Debye model currently being used in some implicit solvent models for computer simulations of solvation free energies of small organic molecules, as well as of biomolecular folding and binding. The analysis is based on the implementation of a charge-dependent Langevin-Debye (qLD) model that is modified by subsequent corrections due to Onsager and Kirkwood. The physical content of the model is elucidated by discussing the general treatment within the LD model of the self-energy of a charge submerged in a dielectric medium for three different limiting conditions and by considering the nonlinear response of the medium. The modified qLD model is used to refine an implicit solvent model (previously applied to protein dynamics). The predictions of the modified implicit solvent model are compared with those from explicit solvent molecular dynamics simulations for the equilibrium conformational populations of 1,2-dimethoxyethane (DME), which is the shortest ether molecule to reproduce the local conformational properties of PEO, a polymer with tremendous technological importance and a wide variety of applications. Because the conformational population preferences of DME change dramatically upon solvation, DME provides a good test case to validate our modified qLD model. PMID:18205504

  4. Effect of the Reaction Field on Molecular Forces and Torques Revealed by an Image-Charge Solvation Model.

    PubMed

    Song, Wei; Lin, Yuchun; Baumketner, Andrij; Deng, Shaozhong; Cai, Wei; Jacobs, Donald J

    2013-01-01

    We recently developed the Image-Charge Solvation Model (ICSM), which is an explicit/implicit hybrid model to accurately account for long-range electrostatic forces in molecular dynamics simulations [Lin et al., J. Chem. Phys., 131, 154103, 2009]. The ICSM has a productive spherical volume within the simulation cell for which key physical properties of bulk water are reproduced, such as density, radial distribution function, diffusion constants and dielectric properties. Although the reaction field (RF) is essential, it typically accounts for less than 2% of the total electrostatic force on a water molecule. This observation motivates investigating further the role of the RF within the ICSM. In this report we focus on distributions of forces and torques on water molecules as a function of distance from the origin and make extensive tests over a range of model parameters where Coulomb forces are decomposed into direct interactions from waters modeled explicitly and the RF. Molecular torques due to the RF typically account for 20% of the total torque, revealing why the RF plays an important role in the dielectric properties of simulated water. Moreover, it becomes clear that the buffer layer in the ICSM is essential to mitigate artifacts caused by the discontinuous change in dielectric constants at the explicit/implicit interface.

  5. Effect of the Reaction Field on Molecular Forces and Torques Revealed by an Image-Charge Solvation Model.

    PubMed

    Song, Wei; Lin, Yuchun; Baumketner, Andrij; Deng, Shaozhong; Cai, Wei; Jacobs, Donald J

    2013-01-01

    We recently developed the Image-Charge Solvation Model (ICSM), which is an explicit/implicit hybrid model to accurately account for long-range electrostatic forces in molecular dynamics simulations [Lin et al., J. Chem. Phys., 131, 154103, 2009]. The ICSM has a productive spherical volume within the simulation cell for which key physical properties of bulk water are reproduced, such as density, radial distribution function, diffusion constants and dielectric properties. Although the reaction field (RF) is essential, it typically accounts for less than 2% of the total electrostatic force on a water molecule. This observation motivates investigating further the role of the RF within the ICSM. In this report we focus on distributions of forces and torques on water molecules as a function of distance from the origin and make extensive tests over a range of model parameters where Coulomb forces are decomposed into direct interactions from waters modeled explicitly and the RF. Molecular torques due to the RF typically account for 20% of the total torque, revealing why the RF plays an important role in the dielectric properties of simulated water. Moreover, it becomes clear that the buffer layer in the ICSM is essential to mitigate artifacts caused by the discontinuous change in dielectric constants at the explicit/implicit interface. PMID:23833681

  6. Appraisal of solvation effects on chemical functional groups: Amides and esters in terms of transferable subgroup contributions

    SciTech Connect

    Alagona, G.; Ghio, C. ); Igual, J. ); Tomasi, J. )

    1989-04-26

    The basic aspects of the solvation of N-methylformamide and methyl formate, obtained and analyzed in other paper on the basis of a full ab initio MO SCF procedure, are here examined by making use of a semiclassical model that replaces the full ab initio calculations with a library of chemical group descriptions derived from wave functions at the 4-31G level. The procedure outlined in this paper permits a sequence of approximations of increasing realism, each related to the introduction of additional physical effects, eventually reaching the ab initio level. Even the lowest levels of the procedure, however, are able to describe the essential aspects of the solvation of the two test molecules.

  7. Anion solvation in alcohols

    SciTech Connect

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

    1996-03-01

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

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

    SciTech Connect

    Zhang, X.; Jonah, C.D.

    1996-04-25

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

  9. 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.

  10. Effects of Water on Solvation Layers of Imidazolium-Type Room Temperature Ionic Liquids on Silica and Mica.

    PubMed

    Sakai, Kenichi; Okada, Kohei; Uka, Akihito; Misono, Takeshi; Endo, Takeshi; Sasaki, Shinya; Abe, Masahiko; Sakai, Hideki

    2015-06-01

    Effects of the addition of water on solvation layers of imidazolium-type room temperature ionic liquids (RT-ILs) have been studied through force curve measurements of atomic force microscopy (AFM). Two kinds of RT-ILs were employed in this study; one is a hydrophilic RT-IL (1-butyl-3-methylimidazolium tetrafluoroborate, BmimBF4), and the other is a hydrophobic one (1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, EmimTFSI). These RT-ILs form solvation layers on hydrophilic solid substances (i.e., silica and mica) in the absence of added water. The addition of water into BmimBF4 resulted in the disruption of the solvation layers and then the formation of an interfacial water phase on silica. In contrast, the formation of the interfacial water phase was not evidenced on mica because of the absence of hydrogen-bonding sites on the mica surface. Interestingly, the addition of water into EmimTFSI induced the formation of the interfacial water phase on the two solid surfaces. In the EmimTFSI system, importantly, significantly greater adhesion forces were observed on silica than on mica. This reflects the different formation mechanisms of the interfacial water phase on the two solid surfaces. We conclude that the hydrogen bonding is a key factor in determining whether water molecules can be adsorbed on the solid surfaces, but it is also necessary to take into account the hydrophilic/hydrophobic nature of the RT-ILs.

  11. Solvation models: theory and validation.

    PubMed

    Purisima, Enrico O; Sulea, Traian

    2014-01-01

    Water plays an active role in many fundamental phenomena in cellular systems such as molecular recognition, folding and conformational equilibria, reaction kinetics and phase partitioning. Hence, our ability to account for the energetics of these processes is highly dependent on the models we use for calculating solvation effects. For example, theoretical prediction of protein-ligand binding modes (i.e., docking) and binding affinities (i.e., scoring) requires an accurate description of the change in hydration that accompanies solute binding. In this review, we discuss the challenges of constructing solvation models that capture these effects, with an emphasis on continuum models and on more recent developments in the field. In our discussion of methods, relatively greater attention will be given to boundary element solutions to the Poisson equation and to nonpolar solvation models, two areas that have become increasingly important but are likely to be less familiar to many readers. The other focus will be upon the trending efforts for evaluating solvation models in order to uncover limitations, biases, and potentially attractive directions for their improvement and applicability. The prospective and retrospective performance of a variety of solvation models in the SAMPL blind challenges will be discussed in detail. After just a few years, these benchmarking exercises have already had a tangible effect in guiding the improvement of solvation models.

  12. Solvation of molecules in superfluid helium enhances the “interaction induced localization” effect

    SciTech Connect

    Walewski, Łukasz Forbert, Harald; Marx, Dominik

    2014-04-14

    Atomic nuclei become delocalized at low temperatures as a result of quantum effects, whereas they are point-like in the high temperature (classical) limit. For non-interacting nuclei, the delocalization upon lowering the temperature is quantitatively described in terms of the thermal de Broglie wavelength of free particles. Clearly, light non-interacting nuclei – the proton being a prominent one – are much more delocalized at low temperatures compared to heavy nuclei, such as non-interacting oxygen having water in mind. However, strong interactions due to chemical bonding in conjunction with ultra-low temperatures characteristic to superfluid helium nanodroplets change this common picture substantially for nuclei in molecules or clusters. It turns out that protons shared in hydrogen bonds undergo an extreme “interaction induced localization” at temperatures on the order of 1 K, which compresses the protonic spatial distributions to the size of the much heavier donor or acceptor atoms, such as O or Cl nuclei, corresponding to about 0.1% of the volume occupied by a non-interacting proton at the same temperature. Moreover, applying our recently developed hybrid ab initio path integral molecular dynamics/bosonic path integral Monte Carlo quantum simulation technique to a HCl/water cluster, HCl(H{sub 2}O){sub 4}, we find that helium solvation has a significant additional localizing effect of up to about 30% in volume. In particular, the solvent-induced excess localization is the stronger the lesser the given nucleus is already localized in the gas phase reference situation.

  13. Solvation effect on conformations of 1,2:dimethoxyethane: charge-dependent nonlinear response in implicit solvent models.

    PubMed

    Jha, Abhishek K; Freed, Karl F

    2008-01-21

    The physical content of and, in particular, the nonlinear contributions from the Langevin-Debye model are illustrated using two applications. First, we provide an improvement in the Langevin-Debye model currently used in some implicit solvent models for computer simulations of solvation free energies of small organic molecules, as well as of biomolecular folding and binding. The analysis is based on the implementation of a charge-dependent Langevin-Debye (qLD) model that is modified by subsequent corrections due to Onsager and Kirkwood. Second, the physical content of the model is elucidated by discussing the general treatment within the LD model of the self-energy of a charge submerged in a dielectric medium for three different limiting conditions and by considering the nonlinear response of the medium. The modified qLD model is used to refine an implicit solvent model (previously applied to protein dynamics). The predictions of the modified implicit solvent model are compared with those from explicit solvent molecular dynamics simulations for the equilibrium conformational populations of 1,2-dimethoxyethane (DME), which is the shortest ether molecule to reproduce the local conformational properties of polyethylene oxide, a polymer with tremendous technological importance and a wide variety of applications. Because the conformational population preferences of DME change dramatically upon solvation, DME is a good test case to validate our modified qLD model. The present analysis of the modified qLD model provides the motivation and tools for studying a wide variety of other interesting systems with heterogeneous dielectric properties and spatial anisotropy.

  14. Attitudinal effects of degrading themes and sexual explicitness in video materials.

    PubMed

    Golde, J A; Strassberg, D S; Turner, C M; Lowe, K

    2000-07-01

    This study examined the independent and interactive effects of sexual explicitness and degrading themes toward women on mens' attitudes following exposure to video presentations of male-female interactions. Subjects were 83 male college students who viewed video vignettes under one of four stimulus conditions: (a) sexually explicit/degrading, (b) sexually explicit/nondegrading, (c) nonexplicit/degrading, and (d) nonexplicit/nondegrading. Results revealed that men exposed to degrading material, regardless of explicitness, were significantly more likely to express attitudes supportive of rape, while explicitness had no significant main or interactive effect on these attitudes. Further, the interaction of explicitness with degradation was found to impact scores on a measure of sexual callousness. Theoretical and clinical implications of these findings are discussed.

  15. Attitudinal effects of degrading themes and sexual explicitness in video materials.

    PubMed

    Golde, J A; Strassberg, D S; Turner, C M; Lowe, K

    2000-07-01

    This study examined the independent and interactive effects of sexual explicitness and degrading themes toward women on mens' attitudes following exposure to video presentations of male-female interactions. Subjects were 83 male college students who viewed video vignettes under one of four stimulus conditions: (a) sexually explicit/degrading, (b) sexually explicit/nondegrading, (c) nonexplicit/degrading, and (d) nonexplicit/nondegrading. Results revealed that men exposed to degrading material, regardless of explicitness, were significantly more likely to express attitudes supportive of rape, while explicitness had no significant main or interactive effect on these attitudes. Further, the interaction of explicitness with degradation was found to impact scores on a measure of sexual callousness. Theoretical and clinical implications of these findings are discussed. PMID:10904993

  16. Effect of lithium chloride on the palisade layer of the Triton-X-100 micelle: two sites for lithium ions as revealed by solvation and rotational dynamics studies.

    PubMed

    Kumbhakar, Manoj; Goel, Teena; Mukherjee, Tulsi; Pal, Haridas

    2005-10-01

    Dynamic Stokes' shift measurements using coumarin 153 as the fluorescence probe have been carried out to explore the effect of added electrolyte, lithium chloride (LiCl), on solvation dynamics in the Triton-X-100 (TX-100) micelle and thus to understand the changes in micellar Palisade layer, especially the entrapped water structures in the Palisade layer. At all concentrations of LiCl, the spectral shift correlation function shows biexponential decay. At lower LiCl concentrations, the longer solvation time is seen to decrease, although the shorter solvation time is not affected much. At higher LiCl concentrations, both longer and shorter solvation times increase with electrolyte concentration. The present observations have been rationalized assuming two possible modes of interaction of the Li+ ions in the micellar palisade layer. For LiCl concentrations below about 1.5 M, the Li+ ions appear to bind preferably to the ether groups of surfactant molecules, and the increased micellar hydration with the added salt effectively makes the solvation dynamics faster. At higher LiCl concentrations, available ether binding sites for the Li+ ions seem to get occupied effectively and the excess Li+ ions start remaining in the Palisade layer as strongly hydrated free ions. Because of strong hydration of the Li+ ions, the mobility of the entrapped water molecules in the micellar Palisade layer decreases significantly, causing the solvation dynamics to slow at higher LiCl concentrations. The fluorescence anisotropy results in the present systems are also in support of the above inferences drawn from solvation dynamics results. The present results with LiCl salt are found to be substantially different than those obtained in our earlier study (Kumbhakar et al. J. Phys. Chem. B 2005, 109, 14168) with salts such as NaCl, KCl, and CsCl. These differences are attributed mainly to the binding of the Li+ ions with the surfactant ether groups, which seems to be unlikely for the other

  17. 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.

  18. The Effect of Explicit Teaching of Comprehension Strategies on Reading Comprehension in Elementary School

    ERIC Educational Resources Information Center

    Atkins, James Grant

    2013-01-01

    This study investigated the effect of explicit teaching of comprehension strategies on the comprehension performance of elementary school students. Two schools with similar demographics, including a significant proportion of students at risk for reading failure, participated in the study. One school utilized an explicit comprehension strategy…

  19. The Effects of Explicit Instruction on French-Speaking Kindergarteners' Understanding of Stories

    ERIC Educational Resources Information Center

    Pesco, Diane; Devlin, Christine

    2015-01-01

    The study examines the effects of a short period of explicit instruction on the narrative comprehension of French-speaking kindergarteners, as measured by story retell and comprehension questions. A group of kindergarteners that received explicit instruction (n = 15) was compared to a control group that was exposed to the same storybooks and…

  20. The effect of implicit and explicit practice in the development of decision making in volleyball serving.

    PubMed

    Lola, Afrodite C; Tzetzis, George C; Zetou, Helen

    2012-04-01

    This experiment investigated the effect of explicit, implicit, and sequential learning (implicit-explicit) on the acquisition and retention of decision-making skill in volleyball. The participants were 60 female novices, ages 10 to 12 years. The experimental groups followed three different methods of training: (a) explicit practice for the development of declarative knowledge, (b) implicit practice for the development of the procedural knowledge, (c) sequential practice (implicit first and then explicit), and (d) control group that participated only in the measurements. A pre-test, a post-test, and a retention test measured the response time and accuracy of the decision-making skill. Analysis indicated that all experimental groups improved over time while the control group did not. The sequential group was faster and more accurate than the implicit group, and the latter was faster and more accurate than the explicit one. The sequential group outperformed implicit and explicit groups on both speed and accuracy of decision. It seems that both explicit and implicit processes, when they take place in sequence, interact positively, and this method improves speed and accuracy of decision making rather than when each mode of learning (implicit or explicit) occurs separately. If the role of working memory is reduced at the early stages of learning, the accumulation of declarative knowledge (explicit learning) may benefit from accumulation of procedural knowledge and enhance decision-making skill. PMID:22755467

  1. The AGBNP2 Implicit Solvation Model.

    PubMed

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

    2009-07-31

    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.

  2. 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

  3. Calix[4]arene-linked bisporphyrin hosts for fullerenes: binding strength, solvation effects, and porphyrin-fullerene charge transfer bands.

    PubMed

    Hosseini, Ali; Taylor, Steven; Accorsi, Gianluca; Armaroli, Nicola; Reed, Christopher A; Boyd, Peter D W

    2006-12-13

    A calix[4]arene scaffolding has been used to construct bisporphyrin ("jaws" porphyrin) hosts for supramolecular binding of fullerene guests. Fullerene affinities were optimized by varying the nature of the covalent linkage of the porphyrins to the calixarenes. Binding constants for C60 and C70 in toluene were explored as a function of substituents at the periphery of the porphyrin, and 3,5-di-tert-butylphenyl groups gave rise to the highest fullerene affinities (26,000 M(-1) for C60). The origin of this high fullerene affinity has been traced to differential solvation effects rather than to electronic effects. Studies of binding constants as a function of solvent (toluene < benzonitrile < dichloromethane < cyclohexane) correlate inversely with fullerene solubility, indicating that desolvation of the fullerene is a major factor determining the magnitude of binding constants. The energetics of fullerene binding have been determined in terms of DelatH and DeltaS and are consistent with an enthalpy-driven, solvation-dependent process. A direct relationship between supramolecular binding of a fullerene guest to a bisporphyrin host and the appearance of a broad NIR absorption band have been established. The energy of this band moves in a predictable manner as a function of the electronic structure of the porphyrin, thereby establishing its origin in porphyrin-to-fullerene charge transfer.

  4. 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…

  5. 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)

  6. Relativistic and Solvation Effects on the Stability of Gold(III) Halides in Aqueous Solution.

    PubMed

    Theilacker, Kolja; Schlegel, H Bernhard; Kaupp, Martin; Schwerdtfeger, Peter

    2015-10-19

    The redox stability of gold halide complexes in aqueous solution has been examined quantum-chemically by a systematic comparison of scalar- and nonrelativistic pseudopotential calculations, using both COSMO and D-COSMO-RS solvent models for water. After a computational benchmarking of density-functional methods against CCSD(T) results for the gas phase decomposition AuX4(-) → AuX2(-) + X2, B3LYP calculations have been used to establish solvent contributions. While relativity clearly enhances the stability of AuX4(-) (X = F, Cl, Br, I) complexes against X2 elimination, solvation favors the lower oxidation state. Solvation and relativity are nonadditive, due to the relativistic reduction of bond polarity. At scalar relativistic D-COSMO-RS level, the reaction AuX4(-) ⇌ AuX2(-) + X2 is computed to be endergonic, except for X = I, where it is slightly exergonic. Under the chosen conditions, partial hydrolysis of AuCl4(-) to AuCl3OH(-) is exergonic. The latter complex in turn is stable against Cl2 elimination. The disproportionation 3 AuCl2(-) ⇌ AuCl4(-) + 2 Au(s) + 2 Cl(-) is clearly exergonic. All of the computed reaction energies at scalar relativistic D-COSMO-RS level agree well with the observed speciation in dilute pH-neutral solutions at ambient temperatures. PMID:26421633

  7. Solvation of transmembrane proteins by isotropic membrane mimetics: a molecular dynamics study.

    PubMed

    Mottamal, Madhusoodanan; Shen, Sui; Guembe, Cristina; Krilov, Goran

    2007-09-27

    Mixtures of organic solvents are often used as membrane mimetics in structure determination of transmembrane proteins by solution NMR; however, the mechanism through which these isotropic solvents mimic the anisotropic environment of cell membranes is not known. Here, we use molecular dynamics simulations to study the solvation thermodynamics of the c-subunit of Escherichia coli F1F0 ATP synthase in membrane mimetic mixtures of methanol, chloroform, and water with varying fractions of components as well as in lipid bilayers. We show that the protein induces a local phase separation of the solvent components into hydrophobic and hydrophilic layers, which provides the anisotropic solvation environment to stabilize the amphiphilic peptide. The extent of this effect varies with solvent composition and is most pronounced in the ternary methanol-chloroform-water mixtures. Analysis of the solvent structure, including the local mole fraction, density profiles, and pair distribution functions, reveals considerable variation among solvent mixtures in the solvation environment surrounding the hydrophobic transmembrane region of the protein. Hydrogen bond analysis indicates that this is primarily driven by the hydrogen-bonding propensity of the essential Asp(61) residue. The impact of the latter on the conformational stability of the solvated protein is discussed. Comparison with the simulations in explicit all-atom models of lipid bilayer indicates a higher flexibility and reduced structural integrity of the membrane mimetic solvated c-subunit. This was particularly true for the deprotonated form of the protein and found to be linked to solvent stabilization of the charged Asp(61).

  8. 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.

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

    PubMed

    Sundararaman, Ravishankar; Goddard, William A

    2015-02-14

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

  10. 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.

  11. 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

  12. Explicit drain current model of junctionless double-gate field-effect transistors

    NASA Astrophysics Data System (ADS)

    Yesayan, Ashkhen; Prégaldiny, Fabien; Sallese, Jean-Michel

    2013-11-01

    This paper presents an explicit drain current model for the junctionless double-gate metal-oxide-semiconductor field-effect transistor. Analytical relationships for the channel charge densities and for the drain current are derived as explicit functions of applied terminal voltages and structural parameters. The model is validated with 2D numerical simulations for a large range of channel thicknesses and is found to be very accurate for doping densities exceeding 1018 cm-3, which are actually used for such devices.

  13. The effect of explicit expectations on initial meditation experiences.

    PubMed

    Woolfolk, R L; Rooney, A J

    1981-12-01

    Although meditation has been employed successfully as a treatment for various stress-related disorders, there is still little evidence clarifying just which aspects of meditation training are responsible for these therapeutic effects. This experiment sought to test the hypothesis that creating two opposite expectations about an initial meditation experience would result in differing physiological and phenomenological responses, even though the same technique was practiced by all subjects. The results of the experiment failed to support this hypothesis.

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

    PubMed

    Gounder, Rajamani; Iglesia, Enrique

    2013-05-01

    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

  15. Prediction of cosolvent effect on solvation free energies and solubilities of organic compounds in supercritical carbon dioxide based on fully atomistic molecular simulations.

    PubMed

    Frolov, Andrey I; Kiselev, Michael G

    2014-10-01

    The solubility of organic compounds in supercritical fluids can be dramatically affected by addition of a suitable cosolvent (entrainer) at small concentrations. This makes the screening of the best-suited cosolvent an important task for the supercritical technology. The present study aims to improve our fundamental understanding of solvation in supercritical CO2 with cosolvents. We address the following questions: (1) How does the solvation free energy depend on the chemical class of an organic solute and the chemical nature of co-solvents? (2) Which intermolecular interactions determine the effect of a cosolvent on the solubility of organic compounds? We performed extensive calculations of solvation free energies of monofunctional organic molecules at infinite dilution in supercritical media by the Bennett's acceptance ratio method based on fully atomistic molecular dynamics sampling. Sixteen monofunctional organic molecules were solvated in pure sc-CO2 and sc-CO2 with addition of 6 molar % of cosolvents of different chemical nature: ethanol, acetone, and n-hexane. Cosolvent-induced solubility enhancement (CISE) factors were also calculated. It was found that formation of significant number of hydrogen bonds between a solute and cosolvent molecules leads to a profound solubility enhancement. The cosolvent effect is proportional to the number of hydrogen bonds. When polar cosolvents do not form hydrogen bonds with solutes, the CISE correlates with the dipole moment of solute molecules. However, the electrostatic interactions have a small impact on the solubility enhancement compared to hydrogen bonding. Addition of a nonpolar cosolvent, n-hexane, has a very little effect on the solvation Gibbs free energy of studied small organic molecules. The observed trends were discussed in line with available experimental data.

  16. Rationalization of the solvation effects on the AtO+ ground-state change.

    PubMed

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

    2013-09-12

    (211)At radionuclide is of considerable interest as a radiotherapeutic agent for targeted alpha therapy in nuclear medicine, but major obstacles remain because the basic chemistry of astatine (At) is not well understood. The AtO(+) cationic form might be currently used for (211)At-labeling protocols in aqueous solution and has proved to readily react with inorganic/organic ligands. But AtO(+) reactivity must be hindered at first glance by spin restriction quantum rules: the ground state of the free cation has a dominant triplet character. Investigating AtO(+) clustered with an increasing number of water molecules and using various flavors of relativistic quantum methods, we found that AtO(+) adopts in solution a Kramers restricted closed-shell configuration resembling a scalar-relativistic singlet. The ground-state change was traced back to strong interactions, namely, attractive electrostatic interactions and charge transfer, with water molecules of the first solvation shell that lift up the degeneracy of the frontier π* molecular orbitals (MOs). This peculiarity brings an alternative explanation to the highly variable reproducibility reported for some astatine reactions: depending on the production protocols (with distillation in gas-phase or "wet chemistry" extraction), (211)At may or may not readily react. PMID:23944251

  17. Intrinsic Optical Activity and Environmental Perturbations: Solvation Effects in Chiral Building Blocks

    NASA Astrophysics Data System (ADS)

    Lemler, Paul M.; Vaccaro, Patrick

    2016-06-01

    The non-resonant interaction of electromagnetic radiation with an isotropic ensemble of chiral molecules, which causes the incident state of linear polarization to undergo a signed rotation, long has served as a metric for gauging the enantiomeric purity of asymmetric syntheses. While the underlying phenomenon of circular birefringence (CB) typically is probed in the condensed phase, recent advances in ultrasensitive circular-differential detection schemes, as exemplified by the techniques of Cavity Ring-Down Polarimetry (CRDP), have permitted the first quantitative analyses of such processes to be performed in rarefied media. Efforts to extend vapor-phase investigations of CB to new families of chiral substrates will be discussed, with particular emphasis directed towards the elucidation of intrinsic (e.g., solvent-free) properties and their mediation by environmental perturbations (e.g., solvation). Specific species targeted by this work will include the stereoselective building blocks phenylpropylene oxide and α-methylbenzyl amine, both of which exhibit pronounced solvent-dependent changes in measured optical activity. The nature of chiroptical response in different environments will be highlighted, with quantum-chemical calculations serving to unravel the structural and electronic provenance of observed behavior.

  18. 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…

  19. Parameterization of the Hamiltonian Dielectric Solvent (HADES) Reaction-Field Method for the Solvation Free Energies of Amino Acid Side-Chain Analogs.

    PubMed

    Zachmann, Martin; Mathias, Gerald; Antes, Iris

    2015-06-01

    Optimization of the Hamiltonian dielectric solvent (HADES) method for biomolecular simulations in a dielectric continuum is presented with the goal of calculating accurate absolute solvation free energies while retaining the model's accuracy in predicting conformational free-energy differences. The solvation free energies of neutral and polar amino acid side-chain analogs calculated by using HADES, which may optionally include nonpolar contributions, were optimized against experimental data to reach a chemical accuracy of about 0.5 kcal mol(-1). The new parameters were evaluated for charged side-chain analogs. The HADES results were compared with explicit-solvent, generalized Born, Poisson-Boltzmann, and QM-based methods. The potentials of mean force (PMFs) between pairs of side-chain analogs obtained by using HADES and explicit-solvent simulations were used to evaluate the effects of the improved parameters optimized for solvation free energies on intermolecular potentials.

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

    PubMed Central

    Wagoner, Jason A.; Baker, Nathan A.

    2006-01-01

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

  1. The effects of implicit and explicit security priming on creative problem solving.

    PubMed

    Mikulincer, Mario; Shaver, Phillip R; Rom, Eldad

    2011-04-01

    Attachment theory is a theory of affect regulation as it occurs in the context of close relationships. Early research focused on regulation of emotions through maintenance of proximity to supportive others (attachment figures) in times of need. Recently, emphasis has shifted to the regulation of emotion, and the benefits of such regulation for exploration and learning, via the activation of mental representations of attachment figures (security priming). We conducted two studies on the effects of implicit and explicit security priming on creative problem solving. In Study 1, implicit security priming (subliminal presentation of attachment figures' names) led to more creative problem solving (compared with control conditions) regardless of dispositional attachment anxiety and avoidance. In Study 2, the effects of explicit security priming (recalling experiences of being well cared for) were moderated by anxiety and avoidance. We discuss the link between attachment and exploration and the different effects of implicit and explicit security priming. PMID:21432691

  2. The effects of implicit and explicit security priming on creative problem solving.

    PubMed

    Mikulincer, Mario; Shaver, Phillip R; Rom, Eldad

    2011-04-01

    Attachment theory is a theory of affect regulation as it occurs in the context of close relationships. Early research focused on regulation of emotions through maintenance of proximity to supportive others (attachment figures) in times of need. Recently, emphasis has shifted to the regulation of emotion, and the benefits of such regulation for exploration and learning, via the activation of mental representations of attachment figures (security priming). We conducted two studies on the effects of implicit and explicit security priming on creative problem solving. In Study 1, implicit security priming (subliminal presentation of attachment figures' names) led to more creative problem solving (compared with control conditions) regardless of dispositional attachment anxiety and avoidance. In Study 2, the effects of explicit security priming (recalling experiences of being well cared for) were moderated by anxiety and avoidance. We discuss the link between attachment and exploration and the different effects of implicit and explicit security priming.

  3. The Effects of Explicit Instruction of Formulaic Sequences on Second-Language Writers

    ERIC Educational Resources Information Center

    Colovic-Markovic, Jelena

    2012-01-01

    The present study investigated the effects of the explicit teaching of formulaic sequences (i.e., academic and topic-induced) on L2 writing. The research examined separately the effects of the treatment on the students' abilities to produce the target formulaic sequences in controlled (i.e., C-tests) and uncontrolled situations (i.e.,…

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

    PubMed

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

    2016-09-14

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

  5. The effects of local prevalence and explicit expectations on search termination times

    PubMed Central

    Kita, Shinichi; Wolfe, Jeremy M.

    2014-01-01

    In visual search tasks, the relative proportions of target-present and -absent trials have important effects on behavior. Miss error rates rise as target prevalence decreases (Wolfe, Horowitz, & Kenner, Nature 435, 439–440, 2005). At the same time, search termination times on target-absent trials become shorter (Wolfe & Van Wert, Current Biology 20, 121–124, 2010). These effects must depend on some implicit or explicit knowledge of the current prevalence. What is the nature of that knowledge? In Experiment 1, we conducted visual search tasks at three levels of prevalence (6%, 50%, and 94%) and analyzed performance as a function of “local prevalence,” the prevalence over the last n trials. The results replicated the usual effects of overall prevalence but revealed only weak or absent effects of local prevalence. In Experiment 2, the overall prevalence in a block of trials was 20%, 50%, or 80%. However, a 100%-valid cue informed observers of the prevalence on the next trial. These explicit cues had a modest effect on target-absent RTs, but explicit expectation could not explain the full prevalence effect. We conclude that observers predict prevalence on the basis of an assessment of a relatively long prior history. Each trial contributes a small amount to that assessment, and this can be modulated but not overruled by explicit instruction. PMID:22006528

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

    PubMed

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

    2011-02-01

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

  7. Interactive effects of explicit emergent structure: a major challenge for cognitive computational modeling.

    PubMed

    French, Robert M; Thomas, Elizabeth

    2015-04-01

    David Marr's (1982) three-level analysis of computational cognition argues for three distinct levels of cognitive information processing-namely, the computational, representational, and implementational levels. But Marr's levels are-and were meant to be-descriptive, rather than interactive and dynamic. For this reason, we suggest that, had Marr been writing today, he might well have gone even farther in his analysis, including the emergence of structure-in particular, explicit structure at the conceptual level-from lower levels, and the effect of explicit emergent structures on the level (or levels) that gave rise to them. The message is that today's cognitive scientists need not only to understand how emergent structures-in particular, explicit emergent structures at the cognitive level-develop but also to understand how they feed back on the sub-structures from which they emerged.

  8. The Effects of Explicit and Implicit Pragmatic Instruction on the Development of Compliments and Compliment Responses

    ERIC Educational Resources Information Center

    Ebadi, Saman; Pourzandi, Mahsa

    2015-01-01

    This study explored the effects of explicit and implicit instructions in the development of EFL learners' speech acts of complimenting (Cs) and complimenting response (CRs). The participants in this research were 56 intermediate EFL learners from a language center, participating as members of intact classes that were divided into three groups of…

  9. Effects of Labeling on Preschoolers' Explicit False Belief Performance: Outcomes of Cognitive Flexibility or Inhibitory Control?

    ERIC Educational Resources Information Center

    Low, Jason; Simpson, Samantha

    2012-01-01

    Executive function mechanisms underpinning language-related effects on theory of mind understanding were examined in a sample of 165 preschoolers. Verbal labels were manipulated to identify relevant perspectives on an explicit false belief task. In Experiment 1 with 4-year-olds (N = 74), false belief reasoning was superior in the fully and…

  10. Transfer-of-Training Effects in Processing Instruction: The Role of Form-Related Explicit Information

    ERIC Educational Resources Information Center

    White, Justin P.; DeMil, Andrew J.

    2013-01-01

    This study compares the effects of processing instruction (PI), structured input (SI), and form-related explicit information (FREI) on a primary target form (i.e., third-person Spanish accusative clitics) and on a secondary form (i.e., third-person Spanish dative clitics). Participants included 151 adult learners enrolled in a beginning-level…

  11. The Effects of Mastery Training and Explicit Feedback on Task Design Preference in a Vocational Setting.

    ERIC Educational Resources Information Center

    Lee, David L.; Belfiore, Phillip J.; Toro-Zambrana, Wanda

    2001-01-01

    A study examined the effects of mastery training and explicit feedback on the selection behavior of two adults with severe mental retardation across two different vocational task designs. Selection behavior was affected by task efficiency only when efficiency was made more salient by pairing task cues with work incentives. (Contains references.)…

  12. Differential Effects of Explicit Form-Focused Instruction on Morphosyntactic Development

    ERIC Educational Resources Information Center

    Xu, Hainu; Lyster, Roy

    2014-01-01

    This study explores whether and to what degree explicit form-focused instruction (FFI) facilitates the use of morphosyntactic forms in second language oral production and also whether it has differential effects on morphosyntactic forms with different linguistic variables. Twenty-seven university-level Chinese EFL participants were randomly…

  13. Effects of Explicit Instruction to "Be Creative" across Domains and Cultures

    ERIC Educational Resources Information Center

    Chen, Chuansheng; Kasof, Joseph; Himsel, Amy; Dmitrieva, Julia; Dong, Qi; Xue, Gui

    2005-01-01

    To explore whether the facilitation effects of an explicit instruction to "be creative" vary across cultures and types of tasks, 248 U.S. and 278 Chinese college students were administered a battery of tests of verbal, artistic, and mathematical creativity. Half of the participants were tested under the standard condition, and the other half under…

  14. The Relative Effects of Explicit Correction and Recasts on Two Target Structures via Two Communication Modes

    ERIC Educational Resources Information Center

    Yilmaz, Yucel

    2012-01-01

    This study investigated the effects of negative feedback type (i.e., explicit correction vs. recasts), communication mode (i.e., face-to-face communication vs. synchronous computer-mediated communication), and target structure salience (i.e., salient vs. nonsalient) on the acquisition of two Turkish morphemes. Forty-eight native speakers of…

  15. The Effects of Explicit Instruction with Manipulatives on the Fraction Skills of Students with Autism

    ERIC Educational Resources Information Center

    Agrawal, Jugnu

    2013-01-01

    This single-subject multiple-baseline across participants study was designed to investigate the effects of explicit instruction with manipulatives on the conceptual and procedural knowledge of addition and subtraction of like and unlike fractions of elementary school students with autism. This study included six 8- to 12-year-old students with…

  16. The Effect of Implicit and Explicit Rules on Customer Greeting and Productivity in a Retail Organization

    ERIC Educational Resources Information Center

    Johnson, Rebecca A.; Houmanfar, Ramona; Smith, Gregory S.

    2010-01-01

    The purpose of this study was to determine the effects of presenting organizational information through implicit and explicit rules on sales-related target behaviors in a retail setting. Results indicated that when organizational information was presented in a specific form, productivity was increased and maintained longer than when presented in…

  17. Alkanesulfonylation. XIII. Solvation effects of the solvent on the competing mechanisms of alkanesulfonylation of phenol under conditions of catalysis by tertiary amines

    SciTech Connect

    Bezrodnyi, V.P.; Lyashchuk, S.N.; Skrypnik, Yu.G.

    1988-11-20

    Change in the nature of the solvent leads to a significant change in the ratio of the competing mechanisms in alkanesulfonylation, i.e., the sulfene (1a) and general base catalysis (1b). The most important role here is played by the polarity of the medium, and with increase in the polarity the predominant path changes from (1b) to (1a). In the case of mechanism (1b) the effects of specific solvation show up more strongly than for mechanism (1a). This is due to differences in the structure of the transition states. A quantitative assessment of the solvation effects on the rate of the competing paths (1a, b) is given.

  18. Charge transfer, bonding conditioning and solvation effect in the activation of the oxygen reduction reaction on unclustered graphitic-nitrogen-doped graphene.

    PubMed

    Ferre-Vilaplana, Adolfo; Herrero, Enrique

    2015-07-01

    The monodentate associative chemisorption of molecular oxygen on unclustered graphitic-nitrogen-doped graphene requires two nitrogen dopants per activated molecule. Significant charge transfers from regions corresponding to distant nitrogen-dopants, the presence of a nitrogen-dopant adjacent to the carbon atom acting as an active site, which favours its transition from a sp(2) hybridization state to sp(3), and the solvation effect turn the investigated mechanism to a favourable process.

  19. Supramolecular Interactions in Secondary Plant Cell Walls: Effect of Lignin Chemical Composition Revealed with the Molecular Theory of Solvation.

    PubMed

    Silveira, Rodrigo L; Stoyanov, Stanislav R; Gusarov, Sergey; Skaf, Munir S; Kovalenko, Andriy

    2015-01-01

    Plant biomass recalcitrance, a major obstacle to achieving sustainable production of second generation biofuels, arises mainly from the amorphous cell-wall matrix containing lignin and hemicellulose assembled into a complex supramolecular network that coats the cellulose fibrils. We employed the statistical-mechanical, 3D reference interaction site model with the Kovalenko-Hirata closure approximation (or 3D-RISM-KH molecular theory of solvation) to reveal the supramolecular interactions in this network and provide molecular-level insight into the effective lignin-lignin and lignin-hemicellulose thermodynamic interactions. We found that such interactions are hydrophobic and entropy-driven, and arise from the expelling of water from the mutual interaction surfaces. The molecular origin of these interactions is carbohydrate-π and π-π stacking forces, whose strengths are dependent on the lignin chemical composition. Methoxy substituents in the phenyl groups of lignin promote substantial entropic stabilization of the ligno-hemicellulosic matrix. Our results provide a detailed molecular view of the fundamental interactions within the secondary plant cell walls that lead to recalcitrance.

  20. Supramolecular Interactions in Secondary Plant Cell Walls: Effect of Lignin Chemical Composition Revealed with the Molecular Theory of Solvation.

    PubMed

    Silveira, Rodrigo L; Stoyanov, Stanislav R; Gusarov, Sergey; Skaf, Munir S; Kovalenko, Andriy

    2015-01-01

    Plant biomass recalcitrance, a major obstacle to achieving sustainable production of second generation biofuels, arises mainly from the amorphous cell-wall matrix containing lignin and hemicellulose assembled into a complex supramolecular network that coats the cellulose fibrils. We employed the statistical-mechanical, 3D reference interaction site model with the Kovalenko-Hirata closure approximation (or 3D-RISM-KH molecular theory of solvation) to reveal the supramolecular interactions in this network and provide molecular-level insight into the effective lignin-lignin and lignin-hemicellulose thermodynamic interactions. We found that such interactions are hydrophobic and entropy-driven, and arise from the expelling of water from the mutual interaction surfaces. The molecular origin of these interactions is carbohydrate-π and π-π stacking forces, whose strengths are dependent on the lignin chemical composition. Methoxy substituents in the phenyl groups of lignin promote substantial entropic stabilization of the ligno-hemicellulosic matrix. Our results provide a detailed molecular view of the fundamental interactions within the secondary plant cell walls that lead to recalcitrance. PMID:26263115

  1. Effect of organic co-solvents on the solvation enthalpies of amino acids and dipeptides in mixed aqueous solutions

    NASA Astrophysics Data System (ADS)

    Badelin, V. G.; Tyunina, E. Yu.

    2011-09-01

    Transition enthalpies (Δtr H o) of substances from water to binary solutions were calculated at 298.15 K on the basis of standard dissolution enthalpies (Δsol H o) for six amino acids and five dipeptides in the mixtures of water with organic solvents of various chemical natures. The enthalpy pair coefficients of interaction h xy for biomolecules with organic component of mixture were estimated within the formalism of the McMillan-Mayer theory. The change in the character of the interaction of the components of solution was demonstrated in dependence on the physicochemical properties of the solvent and nature of the side radical of the dissolved bioorganic substance. Quantitative estimation of the type of interaction of the substance with the solvent was performed on the basis of correlation ratios relating the enthalpy characteristics of bioorganic substances to properties of organic cosolvents. It was shown that in the solutions under study, the effects of both the specific (mainly electron donor) and non-specific solvation of amino acids and peptides are observed.

  2. Driving experience moderates the effect of implicit versus explicit threat priming on hazard perception test.

    PubMed

    Hoffman, Yaakov; Rosenbloom, Tova

    2016-07-01

    Due to the controversial evidence regarding the efficacy of threat campaigns on driving behavior, we addressed the effects of explicit vs. implicit threats. As in other areas of advertisements, we hypothesized that an implicit threat would be more effective, i.e., generate more anxiety than an explicit threat. Furthermore, we hypothesized that such effects would be moderated by driving experience: more experienced drivers when threatened will rely on driving skills and perform in a less cautious manner vs. less experienced drivers who have not yet acquired these skills, and therefore will tend to calm their fear by exercising more caution. Driving behavior in this experimental design was addressed by the Hazard Perception (HP) task. Results were as expected. Anxiety was higher under implicit vs. explicit threat. HP scores however were overall the same for both groups. Implicit priming generated less-cautious behavior in high-experienced drivers while generating more caution for less-experienced drivers. Demonstrating in a single experiment all three driving patterns following threat, namely, no change in driving behavior (whole sample), more cautious driving behavior (less-experience) and less cautious behavior (more-experience), potentially comprises an important step in resolving the aforementioned disparity concerning effects of threat campaigns on driving behavior.

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

    PubMed

    Nakamura, Issei

    2014-05-29

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

  4. Structural Effects of Solvation by 18-Crown-6 on Gaseous Peptides and TrpCage after Electrospray Ionization

    NASA Astrophysics Data System (ADS)

    Bonner, James G.; Hendricks, Nathan G.; Julian, Ryan R.

    2016-08-01

    Significant effort is being employed to utilize the inherent speed and sensitivity of mass spectrometry for rapid structural determination of proteins; however, a thorough understanding of factors influencing the transition from solution to gas phase is critical for correct interpretation of the results from such experiments. It was previously shown that combined use of action excitation energy transfer (EET) and simulated annealing can reveal detailed structural information about gaseous peptide ions. Herein, we utilize this method to study microsolvation of charged groups by retention of 18-crown-6 (18C6) in the gas phase. In the case of GTP (CEGNVRVSRE LAGHTGY), solvation of the 2+ charge state leads to reduced EET, whereas the opposite result is obtained for the 3+ ion. For the mini-protein C-Trpcage, solvation by 18C6 leads to dramatic increase in EET for the 3+ ion. Examination of structural details probed by molecular dynamics calculations illustrate that solvation by 18C6 alleviates the tendency of charged side chains to seek intramolecular solvation, potentially preserving native-like structures in the gas phase. These results suggest that microsolvation may be an important tool for facilitating examination of native-like protein structures in gas phase experiments.

  5. Structural Effects of Solvation by 18-Crown-6 on Gaseous Peptides and TrpCage after Electrospray Ionization

    NASA Astrophysics Data System (ADS)

    Bonner, James G.; Hendricks, Nathan G.; Julian, Ryan R.

    2016-10-01

    Significant effort is being employed to utilize the inherent speed and sensitivity of mass spectrometry for rapid structural determination of proteins; however, a thorough understanding of factors influencing the transition from solution to gas phase is critical for correct interpretation of the results from such experiments. It was previously shown that combined use of action excitation energy transfer (EET) and simulated annealing can reveal detailed structural information about gaseous peptide ions. Herein, we utilize this method to study microsolvation of charged groups by retention of 18-crown-6 (18C6) in the gas phase. In the case of GTP (CEGNVRVSRE LAGHTGY), solvation of the 2+ charge state leads to reduced EET, whereas the opposite result is obtained for the 3+ ion. For the mini-protein C-Trpcage, solvation by 18C6 leads to dramatic increase in EET for the 3+ ion. Examination of structural details probed by molecular dynamics calculations illustrate that solvation by 18C6 alleviates the tendency of charged side chains to seek intramolecular solvation, potentially preserving native-like structures in the gas phase. These results suggest that microsolvation may be an important tool for facilitating examination of native-like protein structures in gas phase experiments.

  6. Effects of labeling on preschoolers' explicit false belief performance: outcomes of cognitive flexibility or inhibitory control?

    PubMed

    Low, Jason; Simpson, Samantha

    2012-01-01

    Executive function mechanisms underpinning language-related effects on theory of mind understanding were examined in a sample of 165 preschoolers. Verbal labels were manipulated to identify relevant perspectives on an explicit false belief task. In Experiment 1 with 4-year-olds (N = 74), false belief reasoning was superior in the fully and protagonist-perspective labeled conditions compared to the child-perspective and nondescript labeling conditions. In Experiment 2 with 3-year-olds (N = 53), labeling the nondominant belief only biased attentional inertia. In Experiment 3 testing generalization in 4-year-olds (N = 38), labeling manipulations translated to improved performance on a second label-free explicit false belief task. These outcomes fit a cognitive flexibility account whereby age changes in the effects of labeling turn on formulating sophisticated conceptual representations.

  7. Grammatical constructions in typical developing children: effects of explicit reinforcement, automatic reinforcement and parity.

    PubMed

    Ostvik, Leni; Eikeseth, Svein; Klintwall, Lars

    2012-01-01

    This study replicated and extended Wright (2006) and Whitehurst, Ironsmith, and Goldfein (1974) by examining whether preschool aged children would increase their use of passive grammatical voice rather than using the more age-appropriate active grammatical construction when the former was modeled by an adult. Results showed that 5 of the 6 participants began using the passive voice after this verbal behavior had been modeled. For 3 of the participants, this change was large. The change occurred even though the adult model explicitly rewarded the participant with praise and stickers for using the active voice, while providing no praise or stickers for using the passive form that was modeled. For 1 participant, the modeling procedure had no effect on use of the passive voice. These results indicate a strong automatic reinforcement effect of achieving parity with the grammatical structures used by adults, compared to the effects of explicit reinforcement by the adult. This might help to explain why children acquire grammatical structures prevalent in their language community apparently without explicit instruction.

  8. Grammatical Constructions in Typical Developing Children: Effects of Explicit Reinforcement, Automatic Reinforcement and Parity

    PubMed Central

    Østvik, Leni; Eikeseth, Svein; Klintwall, Lars

    2012-01-01

    This study replicated and extended Wright (2006) and Whitehurst, Ironsmith, and Goldfein (1974) by examining whether preschool aged children would increase their use of passive grammatical voice rather than using the more age-appropriate active grammatical construction when the former was modeled by an adult. Results showed that 5 of the 6 participants began using the passive voice after this verbal behavior had been modeled. For 3 of the participants, this change was large. The change occurred even though the adult model explicitly rewarded the participant with praise and stickers for using the active voice, while providing no praise or stickers for using the passive form that was modeled. For 1 participant, the modeling procedure had no effect on use of the passive voice. These results indicate a strong automatic reinforcement effect of achieving parity with the grammatical structures used by adults, compared to the effects of explicit reinforcement by the adult. This might help to explain why children acquire grammatical structures prevalent in their language community apparently without explicit instruction. PMID:22754105

  9. The effect of articulatory suppression on implicit and explicit false memory in the DRM paradigm.

    PubMed

    Van Damme, Ilse; Menten, Jan; d'Ydewalle, Gery

    2010-11-01

    Several studies have shown that reliable implicit false memory can be obtained in the DRM paradigm. There has been considerable debate, however, about whether or not conscious activation of critical lures during study is a necessary condition for this. Recent findings have revealed that articulatory suppression prevents subsequent false priming in an anagram task (Lovden & Johansson, 2003). The present experiment sought to replicate and extend these findings to an implicit word stem completion task, and to additionally investigate the effect of articulatory suppression on explicit false memory. Results showed an inhibitory effect of articulatory suppression on veridical memory, as well as on implicit false memory, whereas the level of explicit false memory was heightened. This suggests that articulatory suppression did not merely eliminate conscious lure activation, but had a more general capacity-delimiting effect. The drop in veridical memory can be attributed to diminished encoding of item-specific information. Superficial encoding also limited the spreading of semantic activation during study, which inhibited later false priming. In addition, the lack of item-specific and phenomenological details caused impaired source monitoring at test, resulting in heightened explicit false memory.

  10. Polar solvation and electron transfer

    SciTech Connect

    Not Available

    1993-04-13

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

  11. Solvation dynamics in triton-X-100 and triton-X-165 micelles: effect of micellar size and hydration.

    PubMed

    Kumbhakar, Manoj; Nath, Sukhendu; Mukherjee, Tulsi; Pal, Haridas

    2004-09-22

    Dynamic Stokes' shift measurements using coumarin 153 as the fluorescence probe have been carried out to study solvation dynamics in two nonionic micelles, viz., triton-X-100 (TX-100) and triton-X-165 (TX-165). In both the micelles, the solvent relaxation dynamics is biexponential in nature. While the fast solvation time tau(s1) is seen to be almost similar for both the micelles, the slow solvation time tau(s2) is found to be appreciably smaller in TX-165 than in TX-100 micelle. Dynamic light scattering measurements indicate that the TX-165 micelles are substantially smaller in size than that of TX-100. Assuming similar core size for both the micelles, as expected from the similar chemical structures of the nonpolar ends for both the surfactants, the Palisade layer is also indicated to be substantially thinner for TX-165 micelles than that of TX-100. The aggregation number of TX-165 micelles is also found to be substantially smaller than that of TX-100 micelles. Fluorescence spectral studies of C153 dye in the two micelles indicate that the Palisade layer of TX-165 micelles is more polar than that of TX-100 micelles. Fluorescence anisotropy measurements indicate that the microviscosity in the Palisade layer of TX-165 micelles is also lower than that of TX-100 micelles. Based on these results it is inferred that the structure of the Palisade layer of TX-165 micelles is quite loose and have higher degree hydration in comparison to that of TX-100 micelles. Due to these structural differences in the Palisade layers of TX-165 and TX-100 micelles the solvation dynamics is faster in the former micelles than in the latter. It has been further inferred that in the present systems the collective response of the water molecules at somewhat away from the probes is responsible for the faster component of the solvation time, which does not reflect much of the structural changes of the micellar Palisade layer. On the contrary, the slower solvation time component, which is mainly

  12. Computer simulation of protein solvation, hydrophobic mapping, and the oxygen effect in radiation biology

    SciTech Connect

    Pratt, L.R.; Garcia, A.E.; Hummer, G.

    1997-08-01

    This is the final report of a three-year, Laboratory-Directed Research and Development project at the Los Alamos National Laboratory. Hydrophobic effects are central to the structural stability of biomolecules, particularly proteins, in solution but are not understood at a molecular level. This project developed a new theoretical approach to calculation of hydrophobic effects. This information theory approach can be implemented with experimental, including computer simulation-experimental, information. The new theory is consistent with, builds upon, and subsumes previous integral equation and scaled particle statistical thermodynamic modes of hydrophobic effects. the new theory is sufficiently simple to permit application directly to complex biomolecules in solution and to permit further expansion to incorporate more subtle effects.

  13. To spatially explicitly quantify the indirect effect of disturbances on carbon cycle of Canada's forests

    NASA Astrophysics Data System (ADS)

    Chen, W.; Cihlar, J.; Wang, S.; Zhang, Q.; Ung, C.; Price, D.; Fernandes, R.; Fraser, R.

    2001-12-01

    Disturbances (i.e., fire, insects-induced mortality, and harvesting) affect the carbon cycle of forested ecosystems directly in the year of occurrence and indirectly in many years after. For example, forest fire directly releases a fraction of carbon in biomass and forest floor to the atmosphere. The carbon cycle is also affected indirectly by disturbances which set the disturbed stand to age zero. So far, most studies estimate the indirect effect of disturbances on carbon balance at regional to national scales by aggregated forests in a region or a country into a few units, and largely ignoring the effect of spatial heterogeneity of disturbances and environmental factors. Because the effects of disturbances and environmental factors are usually non-linear, ignoring their spatial heterogeneity may introduce large error in the carbon budget estimates. In order to reduce this potential large error, spatially explicit quantification of the indirect effect of disturbances are urgently needed. Spatially explicit estimates of carbon cycle at 1-km resolution also allow direct testing against field measurements, as well as provide essential information for sustainable development of natural resources. To spatially explicitly quantify the indirect effect of disturbances on carbon cycle, we need first to quantify how stand age affects NPP. Our early results indicated the effect of stand age on NPP is species and site quality dependent. Therefore, age-NPP relationships are needed for all major forest species to carry out the spatially explicitly quantification of indirect effect of disturbances. We will derive these age-NPP relationships using existing yield tables, biomass allometric equations, and recent data on fine root and foliage production. To apply these age-NPP relationships, we need geo-spatial information on species, age, and site quality. Several initiatives have been underway to develop these spatial data layers. Because the NPP derived using these age

  14. Do Young Children Get the Message? The Effects of Repeated Video Viewing on Explicit and Implicit Information

    ERIC Educational Resources Information Center

    Skouteris, Helen; Kelly, Leanne; Dorning, Dominica E.; Calgaro, Kristina; Corns, Ben; Feehan, Emily L.; Hamilton, Fiona; Mahoney, Jessica; Macdonald, Zoe J.; Tamburrini, Sarah; Wood, Christopher

    2007-01-01

    The aim of this study was to explore the effects of repeat viewing on comprehension of explicitly and implicitly presented information in an animated movie. Seventy-three pre-school children watched an animated film and were tested for comprehension after either their single or fifth viewing. Only children's comprehension of explicitly

  15. Effects of Explicit Instruction in Cognitive and Metacognitive Reading Strategies on Iranian EFL Students' Reading Performance and Strategy Transfer

    ERIC Educational Resources Information Center

    Aghaie, Reza; Zhang, Lawrence Jun

    2012-01-01

    This study explored the impact of explicit teaching of reading strategies on English-as-a-foreign-language (EFL) students' reading performance in Iran. The study employed a questionnaire adapted from Chamot and O'Malley's (1994) cognitive and metacognitive strategies framework. To test the effects of explicit teaching of cognitive and…

  16. A Comment on "The Limited Effect of Explicit Instruction on Phrasal Verbs" by Julina A. Magnusson and C. Ray Graham

    ERIC Educational Resources Information Center

    Krashen, Stephen

    2012-01-01

    In previous reviews of studies comparing explicit and implicit instruction (Krashen, 1981, 1982, 1999, 2003), the author argued that explicit instruction will show a positive effect only when the following conditions for the use of the conscious Monitor are met: (1) the acquirer consciously knows the rule or the meaning of the item--that is, has…

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

    PubMed

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

    2014-01-01

    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. PMID:25631536

  18. Structural and energetic effects of the use of polarisable water to solvate proteins

    NASA Astrophysics Data System (ADS)

    Bachmann, Stephan J.; van Gunsteren, Wilfred F.

    2015-09-01

    Using a non-polarisable model (simple-point-charge (SPC)) for liquid water and two polarisable water models (COS/G2, COS/D), the effect of introducing molecular polarisability into the solvent upon protein structure and energetics is investigated for eight proteins, hen egg-white lysozyme (HEWL), major cold shock protein (CspA), protein G (GP), chorismate mutase (CM), the C-terminal domain of the ribosomal protein L7/L12 (RB), the amino terminal domain of phage 434 repressor (GRP), a 12-residue β-hairpin (DNV) and the GCN trigger peptide (GTP), using MD simulation, one 50 ns simulation and four additional 20 ns simulations for each protein and each water model. The differences in overall structural and energetic properties of the proteins induced by the three different water models are small, except for the amino-terminal domain of phage 434 repressor (GRP). The polarisable COS/G2 water model induces a slightly stronger interaction with the proteins modelled using the GROMOS 54A7 force field than the non-polarisable SPC water model, while for the polarisable COS/D water model the opposite effect is observed.

  19. 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

  20. 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.

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

    PubMed

    Frach, Roland; Kast, Stefan M

    2014-12-11

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

  2. Implicit for local effects and explicit for nonlocal effects is unconditionallly stable.

    SciTech Connect

    Anitescu, M.; Layton, W. J.; Pahlevani, F.; Mathematics and Computer Science; Univ. of Pittsburgh

    2004-01-01

    A combination of implicit and explicit timestepping is analyzed for a system of ordinary differential equations (ODEs) motivated by ones arising from spatial discretizations of evolutionary partial differential equations (PDEs). Loosely speaking, the method we consider is implicit in local and stabilizing terms in the underlying PDE and explicit in nonlocal and unstabilizing terms. Unconditional stability and convergence of the numerical scheme are proved by the energy method and by algebraic techniques. This stability result is surprising because usually when different methods are combined, the stability properties of the least stable method plays a determining role in the combination.

  3. Effects of gay identity, gender and explicitness of advertising imagery on gay responses to advertising.

    PubMed

    Oakenfull, Gillian

    2007-01-01

    The present research draws from literature relating to gay identity in psychology and sociology and feminist theory to consider the effect of gay identity and gender on gays' and lesbians' attitudes toward various types of advertising content that are most commonly used to target gay consumers. As such, this study empirically tests whether gay males' and lesbians' responses to gay-oriented advertising content are moderated by individual characteristics: (1) the degree to which they identify as gay, and (2) their gender, and by the explicitness and gender of the gay-oriented advertising imagery.

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

    PubMed

    Wang, Zhi-Xiang; Duan, Yong

    2004-11-15

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

  5. 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

  6. Effect of ionic liquid on the native and denatured state of a protein covalently attached to a probe: Solvation dynamics study

    NASA Astrophysics Data System (ADS)

    Chowdhury, Rajdeep; Mojumdar, Supratik Sen; Chattoraj, Shyamtanu; Bhattacharyya, Kankan

    2012-08-01

    Effect of a room temperature ionic liquid (RTIL, [pmim][Br]) on the solvation dynamics of a probe covalently attached to a protein (human serum albumin (HSA)) has been studied using femtosecond up-conversion. For this study, a solvation probe, 7-diethylamino-3-(4-maleimidophenyl)-4-methylcoumarin (CPM) has been covalently attached to the lone cysteine group (cys-34) of the protein HSA. Addition of 1.5 M RTIL or 6 M GdnHCl causes a red shift of the emission maxima of CPM bound to HSA by 3 nm and 12 nm, respectively. The average solvation time ⟨τs⟩ decreases from 650 ps (in native HSA) to 260 ps (˜2.5 times) in the presence of 1.5 M RTIL and to 60 ps (˜11 times) in the presence of 6 M GdnHCl. This is ascribed to unfolding of the protein by RTIL or GdnHCl and therefore making the probe CPM more exposed. When 1.5 M RTIL is added to the protein denatured by 6 M GdnHCl in advance, a further ˜5 nm red shift along with further ˜2 fold faster solvent relaxation (⟨τ⟩ ˜30 ps) is observed. Our previous fluorescence correlation spectroscopy study [D. K. Sasmal, T. Mondal, S. Sen Mojumdar, A. Choudhury, R. Banerjee, and K. Bhattacharyya, J. Phys. Chem. B 115, 13075 (2011), 10.1021/jp207829y] suggests that addition of RTIL to the protein denatured by 6 M GdnHCl causes a reduction in hydrodynamic radius (rh). It is demonstrated that in the presence of RTIL and GdnHCl, though the protein is structurally more compact, the local environment of CPM is very different from that in the native state.

  7. An explicit-solvent conformation search method using open software

    PubMed Central

    Gaalswyk, Kari

    2016-01-01

    Computer modeling is a popular tool to identify the most-probable conformers of a molecule. Although the solvent can have a large effect on the stability of a conformation, many popular conformational search methods are only capable of describing molecules in the gas phase or with an implicit solvent model. We have developed a work-flow for performing a conformation search on explicitly-solvated molecules using open source software. This method uses replica exchange molecular dynamics (REMD) to sample the conformational states of the molecule efficiently. Cluster analysis is used to identify the most probable conformations from the simulated trajectory. This work-flow was tested on drug molecules α-amanitin and cabergoline to illustrate its capabilities and effectiveness. The preferred conformations of these molecules in gas phase, implicit solvent, and explicit solvent are significantly different. PMID:27280078

  8. Explicit spatial compatibility is not critical to the object handle effect.

    PubMed

    Saccone, Elizabeth J; Churches, Owen; Nicholls, Michael E R

    2016-10-01

    In object perception studies, a response advantage arises when the handle of an object is congruent with the responding hand. This handle effect is thought to reflect increased motor activation of the hand most suited to grasp the object, consistent with affordance theories of object representation. An alternative explanation has been proposed, however, which suggests that the handle effect is related to a simple spatial compatibility effect (the Simon effect). In 3 experiments, we determined whether the handle effect would emerge in the absence of explicit spatial compatibility between handle and response. Stimulus and response location was varied vertically and participants made horizontally orthogonal, bimanual responses to objects' kitchen/garage category, color (as in a traditional Simon effect) or upright/inverted orientation. Categorization and inversion tasks, which relied on object knowledge, elicited a handle effect and a vertical Simon effect regarding stimulus and response locations. When participants judged object color, as per standard Simon effect paradigms, the handle effect disappeared but the Simon effect strengthened. These data demonstrate a dissociation between affordance and spatial compatibility effects and prove that affordance plays an important role in the handle effect. Models that incorporate both affordance and spatial compatibility mechanisms are discussed. (PsycINFO Database Record PMID:27668425

  9. Explicit spatial compatibility is not critical to the object handle effect.

    PubMed

    Saccone, Elizabeth J; Churches, Owen; Nicholls, Michael E R

    2016-10-01

    In object perception studies, a response advantage arises when the handle of an object is congruent with the responding hand. This handle effect is thought to reflect increased motor activation of the hand most suited to grasp the object, consistent with affordance theories of object representation. An alternative explanation has been proposed, however, which suggests that the handle effect is related to a simple spatial compatibility effect (the Simon effect). In 3 experiments, we determined whether the handle effect would emerge in the absence of explicit spatial compatibility between handle and response. Stimulus and response location was varied vertically and participants made horizontally orthogonal, bimanual responses to objects' kitchen/garage category, color (as in a traditional Simon effect) or upright/inverted orientation. Categorization and inversion tasks, which relied on object knowledge, elicited a handle effect and a vertical Simon effect regarding stimulus and response locations. When participants judged object color, as per standard Simon effect paradigms, the handle effect disappeared but the Simon effect strengthened. These data demonstrate a dissociation between affordance and spatial compatibility effects and prove that affordance plays an important role in the handle effect. Models that incorporate both affordance and spatial compatibility mechanisms are discussed. (PsycINFO Database Record

  10. A spatially explicit model for an Allee effect: why wolves recolonize so slowly in Greater Yellowstone.

    PubMed

    Hurford, Amy; Hebblewhite, Mark; Lewis, Mark A

    2006-11-01

    A reduced probability of finding mates at low densities is a frequently hypothesized mechanism for a component Allee effect. At low densities dispersers are less likely to find mates and establish new breeding units. However, many mathematical models for an Allee effect do not make a distinction between breeding group establishment and subsequent population growth. Our objective is to derive a spatially explicit mathematical model, where dispersers have a reduced probability of finding mates at low densities, and parameterize the model for wolf recolonization in the Greater Yellowstone Ecosystem (GYE). In this model, only the probability of establishing new breeding units is influenced by the reduced probability of finding mates at low densities. We analytically and numerically solve the model to determine the effect of a decreased probability in finding mates at low densities on population spread rate and density. Our results suggest that a reduced probability of finding mates at low densities may slow recolonization rate. PMID:16916526

  11. Quantifying solvated electrons' delocalization.

    PubMed

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

    2015-07-28

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

  12. Solvation Behavior of Short-chain Polystyrene Sulfonate in Aqueous Electrolyte Solutions: A Molecular Dyamics Study

    SciTech Connect

    Chialvo, Ariel A; Simonson, J Michael {Mike}

    2005-01-01

    We analyze the solvation behavior of short-chain polystyrene sulfonate (PSS) in aqueous electrolyte solutions by isothernal-isochoric molecular dynamics simulation to determine the solvation effects on the structure and conformation of the polyelectrolyte as a function of the aqueous environment. To that end, we study these aqueous systems including the explicit atomistic description of water, the PSS chain, and their interactions with all species in solution. In addition, we investigate the effect of the degree of sulfonation and its distribution along the PSS chain on the resulting conformation as well as solvation structure. Moreover, we assess the impact of added salts on the net charge of the PSS backbone, placing emphasis on the valence of the counterion and the extent of the ion-pair formation between the sulfonate group and the counterions. Finally, we present evidence for the so-called like-charge attraction between sulfonate groups through the formation of counterion-mediated interchain sulfonate-sulfonate and water-mediated intrachain sulfonate-sulfonate bridges, as well as between unlike counterion-counterion interactions.

  13. Solvation and thermal effects on the optical properties of naturaldyes: a case study on the flavylium cyanin

    NASA Astrophysics Data System (ADS)

    Calzolari, Arrigo; Malcioglu, Baris; Gebauer, Ralph; Varsano, Daniele; Baroni, Stefano

    2011-03-01

    We present a first-principles study of the effects of both hydration and thermal dynamics on the optical properties of a natural anthocyanin dye, namely, cyanin (Cya), in aqueous solution. We combine Car-Parrinello molecular dynamics and time-dependent density functional theory (TDDFT) approaches to simulate the time evolution of UV-vis spectrum of the hydrated Cya molecule at room temperature [2,3]. The spectrum of the dye calculated in the gas phase is characterized by two peaks in the red and in the blue, which would bring about a greenish hue incompatible with the dark purple coloration observed in nature. Describing the effect of the water solvent through a polarizable continuum model does not modify qualitatively the resulting picture. An explicit simulation of both solvent and thermal effects using ab-initio molecular dynamics results instead in a spectrum that is compatible with the observed coloration. This result is analyzed in terms of the spectroscopic effects of molecular distortions, induced by thermal fluctuations.

  14. Solvation and Reaction in Ionic Liquids

    SciTech Connect

    Maroncelli, Mark

    2015-01-15

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

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

    SciTech Connect

    Bickmore, Barry R.; Rosso, Kevin M.; Tadanier, Christopher J.; Bylaska, Eric J.; Doud, Darrin

    2006-08-15

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

  16. Effect of sucrose on chemically and thermally induced unfolding of domain-I of human serum albumin: Solvation dynamics and fluorescence anisotropy study.

    PubMed

    Yadav, Rajeev; Sengupta, Bhaswati; Sen, Pratik

    2016-04-01

    The present study is devoted to understand the effect of sucrose on the hydration dynamics and rotational relaxation dynamics within the domain-I of HSA during chemically as well as thermally induced unfolding. It has been observed that the average solvation time become slower in the presence of sucrose for the lower concentrations of GnHCl, however at higher concentrations of GnHCl the effect of sucrose is almost negligible. From the time resolved fluorescence anisotropy it has been observed that in the lower concentration region of GnHCl the sucrose induced stabilization is small as compared to the higher concentrations of GnHCl. We have concluded that the hydration dynamics plays an important role in the sucrose induced stabilization process at the low concentration region; whereas environmental restriction is responsible at the higher concentration of GnHCl. However, we have observed a negligible stabilizing effect of sucrose towards the temperature induced unfolding.

  17. The Effect of Explicit Instruction on Strategic Reading in a Literacy Methods Course

    ERIC Educational Resources Information Center

    Iwai, Yuko

    2016-01-01

    This study examined the impact of explicit instruction on metacognitive reading strategies among 18 K-8 teacher candidates in a literacy methods course. They received weekly explicit intervention about these strategies over one semester. Collected data included pre- and post-scores of the Metacognitive Awareness of Reading Strategies Inventory…

  18. Aptitude-Treatment Interaction Effects on Explicit Rule Learning: A Latent Growth Curve Analysis

    ERIC Educational Resources Information Center

    Hwu, Fenfang; Pan, Wei; Sun, Shuyan

    2014-01-01

    Finding the match between individuals and educational treatments is the aim of both educators and the aptitude-treatment interaction research paradigm. Using the latent growth curve analysis, the present study investigates the interaction between the type of explicit instructional approaches (deductive vs. explicit-inductive) and the level of…

  19. Effective Reading Instruction for Struggling Readers: The Role of Direct/Explicit Teaching

    ERIC Educational Resources Information Center

    Rupley, William H.; Blair, Timothy R.; Nichols, William D.

    2009-01-01

    Struggling readers are more likely to learn essential reading skills and strategies if the direct or explicit model of instruction is part of the teacher's repertoire of teaching methods. Directly/explicitly teaching reading means imparting new information to students through meaningful teacher-student interactions and teacher guidance of student…

  20. The next trial will be conflicting! Effects of explicit congruency pre-cues on cognitive control.

    PubMed

    Bugg, Julie M; Smallwood, Alicia

    2016-01-01

    The dual mechanisms of control account proposed a role for proactive and reactive mechanisms in minimizing or resolving interference in conflict tasks. Proactive mechanisms are activated in advance of stimulus onset and lead to preparatory biasing of attention in a goal-directed fashion. Reactive mechanisms are triggered post-stimulus onset. Using an explicit, trial-by-trial pre-cueing procedure in a 4-choice color-word Stroop task, we investigated effects of congruency pre-cues on cognitive control. Under conditions of stimulus uncertainty (i.e., each word was associated with multiple, equally probable responses), pre-cue benefits were observed on incongruent trials when cues were 100% valid but not when they were 75% valid. These benefits were selectively found at the longest cue-to-stimulus interval (2,000 ms), consistent with a preparation-dependent proactive control mechanism. By contrast, when a reactive strategy of switching attention to the irrelevant dimension to predict the single correlated response was viable, pre-cue benefits were observed on incongruent trials for all cue-to-stimulus intervals including the shortest that afforded only 500 ms to prepare. The findings (a) suggest a restricted role for the preparation-dependent biasing of attention via proactive control in response to explicit, trial-by-trial pre-cues while (b) highlighting strategies that lead to pre-cue benefits but which appear to reflect primarily reactive use of the information afforded by the pre-cues. We conclude that pre-cues, though available in advance of stimulus onset, may stimulate proactive or reactive minimization of interference. PMID:25522873

  1. Interfacial solvation thermodynamics.

    PubMed

    Ben-Amotz, Dor

    2016-10-19

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

  2. Interfacial solvation thermodynamics

    NASA Astrophysics Data System (ADS)

    Ben-Amotz, Dor

    2016-10-01

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

  3. Effects of solvent (effective medium versus explicit) on the structure of a protein (H3.1)

    NASA Astrophysics Data System (ADS)

    Pandey, Ras; Farmer, Barry

    2015-03-01

    Structure and dynamics of a histone (H3.1) are studied in the presence of effective medium and explicit solvent over a range of temperatures with coarse-grained Monte Carlo simulations. The protein is represented by a coarse-grained chain of residues whose interactions are described by knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions. Each empty lattice site acts as a solvent in effective medium while a fraction of sites are occupied by mobile solvent constituents in explicit solvent medium. The presence of fluctuations with explicit solvent may affect the structure and dynamics of protein differently than that in effective solvent medium. Large scale simulations are performed to analyze the structure of the protein for a range of residue-solvent interactions and temperature, and a number of local and global physical quantities are analyzed. Differences due to type of solvent on the response of some of these quantities as a function of temperature will be presented.

  4. 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.

  5. 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.

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

    PubMed

    de Queiroz, Thiago B; 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.

  7. Adding explicit solvent molecules to continuum solvent calculations for the calculation of aqueous acid dissociation constants.

    PubMed

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

    2006-02-23

    Aqueous acid dissociation free energies for a diverse set of 57 monoprotic acids have been calculated using a combination of experimental and calculated gas and liquid-phase free energies. For ionic species, aqueous solvation free energies were calculated using the recently developed SM6 continuum solvation model. This model combines a dielectric continuum with atomic surface tensions to account for bulk solvent effects. For some of the acids studied, a combined approach that involves attaching a single explicit water molecule to the conjugate base (anion), and then surrounding the resulting anion-water cluster by a dielectric continuum, significantly improves the agreement between the calculated pK(a) value and experiment. This suggests that for some anions, particularly those concentrating charge on a single exposed heteroatom, augmenting implicit solvent calculations with a single explicit water molecule is required, and adequate, to account for strong short-range hydrogen bonding interactions between the anion and the solvent. We also demonstrate the effect of adding several explicit waters by calculating the pK(a) of bicarbonate (HCO(3)(-)) using as the conjugate base carbonate (CO(3)(2-)) bound by up to three explicit water molecules.

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

    PubMed

    Chen, Zhan; Wei, Guo-Wei

    2011-11-21

    to many other classic and quantum models. By using experimental data, we show that the present quantum formulation of our differential geometry based multiscale solvation model improves the prediction of our earlier models, and outperforms some explicit solvation model.

  9. Effects of an 8-week meditation program on the implicit and explicit attitudes toward religious/spiritual self-representations.

    PubMed

    Crescentini, Cristiano; Urgesi, Cosimo; Campanella, Fabio; Eleopra, Roberto; Fabbro, Franco

    2014-11-01

    Explicit self-representations often conflict with implicit and intuitive self-representations, with such discrepancies being seen as a source of psychological tension. Most of previous research on the psychological effects of mindfulness-meditation has assessed people's self-attitudes at an explicit level, leaving unknown whether mindfulness-meditation promotes changes on implicit self-representations. Here, we assessed the changes in implicit and explicit self-related religious/spiritual (RS) representations in healthy participants following an 8-week mindfulness-oriented meditation (MOM) program. Before and after meditation, participants were administered implicit (implicit association test) and explicit (self-reported questionnaires) RS measures. Relative to control condition, MOM led to increases of implicit RS in individuals whit low pre-existing implicit RS and to more widespread increases in explicit RS. On the assumption that MOM practice may enhance the clarity of one's transcendental thoughts and feelings, we argued that MOM allows people to transform their intuitive feelings of implicit RS as well as their explicit RS attitudes.

  10. Separating Cue Encoding from Target Processing in the Explicit Task-Cuing Procedure: Are There "True" Task Switch Effects?

    ERIC Educational Resources Information Center

    Arrington, Catherine M.; Logan, Gordon D.; Schneider, Darryl W.

    2007-01-01

    Six experiments were conducted to separate cue encoding from target processing in explicitly cued task switching to determine whether task switch effects could be separated from cue encoding effects and to determine the nature of the representations produced by cue encoding. Subjects were required to respond to the cue, indicating which cue was…

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

    PubMed Central

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

    2008-01-01

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

  12. Effects of Explicit Teaching and Peer Tutoring on the Reading Achievement of Learning-Disabled and Low-Performing Students in Regular Classrooms.

    ERIC Educational Resources Information Center

    Simmons, Deborah C.; And Others

    1995-01-01

    Examined effects of explicit teaching and peer tutoring on reading achievement of learning-disabled students and nondisabled, low-performing readers in academically integrated classrooms. Found that explicit-teaching students did not achieve reliably better than controls; students in the explicit teaching plus peer tutoring condition scored higher…

  13. Differential solvation of "core" trimannoside complexes of the Dioclea grandiflora lectin and concanavalin A detected by primary solvent isotope effects in isothermal titration microcalorimetry.

    PubMed

    Dam, T K; Oscarson, S; Sacchettini, J C; Brewer, C F

    1998-12-01

    The thermodynamics of binding of the Man/Glc-specific seed lectin from Dioclea grandiflora (DGL) to deoxy analogs of the "core" trimannoside, 3, 6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside was determined by isothermal titration microcalorimetry (ITC) in the first paper of this series (Dam, T. K., Oscarson, S., and Brewer, C. F. (1998) J. Biol. Chem. 273, 32812-32817). The data showed binding of specific hydroxyl groups on all three residues of the trimannoside, similar to that observed for ConA (Gupta, D., Dam, T. K., Oscarson, S., and Brewer, C. F. (1997) J. Biol. Chem. 272, 6388-6392). However, differences exist in the thermodynamics of binding of monodeoxy analogs of the alpha(1-6) Man residue of the trimannoside to the two lectins. The x-ray crystal structure of DGL complexed to the core trimannoside, presented in the second paper in this series (Rozwarski, D. A., Swami, B. M., Brewer, C. F., and Sacchettini, J. C. (1998) J. Biol. Chem. 273, 32818-32825), showed the overall structure of the complex to be similar to that of the ConA-trimannoside complex. Furthermore, the trimannoside is involved in nearly identical hydrogen bonding interactions in both complexes. However, differences were noted in the arrangement of ordered water molecules in the binding sites of the two lectins. The present study presents ITC measurements of DGL and ConA binding to the monodeoxy analogs of the trimannoside in hydrogen oxide (H2O) and deuterium oxide (D2O). The solvent isotope effects present in the thermodynamic binding data provide evidence for altered solvation of the parent trimannoside complexes at sites consistent with the x-ray crystal structures of both lectins. The results indicate that the differences in the thermodynamics of DGL and ConA binding to alpha(1-6) monodeoxy analogs of the trimannoside do not correlate with solvation differences of the parent trimannoside complexes.

  14. The Effect of Implicit–Explicit Followership Congruence on Benevolent Leadership: Evidence from Chinese Family Firms

    PubMed Central

    Wang, Xiao; Peng, Jian

    2016-01-01

    Benevolent leadership, a traditional Chinese leadership style generated under the influence of Confucianism, has been under growing discussion since its proposal. However, existing research has focused mainly on the consequences of benevolent leadership, and research probing into its antecedents is scarce. To fill such research gap, the current study aims to explore the effect of the congruence between implicit positive followership prototype (PFP) and explicit positive followership trait (PFT) on benevolent leadership. Polynomial regression combined with the response surface methodology was used to test the hypotheses herein. The results, based on a sample of 241 leader–follower dyads from four Chinese family firms, indicated the following: (1) benevolent leadership is higher when leader PFP is congruent with follower PFT than when they are incongruent; (2) in cases of congruence, benevolent leadership is higher when leader PFP and follower PFT are both high rather than low; (3) in the case of incongruence, there is no significant difference for the level of benevolent leadership in two scenarios: “low leader PFP – high follower PFT” and “high leader PFP – low follower PFT”. PMID:27375514

  15. The Effect of Implicit-Explicit Followership Congruence on Benevolent Leadership: Evidence from Chinese Family Firms.

    PubMed

    Wang, Xiao; Peng, Jian

    2016-01-01

    Benevolent leadership, a traditional Chinese leadership style generated under the influence of Confucianism, has been under growing discussion since its proposal. However, existing research has focused mainly on the consequences of benevolent leadership, and research probing into its antecedents is scarce. To fill such research gap, the current study aims to explore the effect of the congruence between implicit positive followership prototype (PFP) and explicit positive followership trait (PFT) on benevolent leadership. Polynomial regression combined with the response surface methodology was used to test the hypotheses herein. The results, based on a sample of 241 leader-follower dyads from four Chinese family firms, indicated the following: (1) benevolent leadership is higher when leader PFP is congruent with follower PFT than when they are incongruent; (2) in cases of congruence, benevolent leadership is higher when leader PFP and follower PFT are both high rather than low; (3) in the case of incongruence, there is no significant difference for the level of benevolent leadership in two scenarios: "low leader PFP - high follower PFT" and "high leader PFP - low follower PFT". PMID:27375514

  16. Tobacco Industry Manipulation Messages in Anti-Smoking Public Service Announcements: The Effect of Explicitly Versus Implicitly Delivering Messages

    PubMed Central

    Shadel, William G.; Fryer, Craig S.; Tharp-Taylor, Shannah

    2010-01-01

    Message content in anti-smoking public service announcements (PSAs) can be delivered explicitly (directly with concrete statements) or implicitly (indirectly via metaphor), and the method of delivery may affect the efficacy of those PSAs. The purpose of this study was to conduct an initial test of this hypothesis, using tobacco industry manipulation PSAs in adolescents. A 2 (age: 11-14 years old; 15-17 years old) × 2 (message delivery: implicit, explicit) mixed model design was used. There was a significant main effect of message delivery: Tobacco industry manipulation PSAs that delivered their messages explicitly were associated with stronger levels of smoking resistance self-efficacy compared to tobacco industry manipulation PSAs that delivered their messages implicitly. No significant main effects of age were found nor were any interactions between age and message delivery. These results suggest that message delivery factors should be taken into account when designing anti-smoking PSAs. PMID:20071100

  17. Tobacco industry manipulation messages in anti-smoking public service announcements: the effect of explicitly versus implicitly delivering messages.

    PubMed

    Shadel, William G; Fryer, Craig S; Tharp-Taylor, Shannah

    2010-05-01

    Message content in anti-smoking public service announcements (PSAs) can be delivered explicitly (directly with concrete statements) or implicitly (indirectly via metaphor), and the method of delivery may affect the efficacy of those PSAs. The purpose of this study was to conduct an initial test of this idea using tobacco industry manipulation PSAs in adolescents. A 2 (age: 11-14 years old; 15-17 years old)x2 (message delivery: implicit, explicit) mixed model design was used. There was a significant main effect of message delivery: Tobacco industry manipulation PSAs that delivered their messages explicitly were associated with stronger levels of smoking resistance self-efficacy compared to tobacco industry manipulation PSAs that delivered their messages implicitly. No significant main effects of age were found nor were any interactions between age and message delivery. These results suggest that message delivery factors should be taken into account when designing anti-smoking PSAs. PMID:20071100

  18. Lipid solvation effects contribute to the affinity of Gly-xxx-Gly motif-mediated helix-helix interactions.

    PubMed

    Johnson, Rachel M; Rath, Arianna; Melnyk, Roman A; Deber, Charles M

    2006-07-18

    Interactions between transmembrane helices are mediated by the concave Gly-xxx-Gly motif surface. Whether Gly residues per se are sufficient for selection of this motif has not been established. Here, we used the in vivo TOXCAT assay to measure the relative affinities of all 18 combinations of Gly, Ala, and Ser "small-xxx-small" mutations in glycophorin A (GpA) and bacteriophage M13 major coat protein (MCP) homodimers. Affinity values were compared with the accessibility to a methylene-sized probe of the total surface area of each helix monomer as a measure of solvation by membrane components. A strong inverse correlation was found between nonpolar-group lipid accessibility and dimer affinity (R = 0.75 for GpA, p = 0.013, and R = 0.81 for MCP, p = 0.004), suggesting that lipid as a poor membrane protein solvent, conceptually analogous to water in soluble protein folding, can contribute to dimer stability and help to define helix-helix interfaces.

  19. Dispersion forces between solvated electrons.

    PubMed

    Chuev, Gennady N

    2010-04-14

    Using the path integral centroid approach, we investigate dispersion interactions between electrons solvated in metal-ammonia solutions. We have argued that at finite metal concentrations, the behavior of the solvated electrons is controlled by these interactions. The latter result in a peculiar nonmetal-metal transition, which appears as a sharp dielectric enhancement and a mechanical instability of the system. Our results indicate also that the solvated electrons are to be considered as a two-component mixture consisting of localized and delocalized electrons beyond the critical density corresponding to this mechanical instability.

  20. Effects of Explicit Convection on Global Land-atmosphere Coupling in the Superparameterized CAM

    NASA Astrophysics Data System (ADS)

    Sun, J.; Pritchard, M. S.

    2015-12-01

    Many global climate models are prone to producing land-atmosphere coupling dynamics that are too strong and simplistic. Cumulus and convection parameterizations are natural culprits but the effect of bypassing them with explicitly resolved convection on global land-atmosphere coupling dynamics has not been explored systematically. We apply a suite of modern land-atmosphere coupling diagnostics to isolate the effect of cloud superparameterization (SP) in the Community Atmosphere Model v3.5, focusing on both the land segment (i.e., soil moisture and evapotranspiration relationship) and atmospheric segment (i.e., evapotranspiration and precipitation relationship) in the water pathway of the land-atmosphere feedback loop. Comparing SPCAM3.5 and conventional CAM3.5 in daily timescale, our results show that the Super-Parameterized model reduces the coupling strength in the Central Great Plain in American, and reverses the terrestrial segment coupling sign (from negative to positive) over India. Which are consistent with previous studies and are favorable improvements on the known issues reported in literatures. Analysis of the triggering feedback strength (TFS) and amount feedback strength (AFS) shows that SPCAM3.5 favorably reproduces the patterns of these indices over North America, with probability of afternoon precipitation enhanced by high evaporative fraction along the eastern United States and Mexico, while conventional CAM3.5 does not capture this signal. The links in the soil moisture-precipitation feedback loop are further explored through applying the mixing diagram approach to the diurnal cycles of the land surface and planetary boundary layer variables.

  1. Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions.

    PubMed

    Reif, Maria M; Hünenberger, Philippe H

    2011-04-14

    The raw single-ion solvation free energies computed from atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions (finite or periodic system, system or box size) and treatment of electrostatic interactions (Coulombic, lattice-sum, or cutoff-based) used during these simulations. However, as shown by Kastenholz and Hünenberger [J. Chem. Phys. 124, 224501 (2006)], correction terms can be derived for the effects of: (A) an incorrect solvent polarization around the ion and an incomplete or/and inexact interaction of the ion with the polarized solvent due to the use of an approximate (not strictly Coulombic) electrostatic scheme; (B) the finite-size or artificial periodicity of the simulated system; (C) an improper summation scheme to evaluate the potential at the ion site, and the possible presence of a polarized air-liquid interface or of a constraint of vanishing average electrostatic potential in the simulated system; and (D) an inaccurate dielectric permittivity of the employed solvent model. Comparison with standard experimental data also requires the inclusion of appropriate cavity-formation and standard-state correction terms. In the present study, this correction scheme is extended by: (i) providing simple approximate analytical expressions (empirically-fitted) for the correction terms that were evaluated numerically in the above scheme (continuum-electrostatics calculations); (ii) providing correction terms for derivative thermodynamic single-ion solvation properties (and corresponding partial molar variables in solution), namely, the enthalpy, entropy, isobaric heat capacity, volume, isothermal compressibility, and isobaric expansivity (including appropriate standard-state correction terms). The ability of the correction scheme to produce methodology-independent single-ion solvation free energies based on atomistic simulations is tested in the case of Na(+) hydration, and the nature and magnitude of the correction terms for

  2. Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions

    NASA Astrophysics Data System (ADS)

    Reif, Maria M.; Hünenberger, Philippe H.

    2011-04-01

    The raw single-ion solvation free energies computed from atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions (finite or periodic system, system or box size) and treatment of electrostatic interactions (Coulombic, lattice-sum, or cutoff-based) used during these simulations. However, as shown by Kastenholz and Hünenberger [J. Chem. Phys. 124, 224501 (2006)], 10.1529/biophysj.106.083667, correction terms can be derived for the effects of: (A) an incorrect solvent polarization around the ion and an incomplete or/and inexact interaction of the ion with the polarized solvent due to the use of an approximate (not strictly Coulombic) electrostatic scheme; (B) the finite-size or artificial periodicity of the simulated system; (C) an improper summation scheme to evaluate the potential at the ion site, and the possible presence of a polarized air-liquid interface or of a constraint of vanishing average electrostatic potential in the simulated system; and (D) an inaccurate dielectric permittivity of the employed solvent model. Comparison with standard experimental data also requires the inclusion of appropriate cavity-formation and standard-state correction terms. In the present study, this correction scheme is extended by: (i) providing simple approximate analytical expressions (empirically-fitted) for the correction terms that were evaluated numerically in the above scheme (continuum-electrostatics calculations); (ii) providing correction terms for derivative thermodynamic single-ion solvation properties (and corresponding partial molar variables in solution), namely, the enthalpy, entropy, isobaric heat capacity, volume, isothermal compressibility, and isobaric expansivity (including appropriate standard-state correction terms). The ability of the correction scheme to produce methodology-independent single-ion solvation free energies based on atomistic simulations is tested in the case of Na+ hydration, and the nature and magnitude

  3. The Effects of Explicit Instruction on the Reading Performance of Adolescent English Language Learners with Intellectual Disabilities

    ERIC Educational Resources Information Center

    Reed, Deborah K.

    2013-01-01

    This study sought to determine the effects of explicit phonics instruction and sight word instruction on the letter-sound identification and word reading of 13- to 15-year-old English language learners in the eighth grade who were identified as having intellectual disabilities (ID). Using a randomized single-subject design, four Hispanic students…

  4. More on the Effects of Explicit Information in Instructed SLA: A Partial Replication and a Response to Fernandez (2008)

    ERIC Educational Resources Information Center

    Henry, Nicholas; Culmana, Hillah; VanPattena, Bill

    2009-01-01

    The role of explicit information (EI) as an independent variable in instructed SLA is largely underresearched. Using the framework of processing instruction, however, a series of offline studies has found no effect for EI (e.g., Benati, 2004; Sanz & Morgan-Short, 2004; VanPatten & Oikkenon, 1996). Fernandez (2008) presented two online experiments…

  5. The Effect of Explicit Teaching of Learning Strategies on Students' Reading and Writing in a Japanese Partial Immersion Program.

    ERIC Educational Resources Information Center

    Birch, Gary; And Others

    A study investigated the effect of explicit instruction in reading and writing strategies on student performance in a college-level Japanese partial immersion course. Subjects were five students, four of whom had been subjects of an earlier study of reading and writing strategies and all of whom were training to be Japanese teachers. In class,…

  6. The Effects of Explicit Reading Strategy Instruction and Cooperative Learning on Reading Comprehension in Fourth Grade Students

    ERIC Educational Resources Information Center

    Lencioni, Gina M.

    2013-01-01

    The purpose of this study was to investigate the effects of explicit direct instruction and cooperative learning on reading comprehension in fourth grade students. A quasi-experimental design was used. There were six cognitive and three affective measures used to collect quantitative data. Cognitive measures included California State Test scores,…

  7. The Effects of Mindfulness versus Thought Suppression on Implicit and Explicit Measures of Experiential Avoidance

    ERIC Educational Resources Information Center

    Hooper, Nic; Villatte, Matthieu; Neofotistou, Evi; McHugh, Louise

    2010-01-01

    The current study aimed to provide an implicit measure of experiential avoidance (EA). Fifty undergraduate participants were exposed to an implicit (Implicit Relational Assessment Procedure: IRAP) and an explicit (Acceptance and Action Questionnaire II: AAQ II) measure of EA. Subsequently participant's response latencies on viewing a negatively…

  8. The Effect of Implicit and Explicit Motivation on Recall among Old and Young Adults.

    ERIC Educational Resources Information Center

    McClelland, David C.; Scioli, Anthony; Weaver, Suzanne

    1998-01-01

    Sixty-eight elderly subjects and 77 young adults were compared on implicit and explicit motive levels and on recall of introductions and working memory. Significantly fewer of the elderly scored high in the implicit motives. The elderly participants showed major recall deficits on both tasks but the implicit motives studied enhanced recall for the…

  9. Implementation and Effects of Explicit Reading Comprehension Instruction in Fifth-Grade Classrooms

    ERIC Educational Resources Information Center

    Andreassen, Rune; Braten, Ivar

    2011-01-01

    In this intervention study, teachers tried to implement four instructional principles derived from the literature on research-based, explicit reading comprehension instruction in their fifth-grade classrooms. The principles focused on relevant background knowledge, reading comprehension strategies, reading-group organization, and reading…

  10. Perceived Effects of Sexually Explicit Internet Content: The Third-Person Effect in Singapore.

    ERIC Educational Resources Information Center

    Wu, Wei; Koo, Soh Hoon

    2001-01-01

    Investigates the third-person effect of pornography on the Internet. Notes that congruent with the third-person effect, students from a major Singapore university judged pornographic material on the Internet to have a greater impact on others than on themselves. Reveals evidence for a perceived social distance corollary with children to be more…

  11. EFFECTS OF KETAMINE ON EXPLICIT AND IMPLICIT SUICIDAL COGNITION: A RANDOMIZED CONTROLLED TRIAL IN TREATMENT-RESISTANT DEPRESSION

    PubMed Central

    Price, Rebecca B.; Iosifescu, Dan V.; Murrough, James W.; Chang, Lee C.; Al Jurdi, Rayan K.; Iqbal, Syed Z.; Soleimani, Laili; Charney, Dennis S.; Foulkes, Alexandra L.; Mathew, Sanjay J.

    2014-01-01

    Background Preliminary evidence suggests intravenous ketamine has rapid effects on suicidal cognition, making it an attractive candidate for depressed patients at imminent risk of suicide. In the first randomized controlled trial of ketamine using an anesthetic control condition, we tested ketamine’s acute effects on explicit suicidal cognition and a performance-based index of implicit suicidal cognition (Implicit Association Test; IAT) previously linked to suicidal behavior. Method Symptomatic patients with treatment-resistant unipolar major depression (inadequate response to ≥3 antidepressants) were assessed using a composite index of explicit suicidal ideation (Beck Scale for Suicidal Ideation, Montgomery-Asberg Rating Scale suicide item, Quick Inventory of Depressive Symptoms suicide item) and the IAT to assess suicidality implicitly. Measures were taken at baseline and 24 hr following a single subanesthetic dose of ketamine (n = 36) or midazolam (n = 21), a psychoactive placebo agent selected for its similar, rapid anesthetic effects. Twenty four hours postinfusion, explicit suicidal cognition was significantly reduced in the ketamine but not the midazolam group. Results Fifty three percent of ketamine-treated patients scored zero on all three explicit suicide measures at 24 hr, compared with 24% of the midazolam group (χ2 = 4.6; P = .03). Implicit associations between self- and escape-related words were reduced following ketamine (P = .01; d = .58) but not midazolam (P = .68; d = .09). Ketamine-specific decreases in explicit suicidal cognition were largest in patients with elevated suicidal cognition at baseline, and were mediated by decreases in nonsuicide-related depressive symptoms. Conclusions Intravenous ketamine produces rapid reductions in suicidal cognition over and above active placebo. Further study is warranted to test ketamine’s antisuicidal effects in higher-risk samples. PMID:24668760

  12. The nonmonotonic concentration dependence of the mean activity coefficient of electrolytes is a result of a balance between solvation and ion-ion correlations.

    PubMed

    Vincze, Julianna; Valiskó, Mónika; Boda, Dezso

    2010-10-21

    We propose a simple model to explain the nonmonotonic concentration dependence of the mean activity coefficient of simple electrolytes without using any adjustable parameters. The primitive model of electrolytes is used to describe the interaction between ions computed by the adaptive grand canonical Monte Carlo method. For the dielectric constant of the electrolyte, we use experimental concentration dependent values. This is included through a solvation term in our treatment to describe the interaction between ions and water that changes as the dielectric constant changes with concentration. This term is computed by a Born-treatment fitted to experimental hydration energies. Our results for LiCl, NaCl, KCl, CsCl, NaBr, NaI, MgCl(2), CaCl(2), SrCl(2), and BaCl(2) demonstrate that the principal reason of the nonmonotonic behavior of the activity coefficient is a balance between the solvation and ion-ion correlation terms. This conclusion differs from previous studies that assumed that it is the balance of hard sphere repulsion and electrostatic attraction that produces the nonmonotonic behavior. Our results indicate that the earlier assumption that solvation can be taken into account by a larger, "solvated" ionic radius should be reconsidered. To explain second order effects (such as dependence on ionic size), we conclude that explicit water models are needed.

  13. Preferential solvation: dividing surface vs excess numbers.

    PubMed

    Shimizu, Seishi; Matubayasi, Nobuyuki

    2014-04-10

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

  14. Preferential solvation: dividing surface vs excess numbers.

    PubMed

    Shimizu, Seishi; Matubayasi, Nobuyuki

    2014-04-10

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

  15. 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.

  16. Effect of coordinate frame compatibility on the transfer of implicit and explicit learning across limbs.

    PubMed

    Poh, Eugene; Carroll, Timothy J; Taylor, Jordan A

    2016-09-01

    Insights into the neural representation of motor learning can be obtained by investigating how learning transfers to novel task conditions. We recently demonstrated that visuomotor rotation learning transferred strongly between left and right limbs when the task was performed in a sagittal workspace, which afforded a consistent remapping for the two limbs in both extrinsic and joint-based coordinates. In contrast, transfer was absent when performed in horizontal workspace, where the extrinsically defined perturbation required conflicting joint-based remapping for the left and right limbs. Because visuomotor learning is thought to be supported by both implicit and explicit forms of learning, however, it is unclear to what extent these distinct forms of learning contribute to interlimb transfer. In this study, we assessed the degree to which interlimb transfer, following visuomotor rotation training, reflects explicit vs. implicit learning by obtaining verbal reports of participants' aiming direction before each movement. We also determined the extent to which these distinct components of learning are constrained by the compatibility of coordinate systems by comparing transfer between groups of participants who reached to targets arranged in the horizontal and sagittal planes. Both sagittal and horizontal conditions displayed complete transfer of explicit learning to the untrained limb. In contrast, transfer of implicit learning was incomplete, but the sagittal condition showed greater transfer than the horizontal condition. These findings suggest that explicit strategies developed with one limb can be fully implemented in the opposite limb, whereas implicit transfer depends on the degree to which new sensorimotor maps are spatially compatible for the two limbs.

  17. Priming effects from young-old to very old age on a word-stem completion task: minimizing explicit contamination.

    PubMed

    Spaan, Pauline E J; Raaijmakers, Jeroen G W

    2011-01-01

    We investigated the size of repetition priming effects from young-old to very old age using a newly developed Word-Stem Completion (WSC) task. Retrospectively, we examined the role of explicit, intentional retrieval strategies in priming. We constructed our task by taking factors into account that were known to complicate the measurement of significant and valid priming effects. Within our sample of 170 cognitively healthy elderly persons of 55-94 years old, we found no effects on priming of age, gender, education, intelligence, cognitive status, memory complaints, or depressive symptoms. Participants that subsequent to task administration reported awareness of the study-test relationship obtained higher priming scores. However, analysis of stem-completion times showed that explicit contamination during the task was unlikely. The results suggest that WSC priming is age-invariant up to very old age. This task with increased validity might contribute to the differentiation with Alzheimer's disease by improving specificity of assessment.

  18. Solvation Effects on the Static and Dynamic First-Order Electronic and Vibrational Hyperpolarizabilities of Uracil: A Polarized Continuum Model Investigation

    PubMed Central

    Alparone, Andrea

    2013-01-01

    Electronic (βe) and vibrational (βv) first-order hyperpolarizabilities of uracil were determined in gas and water solution using the Coulomb-attenuating Density Functional Theory level with the Dunning's correlation-consistent aug-cc-pVDZ basis set. Frequency-dependent βe values were computed for the Second Harmonic Generation (SHG) and Electric Optical Pockels Effect (EOPE) nonlinear optical phenomena. The Polarized Continuum Model was employed to study the solvent effects on the electronic and vibrational properties. The introduction of solvation contributions increases the βe(static) value by ca. 110%. In comparison, smaller enhancements are found for the βe(EOPE) and βe(SHG) data evaluated at the typical wavelength of 694 nm (by 40–50%). The gas-water hyperpolarizability difference was rationalised through a density analysis study. The magnitudes of the vibrational first-order hyperpolarizabilities are comparable to their electronic counterparts and noticeably increase in solution: βv(EOPE) ~ βe(EOPE) in aqueous phase at λ = 694 nm. Analysis of the IR and Raman spectra is useful to elucidate the most important contributing modes to the vibrational first-order hyperpolarizabilities. PMID:24453886

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

    PubMed

    Das, Siddhartha; Chakraborty, Suman

    2011-08-01

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

  20. Effects of Reliability and Global Context on Explicit and Implicit Measures of Sensed Hand Position in Cursor-Control Tasks

    PubMed Central

    Rand, Miya K.; Heuer, Herbert

    2016-01-01

    In a cursor-control task in which the motion of the cursor is rotated randomly relative to the movement of the hand, the sensed directions of hand and cursor are mutually biased. In our previous study, we used implicit and explicit measures of the bias of sensed hand direction toward the direction of the cursor and found different characteristics. The present study serves to explore further differences and commonalities of these measures. In Experiment 1, we examined the effects of different relative reliabilities of visual and proprioceptive information on the explicitly and implicitly assessed bias of sensed hand direction. In two conditions, participants made an aiming movement and returned to the start position immediately or after a delay of 6 s during which the cursor was no longer visible. The unimodal proprioceptive information on final hand position in the delayed condition served to increase its relative reliability. As a result, the bias of sensed hand direction toward the direction of the cursor was reduced for the explicit measure, with a complementary increase of the bias of sensed cursor direction, but unchanged for the implicit measure. In Experiment 2, we examined the influence of global context, specifically of the across-trial sequence of judgments of hand and cursor direction. Both explicitly and implicitly assessed biases of sensed hand direction did not significantly differ between the alternated condition (trial-to-trial alternations of judgments of hand and cursor direction) and the blocked condition (judgments of hand or cursor directions in all trials). They both substantially decreased from the alternated to the randomized condition (random sequence of judgments of hand and cursor direction), without a complementary increase of the bias of sensed cursor direction. We conclude that our explicit and implicit measures are equally sensitive to variations of coupling strength as induced by the variation of global context in Experiment 2, but

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

    PubMed

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

    2015-03-28

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

  2. Advances in computational solvation thermodynamics

    NASA Astrophysics Data System (ADS)

    Wyczalkowski, Matthew A.

    The aim of this thesis is to develop improved methods for calculating the free energy, entropy and enthalpy of solvation from molecular simulations. Solvation thermodynamics of model compounds provides quantitative measurements used to analyze the stability of protein conformations in aqueous milieus. Solvation free energies govern the favorability of the solvation process, while entropy and enthalpy decompositions give insight into the molecular mechanisms by which the process occurs. Computationally, a coupling parameter lambda modulates solute-solvent interactions to simulate an insertion process, and multiple lengthy simulations at a fixed lambda value are typically required for free energy calculations to converge; entropy and enthalpy decompositions generally take 10-100 times longer. This thesis presents three advances which accelerate the convergence of such calculations: (1) Development of entropy and enthalpy estimators which combine data from multiple simulations; (2) Optimization of lambda schedules, or the set of parameter values associated with each simulation; (3) Validation of Hamiltonian replica exchange, a technique which swaps lambda values between two otherwise independent simulations. Taken together, these techniques promise to increase the accuracy and precision of free energy, entropy and enthalpy calculations. Improved estimates, in turn, can be used to investigate the validity and limits of existing solvation models and refine force field parameters, with the goal of understanding better the collapse transition and aggregation behavior of polypeptides.

  3. 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.

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

    PubMed

    Kroutil, Ondřej; Minofar, Babak; Kabeláč, Martin

    2016-09-01

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

  5. Molecular correlations and solvation in simple fluids.

    PubMed

    Barbosa, Marco A A; Widom, B

    2010-06-01

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

  6. Molecular correlations and solvation in simple fluids.

    PubMed

    Barbosa, Marco A A; Widom, B

    2010-06-01

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

  7. 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

  8. Small molecule solvation changes due to the presence of salt are governed by the cost of solvent cavity formation and dispersion.

    PubMed

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

    2014-12-14

    We are interested in the free energies of transferring nonpolar solutes into aqueous NaCl solutions with salt concentrations upwards of 2 M, the Hofmeister regime. We use the semi-explicit assembly (SEA) computational model to represent these electrolyte solutions. We find good agreement with experiments (Setschenow coefficients) on 43 nonpolar and polar solutes and with TIP3P explicit-solvent simulations. Besides being much faster than explicit solvent calculations, SEA is more accurate than the PB models we tested, successfully capturing even subtle salt effects in both the polar and nonpolar components of solvation. We find that the salt effects are mainly due to changes in the cost of forming nonpolar cavities in aqueous NaCl solutions, and not mainly due to solute-ion electrostatic interactions.

  9. Charged patchy particle models in explicit salt: Ion distributions, electrostatic potentials, and effective interactions

    SciTech Connect

    Yigit, Cemil; Dzubiella, Joachim; Heyda, Jan

    2015-08-14

    We introduce a set of charged patchy particle models (CPPMs) in order to systematically study the influence of electrostatic charge patchiness and multipolarity on macromolecular interactions by means of implicit-solvent, explicit-ion Langevin dynamics simulations employing the Gromacs software. We consider well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size which are composed of discrete atoms. The studied mono- and multipole moments of the CPPMs are comparable to those of globular proteins with similar size. We first characterize ion distributions and electrostatic potentials around a single CPPM. Although angle-resolved radial distribution functions reveal the expected local accumulation and depletion of counter- and co-ions around the patches, respectively, the orientation-averaged electrostatic potential shows only a small variation among the various CPPMs due to space charge cancellations. Furthermore, we study the orientation-averaged potential of mean force (PMF), the number of accumulated ions on the patches, as well as the CPPM orientations along the center-to-center distance of a pair of CPPMs. We compare the PMFs to the classical Derjaguin-Verwey-Landau-Overbeek theory and previously introduced orientation-averaged Debye-Hückel pair potentials including dipolar interactions. Our simulations confirm the adequacy of the theories in their respective regimes of validity, while low salt concentrations and large multipolar interactions remain a challenge for tractable theoretical descriptions.

  10. Charged patchy particle models in explicit salt: Ion distributions, electrostatic potentials, and effective interactions.

    PubMed

    Yigit, Cemil; Heyda, Jan; Dzubiella, Joachim

    2015-08-14

    We introduce a set of charged patchy particle models (CPPMs) in order to systematically study the influence of electrostatic charge patchiness and multipolarity on macromolecular interactions by means of implicit-solvent, explicit-ion Langevin dynamics simulations employing the Gromacs software. We consider well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size which are composed of discrete atoms. The studied mono- and multipole moments of the CPPMs are comparable to those of globular proteins with similar size. We first characterize ion distributions and electrostatic potentials around a single CPPM. Although angle-resolved radial distribution functions reveal the expected local accumulation and depletion of counter- and co-ions around the patches, respectively, the orientation-averaged electrostatic potential shows only a small variation among the various CPPMs due to space charge cancellations. Furthermore, we study the orientation-averaged potential of mean force (PMF), the number of accumulated ions on the patches, as well as the CPPM orientations along the center-to-center distance of a pair of CPPMs. We compare the PMFs to the classical Derjaguin-Verwey-Landau-Overbeek theory and previously introduced orientation-averaged Debye-Hückel pair potentials including dipolar interactions. Our simulations confirm the adequacy of the theories in their respective regimes of validity, while low salt concentrations and large multipolar interactions remain a challenge for tractable theoretical descriptions. PMID:26277163

  11. The cooperation effect of noise and an external signal on implicit and explicit coherence resonances in the brusselator system

    NASA Astrophysics Data System (ADS)

    Shi, J.-C.

    2010-04-01

    The brusselator system subject to noise and an external signal is investigated in this work. The results show that both implicit coherence resonance and explicit coherence biresonance are exhibited in the absence of external signal. When an external signal is introduced into the system, explicit coherence biresonance is eliminated, whereas implicit coherence resonance is enhanced, and the enhanced implicit coherence resonance is attributed to the internal signal generated from noise-induced oscillations, not to the external signal. When an external signal and noise are added to the same control parameter, implicit coherence resonance is enhanced; when they are added to two control parameters separately, implicit coherence resonance is suppressed. Furthermore, above the critical noise intensity, the effect of the external signal on coherent behaviors is destroyed.

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

    PubMed Central

    Baker, Nathan A.; McCammon, J. Andrew

    2008-01-01

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

  13. Preparation of cerium halide solvate complexes

    DOEpatents

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

    2013-08-06

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

  14. Effects of explicit teacher-implemented phoneme awareness instruction in 4-year-olds.

    PubMed

    Tyler, Ann A; Osterhouse, Heather; Wickham, Katherine; Mcnutt, Robert; Shao, Yuanyuan

    2014-01-01

    The purpose of this study was to determine whether gains would be observed in an integrated group of 4-year-olds when phoneme awareness skills were explicitly taught by trained early childhood educators. In a quasi-experimental design with a delayed treatment approach, one classroom (N = 14) was randomly assigned to receive the instructional program in fall, while a second classroom (N = 10) served as a control and subsequently received the program in spring. Baseline assessment of speech and language skills indicated there were four participants with speech and/or language impairments. The teacher training involved an initial workshop and weekly hour-long mentoring meetings; the program was provided for 20 min a day, 4 d a week, for 10 weeks. Outcome measures of phoneme awareness and letter knowledge skills were obtained from non-standardized tasks administered pre-instruction and post-instruction, at mid-year and end-year points. When each classroom received the phoneme instruction, participants made gains in letter knowledge and phoneme level skills in comparison with group performance under regular instruction. These gains were statistically significant for phoneme blending and letter knowledge. Using an aggregate of all outcome measures, the gain for each classroom when under instruction was statistically significant as compared with when that same classroom was receiving the regular curriculum. Children with speech and/or language impairment responded more variably. Gains in the more difficult phoneme awareness skill of blending suggest the potential for marked change with an intensive, explicit classroom instruction and hold promise for SLPs collaborating with preschool teachers to provide time-efficient PA instruction.

  15. Effects of learning with explicit elaboration on implicit transfer of visuomotor sequence learning.

    PubMed

    Tanaka, Kanji; Watanabe, Katsumi

    2013-08-01

    Intervals between stimuli and/or responses have significant influences on sequential learning. In the present study, we investigated whether transfer would occur even when the intervals and the visual configurations in a sequence were drastically changed so that participants did not notice that the required sequences of responses were identical. In the experiment, two (or three) sequential button presses comprised a "set," and nine (or six) consecutive sets comprised a "hyperset." In the first session, participants learned either a 2 × 9 or 3 × 6 hyperset by trial and error until they completed it 20 times without error. In the second block, the 2 × 9 (3 × 6) hyperset was changed into the 3 × 6 (2 × 9) hyperset, resulting in different visual configurations and intervals between stimuli and responses. Participants were assigned into two groups: the Identical and Random groups. In the Identical group, the sequence (i.e., the buttons to be pressed) in the second block was identical to that in the first block. In the Random group, a new hyperset was learned. Even in the Identical group, no participants noticed that the sequences were identical. Nevertheless, a significant transfer of performance occurred. However, in the subsequent experiment that did not require explicit trial-and-error learning in the first session, implicit transfer in the second session did not occur. These results indicate that learning with explicit elaboration strengthens the implicit representation of the sequence order as a whole; this might occur independently of the intervals between elements and enable implicit transfer.

  16. Transition states and energetics of nucleophilic additions of thiols to substituted α,β-unsaturated ketones: substituent effects involve enone stabilization, product branching, and solvation.

    PubMed

    Krenske, Elizabeth H; Petter, Russell C; Zhu, Zhendong; Houk, K N

    2011-06-17

    CBS-QB3 enthalpies of reaction have been computed for the conjugate additions of MeSH to six α,β-unsaturated ketones. Compared with addition to methyl vinyl ketone, the reaction becomes 1-3 kcal mol(-1) less exothermic when an α-Me, β-Me, or β-Ph substituent is present on the C=C bond. The lower exothermicity for the substituted enones occurs because the substituted reactant is stabilized more by hyperconjugation or conjugation than the product is stabilized by branching. Substituent effects on the activation energies for the rate-determining step of the thiol addition (reaction of the enone with MeS(-)) were also computed. Loss of reactant stabilization, and not steric hindrance, is the main factor responsible for controlling the relative activation energies in the gas phase. The substituent effects are further magnified in solution; in water (simulated by CPCM calculations), the addition of MeS(-) to an enone is disfavored by 2-6 kcal mol(-1) when one or two methyl groups are present on the C=C bond (ΔΔG(‡)). The use of CBS-QB3 gas-phase energies in conjunction with CPCM solvation corrections provides kinetic data in good agreement with experimental substituent effects. When the energetics of the thiol additions were calculated with several popular density functional theory and ab initio methods (B3LYP, MPW1PW91, B1B95, PBE0, B2PLYP, and MP2), some substantial inaccuracies were noted. However, M06-2X (with a large basis set), B2PLYP-D, and SCS-MP2 gave results within 1 kcal mol(-1) of the CBS-QB3 benchmark values.

  17. The Effectiveness of Using an Explicit Language Learning Strategy-Based Instruction in Developing Secondary School Students' EFL Listening Comprehension Skills

    ERIC Educational Resources Information Center

    Amin, Iman Abdul-Reheem; Amin, Magdy Mohammad; Aly, Mahsoub Abdul-Sadeq

    2011-01-01

    The present study aimed at exploring the effectiveness of using explicit language learning strategy-based instruction in developing secondary school students' EFL listening comprehension skills. It was hypothesized that using explicit strategy-based instruction would develop students' EFL listening comprehension skill and its sub-skills. The…

  18. Computation of Atomic Solvent Accessible Surface Areas and Gradients for the Calculation of Solvation Energy and Forces on Molecules

    NASA Astrophysics Data System (ADS)

    Hummel, Michelle; Fennel, Christopher; Coutsias, Evangelos; Dill, Kenneth; Brini, Emiliano

    2014-03-01

    Many models for the calculation of solvation energy and forces on a molecule involve atomic solvent accessible surface areas and their gradients. We present analytical formulas for such areas and gradients which utilize the Delaunay tetrahedrization of a molecule and its subset called the α-complex. These formulas have been implemented in a fast computer program in conjunction with a solvation approach called Semi Explicit Assembly (SEA), and has shown to produce quick and physically accurate results.

  19. Combined effects of solvation and aggregation propensity on the final supramolecular structures adopted by hydrophobic, glycine-rich, elastin-like polypeptides.

    PubMed

    Salvi, Anna M; Moscarelli, Pasquale; Bochicchio, Brigida; Lanza, Giuseppe; Castle, James E

    2013-05-01

    Previous work on elastin-like polypeptides (ELPs) made of hydrophobic amino acids of the type XxxGlyGlyZzzGly (Xxx, Zzz = Val, Leu) has consistently shown that differing dominant supramolecular structures were formed when the suspending media were varied: helical, amyloid-like fibers when suspended in water and globules evolving into "string of bead" structures, poly(ValGlyGlyValGly), or cigar-like bundles, poly(ValGlyGlyLeuGly), when suspended in methyl alcohol. Comparative experiments with poly(LeuGlyGlyValGly) have further indicated that the interface energy plays a significant role and that solvation effects act in concomitance with the intrinsic aggregation propensity of the repeat sequence. Continuing our investigation on ELPs using surface (X-ray photoelectron spectroscopy, atomic force microscopy) and bulk (circular dichroism, Fourier transform infrared spectroscopy) techniques for their characterization, here we have compared the effect of suspending solvents (H(2)O, dimethylsulfoxide, ethylene glycol, and MeOH) on poly(ValGlyGlyValGly), the polypeptide most inclined to form long and well-refined helical fibers in water, searching for the signature of intermolecular interactions occurring between the polypeptide chains in the given suspension. The influence of sequence specificities has been studied by comparing poly(ValGlyGlyValGly) and poly(LeuGlyGlyValGly) with a similar degree of polymerization. Deposits on substrates of the polypeptides were characterized taking into account the differing evaporation rate of solvents, and tests on their stability in ultra high vacuum were performed. Finally, combining experimental and computational studies, we have revaluated the three-dimensional modeling previously proposed for the supramolecular assembly in water of poly(ValGlyGlyValGly). The results were discussed and rationalized also in the light of published data. PMID:23426573

  20. 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

  1. 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

  2. Effects of brief mindful acceptance induction on implicit dysfunctional attitudes and concordance between implicit and explicit dysfunctional attitudes.

    PubMed

    Keng, Shian-Ling; Seah, Stanley T H; Tong, Eddie M W; Smoski, Moria

    2016-08-01

    Mindfulness-based interventions have been shown to be effective in alleviating depressive symptoms. While much work has examined the effects of mindfulness training on subjective symptoms and experiences, and less is known regarding whether mindfulness training may alter relatively uncontrollable cognitive processes associated with depressed mood, particularly implicit dysfunctional attitudes. The present study examined the effects of a brief mindful acceptance induction on implicit dysfunctional attitudes and degree of concordance between implicit and explicit dysfunctional attitudes in the context of sad mood. A total of 79 adult participants with elevated depressive symptoms underwent an autobiographical mood induction procedure before being randomly assigned to mindful acceptance or thought wandering inductions. Results showed that the effect of mindful acceptance on implicit dysfunctional attitude was significantly moderated by trait mindfulness. Participants high on trait mindfulness demonstrated significant improvements in implicit dysfunctional attitudes following the mindful acceptance induction. Those low on trait mindfulness demonstrated significantly worse implicit dysfunctional attitudes following the induction. Significantly greater levels of concordance between implicit and explicit dysfunctional attitudes were observed in the mindful acceptance condition versus the thought wandering condition. The findings highlight changes in implicit dysfunctional attitudes and improvements in self-concordance as two potential mechanisms underlying the effects of mindfulness-based interventions.

  3. 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.

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

    PubMed

    Chaban, Vitaly V; Prezhdo, Oleg V

    2016-03-10

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

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

    PubMed

    Chaban, Vitaly V; Prezhdo, Oleg V

    2016-03-10

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  7. Theoretical study on the ground state intramolecular proton transfer (IPT) and solvation effect in two Schiff bases formed by 2-aminopyridine with 2-hydroxy-1- naphthaldehyde and 2-hydroxy salicylaldehyde.

    PubMed

    Tezer, N; Karakus, N

    2009-03-01

    The tautomerization mechanism the isolated and monohydrated forms of two Schiff bases 1 and 2, and the effect of solvation on the proton transfer from enol-imine form to the keto-enamine form have been investigated using the B3LYP hybrid density functional method at the 6-31G** basis set level. The barrier heights for H(2)O-assisted reactions are significantly lower than that of unassisted tautomerization reaction in the gas phase. Nonspecific solvent effects have also been taken into account by using the continuum model (IPCM) of four different solvent. The tautomerization energies and the potential energy barriers are decreased by increasing solvent polarity.

  8. Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data.

    PubMed

    Bottaro, Sandro; Lindorff-Larsen, Kresten; Best, Robert B

    2013-12-10

    The development of accurate implicit solvation models with low computational cost is essential for addressing many large-scale biophysical problems. Here, we present an efficient solvation term based on a Gaussian solvent-exclusion model (EEF1) for simulations of proteins in aqueous environment, with the primary aim of having a good overlap with explicit solvent simulations, particularly for unfolded and disordered states - as would be needed for multiscale applications. In order to achieve this, we have used a recently proposed coarse-graining procedure based on minimization of an entropy-related objective function to train the model to reproduce the equilibrium distribution obtained from explicit water simulations. Via this methodology, we have optimized both a charge screening parameter and a backbone torsion term against explicit solvent simulations of an α-helical and a β-stranded peptide. The performance of the resulting effective energy function, termed EEF1-SB, is tested with respect to the properties of folded proteins, the folding of small peptides or fast-folding proteins, and NMR data for intrinsically disordered proteins. The results show that EEF1-SB provides a reasonable description of a wide range of systems, but its key advantage over other methods tested is that it captures very well the structure and dimension of disordered or weakly structured peptides. EEF1-SB is thus a computationally inexpensive (~ 10 times faster than Generalized-Born methods) and transferable approximation for treating solvent effects. PMID:24748852

  9. Alphabetical knowledge from whole words training: effects of explicit instruction and implicit experience on learning script segmentation.

    PubMed

    Bitan, T; Karni, A

    2003-05-01

    We investigated the possibility that pattern segmentation skills, specifically, phonological decoding, evolve implicitly in adult readers given training in an artificial script. In this Morse-like script each phoneme was represented by 2-3 discrete symbols. Subjects were trained in five consecutive sessions, on reading six nonsense words using a forced choice task that required translating symbol strings to sound patterns written in Latin letters. Three training conditions were compared within subject in terms of the time-course of learning and the ability to generalize the acquired knowledge (transfer): alphabetical whole words with letter decoding instruction (Explicit); alphabetical whole words (Implicit), and non-alphabetical whole words (Arbitrary). In separate blocks in each training session, a visual-matching task was administered using the same stimuli. Our results show: (a). that while all three training conditions were equally effective in terms of magnitude and time-course of learning accurate translation, each training condition resulted in a different type of knowledge (i.e. differential transfer). (b). Declarative knowledge of letters evolved from training on whole words only in subjects with previous experience in Explicit training. However, even with declarative knowledge of the specific letters subjects did not develop general letter segmentation skills. (c). Contrary to the robust transfer of learning gains to different stimuli within a given task, there was no significant transfer across tasks indicating that the locus of learning was task dependent. Altogether our results suggest that even given explicit letter instruction, training on word decoding may result in letter recognition rather than in alphabetic segmentation skills. PMID:12706213

  10. Explicit formulas for 2nd-order driving terms due to sextupoles and chromatic effects of quadrupoles.

    SciTech Connect

    Wang, C-X. )

    2012-04-25

    Optimization of nonlinear driving terms have become a useful tool for designing storage rings, especially modern light sources where the strong nonlinearity is dominated by the large chromatic effects of quadrupoles and strong sextupoles for chromaticity control. The Lie algebraic method is well known for computing such driving terms. However, it appears that there was a lack of explicit formulas in the public domain for such computation, resulting in uncertainty and/or inconsistency in widely used codes. This note presents explicit formulas for driving terms due to sextupoles and chromatic effects of quadrupoles, which can be considered as thin elements. The computation is accurate to the 4th-order Hamiltonian and 2nd-order in terms of magnet parameters. The results given here are the same as the APS internal note AOP-TN-2009-020. This internal nte has been revised and published here as a Light Source Note in order to get this information into the public domain, since both ELEGANT and OPA are using these formulas.

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

    NASA Astrophysics Data System (ADS)

    Pertsin, Alexander J.; Grunze, Michael

    2003-05-01

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

  12. The effects of an ionic liquid on unimolecular substitution processes: the importance of the extent of transition state solvation.

    PubMed

    Keaveney, Sinead T; White, Benjamin P; Haines, Ronald S; Harper, Jason B

    2016-02-28

    The reaction of bromodiphenylmethane and 3-chloropyridine, which proceeds concurrently through both unimolecular and bimolecular mechanisms, was examined in mixtures of acetonitrile and an ionic liquid. As predicted, the bimolecular rate constant (k2) gradually increased as the amount of ionic liquid in the reaction mixture increased, as a result of a minor enthalpic cost offset by a more significant entropic benefit. Addition of an ionic liquid had a substantial effect on the unimolecular rate constant (k1) of the reaction, with at least a 5-fold rate enhancement relative to acetonitrile, which was found to be due to a significant decrease in the enthalpy of activation, partially offset by the associated decrease in the entropy of activation. This is in contrast to the effects seen previously for aliphatic carbocation formation, where the entropic cost dominated reaction outcome. This change is attributed to a lessened ionic liquid-transition state interaction, as the incipient charges in the transition state were delocalized across the neighbouring π systems. By varying the mole fraction of ionic liquid in the reaction mixture the ratio between k1 and k2 could be altered, highlighting the potential to use ionic liquids to control which pathway a reaction proceeds through.

  13. The effects of an ionic liquid on unimolecular substitution processes: the importance of the extent of transition state solvation.

    PubMed

    Keaveney, Sinead T; White, Benjamin P; Haines, Ronald S; Harper, Jason B

    2016-02-28

    The reaction of bromodiphenylmethane and 3-chloropyridine, which proceeds concurrently through both unimolecular and bimolecular mechanisms, was examined in mixtures of acetonitrile and an ionic liquid. As predicted, the bimolecular rate constant (k2) gradually increased as the amount of ionic liquid in the reaction mixture increased, as a result of a minor enthalpic cost offset by a more significant entropic benefit. Addition of an ionic liquid had a substantial effect on the unimolecular rate constant (k1) of the reaction, with at least a 5-fold rate enhancement relative to acetonitrile, which was found to be due to a significant decrease in the enthalpy of activation, partially offset by the associated decrease in the entropy of activation. This is in contrast to the effects seen previously for aliphatic carbocation formation, where the entropic cost dominated reaction outcome. This change is attributed to a lessened ionic liquid-transition state interaction, as the incipient charges in the transition state were delocalized across the neighbouring π systems. By varying the mole fraction of ionic liquid in the reaction mixture the ratio between k1 and k2 could be altered, highlighting the potential to use ionic liquids to control which pathway a reaction proceeds through. PMID:26842921

  14. Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex.

    PubMed

    Rungnim, Chompoonut; Phunpee, Sarunya; Kunaseth, Manaschai; Namuangruk, Supawadee; Rungsardthong, Kanin; Rungrotmongkol, Thanyada; Ruktanonchai, Uracha

    2015-01-01

    Cyclodextrins (CDs) have been extensively utilized as host molecules to enhance the solubility, stability and bioavailability of hydrophobic drug molecules through the formation of inclusion complexes. It was previously reported that the use of co-solvents in such studies may result in ternary (host:guest:co-solvent) complex formation. The objective of this work was to investigate the effect of ethanol as a co-solvent on the inclusion complex formation between α-mangostin (α-MGS) and β-CD, using both experimental and theoretical studies. Experimental phase-solubility studies were carried out in order to assess complex formation, with the mechanism of association being probed using a mathematical model. It was found that α-MGS was poorly soluble at low ethanol concentrations (0-10% v/v), but higher concentrations (10-40% v/v) resulted in better α-MGS solubility at all β-CD concentrations studied (0-10 mM). From the equilibrium constant calculation, the inclusion complex is still a binary complex (1:1), even in the presence of ethanol. The results from our theoretical study confirm that the binding mode is binary complex and the presence of ethanol as co-solvent enhances the solubility of α-MGS with some effects on the binding affinity with β-CD, depending on the concentration employed. PMID:26734079

  15. Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex

    PubMed Central

    Rungnim, Chompoonut; Phunpee, Sarunya; Kunaseth, Manaschai; Namuangruk, Supawadee; Rungsardthong, Kanin

    2015-01-01

    Summary Cyclodextrins (CDs) have been extensively utilized as host molecules to enhance the solubility, stability and bioavailability of hydrophobic drug molecules through the formation of inclusion complexes. It was previously reported that the use of co-solvents in such studies may result in ternary (host:guest:co-solvent) complex formation. The objective of this work was to investigate the effect of ethanol as a co-solvent on the inclusion complex formation between α-mangostin (α-MGS) and β-CD, using both experimental and theoretical studies. Experimental phase-solubility studies were carried out in order to assess complex formation, with the mechanism of association being probed using a mathematical model. It was found that α-MGS was poorly soluble at low ethanol concentrations (0–10% v/v), but higher concentrations (10–40% v/v) resulted in better α-MGS solubility at all β-CD concentrations studied (0–10 mM). From the equilibrium constant calculation, the inclusion complex is still a binary complex (1:1), even in the presence of ethanol. The results from our theoretical study confirm that the binding mode is binary complex and the presence of ethanol as co-solvent enhances the solubility of α-MGS with some effects on the binding affinity with β-CD, depending on the concentration employed. PMID:26734079

  16. Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex.

    PubMed

    Rungnim, Chompoonut; Phunpee, Sarunya; Kunaseth, Manaschai; Namuangruk, Supawadee; Rungsardthong, Kanin; Rungrotmongkol, Thanyada; Ruktanonchai, Uracha

    2015-01-01

    Cyclodextrins (CDs) have been extensively utilized as host molecules to enhance the solubility, stability and bioavailability of hydrophobic drug molecules through the formation of inclusion complexes. It was previously reported that the use of co-solvents in such studies may result in ternary (host:guest:co-solvent) complex formation. The objective of this work was to investigate the effect of ethanol as a co-solvent on the inclusion complex formation between α-mangostin (α-MGS) and β-CD, using both experimental and theoretical studies. Experimental phase-solubility studies were carried out in order to assess complex formation, with the mechanism of association being probed using a mathematical model. It was found that α-MGS was poorly soluble at low ethanol concentrations (0-10% v/v), but higher concentrations (10-40% v/v) resulted in better α-MGS solubility at all β-CD concentrations studied (0-10 mM). From the equilibrium constant calculation, the inclusion complex is still a binary complex (1:1), even in the presence of ethanol. The results from our theoretical study confirm that the binding mode is binary complex and the presence of ethanol as co-solvent enhances the solubility of α-MGS with some effects on the binding affinity with β-CD, depending on the concentration employed.

  17. The generalizability of gender bias: Testing the effects of contextual, explicit, and implicit sexism on labor arbitration decisions.

    PubMed

    Girvan, Erik J; Deason, Grace; Borgida, Eugene

    2015-10-01

    Decades of social-psychological research show that gender bias can result from features of the social context and from individual-level psychological predispositions. Do these sources of bias impact legal decisions, which are frequently made by people subject to factors that have been proposed to reduce bias (training and accountability)? To answer the question, we examined the potential for 3 major social-psychological theories of gender bias (role-congruity theory, ambivalent sexism, and implicit bias) to predict outcomes of labor arbitration decisions. In the first study, undergraduate students and professional arbitrators made decisions about 2 mock arbitration cases in which the gender of the employee-grievants was experimentally manipulated. Student participants' decisions showed the predicted gender bias, whereas the decisions of experienced professionals did not. Individual-level attitudes did not predict the extent of the observed bias and accountability did not attenuate it. In the second study, arbitrators' explicit and implicit gender attitudes were significant predictors of their decisions in published cases. The laboratory and field results suggest that context, expertise, and implicit and explicit attitudes are relevant to legal decision-making, but that laboratory experiments alone may not fully capture the nature of their effect on legal professionals' decisions in real cases.

  18. Effects of supported electronic text and explicit instruction on science comprehension by students with autism spectrum disorder

    NASA Astrophysics Data System (ADS)

    Knight, Victoria Floyd

    Supported electronic text (eText), or text that has been altered to increase access and provide support to learners, may promote comprehension of science content for students with disabilities. According to CAST, Book Builder(TM) uses supported eText to promote reading for meaning for all students. Although little research has been conducted in the area of supported eText for students with autism spectrum disorders (ASD), technology (e.g., computer assisted instruction) has been used for over 35 years to instruct students with ASD in academic areas. The purpose of this study was to evaluate the effects of a supported eText and explicit instruction on the science vocabulary and comprehension of four middle school students with ASD. Researchers used a multiple probe across participants design to evaluate the Book Builder (TM) program on measures of vocabulary, literal comprehension, and application questions. Results indicated a functional relation between the Book Builder(TM) and explicit instruction (i.e., model-lead-test, examples and non-examples, and referral to the definition) and the number of correct responses on the probe. In addition, students were able to generalize concepts to untrained exemplars. Finally, teachers and students validate the program as practical and useful.

  19. Effect of the explicit flexibility of the InhA enzyme from Mycobacterium tuberculosis in molecular docking simulations

    PubMed Central

    2011-01-01

    Background Protein/receptor explicit flexibility has recently become an important feature of molecular docking simulations. Taking the flexibility into account brings the docking simulation closer to the receptors’ real behaviour in its natural environment. Several approaches have been developed to address this problem. Among them, modelling the full flexibility as an ensemble of snapshots derived from a molecular dynamics simulation (MD) of the receptor has proved very promising. Despite its potential, however, only a few studies have employed this method to probe its effect in molecular docking simulations. We hereby use ensembles of snapshots obtained from three different MD simulations of the InhA enzyme from M. tuberculosis (Mtb), the wild-type (InhA_wt), InhA_I16T, and InhA_I21V mutants to model their explicit flexibility, and to systematically explore their effect in docking simulations with three different InhA inhibitors, namely, ethionamide (ETH), triclosan (TCL), and pentacyano(isoniazid)ferrate(II) (PIF). Results The use of fully-flexible receptor (FFR) models of InhA_wt, InhA_I16T, and InhA_I21V mutants in docking simulation with the inhibitors ETH, TCL, and PIF revealed significant differences in the way they interact as compared to the rigid, InhA crystal structure (PDB ID: 1ENY). In the latter, only up to five receptor residues interact with the three different ligands. Conversely, in the FFR models this number grows up to an astonishing 80 different residues. The comparison between the rigid crystal structure and the FFR models showed that the inclusion of explicit flexibility, despite the limitations of the FFR models employed in this study, accounts in a substantial manner to the induced fit expected when a protein/receptor and ligand approach each other to interact in the most favourable manner. Conclusions Protein/receptor explicit flexibility, or FFR models, represented as an ensemble of MD simulation snapshots, can lead to a more realistic

  20. Picosecond dynamics of benzophenone anion solvation

    SciTech Connect

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

    1993-01-14

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

  1. Explicit Input Enhancement: Effects on Target and Non-Target Aspects of Second Language Acquisition

    ERIC Educational Resources Information Center

    Gascoigne, Carolyn

    2006-01-01

    Many recent studies have examined the effectiveness of various types of input enhancement. The following study expands this line of inquiry to include technological applications of language learning by comparing the effectiveness of the computer application of diacritics to a traditional pen-and-paper process among beginning students of French and…

  2. Applications of Optical Spectroscopy in Studies on Energy & Electron Transfer and Solvation Effects in Nanoscale and Molecular Systems

    NASA Astrophysics Data System (ADS)

    Oh, Megan H. J.

    This thesis describes three investigations, ranging in subject matters, all of which relating to systems capable of photoinduced reactions involving energy or electron transfer. The phenomenon and the effects of environment in the various systems are explored using different methodologies of optical spectroscopy. As the chapters progress, different investigations introduce and build on fundamental concepts encountered and in complexity of the methodologies used to explore the systems. The first chapter introduces the preparation of water-soluble CdSe nanocrystal clusters. The clusters, created using a protein, are 3-D close-packed self-assemblies of nanocrystals. Due to this close-packed nature, electronic interactions between the nanocrystals allow for energy migration within the cluster. The structural and optical properties of the clusters were described. Then using steady-state spectroscopy, properties of the original nanocrystals were compared to that of the cluster to determine the consequence of nanocrystal coupling interactions and their potential use toward the development of artificial light-harvesting systems. In the second chapter, CdSe nanocrystals are functionalized with a unique electro-active polymer, and the electron transfer between the nanocrystal and the electro-active polymer adsorbate is investigated. Using fluorescence decay measurements, the electron transfer reaction inherent to the system with respect to a comprehensive range of dielectric solvents was explored. The study illustrates the high complexity of seemingly typical nanocrystal-based systems and provides general awareness of what factors need to be considered when dealing with such systems. The final chapter starts with an informal review of ultrafast nonlinear spectroscopy, focusing on two methods, three-pulse photon echo peak shift (3PEPS) and two-dimensional photon echo (2DPE) electronic spectroscopy, and how they are related. A straightforward approach for extracting 3PEPS data

  3. Effects of explicit knowledge and predictability on auditory distraction and target performance.

    PubMed

    Max, Caroline; Widmann, Andreas; Schröger, Erich; Sussman, Elyse

    2015-11-01

    This study tested effects of task requirements and knowledge on auditory distraction effects. This was done by comparing the response to a pitch change (an irrelevant, distracting tone feature) that occurred predictably in a tone sequence (every 5th tone) under different task conditions. The same regular sound sequence was presented with task conditions varying in what information the participant was given about the predictability of the pitch change, and when this information was relevant for the task to be performed. In all conditions, participants performed a tone duration judgment task. Behavioral and event-related brain potential (ERP) measures were obtained to measure distraction effects and deviance detection. Predictable deviants produced behavioral distraction effects in all conditions. However, the P3a amplitude evoked by the predictable pitch change was largest when participants were uninformed about the regular structure of the sound sequence, showing an effect of knowledge on involuntary orienting of attention. In contrast, the mismatch negativity (MMN) component was only modulated when the regularity was relevant for the task and not by stimulus predictability itself. P3a and behavioral indices of distraction were not fully concordant. Overall, our results show differential effects of knowledge and predictability on auditory distraction effects indexed by neurophysiological (P3a) and behavioral measures.

  4. Maleic acid solvation in mixed water-ethanol solvents

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  5. Spin crossover and solvate effects in 1D Fe{sup II} chain compounds containig Bis(dipyridylamine)-linked triazine ligands.

    SciTech Connect

    Ross, , T. M.; Moubaraki, B.; Turner, D. R.; Halder, G. J.; Chastanet, G.; Neville, S. M.; Cashion, J. D.; Letard, J. F.; Batten, S. R.; Murray, K. S.

    2011-03-01

    A series of 1D polymeric FeII spin crossover (SCO) compounds of type trans-[FeII(NCX)2(L)] Solvent has been synthesised {l_brace}L = DPPyT = 1-[4,6-bis(dipyridin-2-ylamino)-1,3,5-triazin-2-yl]pyridin-4(1H)-one for 1-4{r_brace}; NCX = NCS- for 1 and 2, NCSe- for 3 and 4; Solvent = 2.5CH2Cl2 for 1, 2CHCl3 {center_dot} 0.5CH3OH for 2 and 4, CH2Cl2 for 3; L = DPT (6-phenoxy-N2,N2,N4,N4-tetra-2-pyridinyl-1,3,5-triazine-2,4-diamine) for 5; NCX = NCS- for 5; Solvent = 2CH3OH {center_dot} H2O for 5; L = DQT {l_brace}4-[4,6-bis(dipyridin-2-ylamino)-1,3,5-triazin-2-yloxy]phenol{r_brace} for 6-8; NCX- = NCS- for 6; Solvent = 2CH2Cl2 for 6; NCX- = NCSe- for 7; Solvent = CH2Cl2 {center_dot} CH2ClCH2Cl for 7; NCX- = NCSe- for 8; Solvent = 1.5CH2Cl2 {center_dot} 0.5CH3OH for 8. Two mononuclear complexes, trans-[FeII(NCS)2(DPT)2] {center_dot} 2CH3OH (9) and trans-[FeII(NCSe)2(DPT)2] {center_dot} 2CH3OH (10), contained the L ligand in a terminal bidentate coordination mode. As well as variations made in the NCX- ligands, variations were also made in substituent groups on the s-triazine 'core' of L to investigate their intermolecular/supramolecular role in crystal packing and, thus, their influence on SCO properties. All the complexes crystallised as solvates, and the influence of the latter on the magnetism and spin transitions was explored. A wide range of physical methods was employed, as a function of temperature, viz. crystallography, PXRD (synchrotron), susceptibilities, LIESST and Moessbauer effect, in order to probe magnetostructural correlations in these 1D families. New examples of half-crossovers, with ordered -LS-HS-LS-HS- intrachain states existing below T1/2, have been observed and comparisons made to related one- or two-step systems. All the observed transitions are gradual and non-hysteretic, and brief comments are made in relation to recent theoretical models for cooperativity, developed elsewhere.

  6. Updated Abraham solvation parameters for polychlorinated biphenyls.

    PubMed

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

    2010-09-15

    This study shows that the recently published polychlorinated biphenyl (PCB) Abraham solvation parameters predict PCB air-n-hexadecane and n-octanol-water partition coefficients very poorly, especially for highly ortho-chlorinated congeners. Therefore, an updated set of PCB solvation parameters was derived from four PCB properties and associated Abraham solvation equations. Additionally, the influence of ortho-chlorination on PCB solvent accessible volume and surface area was investigated. The updated PCB solvation parameters were tested on partitioning between five other phase combinations. Compared to the original PCB solvation parameter set, the updated PCB solvation parameters resulted in substantially improved estimates from Abraham solvation equations for (subcooled) liquid vapor pressures, aqueous solubilities, HPLC capacity factors, and for coefficients of air-n-hexadecane, air-water, organic carbon-water, and n-octanol-water partitioning. For water to polydimethyl siloxane and sodium dodecylsulphate (SDS) partitioning, the updated PCB solvation parameters yielded no improvement compared to the original data set. The main difference between the updated and the original parameter set is that updated PCB McGowan specific volumes depend on the degree of ortho-chlorination, which is qualitatively confirmed by trends in the PCB solvent accessible volumes and surface areas. The use of the updated PCB solvation parameters instead of the original values is therefore recommended.

  7. Solvates of Dasatinib: Diversity and Isostructurality.

    PubMed

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

    2016-04-01

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

  8. The Effects of Explicit Instruction on the Writing Ability of a Student with Noonan Syndrome

    ERIC Educational Resources Information Center

    Asaro-Saddler, Kristie; Saddler, Bruce; Ellis-Robinson, Tammy

    2014-01-01

    In this study, we sought to determine the effectiveness of a sentence creation intervention on the sentence writing ability of a young writer with Noonan Syndrome. Noonan syndrome is an autosomal dominant condition characterized by shortness in stature, with neck and ear anomalies, hypertelorism, ptosis of the eyelids, low set ears, and instances…

  9. The Role of Exposure Condition in the Effectiveness of Explicit Correction

    ERIC Educational Resources Information Center

    Yilmaz, Yucel

    2016-01-01

    This article reports on a study that investigated the effects of two feedback exposure conditions on the acquisition of two Turkish morphemes. The study followed a randomized experimental design with an immediate and a delayed posttest. Forty-two Chinese-speaking learners of Turkish were randomly assigned to one of three groups: receivers,…

  10. The Effects of Explicit Word Recognition Training on Japanese EFL Learners

    ERIC Educational Resources Information Center

    Burrows, Lance; Holsworth, Michael

    2016-01-01

    This study is a quantitative, quasi-experimental investigation focusing on the effects of word recognition training on word recognition fluency, reading speed, and reading comprehension for 151 Japanese university students at a lower-intermediate reading proficiency level. Four treatment groups were given training in orthographic, phonological,…

  11. Effects of sleep loss, time of day, and extended mental work on implicit and explicit learning of sequences

    NASA Technical Reports Server (NTRS)

    Heuer, H.; Spijkers, W.; Kiesswetter, E.; Schmidtke, V.

    1998-01-01

    Tacit knowledge is part of many professional skills and can be studied experimentally with implicit-learning paradigms. The authors explored the effects of 2 different stressors, loss of sleep and mental fatigue, on implicit learning in a serial-response time (RT) task. In the 1st experiment, 1 night of sleep deprivation was shown to impair implicit but not explicit sequence learning. In the 2nd experiment, no impairment of both types of sequence learning was found after 1.5 hr of mental work. Serial-RT performance, in contrast, suffered from both stressors. These findings suggest that sleep deprivation induces specific risks for automatic, skill-based behavior that are not present in consciously controlled performance.

  12. A unifying modeling of plant shoot gravitropism with an explicit account of the effects of growth

    PubMed Central

    Bastien, Renaud; Douady, Stéphane; Moulia, Bruno

    2014-01-01

    Gravitropism, the slow reorientation of plant growth in response to gravity, is a major determinant of the form and posture of land plants. Recently a universal model of shoot gravitropism, the AC model, was presented, in which the dynamics of the tropic movement is only determined by the conflicting controls of (1) graviception that tends to curve the plants toward the vertical, and (2) proprioception that tends to keep the stem straight. This model was found to be valid for many species and over two orders of magnitude of organ size. However, the motor of the movement, the elongation, was purposely neglected in the AC model. If growth effects are to be taken into account, it is necessary to consider the material derivative, i.e., the rate of change of curvature bound to expanding and convected organ elements. Here we show that it is possible to rewrite the material equation of curvature in a compact simplified form that directly expresses the curvature variation as a function of the median elongation and of the distribution of the differential growth. By using this extended model, called the ACĖ model, growth is found to have two main destabilizing effects on the tropic movement: (1) passive orientation drift, which occurs when a curved element elongates without differential growth, and (2) fixed curvature, when an element leaves the elongation zone and is no longer able to actively change its curvature. By comparing the AC and ACĖ models to experiments, these two effects are found to be negligible. Our results show that the simplified AC mode can be used to analyze gravitropism and posture control in actively elongating plant organs without significant information loss. PMID:24782876

  13. The emergence of the rescue effect from explicit within- and between-patch dynamics in a metapopulation

    PubMed Central

    Eriksson, Anders; Elías-Wolff, Federico; Mehlig, Bernhard; Manica, Andrea

    2014-01-01

    Immigration can rescue local populations from extinction, helping to stabilize a metapopulation. Local population dynamics is important for determining the strength of this rescue effect, but the mechanistic link between local demographic parameters and the rescue effect at the metapopulation level has received very little attention by modellers. We develop an analytical framework that allows us to describe the emergence of the rescue effect from interacting local stochastic dynamics. We show this framework to be applicable to a wide range of spatial scales, providing a powerful and convenient alternative to individual-based models for making predictions concerning the fate of metapopulations. We show that the rescue effect plays an important role in minimizing the increase in local extinction probability associated with high demographic stochasticity, but its role is more limited in the case of high local environmental stochasticity of recruitment or survival. While most models postulate the rescue effect, our framework provides an explicit mechanistic link between local dynamics and the emergence of the rescue effect, and more generally the stability of the whole metapopulation. PMID:24523274

  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. Differential geometry based solvation model II: Lagrangian formulation.

    PubMed

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

    2011-12-01

    computation, thanks to the equivalence of the Laplace-Beltrami operator in the two representations. The coupled partial differential equations (PDEs) are solved with an iterative procedure to reach a steady state, which delivers desired solvent-solute interface and electrostatic potential for problems of interest. These quantities are utilized to evaluate the solvation free energies and protein-protein binding affinities. A number of computational methods and algorithms are described for the interconversion of Lagrangian and Eulerian representations, and for the solution of the coupled PDE system. The proposed approaches have been extensively validated. We also verify that the mean curvature flow indeed gives rise to the minimal molecular surface and the proposed variational procedure indeed offers minimal total free energy. Solvation analysis and applications are considered for a set of 17 small compounds and a set of 23 proteins. The salt effect on protein-protein binding affinity is investigated with two protein complexes by using the present model. Numerical results are compared to the experimental measurements and to those obtained by using other theoretical methods in the literature.

  16. Differential geometry based solvation model II: Lagrangian formulation

    PubMed Central

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

    2010-01-01

    the purpose of computation, thanks to the equivalence of the Laplace-Beltrami operator in the two representations. The coupled partial differential equations (PDEs) are solved with an iterative procedure to reach a steady state, which delivers desired solvent-solute interface and electrostatic potential for problems of interest. These quantities are utilized to evaluate the solvation free energies and protein-protein binding affinities. A number of computational methods and algorithms are described for the interconversion of Lagrangian and Eulerian representations, and for the solution of the coupled PDE system. The proposed approaches have been extensively validated. We also verify that the mean curvature flow indeed gives rise to the minimal molecular surface (MMS) and the proposed variational procedure indeed offers minimal total free energy. Solvation analysis and applications are considered for a set of 17 small compounds and a set of 23 proteins. The salt effect on protein-protein binding affinity is investigated with two protein complexes by using the present model. Numerical results are compared to the experimental measurements and to those obtained by using other theoretical methods in the literature. PMID:21279359

  17. Explicit Nature of Science and Argumentation Instruction in the Context of Socioscientific Issues: An Effect on Student Learning and Transfer

    ERIC Educational Resources Information Center

    Khishfe, Rola

    2014-01-01

    The purpose of the study was two-fold: to (a) investigate the influence of explicit nature of science (NOS) and explicit argumentation instruction in the context of a socioscientific issue on the argumentation skills and NOS understandings of students, and (b) explore the transfer of students' NOS understandings and argumentation skills…

  18. Graphophonological processes in dyslexic readers of French: a longitudinal study of the explicitness effect of tasks.

    PubMed

    Daigle, Daniel; Berthiaume, Rachel; Plisson, Anne; Demont, Elisabeth

    2012-07-01

    Given the well-acknowledged phonological deficit found in dyslexic children, this study was aimed at investigating graphophonological processes in dyslexic readers of French over a 1-year period. Among the different types of phonological processing can be distinguished those related to phonological awareness based on knowledge of the oral language and graphophonological processes based on correspondences between the oral and the written language. In this study, we evaluated graphophonemic and graphosyllabic processes using, in each case, two different tasks varying in the degree of cognitive constraint associated with the task (CC- vs CC+). Twenty 11 year-old dyslexic students were compared with younger normal-readers of the same reading level (RA, n=26) and to normal-readers of the same age (CA, n=24). Two variables were considered in the analyses: accuracy and response latency. Results show that dyslexic readers do process written items at the graphophonological level. Also, results indicate main effects of task (CC- vs CC+), time (T1 vs T2), and group (DYS vs RA vs CA). In general, dyslexic participants' performances are comparable to those of RA and differ from those of CA. PMID:22441904

  19. Compton scattering from the proton in an effective field theory with explicit Delta degrees of freedom

    NASA Astrophysics Data System (ADS)

    McGovern, J. A.; Phillips, D. R.; Grießhammer, H. W.

    2013-01-01

    We analyse the proton Compton-scattering differential cross section for photon energies up to 325 MeV using Chiral Effective Field Theory (χEFT) and extract new values for the electric and magnetic polarisabilities of the proton. Our approach builds in the key physics in two different regimes: photon energies ω ≲ m π ("low energy"), and the higher energies where the Δ(1232) resonance plays a key role. The Compton amplitude is complete at N4LO, {O}( {e^2 δ ^4 } ), in the low-energy region, and at NLO, {O}( {e^2 δ ^0 } ), in the resonance region. Throughout, the Delta-pole graphs are dressed with π N loops and γN Δ vertex corrections. A statistically consistent database of proton Compton experiments is used to constrain the free parameters in our amplitude: the M1 γN Δ transition strength b 1 (which is fixed in the resonance region) and the polarisabilities α E1 and β M1 (which are fixed from data below 170 MeV). In order to obtain a reasonable fit, we find it necessary to add the spin polarisability γ M1 M1 as a free parameter, even though it is, strictly speaking, predicted in χEFT at the order to which we work. We show that the fit is consistent with the Baldin sum rule, and then use that sum rule to constrain α E1 + β M1. In this way we obtain α E1 = [10.65 ± 0.35(stat) ± 0.2(Baldin) ± 0.3(theory)] × 10-4 fm3 and β M1 = [3.15 ∓ 0.35(state) ± 0.2(Baldin) ∓ 0.3()theory] × 10-4 fm3, with χ2 = 113.2 for 135 degrees of freedom. A detailed rationale for the theoretical uncertainties assigned to this result is provided.

  20. 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

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

    PubMed

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

    2016-09-13

    The optical spectra of 5-methylcytidine in three different solvents (tetrahydrofuran, acetonitrile, and water) is measured, showing that both the absorption and the emission maximum in water are significantly blue-shifted (0.08 eV). The absorption spectra are simulated based on CAM-B3LYP/TD-DFT calculations but including solvent effects with three different approaches: (i) a hybrid implicit/explicit full quantum mechanical approach, (ii) a mixed QM/MM static approach, and (iii) a QM/MM method exploiting the structures issuing from molecular dynamics classical simulations. Ab-initio Molecular dynamics simulations based on CAM-B3LYP functionals have also been performed. The adopted approaches all reproduce the main features of the experimental spectra, giving insights on the chemical-physical effects responsible for the solvent shifts in the spectra of 5-methylcytidine and providing the basis for discussing advantages and limitations of the adopted solvation models. PMID:27529792

  2. Variational approach for nonpolar solvation analysis.

    PubMed

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

    2012-08-28

    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

  3. Studies of ion solvation using pulse radiolysis

    SciTech Connect

    Jonah, C.D.; Lin, Yi.

    1991-01-01

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

  4. Peptide adsorption on a hydrophobic surface results from an interplay of solvation, surface, and intrapeptide forces.

    PubMed

    Horinek, D; Serr, A; Geisler, M; Pirzer, T; Slotta, U; Lud, S Q; Garrido, J A; Scheibel, T; Hugel, T; Netz, R R

    2008-02-26

    The hydrophobic effect, i.e., the poor solvation of nonpolar parts of molecules, plays a key role in protein folding and more generally for molecular self-assembly and aggregation in aqueous media. The perturbation of the water structure accounts for many aspects of protein hydrophobicity. However, to what extent the dispersion interaction between molecular entities themselves contributes has remained unclear. This is so because in peptide folding interactions and structural changes occur on all length scales and make disentangling various contributions impossible. We address this issue both experimentally and theoretically by looking at the force necessary to peel a mildly hydrophobic single peptide molecule from a flat hydrophobic diamond surface in the presence of water. This setup avoids problems caused by bubble adsorption, cavitation, and slow equilibration that complicate the much-studied geometry with two macroscopic surfaces. Using atomic-force spectroscopy, we determine the mean desorption force of a single spider-silk peptide chain as F = 58 +/- 8 pN, which corresponds to a desorption free energy of approximately 5 k(B)T per amino acid. Our all-atomistic molecular dynamics simulation including explicit water correspondingly yields the desorption force F = 54 +/- 15 pN. This observation demonstrates that standard nonpolarizable force fields used in classical simulations are capable of resolving the fine details of the hydrophobic attraction of peptides. The analysis of the involved energetics shows that water-structure effects and dispersive interactions give contributions of comparable magnitude that largely cancel out. It follows that the correct modeling of peptide hydrophobicity must take the intimate coupling of solvation and dispersive effects into account.

  5. Selective nonspecific solvation under dielectric saturation and fluorescence spectra of dye solutions in binary solvents.

    PubMed

    Bakhshiev, N G; Kiselev, M B

    1991-09-01

    The influence of selective nonspecific solvation on the fluorescence spectra of three substitutedN-methylphthalimides in a binary solvent system consisting of a nonpolar (n-heptane) and a polar (pyridine) component has been studied under conditions close to dielectric saturation. The substantially nonlinearity of the effect is confirmation that the spectral shifts of fluorescence bands depend on the number of polar solvent molecules involved in solvating the dye molecule. The measured fluorescence spectral shifts determined by substituting one nonpolar solvent molecula with a polar one in the proximity of the dye molecule agree quantitatively with the forecasts of the previously proposed semiempirical theory which describes this nonlinear solvation phenomenon.

  6. Computational protein design is a challenge for implicit solvation models.

    PubMed

    Jaramillo, Alfonso; Wodak, Shoshana J

    2005-01-01

    Increasingly complex schemes for representing solvent effects in an implicit fashion are being used in computational analyses of biological macromolecules. These schemes speed up the calculations by orders of magnitude and are assumed to compromise little on essential features of the solvation phenomenon. In this work we examine this assumption. Five implicit solvation models, a surface area-based empirical model, two models that approximate the generalized Born treatment and a finite difference Poisson-Boltzmann method are challenged in situations differing from those where these models were calibrated. These situations are encountered in automatic protein design procedures, whose job is to select sequences, which stabilize a given protein 3D structure, from a large number of alternatives. To this end we evaluate the energetic cost of burying amino acids in thousands of environments with different solvent exposures belonging, respectively, to decoys built with random sequences and to native protein crystal structures. In addition we perform actual sequence design calculations. Except for the crudest surface area-based procedure, all the tested models tend to favor the burial of polar amino acids in the protein interior over nonpolar ones, a behavior that leads to poor performance in protein design calculations. We show, on the other hand, that three of the examined models are nonetheless capable of discriminating between the native fold and many nonnative alternatives, a test commonly used to validate force fields. It is concluded that protein design is a particularly challenging test for implicit solvation models because it requires accurate estimates of the solvation contribution of individual residues. This contrasts with native recognition, which depends less on solvation and more on other nonbonded contributions.

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

    PubMed

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

    2015-02-10

    Modeling of macromolecular structures and interactions represents an important challenge for computational biology, involving different time and length scales. However, this task can be facilitated through the use of coarse-grained (CG) models, which reduce the number of degrees of freedom and allow efficient exploration of complex conformational spaces. This article presents a new CG protein model named SIRAH, developed to work with explicit solvent and to capture sequence, temperature, and ionic strength effects in a topologically unbiased manner. SIRAH is implemented in GROMACS, and interactions are calculated using a standard pairwise Hamiltonian for classical molecular dynamics simulations. We present a set of simulations that test the capability of SIRAH to produce a qualitatively correct solvation on different amino acids, hydrophilic/hydrophobic interactions, and long-range electrostatic recognition leading to spontaneous association of unstructured peptides and stable structures of single polypeptides and protein-protein complexes. PMID:26575407

  8. Segue between Favorable and Unfavorable Solvation

    SciTech Connect

    Maibaum, Lutz; Chandler, David

    2007-03-21

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

  9. Adolescents' use of sexually explicit Internet material and their sexual attitudes and behavior: Parallel development and directional effects.

    PubMed

    Doornwaard, Suzan M; Bickham, David S; Rich, Michael; ter Bogt, Tom F M; van den Eijnden, Regina J J M

    2015-10-01

    Although research has repeatedly demonstrated that adolescents' use of sexually explicit Internet material (SEIM) is related to their endorsement of permissive sexual attitudes and their experience with sexual behavior, it is not clear how linkages between these constructs unfold over time. This study combined 2 types of longitudinal modeling, mean-level development and cross-lagged panel modeling, to examine (a) developmental patterns in adolescents' SEIM use, permissive sexual attitudes, and experience with sexual behavior, as well as whether these developments are related; and (b) longitudinal directionality of associations between SEIM use on the 1 hand and permissive sexual attitudes and sexual behavior on the other hand. We used 4-wave longitudinal data from 1,132 7th through 10th grade Dutch adolescents (M(age) T1 = 13.95; 52.7% boys) and estimated multigroup models to test for moderation by gender. Mean-level developmental trajectories showed that boys occasionally and increasingly used SEIM over the 18-month study period, which co-occurred with increases in their permissive attitudes and their experience with sexual behavior. Cross-lagged panel models revealed unidirectional effects from boys' SEIM use on their subsequent endorsement of permissive attitudes, but no consistent directional effects between their SEIM use and sexual behavior. Girls showed a similar pattern of increases in experience with sexual behavior, but their SEIM use was consistently low and their endorsement of permissive sexual attitudes decreased over the 18-month study period. In contrast to boys, girls' SEIM use was not longitudinally related to their sexual attitudes and behavior. Theoretical and practical implications of these gender-specific findings are discussed. (PsycINFO Database Record PMID:26376287

  10. Adolescents' use of sexually explicit Internet material and their sexual attitudes and behavior: Parallel development and directional effects.

    PubMed

    Doornwaard, Suzan M; Bickham, David S; Rich, Michael; ter Bogt, Tom F M; van den Eijnden, Regina J J M

    2015-10-01

    Although research has repeatedly demonstrated that adolescents' use of sexually explicit Internet material (SEIM) is related to their endorsement of permissive sexual attitudes and their experience with sexual behavior, it is not clear how linkages between these constructs unfold over time. This study combined 2 types of longitudinal modeling, mean-level development and cross-lagged panel modeling, to examine (a) developmental patterns in adolescents' SEIM use, permissive sexual attitudes, and experience with sexual behavior, as well as whether these developments are related; and (b) longitudinal directionality of associations between SEIM use on the 1 hand and permissive sexual attitudes and sexual behavior on the other hand. We used 4-wave longitudinal data from 1,132 7th through 10th grade Dutch adolescents (M(age) T1 = 13.95; 52.7% boys) and estimated multigroup models to test for moderation by gender. Mean-level developmental trajectories showed that boys occasionally and increasingly used SEIM over the 18-month study period, which co-occurred with increases in their permissive attitudes and their experience with sexual behavior. Cross-lagged panel models revealed unidirectional effects from boys' SEIM use on their subsequent endorsement of permissive attitudes, but no consistent directional effects between their SEIM use and sexual behavior. Girls showed a similar pattern of increases in experience with sexual behavior, but their SEIM use was consistently low and their endorsement of permissive sexual attitudes decreased over the 18-month study period. In contrast to boys, girls' SEIM use was not longitudinally related to their sexual attitudes and behavior. Theoretical and practical implications of these gender-specific findings are discussed. (PsycINFO Database Record

  11. Losing on all fronts: the effects of negative versus positive person-based campaigns on implicit and explicit evaluations of political candidates.

    PubMed

    Carraro, Luciana; Gawronski, Bertram; Castelli, Luigi

    2010-09-01

    The current research investigated the effects of negative as compared to positive person-based political campaigns on explicit and implicit evaluations of the involved candidates. Participants were presented with two political candidates and statements that one of them ostensibly said during the last political campaign. For half of the participants, the campaign included positive remarks about the source of the statement (positive campaign); for the remaining half, the campaign included negative remarks about the opponent (negative campaign). Afterwards, participants completed measures of explicit and implicit evaluations of both candidates. Results indicate that explicit evaluations of the source, but not the opponent, were less favourable after negative as compared to positive campaigns. In contrast, implicit evaluations were less favourable for both candidates after negative campaigns. The results are discussed in terms of associative and propositional processes, highlighting the importance of associative processes in political decision making.

  12. Explicit Compact Surface-Potential and Drain-Current Models for Generic Asymmetric Double-Gate Metal-Oxide-Semiconductor Field-Effect Transistors

    NASA Astrophysics Data System (ADS)

    Zhu, Zhaomin; Zhou, Xing; Chandrasekaran, Karthik; Rustagi, Subhash C.; See, Guan Huei

    2007-04-01

    In this paper, explicit surface potentials for undoped asymmetric-double-gate (a-DG) metal-oxide-semiconductor field-effect transistors (MOSFETs) suitable for compact model development are presented for the first time. The model is physically derived from Poisson’s equation in each region of operation and adopted in a unified regional approach. The proposed model is physically scalable with oxide/channel thicknesses and has been verified with generic implicit solutions for independent gate biases as well as for different gate/oxide materials. The model is extendable to silicon-on-insulator (SOI) and symmetric-DG (s-DG) MOSFETs. Finally, a continuous, explicit drain-current equation has been derived on the basis of the developed explicit surface-potential solutions.

  13. Task engagement and escape maintained challenging behavior: differential effects of general and explicit cues when implementing a signaled delay in the delivery of reinforcement.

    PubMed

    Reichle, Joe; Johnson, LeAnne; Monn, Emily; Harris, Michael

    2010-06-01

    This study was designed to evaluate the effects of explicit and general delay cues when implementing a tolerance for a delay in the delivery of a reinforcement procedure to increase task engagement and decrease escape maintained challenging behavior. Two preschool children with autism participated in an alternating treatments design with changing criterions for task engagement. For both children, descriptive and experimental analyses verified that the challenging behavior functioned to escape instructional task demands. Subsequently, two types of tasks were identified for each participant with assignment to either the explicit or general cue procedures. Both participants demonstrated increased task engagement with concurrent decreases in challenging behavior with both types of delay cues, though rate of successful work unit completion advanced more quickly with explicit delay cues.

  14. 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.

  15. The Effect of Using an Explicit General Problem Solving Teaching Approach on Elementary Pre-Service Teachers' Ability to Solve Heat Transfer Problems

    ERIC Educational Resources Information Center

    Mataka, Lloyd M.; Cobern, William W.; Grunert, Megan L.; Mutambuki, Jacinta; Akom, George

    2014-01-01

    This study investigate the effectiveness of adding an "explicit general problem solving teaching strategy" (EGPS) to guided inquiry (GI) on pre-service elementary school teachers' ability to solve heat transfer problems. The pre-service elementary teachers in this study were enrolled in two sections of a chemistry course for…

  16. The Effectiveness of Explicit Individualized Phonemic Awareness Instruction by a Speech-Language Pathologist to Preschool Children with Phonological Speech Disorders

    ERIC Educational Resources Information Center

    Nullman, Susan L.

    2009-01-01

    This study investigated the effects of an explicit individualized phonemic awareness intervention administered by a speech-language pathologist to 4 prekindergarten children with phonological speech sound disorders. Research has demonstrated that children with moderate-severe expressive phonological disorders are at-risk for poor literacy…

  17. Task Engagement and Escape Maintained Challenging Behavior: Differential Effects of General and Explicit Cues when Implementing a Signaled Delay in the Delivery of Reinforcement

    ERIC Educational Resources Information Center

    Reichle, Joe; Johnson, LeAnne; Monn, Emily; Harris, Michael

    2010-01-01

    This study was designed to evaluate the effects of explicit and general delay cues when implementing a tolerance for a delay in the delivery of a reinforcement procedure to increase task engagement and decrease escape maintained challenging behavior. Two preschool children with autism participated in an alternating treatments design with changing…

  18. Effects of Explicit Reading Strategies Instruction and Peer Tutoring on Second and Fifth Graders' Reading Comprehension and Self-Efficacy Perceptions

    ERIC Educational Resources Information Center

    Van Keer, Hilde; Verhaeghe, Jean Pierre

    2005-01-01

    The authors evaluated the effectiveness of explicit reading comprehension strategies instruction, followed by practice in teacher-led whole-class activities (STRAT), reciprocal same-age (STRAT + SA) peer-tutoring activities, or cross-age peer-tutoring activities (STRAT + CA) on 2nd and 5th graders' reading comprehension and self-efficacy…

  19. The Effect of Explicit and Direct Generative Strategy Training and Working Memory on Word Problem-Solving Accuracy in Children at Risk for Math Difficulties

    ERIC Educational Resources Information Center

    Swanson, H. Lee; Moran, Amber; Lussier, Cathy; Fung, Wenson

    2014-01-01

    The purpose of this study was to investigate the effectiveness of explicit, direct, and generative strategy training and working memory capacity (WMC) on mathematical word problem-solving accuracy in elementary schoolchildren. In this study, children in third grade ("N" = 82) identified as at risk for math difficulties (MD) were randomly…

  20. Preferential Solvation in Binary and Ternary Mixtures.

    PubMed

    Pallewela, Gayani N; Smith, Paul E

    2015-12-24

    Preferential solvation has become a useful tool to help characterize and understand the properties of liquid mixtures. Here, we provide a new quantitative measure of preferential solvation in binary and ternary mixtures that uses Kirkwood-Buff integrals as input, but differs from traditional measures. The advantages of the new measure are highlighted and compared with established literature approaches. Molecular dynamics simulations are performed to further investigate the nature of binary mixtures, as described by the new and existing measures of preferential solvation. It is shown that the new measure of preferential solvation is rigorous, has a simple physical interpretation, can be easily related to the underlying thermodynamic properties of the mixture, and naturally leads to zero values for ideal mixtures.

  1. Prevention of Intraoperative Awareness with Explicit Recall in an Unselected Surgical Population: A Randomized Comparative Effectiveness Trial

    PubMed Central

    Mashour, George A.; Shanks, Amy; Tremper, Kevin K.; Kheterpal, Sachin; Turner, Christopher R.; Ramachandran, Satya Krishna; Picton, Paul; Schueller, Christa; Morris, Michelle; Vandervest, John C.; Lin, Nan; Avidan, Michael S.

    2012-01-01

    Background Intraoperative awareness with explicit recall occurs in approximately 0.15% of all surgical cases. Efficacy trials based on the Bispectral Index™ (BIS) monitor and anesthetic concentrations have focused on high-risk patients, but there are no effectiveness data applicable to an unselected surgical population. Methods We conducted a randomized controlled trial of unselected surgical patients at three hospitals of a tertiary academic medical center. Surgical cases were randomized to alerting algorithms based on either BIS values or anesthetic concentrations. The primary outcome was the incidence of definite intraoperative awareness; prespecified secondary outcomes included postanesthetic recovery variables. Results The study was terminated due to futility. At interim analysis the incidence of definite awareness was 0.12% (11/9376) (95% CI 0.07 to 0.21%) in the anesthetic concentration group and 0.08% (8/9460) (95% CI 0.04 to 0.16%) in the BIS group (p = 0.48). There was no significant difference between the two groups in terms of meeting criteria for recovery room discharge or incidence of nausea and vomiting. By post hoc secondary analysis, the BIS protocol was associated with a 4.7-fold reduction in definite or possible awareness events compared to a cohort receiving no intervention (p = 0.001; 95% CI 1.7 to 13.1). Conclusion This negative trial could not detect a difference in the incidence of definite awareness or recovery variables between monitoring protocols based on either BIS values or anesthetic concentration. By post hoc analysis, a protocol based on BIS monitoring reduced the incidence of definite or possible intraoperative awareness compared to routine care. PMID:22990178

  2. The Effect of Explicit-Reflective and Historical Approach on Preservice Elementary Teachers' Views of Nature of Science

    ERIC Educational Resources Information Center

    Pekbay, Canay; Yilmaz, Serkan

    2015-01-01

    This study aims to explore the influence of nature of science (NOS) activities based on explicit-reflective and historical approach on preservice elementary teachers' views of NOS aspects. Mixed-method approach including both qualitative and quantitative methods was used. The sample consisted of 83 preservice elementary teachers of a public…

  3. Relative Effects of Explicit and Implicit Feedback: The Role of Working Memory Capacity and Language Analytic Ability

    ERIC Educational Resources Information Center

    Yilmaz, Yucel

    2013-01-01

    The purpose of this study is to investigate the role of two cognitive factors (i.e. working memory capacity [WMC] and language analytic ability [LAA]) in the extent to which L2 learners benefit from two different types of feedback (i.e. explicit correction and recasts). Forty-eight adult native speakers of English, who had no previous exposure to…

  4. Effect of explicit representation of detailed stratigraphy on brine and gas flow at the Waste Isolation Pilot Plant

    SciTech Connect

    Christian-Frear, T.L.; Webb, S.W.

    1996-04-01

    Stratigraphic units of the Salado Formation at the Waste Isolation Pilot Plant (WIPP) disposal room horizon includes various layers of halite, polyhalitic halite, argillaceous halite, clay, and anhydrite. Current models, including those used in the WIPP Performance Assessment calculations, employ a ``composite stratigraphy`` approach in modeling. This study was initiated to evaluate the impact that an explicit representation of detailed stratigraphy around the repository may have on fluid flow compared to the simplified ``composite stratigraphy`` models currently employed. Sensitivity of model results to intrinsic permeability anisotropy, interbed fracturing, two-phase characteristic curves, and gas-generation rates were studied. The results of this study indicate that explicit representation of the stratigraphy maintains higher pressures and does not allow as much fluid to leave the disposal room as compared to the ``composite stratigraphy`` approach. However, the differences are relatively small. Gas migration distances are also different between the two approaches. However, for the two cases in which explicit layering results were considerably different than the composite model (anisotropic and vapor-limited), the gas-migration distances for both models were negligible. For the cases in which gas migration distances were considerable, van Genuchten/Parker and interbed fracture, the differences between the two models were fairly insignificant. Overall, this study suggests that explicit representation of the stratigraphy in the WIPP PA models is not required for the parameter variations modeled if ``global quantities`` (e.g., disposal room pressures, net brine and gas flux into and out of disposal rooms) are the only concern.

  5. Teaching Pragmatic Awareness of Spoken Requests to Chinese EAP Learners in the UK: Is Explicit Instruction Effective?

    ERIC Educational Resources Information Center

    Halenko, Nicola; Jones, Christian

    2011-01-01

    The aim of this study is to evaluate the impact of explicit interventional treatment on developing pragmatic awareness and production of spoken requests in an EAP context (taken here to mean those studying/using English for academic purposes in the UK) with Chinese learners of English at a British higher education institution. The study employed…

  6. Adolescents' Use of Sexually Explicit Internet Material and Their Sexual Attitudes and Behavior: Parallel Development and Directional Effects

    ERIC Educational Resources Information Center

    Doornwaard, Suzan M.; Bickham, David S.; Rich, Michael; ter Bogt, Tom F. M.; van den Eijnden, Regina J. J. M.

    2015-01-01

    Although research has repeatedly demonstrated that adolescents' use of sexually explicit Internet material (SEIM) is related to their endorsement of permissive sexual attitudes and their experience with sexual behavior, it is not clear how linkages between these constructs unfold over time. This study combined 2 types of longitudinal modeling,…

  7. Effects of Learning Strategies and Motivation on Implicit vs. Explicit Instructional Approaches for Spanish L2 Vocabulary

    ERIC Educational Resources Information Center

    Hervas, David

    2010-01-01

    Under the premise that vocabulary learning in a Spanish as a second language in-class environment may be affected by the instructional approach adopted by the instructors or the materials followed, this study explores the influence of rather distant teaching styles, such as implicit and explicit approaches, on the learning outcome of Spanish…

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

    PubMed

    Cabot, Rafel; Hunter, Christopher A

    2010-04-21

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

  9. The relation between the structure of the first solvation shell and the IR spectra of aqueous solutions.

    PubMed

    Kumar, Revati; Keyes, Tom

    2012-01-01

    The spectroscopic signatures of solvated anions and cations, in the O-H stretch region of water, are studied using the POLIR potential. Shifts in the spectra are shown to correlate very well with the distribution of a particular hydrogen bond angle for the waters in the first solvation shell. The results indicate that the spectral shifts might be predicted from MD simulations in a computationally convenient fashion, avoiding an explicit calculation of the spectra, as first suggested by Sharp et al. (J Chem Phys 114(4):1791-1796, 2001). PMID:23277671

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

    PubMed

    Sedlmeier, Felix; Netz, Roland R

    2013-03-21

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

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

    SciTech Connect

    Sedlmeier, Felix; Netz, Roland R.

    2013-03-21

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

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

    NASA Astrophysics Data System (ADS)

    Sedlmeier, Felix; Netz, Roland R.

    2013-03-01

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

  13. Effects of compatibility of polymer binders with solvate ionic liquid electrolytes on discharge and charge reactions of lithium-sulfur batteries

    NASA Astrophysics Data System (ADS)

    Nakazawa, Toshitada; Ikoma, Ai; Kido, Ryosuke; Ueno, Kazuhide; Dokko, Kaoru; Watanabe, Masayoshi

    2016-03-01

    Electrochemical reactions in Li-S cells with a solvate ionic liquid (SIL) electrolyte composed of tetraglyme (G4) and Li[TFSA] (TFSA: bis(trifluoromethanesulfonyl)amide) are studied. The sulfur cathode (S cathode) comprises sulfur, carbon powder, and a polymer binder. Poly(ethylene oxide) (PEO) and poly(vinyl alcohol) (PVA-x) with different degrees of saponification (x%) are used as binders to prepare the composite cathodes. For the Li-S cell containing PEO binder, lithium polysulfides (Li2Sm, 2 ≤ m ≤ 8), reaction intermediates of the S cathode, dissolve into the electrolyte, and Li2Sm acts as a redox shuttle in the Li-S cell. In contrast, in the Li-S cell with PVA-x binder, the dissolution of Li2Sm is suppressed, leading to high columbic efficiencies during charge-discharge cycles. The compatibility of the PVA-x binder with the SIL electrolyte changes depending on the degree of saponification. Decreasing the degree of saponification leads to increased electrolyte uptake by the PVA-x binder, increasing the charge and discharge capacities of Li-S cell. The rate capability of Li-S cell is also enhanced by the partial swelling of the PVA-x binder. The enhanced performance of Li-S cell containing PVA-x is attributed to the lowering of resistance of Li+ ion transport in the composite cathode.

  14. Solvatochromism and the solvation structure of benzophenone

    NASA Astrophysics Data System (ADS)

    Elenewski, Justin E.; C Hackett, John

    2013-06-01

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

  15. 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).

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

    PubMed

    Jeschke, Steffen; Wiemhöfer, Hans-Dieter

    2016-03-15

    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 C=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 C=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)). PMID:26774812

  17. The tempting effect of forbidden foods. High calorie content evokes conflicting implicit and explicit evaluations in restrained eaters.

    PubMed

    Hoefling, Atilla; Strack, Fritz

    2008-11-01

    In this study, restrained and unrestrained eaters' immediate evaluations of high calorie content and low calorie content were measured, both when being deprived of food and when satiated. As an indirect measure, the Extrinsic Affective Simon Task (EAST) [De Houwer, J. (2003). The Extrinsic Affective Simon Task. Experimental Psychology, 50, 77-85.] was used. Explicit attitudes towards high calorie content and low calorie content were also assessed. Food deprivation was found to boost the value of food for all subjects on an impulsive level of information processing. More importantly, it was also found that restrained eaters exhibit a dissociative pattern of positive implicit and negative explicit attitudes towards high calorie content, but not towards low calorie content. Furthermore, restrained eaters evaluated high calorie content more negative than unrestrained eaters on an explicit level, but more positive on an implicit level. Results from this study are twofold. First, they suggest that conflicting evaluative reactions from two systems of information processing may play a central role in the restrained eater's dilemma. Second, individual differences between restrained and unrestrained eaters' attitudes towards high calorie content should further be investigated.

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

    SciTech Connect

    Wishart,J.F.

    2008-09-29

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

  19. 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

  20. Perceived Effects of Sexually Explicit Media among Men who have Sex with Men and Psychometric Properties of the Pornography Consumption Effects Scale (PCES)

    PubMed Central

    Hald, Gert Martin; Smolenski, Derek; Simon Rosser, B. R.

    2012-01-01

    Introduction Researchers have proposed that consumption of Sexually Explicit Media (SEM) may not only adversely influence sexual attitudes and behaviors of Men Who Have Sex with Men (MSM) but (also) play a positive role in the development and sexual education of MSM, be a major source of sexual information for MSM, and provide validation, understanding, and confirmation of MSM’s sexual orientation. However, such claims are in urgent need of empirical validation as is the development of psychometrically sound and easily implemented instruments able to reliably assist such validations. Aim To investigate how MSM who consume SEM self-perceive the impact of SEM on their STI-related sexual risk behaviors (i.e. anal intercourse), sexual knowledge, enjoyment of sex, interest in sex, attitudes toward sex, and understanding of their sexual orientation. Further, to provide a thorough psychometric validation of a reduced and reworked version of the Pornography Consumption Effect Scale. Main Outcomes Measures A revised version of the Pornography Consumption Effect Scale (PCES) by Hald and Malamuth (2008). Results This study found that 97% of MSM reported positive effects of SEM consumption on their sexual knowledge, enjoyment of and interest in sex, attitudes toward sex, and understanding of their sexual orientation. Only 3 % reported any negative effects of their SEM consumption. SEM consumption was found to significantly increase consumers’ interest in having protected anal intercourse while not significantly influencing their interests in having unprotected anal intercourse. The revised version of the PCES showed excellent psychometric performance. Conclusion The study found that MSM generally report positive effects of their consumption of sexually explicit materials in areas related to their sexual knowledge, attitudes, behaviors, and orientation. This finding could have important implications for the sexual health and well-being of MSM by suggesting that SEM

  1. Nonequilibrium solvation for vertical photoemission and photoabsorption processes using the symmetry-adapted cluster-configuration interaction method in the polarizable continuum model

    NASA Astrophysics Data System (ADS)

    Fukuda, Ryoichi; Ehara, Masahiro; Nakatsuji, Hiroshi; Cammi, Roberto

    2011-03-01

    In this paper, we present the theory and implementation of a nonequilibrium solvation model for the symmetry-adapted cluster (SAC) and symmetry-adapted cluster-configuration interaction (SAC-CI) method in the polarizable continuum model. For nonequilibrium solvation, we adopted the Pekar partition scheme in which solvent charges are divided into dynamical and inertial components. With this nonequilibrium solvation scheme, a vertical transition from an initial state to a final state may be described as follows: the initial state is described by equilibrium solvation, while in the final state, the inertial component remains in the solvation for the initial state; the dynamical component will be calculated self-consistently for the final state. The present method was applied to the vertical photoemission and absorption of s-trans acrolein and methylenecyclopropene. The effect of nonequilibrium solvation was significant for a polar solvent.

  2. Computational studies on intermolecular interactions in solvation

    NASA Astrophysics Data System (ADS)

    Song, Weiping

    This thesis presents the results of computational studies of intermolecular interactions in various contexts. We first investigated the relation between solute-solvent intermolecular interactions and local density augmentation in supercritical solvation. The phenomenon of interest is the excess density that exists in the neighborhood of an attractive solute in a supercritical solvent in the vicinity of the critical point. In Chapter 2, we examined the ability of various measures of the strength of solute-solvent interactions, calculated from all-atom potential functions, to correlate the extent of local density augmentation in both experimental and model solvents. The Gibbs Ensemble Monte Carlo (GEMC) method enables us to calculate phase equilibrium in pure substances and mixtures. It provides a convenient way to test and develop model potentials. In Chapter 3 we present some methodological aspects of such calculations, the issues related to approach to critical points and finite-size effects and applications to simple fluids. Chapter 4 then describes a simplified 2-site potential model for simulating supercritical fluoroform. The GEMC method was used to simulate the vapor-liquid coexistence curve of the model fluid and the dynamic properties were studied by performing NVT molecular dynamics (MD) simulations. The results show that despite its simplicity, this model is able to reproduce many important properties of supercritical fluoroform, making it useful in molecular simulations of supercritical solvation. In the above two studies, the intermolecular interactions are described by a sum of pair-wise additive Lennard-Jones + Coulomb terms. The standard Lorentz-Berthelot combining rules (geometric mean rule for well depth and arithmetic mean rule for collision diameter) are commonly applied to account for the unlike pair Lennard-Jones parameters. In Chapter 5, we examined the applicability of the combining rules for modeling alkane-perfluoroalkane interactions. It

  3. Water-enhanced solvation of organics

    SciTech Connect

    Lee, J.H.

    1993-07-01

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

  4. The effectiveness of a highly explicit, teacher-directed strategy instruction routine: changing the writing performance of students with learning disabilities.

    PubMed

    Troia, Gary A; Graham, Steve

    2002-01-01

    This study examined the effectiveness of a highly explicit, teacher-directed instructional routine used to teach three planning strategies for writing to fourth and fifth graders with learning disabilities. In comparison to peers who received process writing instruction, children who were taught the three planning strategies-goal setting, brainstorming, and organizing-spent more time planning stories in advance of writing and produced stories that were qualitatively better. One month after the end of instruction, students who had been taught the strategies not only maintained their advantage in story quality but also produced longer stories than those produced by their peers who were taught process writing. However, the highly explicit, teacher-directed strategy instructional routine used in this study did not promote transfer to an uninstructed genre, persuasive essay writing. These findings are discussed in terms of their relevance to effective writing instruction practices for students with learning disabilities.

  5. Hyperbolic heat conduction problems involving non-Fourier effects - Numerical simulations via explicit Lax-Wendroff/Taylor-Galerkin finite element formulations

    NASA Technical Reports Server (NTRS)

    Tamma, Kumar K.; Namburu, Raju R.

    1989-01-01

    Numerical simulations are presented for hyperbolic heat-conduction problems that involve non-Fourier effects, using explicit, Lax-Wendroff/Taylor-Galerkin FEM formulations as the principal computational tool. Also employed are smoothing techniques which stabilize the numerical noise and accurately predict the propagating thermal disturbances. The accurate capture of propagating thermal disturbances at characteristic time-step values is achieved; numerical test cases are presented which validate the proposed hyperbolic heat-conduction problem concepts.

  6. 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

  7. 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

  8. Implicit and Explicit Instruction of Spelling Rules

    ERIC Educational Resources Information Center

    Kemper, M. J.; Verhoeven, L.; Bosman, A. M. T.

    2012-01-01

    The study aimed to compare the differential effectiveness of explicit and implicit instruction of two Dutch spelling rules. Students with and without spelling disabilities were instructed a spelling rule either implicitly or explicitly in two experiments. Effects were tested in a pretest-intervention-posttest control group design. Experiment 1…

  9. On the performance of continuum solvation methods. A comment on "Universal approaches to solvation modeling".

    PubMed

    Klamt, Andreas; Mennucci, Benedetta; Tomasi, Jacopo; Barone, Vincenzo; Curutchet, Carles; Orozco, Modesto; Luque, F Javier

    2009-04-21

    In a recent Account, Cramer and Truhlar presented a comparison between the SM8 method and standard versions of other continuum solvation models implemented in widely available quantum mechanical programs. In that Account, the SM8 model was found to lead to "considerably smaller errors for aqueous and nonaqueous free energies of solvation for neutrals, cations, and anions, with particularly good performance for nonaqueous data". Here, we demonstrate that competing solvation methods are indeed as accurate as the SM8 method, if they are applied with the same rigor.

  10. 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.

  11. 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.

  12. Close relationships and the working self-concept: implicit and explicit effects of priming attachment on agency and communion.

    PubMed

    Bartz, Jennifer A; Lydon, John E

    2004-11-01

    Two studies investigated how contextually activating attachment relationships influences the working self-concept in terms of agency and communion. In Study 1, 245 participants were primed with a secure, avoidant, or anxious-ambivalent relationship and the implicit accessibility of agency and communion was assessed using word fragments. Activating a secure relationship increased the accessibility of communion, whereas activating an anxious-ambivalent relationship increased the accessibility of agency. In Study 2, 123 participants were primed with a secure, preoccupied, avoidant-dismissive, or avoidant-fearful relationship and explicit self-perceptions of agency and communion traits were assessed using the Extended Personality Attributes Questionnaire (EPAQ). Gender interacted with the attachment prime, such that men primed with a secure relationship reported higher communion than did men primed with an avoidant (dismissive or fearful) relationship, whereas women primed with an anxious (preoccupied or fearful) relationship reported higher agency than did women primed with a secure relationship.

  13. Solvation dynamics and energetics of intramolecular hydride transfer reactions in biomass conversion.

    PubMed

    Mushrif, Samir H; Varghese, Jithin J; Krishnamurthy, Chethana B

    2015-02-21

    Hydride transfer changes the charge structure of the reactant and thus, may induce reorientation/reorganization of solvent molecules. This solvent reorganization may in turn alter the energetics of the reaction. In the present work, we investigate the intramolecular hydride transfer by taking Lewis acid catalyzed glucose to fructose isomerization as an example. The C2-C1 hydride transfer is the rate limiting step in this reaction. Water and methanol are used as solvents and hydride transfer is simulated in the presence of explicit solvent molecules, treated quantum mechanically and at a finite temperature, using Car-Parrinello molecular dynamics (CPMD) and metadynamics. Activation free energy barrier for hydride transfer in methanol is found to be 50 kJ mol(-1) higher than that in water. In contrast, in density functional theory calculations, using an implicit solvent environment, the barriers are almost identical. Analysis of solvent dynamics and electronic polarization along the molecular dynamics trajectory and the results of CPMD-metadynamics simulation of the hydride transfer process in the absence of any solvent suggest that higher barrier in methanol is a result of non-equilibrium solvation. Methanol undergoes electronic polarization during the hydride transfer step. However, its molecular orientational relaxation is a much slower process that takes place after the hydride transfer, over an extended timescale. This results in non-equilibrium solvation. Water, on the other hand, does not undergo significant electronic polarization and thus, has to undergo minimal molecular reorientation to provide near equilibrium solvation to the transition state and an improved equilibrium solvation to the post hydride shift product state. Hence, the hydride transfer step is also observed to be exergonic in water and endergonic in methanol. The aforementioned explanation is juxtaposed to enzyme catalyzed charge transfer reactions, where the enhanced solvation of the

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

    PubMed

    Sedov, I A; Magsumov, T I

    2015-07-16

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

  15. 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.)

  16. 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

  17. 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.

  18. Effects of gambling-related cues on the activation of implicit and explicit gambling outcome expectancies in regular gamblers.

    PubMed

    Stewart, Melissa J; Yi, Sunghwan; Stewart, Sherry H

    2014-09-01

    The current research examined whether the presentation of gambling-related cues facilitates the activation of gambling outcome expectancies using both reaction time (RT) and self-report modes of assessment. Gambling outcome expectancies were assessed by having regular casino or online gamblers (N = 58) complete an outcome expectancy RT task, as well as a self-report measure of gambling outcome expectancies, both before and after exposure to one of two randomly assigned cue conditions (i.e., casino or control video). Consistent with hypotheses, participants exposed to gambling-related cues (i.e., casino cue video condition) responded faster to positive outcome expectancy words preceded by gambling prime relative to non-gambling prime pictures on the post-cue RT task. Similarly, participants in the casino cue video condition self-reported significantly stronger positive gambling outcome expectancies than those in the control cue video condition following cue exposure. Activation of negative gambling outcome expectancies was not observed on either the RT task or self-report measure. The results indicate that exposure to gambling cues activates both implicit and explicit positive gambling outcome expectancies among regular gamblers.

  19. The effects of gay sexually explicit media on the HIV risk behavior of men who have sex with men.

    PubMed

    Rosser, B R Simon; Smolenski, Derek J; Erickson, Darin; Iantaffi, Alex; Brady, Sonya S; Grey, Jeremy A; Hald, Gert Martin; Horvath, Keith J; Kilian, Gunna; Træen, Bente; Wilkerson, J Michael

    2013-05-01

    This study sought to study consumption patterns of gay-oriented sexually explicit media (SEM) by men who have sex with men (MSM); and to investigate a hypothesized relationship between gay SEM consumption and HIV risk behavior. Participants were 1,391 MSM living in the US, recruited online to complete a SEM consumption and sexual risk survey. Almost all (98.5 %) reported some gay SEM exposure over the last 90 days. While 41 % reported a preference to watch actors perform anal sex without condoms (termed "bareback SEM"), 17 % preferred to actors perform anal sex with condoms (termed "safer sex SEM") and 42 % reported no preference. Overall SEM consumption was not associated with HIV risk; however participants who watched more bareback SEM reported significantly greater odds of engaging in risk behavior. The results suggest that a preference for bareback SEM is associated with engaging in risk behavior. More research to understand how MSM develop and maintain preferences in viewing SEM, and to identify new ways to use SEM in HIV prevention, is recommended. PMID:23564010

  20. Individual-Based Spatially-Explicit Model of an Herbivore and Its Resource: The Effect of Habitat Reduction and Fragmentation

    SciTech Connect

    Kostova, T; Carlsen, T; Kercher, J

    2002-06-17

    We present an individual-based, spatially-explicit model of the dynamics of a small mammal and its resource. The life histories of each individual animal are modeled separately. The individuals can have the status of residents or wanderers and belong to behaviorally differing groups of juveniles or adults and males or females. Their territory defending and monogamous behavior is taken into consideration. The resource, green vegetation, grows depending on seasonal climatic characteristics and is diminished due to the herbivore's grazing. Other specifics such as a varying personal energetic level due to feeding and starvation of the individuals, mating preferences, avoidance of competitors, dispersal of juveniles, as a result of site overgrazing, etc. are included in the model. We determined model parameters from real data for the species Microtus ochrogaster (prairie vole). The simulations are done for a case of an enclosed habitat without predators or other species competitors. The goal of the study is to find the relation between size of habitat and population persistence. The experiments with the model show the populations go extinct due to severe overgrazing, but that the length of population persistence depends on the area of the habitat as well as on the presence of fragmentation. Additionally, the total population size of the vole population obtained during the simulations exhibits yearly fluctuations as well as multi-yearly peaks of fluctuations. This dynamics is similar to the one observed in prairie vole field studies.

  1. The Effects of Gay Sexually Explicit Media on the HIV Risk Behavior of Men who have Sex with Men

    PubMed Central

    Simon Rosser, B. R.; Smolenski, Derek J.; Erickson, Darin; Iantaffi, Alex; Brady, Sonya S.; Galos, Dylan L.; Grey, Jeremy A.; Hald, Gert Martin; Horvath, Keith J.; Kilian, Gunna; Træen, Bente; Wilkerson, J. Michael

    2013-01-01

    This study sought to study consumption patterns of gay-oriented sexually explicit media (SEM) by men who have sex with men (MSM); and to investigate a hypothesized relationship between gay SEM consumption and HIV risk behavior. Participants were 1391 MSM living in the US, recruited online to complete a SEM consumption and sexual risk survey. Almost all (98.5%) reported some gay SEM exposure over the last 90 days. While 41% reported a preference to watch actors perform anal sex without condoms (termed “bareback SEM”), 17% preferred to actors perform anal sex with condoms (termed “safer sex SEM”) and 42% reported no preference. Overall SEM consumption was not associated with HIV risk; however participants who watched more bareback SEM reported significantly greater odds of engaging in risk behavior. The results suggest that a preference for bareback SEM is associated with engaging in risk behavior. More research to understand how MSM develop and maintain preferences in viewing SEM, and to identify new ways to use SEM in HIV prevention, is recommended. PMID:23564010

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  3. Solvation of the fluorine containing anions and their lithium salts in propylene carbonate and dimethoxyethane.

    PubMed

    Chaban, Vitaly

    2015-07-01

    Electrolyte solutions based on the propylene carbonate (PC)-dimethoxyethane (DME) mixtures are of significant importance and urgency due to emergence of lithium-ion batteries. Solvation and coordination of the lithium cation in these systems have been recently attended in detail. However, analogous information concerning anions (tetrafluoroborate, hexafluorophosphate) is still missed. This work reports PM7-MD simulations (electronic-structure level of description) to include finite-temperature effects on the anion solvation regularities in the PC-DME mixture. The reported result evidences that the anions appear weakly solvated. This observation is linked to the absence of suitable coordination sites in the solvent molecules. In the concentrated electrolyte solutions, both BF4(-) and PF6(-) prefer to exist as neutral ion pairs (LiBF4, LiPF6). PMID:26067106

  4. Free energies of solvation for peptides and polypeptides using SCRF methods

    NASA Astrophysics Data System (ADS)

    Alemán, Carlos; Ishiki, Hamilton Mitsugu; Armelin, Elaine A.; Abrahão Junior, Odonírio; Galembeck, Sergio E.

    1998-07-01

    The effects of the aqueous solvent in the conformational preferences of peptides and homopeptides have been investigated using two different and widely used self-consistent reaction-field models. The free energies of solvation were predicted using the polarizable continuum model developed by Tomasi and co-workers and adapted to semi-empirical hamiltonians by Orozco and Luque, and the solvation model developed by Cramer and Truhlar. The set of compounds investigated is constituted by five dipeptides with different chemical nature and structural properties as well as by two homopeptides in which the size of the polypeptidic chain was varied. Results provided by the different methods are compared and discussed.

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

    PubMed

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

    2014-08-21

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

  6. 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

  7. Parameter optimization in differential geometry based solvation models.

    PubMed

    Wang, Bao; Wei, G W

    2015-10-01

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

  8. Effects of explicit and implicit prompts on students' inquiry practices in computer-supported learning environments in high school earth science

    NASA Astrophysics Data System (ADS)

    Fang, Su-Chi; Hsu, Ying-Shao; Hsu, Wei Hsiu

    2016-07-01

    The study explored how to best use scaffolds for supporting students' inquiry practices in computer-supported learning environments. We designed a series of inquiry units assisted with three versions of written inquiry prompts (generic and context-specific); that is, three scaffold-fading conditions: implicit, explicit, and fading. We then examined how the three scaffold-fading conditions influenced students' conceptual understanding, understanding of scientific inquiry, and inquiry abilities. Three grade-10 classes (N = 105) participated in this study; they were randomly assigned to and taught in the three conditions. Data-collection procedures included a pretest-posttest approach and in-depth observations of the target students. The findings showed that after these inquiry units, all of the students exhibited significant learning gains in conceptual knowledge and performed better inquiry abilities regardless of which condition was used. The explicit and fading conditions were more effective in enhancing students' understanding of scientific inquiry. The fading condition tended to better support the students' development of inquiry abilities and help transfer these abilities to a new setting involving an independent socioscientific task about where to build a dam. The results suggest that fading plays an essential role in enhancing the effectiveness of scaffolds.

  9. Explicit Fourier wavefield operators

    NASA Astrophysics Data System (ADS)

    Ferguson, R. J.; Margrave, G. F.

    2006-04-01

    Explicit wavefield extrapolators are based on direct analytic mathematical formulae that express the output as an extrapolation operator acting on the input, while implicit methods usually require the calculation of the numerical inverse of a matrix to obtain the output. Typically, explicit methods are faster than implicit methods, and they often give more insight into the physics of the wave propagation, but they often suffer from instability. Four different explicit extrapolators based on Fourier theory are presented and analysed. They are: PS (ordinary phase shift), GPSPI (generalized phase shift plus interpolation), NSPS (non-stationary phase shift) and SNPS (symmetric non-stationary phase shift). A formal proof is given that NSPS in a direction orthogonal to the velocity gradient is the mathematical adjoint process to GPSPI in the opposite direction. This motivates the construction of SNPS that combines NSPS and GPSPI in a symmetric fashion. This symmetry (under interchange of input and output lateral coordinates) is required by reciprocity arguments. PS and SNPS are symmetric while NSPS and GPSPI are not. A numerical stability study using SVD (singular value decomposition) shows that all of these extrapolators can become unstable for strong lateral velocity gradients. Unstable operators allow amplitudes to grow non-physically in a recursion. Stability is enhanced by introducing a small (~3 per cent) imaginary component to the velocities. This causes a numerical attenuation that tends to stabilize the operators but does not address the cause of the instability. For the velocity model studied (a very challenging case) GPSPI and NSPS have exactly the same instability while SNPS is always more stable. Instability manifests in a complicated way as a function of extrapolation step size, frequency, velocity gradient, and strength of numerical attenuation. The SNPS operator can be stabilized over a wide range of conditions with considerably less attenuation than is

  10. 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.

  11. Explicit superconic curves.

    PubMed

    Cho, Sunggoo

    2016-09-01

    Conics and Cartesian ovals are extremely important curves in various fields of science. In addition, aspheric curves based on conics are useful in optical design. Superconic curves, recently suggested by Greynolds, are extensions of both conics and Cartesian ovals and have been applied to optical design. However, they are not extensions of aspheric curves based on conics. In this work, we investigate another type of superconic curves. These superconic curves are extensions of not only conics and Cartesian ovals but also aspheric curves based on conics. Moreover, these are represented in explicit form, while Greynolds's superconic curves are in implicit form. PMID:27607506

  12. 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

  13. Why is Benzene Soluble in Water? Role of OH/π Interaction in Solvation.

    PubMed

    Takahashi, Hideaki; Suzuoka, Daiki; Morita, Akihiro

    2015-03-10

    The XH/π interaction (X = C, N, or O) plays an essential role in a variety of fundamental processes in condensed phase, and it attracts broad interests in the fields of chemistry and biochemistry in recent years. This issue has a direct relevance to an intriguing phenomenon that a benzene molecule exhibits a negative solvation free energy of -0.87 kcal/mol in ambient water though it is a typical nonpolar organic solute. In this work, we developed a novel method to analyze the free energy δμ due to the electron density fluctuation of a solute in solution to clarify the mechanism responsible for the affinity of benzene to bulk water. Explicitly, the free energy δμ is decomposed into contributions from σ and π electrons in π-conjugated systems on the basis of the QM/MM method combined with a theory of solutions. With our analyses, the free energy δμ(π) arising from the fluctuation of π electrons in benzene was obtained as -0.94 kcal/mol and found to be the major source of the affinity of benzene to water. Thus, the role of π electrons in hydration is quantified for the first time with our analyses. Our method was applied to phenyl methyl ether (PME) in water solution to examine the substituent effects of the electron donating group (EDG) on the hydration of a π-conjugated system. The delocalization effect of the π electrons on hydration was also investigated performing the decomposition analyses for ethene and 1,3-butadiene molecules in water solutions. It was revealed that the stabilization due to δμ(π) for butadiene (-0.76 kcal/mol) is about three times as large as that for ethene (-0.26 kcal/mol), which suggests the importance of the delocalization effect of the π electrons in mediating the affinity to polar solvent. PMID:26579767

  14. Why is Benzene Soluble in Water? Role of OH/π Interaction in Solvation.

    PubMed

    Takahashi, Hideaki; Suzuoka, Daiki; Morita, Akihiro

    2015-03-10

    The XH/π interaction (X = C, N, or O) plays an essential role in a variety of fundamental processes in condensed phase, and it attracts broad interests in the fields of chemistry and biochemistry in recent years. This issue has a direct relevance to an intriguing phenomenon that a benzene molecule exhibits a negative solvation free energy of -0.87 kcal/mol in ambient water though it is a typical nonpolar organic solute. In this work, we developed a novel method to analyze the free energy δμ due to the electron density fluctuation of a solute in solution to clarify the mechanism responsible for the affinity of benzene to bulk water. Explicitly, the free energy δμ is decomposed into contributions from σ and π electrons in π-conjugated systems on the basis of the QM/MM method combined with a theory of solutions. With our analyses, the free energy δμ(π) arising from the fluctuation of π electrons in benzene was obtained as -0.94 kcal/mol and found to be the major source of the affinity of benzene to water. Thus, the role of π electrons in hydration is quantified for the first time with our analyses. Our method was applied to phenyl methyl ether (PME) in water solution to examine the substituent effects of the electron donating group (EDG) on the hydration of a π-conjugated system. The delocalization effect of the π electrons on hydration was also investigated performing the decomposition analyses for ethene and 1,3-butadiene molecules in water solutions. It was revealed that the stabilization due to δμ(π) for butadiene (-0.76 kcal/mol) is about three times as large as that for ethene (-0.26 kcal/mol), which suggests the importance of the delocalization effect of the π electrons in mediating the affinity to polar solvent.

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. Temperature-dependent solvation modulates the dimensions of disordered proteins

    PubMed Central

    Wuttke, René; Hofmann, Hagen; Nettels, Daniel; Borgia, Madeleine B.; Mittal, Jeetain; Best, Robert B.; Schuler, Benjamin

    2014-01-01

    For disordered proteins, the dimensions of the chain are an important property that is sensitive to environmental conditions. We have used single-molecule Förster resonance energy transfer to probe the temperature-induced chain collapse of five unfolded or intrinsically disordered proteins. Because this behavior is sensitive to the details of intrachain and chain–solvent interactions, the collapse allows us to probe the physical interactions governing the dimensions of disordered proteins. We find that each of the proteins undergoes a collapse with increasing temperature, with the most hydrophobic one, λ-repressor, undergoing a reexpansion at the highest temperatures. Although such a collapse might be expected due to the temperature dependence of the classical “hydrophobic effect,” remarkably we find that the largest collapse occurs for the most hydrophilic, charged sequences. Using a combination of theory and simulation, we show that this result can be rationalized in terms of the temperature-dependent solvation free energies of the constituent amino acids, with the solvation properties of the most hydrophilic residues playing a large part in determining the collapse. PMID:24706910

  20. Temperature-dependent solvation modulates the dimensions of disordered proteins.

    PubMed

    Wuttke, René; Hofmann, Hagen; Nettels, Daniel; Borgia, Madeleine B; Mittal, Jeetain; Best, Robert B; Schuler, Benjamin

    2014-04-01

    For disordered proteins, the dimensions of the chain are an important property that is sensitive to environmental conditions. We have used single-molecule Förster resonance energy transfer to probe the temperature-induced chain collapse of five unfolded or intrinsically disordered proteins. Because this behavior is sensitive to the details of intrachain and chain-solvent interactions, the collapse allows us to probe the physical interactions governing the dimensions of disordered proteins. We find that each of the proteins undergoes a collapse with increasing temperature, with the most hydrophobic one, λ-repressor, undergoing a reexpansion at the highest temperatures. Although such a collapse might be expected due to the temperature dependence of the classical "hydrophobic effect," remarkably we find that the largest collapse occurs for the most hydrophilic, charged sequences. Using a combination of theory and simulation, we show that this result can be rationalized in terms of the temperature-dependent solvation free energies of the constituent amino acids, with the solvation properties of the most hydrophilic residues playing a large part in determining the collapse.

  1. Quantum mechanical continuum solvation models for ionic liquids.

    PubMed

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

    2012-08-01

    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.

  2. Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies

    SciTech Connect

    Daily, Michael D.; Chun, Jaehun; Heredia-Langner, Alejandro; Wei, Guowei; Baker, Nathan A.

    2013-11-28

    Implicit solvent models are important tools for calculating solvation free energies for chemical and biophysical studies since they require fewer computational resources but can achieve accuracy comparable to that of explicit-solvent models. In past papers, geometric flow-based solvation models have been established for solvation analysis of small and large compounds. In the present work, the use of realistic experiment-based parameter choices for the geometric flow models is studied. We find that the experimental parameters of solvent internal pressure p = 172 MPa and surface tension γ = 72 mN/m produce solvation free energies within 1 RT of the global minimum root-mean-squared deviation from experimental data over the expanded set. Our results demonstrate that experimental values can be used for geometric flow solvent model parameters, thus eliminating the need for additional parameterization. We also examine the correlations between optimal values of p and γ which are strongly anti-correlated. Geometric analysis of the small molecule test set shows that these results are inter-connected with an approximately linear relationship between area and volume in the range of molecular sizes spanned by the data set. In spite of this considerable degeneracy between the surface tension and pressure terms in the model, both terms are important for the broader applicability of the model.

  3. Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies

    NASA Astrophysics Data System (ADS)

    Daily, Michael D.; Chun, Jaehun; Heredia-Langner, Alejandro; Wei, Guowei; Baker, Nathan A.

    2013-11-01

    Implicit solvent models are important tools for calculating solvation free energies for chemical and biophysical studies since they require fewer computational resources but can achieve accuracy comparable to that of explicit-solvent models. In past papers, geometric flow-based solvation models have been established for solvation analysis of small and large compounds. In the present work, the use of realistic experiment-based parameter choices for the geometric flow models is studied. We find that the experimental parameters of solvent internal pressure p = 172 MPa and surface tension γ = 72 mN/m produce solvation free energies within 1 RT of the global minimum root-mean-squared deviation from experimental data over the expanded set. Our results demonstrate that experimental values can be used for geometric flow solvent model parameters, thus eliminating the need for additional parameterization. We also examine the correlations between optimal values of p and γ which are strongly anti-correlated. Geometric analysis of the small molecule test set shows that these results are inter-connected with an approximately linear relationship between area and volume in the range of molecular sizes spanned by the data set. In spite of this considerable degeneracy between the surface tension and pressure terms in the model, both terms are important for the broader applicability of the model.

  4. Spatially explicit integrated modeling and economic valuation of climate driven land use change and its indirect effects.

    PubMed

    Bateman, Ian; Agarwala, Matthew; Binner, Amy; Coombes, Emma; Day, Brett; Ferrini, Silvia; Fezzi, Carlo; Hutchins, Michael; Lovett, Andrew; Posen, Paulette

    2016-10-01

    We present an integrated model of the direct consequences of climate change on land use, and the indirect effects of induced land use change upon the natural environment. The model predicts climate-driven shifts in the profitability of alternative uses of agricultural land. Both the direct impact of climate change and the induced shift in land use patterns will cause secondary effects on the water environment, for which agriculture is the major source of diffuse pollution. We model the impact of changes in such pollution on riverine ecosystems showing that these will be spatially heterogeneous. Moreover, we consider further knock-on effects upon the recreational benefits derived from water environments, which we assess using revealed preference methods. This analysis permits a multi-layered examination of the economic consequences of climate change, assessing the sequence of impacts from climate change through farm gross margins, land use, water quality and recreation, both at the individual and catchment scale. PMID:27343434

  5. Spatially explicit integrated modeling and economic valuation of climate driven land use change and its indirect effects.

    PubMed

    Bateman, Ian; Agarwala, Matthew; Binner, Amy; Coombes, Emma; Day, Brett; Ferrini, Silvia; Fezzi, Carlo; Hutchins, Michael; Lovett, Andrew; Posen, Paulette

    2016-10-01

    We present an integrated model of the direct consequences of climate change on land use, and the indirect effects of induced land use change upon the natural environment. The model predicts climate-driven shifts in the profitability of alternative uses of agricultural land. Both the direct impact of climate change and the induced shift in land use patterns will cause secondary effects on the water environment, for which agriculture is the major source of diffuse pollution. We model the impact of changes in such pollution on riverine ecosystems showing that these will be spatially heterogeneous. Moreover, we consider further knock-on effects upon the recreational benefits derived from water environments, which we assess using revealed preference methods. This analysis permits a multi-layered examination of the economic consequences of climate change, assessing the sequence of impacts from climate change through farm gross margins, land use, water quality and recreation, both at the individual and catchment scale.

  6. The Effect of Explicit Instruction of Meta Cognitive Learning Strategies on Promoting Jordanian Language Learners' Reading Competence

    ERIC Educational Resources Information Center

    Al-Ghazo, Abeer

    2016-01-01

    The main purpose of the present study was to investigate the effect of met cognitive strategies on reading comprehension among Jordanian university students. The participants of this research consists of two classes of English Course , Level one with 60 students, 30 in the control group and 30 in the experimental group. Then, Metacognitive reading…

  7. The Synergistic Effect of Teaching a Combined Explicit Movement and Phonological Awareness Program to Preschool Aged Students

    ERIC Educational Resources Information Center

    Callcott, Deborah; Hammond, Lorraine; Hill, Susan

    2015-01-01

    While movement is critical to young children's development, there is an ongoing debate about the time devoted to teaching movement in early childhood classrooms. Nevertheless, research has established a link between specific precursor motor skills and early literacy development. This study investigated the synergistic effect of practising specific…

  8. Effects of beta blockade, PTSD diagnosis, and explicit threat on the extinction and retention of an aversively conditioned response.

    PubMed

    Orr, Scott P; Milad, Mohammed R; Metzger, Linda J; Lasko, Natasha B; Gilbertson, Mark W; Pitman, Roger K

    2006-10-01

    An aversively conditioned SC response was assessed in 18 males meeting DSM-IV criteria for chronic posttraumatic stress disorder (PTSD) and 10 trauma-exposed males who never developed PTSD. Effects of beta blockade on acquisition and retention of a conditioned response (CR) were examined by administering propranolol HCl before acquisition or following extinction trials. Retention of the CR was assessed 1 week following acquisition under conditions of non-threat and threat. Conditioned stimuli were colored circles and the unconditioned stimulus (UCS) was a "highly annoying" electrical stimulus. The propranolol failed to produce any measurable effects on acquisition or retention of the CR and there was no evidence of increased conditionability in individuals diagnosed with PTSD. One week following acquisition, the differential CR to the reinforced stimulus was evident only in the threat condition. This suggests that belief in the presence of a threat is necessary and sufficient for activating a previously established CR.

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

    PubMed Central

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

    2013-01-01

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

  10. 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.

  11. An explicit approach to capture diffusive effects in finite water-content method for solving vadose zone flow

    NASA Astrophysics Data System (ADS)

    Zhu, Jianting; Ogden, Fred L.; Lai, Wencong; Chen, Xiangfeng; Talbot, Cary A.

    2016-04-01

    Vadose zone flow problems are usually solved from the Richards equation. Solution to the Richards equation is generally challenging because the hydraulic conductivity and diffusivity in the equation are strongly non-linear functions of water content. The finite water-content method was proposed as an alternative general solution method of the vadose zone flow problem for infiltration, falling slugs, and vadose zone response to water table dynamics based on discretizing the water content domain into numerous bins instead of the traditional spatial discretization. In this study, we develop an improved approach to the original finite water-content method (referred to as TO method hereinafter) that better simulates diffusive effects but retains the robustness of the TO method. The approach treats advection and diffusion separately and considers diffusion on a bin by bin basis. After discretizing into water content bins, we treat the conductivity and diffusivity in individual bins as water content dependent constant evaluated at given water content corresponding to each bin. For each bin, we can solve the flow equations analytically since the hydraulic conductivity and diffusivity can be treated as a constant. We then develop solutions for each bin to determine the diffusive water amounts at each time step. The water amount ahead of the convective front for each bin is redistributed among water content bins to account for diffusive effects. The application of developed solution is straightforward only involving algebraic manipulations at each time step. The method can mainly improve water content profiles, but has no significant difference for the total infiltration rate and cumulative infiltration compared to the TO method. Although the method separately deals with advection and diffusion, it can account for the coupling effects of advection and diffusion reasonably well.

  12. An integrated experimental and theoretical approach to the spectroscopy of organic-dye-sensitized TiO₂ heterointerfaces: disentangling the effects of aggregation, solvation, and surface protonation.

    PubMed

    Marotta, Gabriele; Lobello, Maria Grazia; Anselmi, Chiara; Barozzino Consiglio, Gabriella; Calamante, Massimo; Mordini, Alessandro; Pastore, Mariachiara; De Angelis, Filippo

    2014-04-14

    We report a joint experimental and computational study into the spectroscopic properties of a prototypical D5 organic dye, both in solution and adsorbed on a TiO2 surface, with the aim of modeling and quantifying the UV/Vis spectral shifts that occur in the different explored environments. Going from the dye in solution to dye-sensitized TiO2, various factors may shift the position of the UV/Vis absorption maximum, both towards longer and shorter wavelengths. Here we have focused on the effect of dye aggregation on TiO2, surface protonation, and solvent effects. The D5 dye forms stable aggregates on the TiO2 surface that cause spectral blueshifts. We used different sensitization conditions to vary the dye loading and thus the extent of dye aggregation. For each sensitization condition, we explored protonated and native TiO2 films. Computational modeling of different dimeric aggregates with increasing intermolecular interactions and simulation of the associated optical responses also confirm the observed spectral blueshifts. Our results show that both the presence of surface protons and solvent stabilize the excited state of the adsorbed dye molecules, which causes a marked redshift in the absorption maximum and thus moves in the opposite direction to the shift due to the increase in the surface coverage.

  13. Solvation of proteins: linking thermodynamics to geometry.

    PubMed

    Hansen-Goos, Hendrik; Roth, Roland; Mecke, Klaus; Dietrich, S

    2007-09-21

    We calculate the solvation free energy of proteins in the tube model of Banavar and Maritan [Rev. Mod. Phys. 75, 23 (2003)10.1103/RevModPhys.75.23] using morphological thermodynamics which is based on Hadwiger's theorem of integral geometry. Thereby we extend recent results by Snir and Kamien [Science 307, 1067 (2005)10.1126/science.1106243] to hard-sphere solvents at finite packing fractions and obtain new conclusions. Depending on the solvent properties, parameter regions are identified where the beta sheet, the optimal helix, or neither is favored.

  14. Large-scale organization of tropical convection in two-dimensional explicit numerical simulations: Effects of interactive radiation

    NASA Astrophysics Data System (ADS)

    Grabowski, Wojciech W.; Moncrieff, Mitchell W.

    2002-10-01

    We examine interactions among radiative processes, water vapour, clouds, and the multi-scale organization of tropical convection in two-dimensional idealized cloud-resolving simulations using planetary-scale horizontal domains. We extend our earlier study where radiative cooling was prescribed. Therein, deep convection spontaneously organized into two primary scales: westward travelling mesoscale convective systems on a scale of a few hundred kilometres and the eastward-propagating envelopes of convection spanning thousands of kilometres. These envelopes represented large-scale convectively coupled gravity waves, two-dimensional non-rotating analogues of equatorially trapped Kelvin waves. Interactive radiation introduces a new mechanism of large-scale convective organization. Weak overturning circulations, steered by the mean wind and of a few thousand kilometres in scale, gradually develop. This overturning is a manifestation of the baroclinic response to horizontal gradients of radiative heating established between the moist and dry regions, which causes a spontaneous positive feedback among large-scale dynamics, water vapour, clouds, and radiation. The mechanism is as follows: the convective systems maintain the humidity (vapour and cloud) in the ascending branch which, in turn, maintains the differential radiative heating. Conversely, the large-scale overturning provides the large-scale dynamical forcing that maintains the deep convection. This quantifies recent idealized studies that applied convective parametrizations. The radiatively driven overturning and the deep convection are modulated by large-scale convectively coupled gravity waves responsible for the large-scale envelopes reported earlier. A series of sensitivity tests, including the effects of environmental shear, demonstrate the robustness of these results.

  15. 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.

  16. Lady Liberty and Godfather Death as candidates for linguistic relativity? Scrutinizing the gender congruency effect on personified allegories with explicit and implicit measures.

    PubMed

    Bender, Andrea; Beller, Sieghard; Klauer, Karl Christoph

    2016-01-01

    Linguistic relativity--the idea that language affects thought by way of its grammatical categorizations--has been controversially debated for decades. One of the contested cases is the grammatical gender of nouns, which is claimed to affect how their referents are conceptualized (i.e., as rather female or male in congruence with the grammatical gender of the noun), especially when used allegorically. But is this association strong enough to be detected in implicit measures, and, if so, can we disentangle effects of grammatical gender and allegorical association? Three experiments with native speakers of German tackled these questions. They revealed a gender congruency effect on allegorically used nouns, but this effect was stronger with an explicit measure (assignment of biological sex) than with an implicit measure (Extrinsic Affective Simon Task) and disappeared in the implicit measure when grammatical gender and allegorical associations were set into contrast. Taken together, these findings indicate that the observed congruency effect was driven by the association of nouns with personifications rather than by their grammatical gender. In conclusion, we also discuss implications of these findings for linguistic relativity.

  17. 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.

  18. DFT-based simulations of IR amide I' spectra for a small protein in solution. Comparison of explicit and empirical solvent models.

    PubMed

    Grahnen, Johan A; Amunson, Krista E; Kubelka, Jan

    2010-10-14

    Infrared (IR) amide I' spectra are widely used for investigations of the structural properties of proteins in aqueous solution. For analysis of the experimental data, it is necessary to separate the spectral features due to the backbone conformation from those arising from other factors, in particular the interaction with solvent. We investigate the effects of solvation on amide I' spectra for a small 40-residue helix-turn-helix protein by theoretical simulations based on density functional theory (DFT). The vibrational force fields and intensity parameters for the protein amide backbone are constructed by transfer from smaller heptaamide fragments; the side chains are neglected in the DFT calculations. Solvent is modeled at two different levels: first as explicit water hydrogen bonded to the surface amide groups, treated at the same DFT level, and, second, using the electrostatic map approach combined with molecular dynamics (MD) simulation. Motional narrowing of the spectral band shapes due to averaging over the fast solvent fluctuation is introduced by use of the time-averaging approximation (TAA). The simulations are compared with the experimental amide I', including two (13)C isotopically edited spectra, corrected for the side-chain signals. Both solvent models are consistent with the asymmetric experimental band shape, which arises from the differential solvation of the amide backbone. However, the effects of (13)C isotopic labeling are best captured by the gas-phase calculations. The limitations of the solvent models and implications for the theoretical simulations of protein amide vibrational spectra are discussed.

  19. 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.

  20. Partial solvation parameters and mixture thermodynamics.

    PubMed

    Panayiotou, Costas

    2012-06-21

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

  1. 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.

  2. Inversion of the electric field driven by ionic solvation energy

    NASA Astrophysics Data System (ADS)

    Guerrero Garcia, Guillermo; Solis, Francisco; Olvera de La Cruz, Monica

    2014-03-01

    In previous studies, Monte Carlo simulations have suggested the possibility of inverting the electric field near a liquid/liquid interface due to excluded volume effects, ionic size asymmetry, and image charges at high electrolyte concentrations in the absence of ion transfer. In this work, we develop a mean field theory and coarse grained simulations to study the ion transfer between the two immiscible electrolytes in the presence of an electric field. Our calculations suggest a novel mechanism to invert the electric field near confined oil/water interfaces based on differences of the ionic solvation energy in both liquid media. We thank the support of the Office of the Secretary of Defense under the NSSEFF program award number FA9550-10-1-0167.

  3. Microscopic probing of the size dependence in hydrophobic solvation

    SciTech Connect

    Huang Ningdong; Nordlund, Dennis; Huang Congcong; Weiss, Thomas M.; Acremann, Yves; Schlesinger, Daniel; Pettersson, Lars G. M.; Tyliszczak, Tolek; Nilsson, Anders

    2012-02-21

    We report small angle x-ray scattering data demonstrating the direct experimental microscopic observation of the small-to-large crossover behavior of hydrophobic effects in hydrophobic solvation. By increasing the side chain length of amphiphilic tetraalkyl-ammonium (C{sub n}H{sub 2n+1}){sub 4}N{sup +} (R{sub 4}N{sup +}) cations in aqueous solution we observe diffraction peaks indicating association between cations at a solute size between 4.4 and 5 A, which show temperature dependence dominated by hydrophobic attraction. Using O K-edge x-ray absorption we show that small solutes affect hydrogen bonding in water similar to a temperature decrease, while large solutes affect water similar to a temperature increase. Molecular dynamics simulations support, and provide further insight into, the origin of the experimental observations.

  4. A Theory of Solvation Effects on Viscosity

    NASA Astrophysics Data System (ADS)

    Yamakita, Tomofumi; Yoshimori, Akira

    2015-04-01

    We formulate a theory for calculating the viscosity of a dilute solution, considering the solute-solvent interaction. We consider an inhomogeneous density distribution of solvent particles caused by the interaction, using the equilibrium solute-solvent radial distribution function. The theory is a microscopic extension of Einstein's viscosity formula. We formulate the theory by a perturbation expansion, assuming that a solvent particle is much smaller than a solute particle. From the perturbation theory, we obtain hydrodynamic equations with new boundary conditions on the surface of the solute. The theory is applied to a system with a simple radial distribution function.

  5. Continuous medium theory for nonequilibrium solvation: III. Solvation shift by monopole approximation and multipole expansion in spherical cavity.

    PubMed

    Zhu, Quan; Fu, Ke-Xiang; Li, Xiang-Yuan; Gong, Zhen; Ma, Jian-Yi

    2005-03-01

    According to the classical electrodynamics, a new and reasonable method about electrostatic energy decomposition of the solute-solvent system has been proposed in this work by introducing the concept of spring energy. This decomposition in equilibrium solvation gives the clear comprehension for different parts of total electrostatic free energy. Logically extending this cognition to nonequilibrium leads to the new formula of electrostatic free energy of nonequilibrium state. Furthermore, the general solvation shift for light absorption/emission has been reformulated and applied to the ideal sphere case with the monopole approximation and multipole expansion. Solvation shifts in vertical ionizations of atomic ions of some series of main group elements have been investigated with monopole approximation, and the variation tendency of the solvation shift versus atomic number has been discussed. Moreover, the solvation shift in photoionization of nitrate anion in glycol has been investigated by the multipole expansion method.

  6. 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.

  7. Coarse-grained ions without charges: Reproducing the solvation structure of NaCl in water using short-ranged potentials

    NASA Astrophysics Data System (ADS)

    DeMille, Robert C.; Molinero, Valeria

    2009-07-01

    A coarse-grained model of NaCl in water is presented where the ions are modeled without charge to avoid computationally challenging electrostatics. A monatomic model of water [V. Molinero and E. B. Moore, J. Phys. Chem. B 113, 4008 (2009)] is used as the basis for this coarse-grain approach. The ability of Na+ to disrupt the native tetrahedral arrangement of water molecules, and of Cl- to integrate within this organization, is preserved in this mW-ion model through parametrization focused on water's solvation of these ions. This model successfully reproduces the structural effect of ions on water, referenced to observations from experiments and atomistic molecular dynamics simulations, while using extremely short-ranged potentials. Without Coulomb interactions the model replicates details of the ion-water structure such as distinguishing contact and solvent-separated ion pairs and the free energy barriers between them. The approach of mimicking ionic effects with short-ranged interactions results in performance gains of two orders of magnitude compared to Ewald methods. Explored over a broad range of salt concentration, the model reproduces the solvation structure and trends of diffusion relative to atomistic simulations and experimental results. The functional form of the mW-ion model can be parametrized to represent other electrolytes. With increased computational efficiency and reliable structural fidelity, this model promises to be an asset for accessing significantly longer simulation time scales with an explicit solvent in a coarse-grained system involving, for example, polyelectrolytes such as proteins, nucleic acids, and fuel-cell membranes.

  8. Dielectric spectra of ionic liquids and their conversion to solvation dynamics: a detailed computational analysis of polarizable systems.

    PubMed

    Schmollngruber, Michael; Schröder, Christian; Steinhauser, Othmar

    2014-06-14

    For the three molecular ionic liquids 1-ethyl-3-methylimidazolium tetrafluoroborate, 1-ethyl-3-methylimidazolium trifluoromethanesulfonate and 1-butyl-3-methylimidazolium tetrafluoroborate, dielectric spectra were calculated from molecular dynamics simulations based on polarizable force fields. Using the reaction field continuum model the dielectric spectra were converted to the solvation dynamics of coumarin 153. It is shown in detail that the inclusion of the static conductivity in this model is essential. When simplifying the dielectric spectrum to the static conductivity hyperbola, the solvation response function becomes mono-exponential. Taking into account the frequency dependence of the conductivity, the typical two time-regimes of the solvation response function in ionic liquids are already obtained. However, the mean relaxation time remains the same. When converting the complete dielectric spectrum, i.e. also including frequency-dependent dielectric permittivity, quantitative changes are observed, but the qualitative shape is conserved. In accordance with previous experimental studies, solvation dynamics in ionic liquids predicted by the reaction field continuum model is too fast for longer times. This correlates with the suppression of the fine structure of the dielectric spectrum at low frequencies by the static conductivity hyperbola. By scaling down the static conductivity this effect can be partially amended. In addition to the impact of the solvent dielectric spectrum on solvation dynamics, solute-specific effects, i.e. anisotropy in shape and charge distribution as well as polarizability, were also studied.

  9. 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.

  10. The Clusters-in-a-Liquid Approach for Solvation: New Insights from the Conformer Specific Gas Phase Spectroscopy and Vibrational Optical Activity Spectroscopy

    PubMed Central

    Perera, Angelo S.; Thomas, Javix; Poopari, Mohammad R.; Xu, Yunjie

    2016-01-01

    Vibrational optical activity spectroscopies, namely vibrational circular dichroism (VCD) and Raman optical activity (ROA), have been emerged in the past decade as powerful spectroscopic tools for stereochemical information of a wide range of chiral compounds in solution directly. More recently, their applications in unveiling solvent effects, especially those associated with water solvent, have been explored. In this review article, we first select a few examples to demonstrate the unique sensitivity of VCD spectral signatures to both bulk solvent effects and explicit hydrogen-bonding interactions in solution. Second, we discuss the induced solvent chirality, or chiral transfer, VCD spectral features observed in the water bending band region in detail. From these chirality transfer spectral data, the related conformer specific gas phase spectroscopic studies of small chiral hydration clusters, and the associated matrix isolation VCD experiments of hydrogen-bonded complexes in cold rare gas matrices, a general picture of solvation in aqueous solution emerges. In such an aqueous solution, some small chiral hydration clusters, rather than the chiral solutes themselves, are the dominant species and are the ones that contribute mainly to the experimentally observed VCD features. We then review a series of VCD studies of amino acids and their derivatives in aqueous solution under different pHs to emphasize the importance of the inclusion of the bulk solvent effects. These experimental data and the associated theoretical analyses are the foundation for the proposed “clusters-in-a-liquid” approach to account for solvent effects effectively. We present several approaches to identify and build such representative chiral hydration clusters. Recent studies which applied molecular dynamics simulations and the subsequent snapshot averaging approach to generate the ROA, VCD, electronic CD, and optical rotatory dispersion spectra are also reviewed. Challenges associated with

  11. The clusters-in-a-liquid approach for solvation: New insights from the conformer specific gas phase spectroscopy and vibrational optical activity spectroscopy

    NASA Astrophysics Data System (ADS)

    Xu, Yunjie; Perera, Angelo; Thomas, Javix; Poopari, Mohammad

    2016-02-01

    Vibrational optical activity spectroscopies, namely vibrational circular dichroism (VCD) and Raman optical activity (ROA), have been emerged in the past decade as a powerful spectroscopic tool for stereochemical information of a wide range of chiral compounds in solution directly. More recently, their applications in unveiling solvent effects, especially those associated with water solvent, have been explored. In this review article, we first select a few examples to demonstrate the unique sensitivity of VCD spectral signatures to both bulk solvent effects and explicit hydrogen-bonding interactions in solution. Second, we discuss the induced solvent chirality, or chiral transfer, VCD spectral features observed at the water bending band region in detail. From these chirality transfer spectral data, the related conformer specific gas phase spectroscopic studies of small chiral hydration clusters, and the associated matrix isolation VCD experiments of hydrogen-bonded complexes in cold rare gas matrices, a general picture of solvation in aqueous solution emerges. In such an aqueous solution, some small chiral hydration clusters, rather than the chiral solutes themselves, are the dominant species and are the ones who contribute mainly to the experimentally observed VCD features. We then review a series of VCD studies of amino acids and their derivatives in aqueous solution under different pHs to emphasize the importance of the inclusion of the bulk solvent effects. These experimental data and the associated theoretical analyses are the foundation for the proposed “clusters-in-a-liquid” approach to account for solvent effects effectively. We present several approaches to identify and build such representative chiral hydration clusters. Recent studies which applied molecular dynamics simulations and the subsequent snapshot averaging approach to generate the ROA, electronic CD, and optical rotatory dispersion spectra are also reviewed. Challenges associated with the

  12. The Explicit Teaching of Reading.

    ERIC Educational Resources Information Center

    Hancock, Joelie, Ed.

    Exploring the explicit teaching of reading, this book is the result of a group of Australian teachers who took a closer look at their teaching so that they could be clearer to their kindergarten through middle-school students. Chapter 1 is based on a presentation at a Saturday inservice program on explicit teaching. Chapters 2-9 were written by…

  13. Effect of pH on the Aggregation of α-syn12 Dimer in Explicit Water by Replica-Exchange Molecular Dynamics Simulation

    PubMed Central

    Cao, Zanxia; Zhang, Xiumei; Liu, Lei; Zhao, Liling; Li, Haiyan; Wang, Jihua

    2015-01-01

    The dimeric structure of the N-terminal 12 residues drives the interaction of α-synuclein protein with membranes. Moreover, experimental studies indicated that the aggregation of α-synuclein is faster at low pH than neutral pH. Nevertheless, the effects of different pH on the structural characteristics of the α-syn12 dimer remain poorly understood. We performed 500 ns temperature replica exchange molecular dynamics (T-REMD) simulations of two α-syn12 peptides in explicit solvent. The free energy surfaces contain ten highly populated regions at physiological pH, while there are only three highly populated regions contained at acidic pH. The anti-parallel β-sheet conformations were found as the lowest free energy state. Additionally, these states are nearly flat with a very small barrier which indicates that these states can easily transit between themselves. The dimer undergoes a disorder to order transition from physiological pH to acidic pH and the α-syn12 dimer at acidic pH involves a faster dimerization process. Further, the Lys6–Asp2 contact may prevent the dimerization. PMID:26114384

  14. Redefining solubility parameters: the partial solvation parameters.

    PubMed

    Panayiotou, Costas

    2012-03-21

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

  15. 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.

  16. Polar solvation dynamics of lysozyme from molecular dynamics studies

    NASA Astrophysics Data System (ADS)

    Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy

    2012-05-01

    The solvation dynamics of a protein are believed to be sensitive to its secondary structures. We have explored such sensitivity in this article by performing room temperature molecular dynamics simulation of an aqueous solution of lysozyme. Nonuniform long-time relaxation patterns of the solvation time correlation function for different segments of the protein have been observed. It is found that relatively slower long-time solvation components of the α-helices and β-sheets of the protein are correlated with lower exposure of their polar probe residues to bulk solvent and hence stronger interactions with the dynamically restricted surface water molecules. These findings can be verified by appropriate experimental studies.

  17. 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.

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

    SciTech Connect

    Borowiak-Resterna, A.; Szymanowski, J.

    2000-01-01

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

  19. The Effectiveness of the Conceptual Change Approach, Explicit Reflective Approach, and Course Book by the Ministry of Education on the Views of the Nature of Science and Conceptual Change in Light Unit

    ERIC Educational Resources Information Center

    Cil, Emine; Cepni, Salih

    2012-01-01

    The aim of this study was to analyze the effectiveness of the conceptual change approach, explicit reflective approach, and the course book by the Ministry of Education on the views toward the nature of science and conceptual change in the Light unit. Three study groups were selected from several seventh grade classes. Two of the three classes,…

  20. Interaction Effects between Exposure to Sexually Explicit Online Materials and Individual, Family, and Extrafamilial Factors on Hong Kong High School Students' Beliefs about Gender Role Equality and Body-Centered Sexuality

    ERIC Educational Resources Information Center

    To, Siu-ming; Kan, Siu-mee Iu; Ngai, Steven Sek-yum

    2015-01-01

    This study examined the interaction effects between Hong Kong adolescents' exposure to sexually explicit online materials (SEOM) and individual, family, peer, and cultural factors on their beliefs about gender role equality and body-centered sexuality. Based on a survey design with a sample of 503 high school students in Hong Kong, the results…

  1. From Asking to Answering: Making Questions Explicit

    ERIC Educational Resources Information Center

    Washington, Gene

    2006-01-01

    "From Asking To Answering: Making Questions Explicit" describes a pedagogical procedure the author has used in writing classes (expository, technical and creative) to help students better understand the purpose, and effect, of text-questions. It accomplishes this by means of thirteen discrete categories (e.g., CLAIMS, COMMITMENT, ANAPHORA, or…

  2. Explicit Instruction in Core Reading Programs

    ERIC Educational Resources Information Center

    Reutzel, D. Ray; Child, Angela; Jones, Cindy D.; Clark, Sarah K.

    2014-01-01

    The purpose of this study was to conduct a content analysis of the types and occurrences of explicit instructional moves recommended for teaching five essentials of effective reading instruction in grades 1, 3, and 5 core reading program teachers' editions in five widely marketed core reading programs. Guided practice was the most frequently…

  3. Solvation enthalpies of hydrocarbons in water-alcohol solutions

    SciTech Connect

    Antonova, O.A.; Batov, D.V.; Korolev, V.P.

    1994-03-20

    It was found that the enthalpies of solvation of alkanes and xenon in water-alcohol mixtures vary, following a parabolic law relative to the density of the cohesion energy of a mixed solvent ({rho}). The general relationships were obtained for calculation of the solvation enthalpy of alkanes as a function of {rho} of the mixture and of the size of the solute particles. 14 refs., 6 figs.

  4. Explicit Substitutions and All That

    NASA Technical Reports Server (NTRS)

    Ayala-Rincon, Mauricio; Munoz, Cesar; Busnell, Dennis M. (Technical Monitor)

    2000-01-01

    Explicit substitution calculi are extensions of the Lambda-calculus where the substitution mechanism is internalized into the theory. This feature makes them suitable for implementation and theoretical study of logic-based tools such as strongly typed programming languages and proof assistant systems. In this paper we explore new developments on two of the most successful styles of explicit substitution calculi: the lambda(sigma)- and lambda(s(e))-calculi.

  5. Explicit Substitutions and All That

    NASA Technical Reports Server (NTRS)

    Ayala-Rincon, Mauricio; Munoz, Cesar

    2000-01-01

    Explicit substitution calculi are extensions of the lambda-calculus where the substitution mechanism is internalized into the theory. This feature makes them suitable for implementation and theoretical study of logic-based tools such as strongly typed programming languages and proof assistant systems. In this paper we explore new developments on two of the most successful styles of explicit substitution calculi: the lambda sigma- and lambda S(e)-calculi.

  6. Sensitivity of Solvation Environment to Oxidation State and Position in the Early Actinide Period.

    PubMed

    Clark, Aurora E; Samuels, Alex; Wisuri, Katy; Landstrom, Sarah; Saul, Tessa

    2015-07-01

    The aqueous solvation of U-Pu in the III-VI oxidation states has been examined using density functional theory and hydrated cluster models of the form An(H2O)30(4+/3+) and AnO2(H2O)30(2+/+) embedded within a polarizable continuum model to approximate the effect of bulk water. The structural features are compared to available data from extended X-ray absorption fine structure. Then, using a multiple-scattering approach, the X-ray absorption near-edge spectra (XANES) have been simulated and compared to experiment. These structural data are complemented by a detailed thermodynamic analysis using a recently benchmarked protocol. The structural, spectroscopic, and thermodynamic information has been used to assign the primary solvation environments in water, with an emphasis upon understanding how oxidation state and position in the period modifies the hydration number and equilibrium between different solvation shell environments. Tetravalent U is proposed to exist in equilibrium between the 8- and 9-coordinate species. Moving to the right of the period, Np(IV) and Pu(IV) exist solely as the octa-aquo species. Reduction to the trivalent ions leads to thermodynamic favorability for this solvation environment, whose features reproduce the XANES spectra. The actinyl dications (AnO2(2+)) of U and Np have a preferred environment in the equatorial plane consisting of 5 solvating waters; however, changes to the ionic radius and electronic structure at Pu leads to an equilibrium between the 4- and 5-coordinate species for PuO2(2+). Reduction of the dications to form the monocations generally leads to a preference for the 4-coordinate primary solvation shell, with an equilibrium existing for uranyl, while the neptunyl and plutonyl species exist solely as AnO2(H2O)4(+). These data provide accurate thermodynamic information for several rare species and the combined thermodynamic, structural, and spectroscopic approach reveals trends in hydration behavior across actinide oxidation

  7. USING THE ECLPSS SOFTWARE ENVIRONMENT TO BUILD A SPATIALLY EXPLICIT COMPONENT-BASED MODEL OF OZONE EFFECTS ON FOREST ECOSYSTEMS. (R827958)

    EPA Science Inventory

    We have developed a modeling framework to support grid-based simulation of ecosystems at multiple spatial scales, the Ecological Component Library for Parallel Spatial Simulation (ECLPSS). ECLPSS helps ecologists to build robust spatially explicit simulations of ...

  8. Effects of Explicit and Implicit Prompts on Students' Inquiry Practices in Computer-Supported Learning Environments in High School Earth Science

    ERIC Educational Resources Information Center

    Fang, Su-Chi; Hsu, Ying-Shao; Hsu, Wei Hsiu

    2016-01-01

    The study explored how to best use scaffolds for supporting students' inquiry practices in computer-supported learning environments. We designed a series of inquiry units assisted with three versions of written inquiry prompts (generic and context-specific); that is, three scaffold-fading conditions: implicit, explicit, and fading. We then…

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

    PubMed

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

    2011-12-01

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

  10. 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.

  11. Solvation of uranyl(II) and europium(III) cations and their chloro complexes in a room-temperature ionic liquid. A theoretical study of the effect of solvent "humidity".

    PubMed

    Chaumont, Alain; Wipff, Georges

    2004-09-20

    We report a molecular dynamics study of the solvation of the UO2(2+) and Eu3+ cations and their chloro complexes in the [BMI][PF6][H2O] "humid" room-temperature ionic liquid (IL) composed of 1-butyl-3-methylimidazolium+ and PF6- ions and H2O in a 1:1:1 ratio. When compared to the results obtained in dry [BMI][PF6], the present results reveal the importance of water. The "naked" cations form UO2(H2O)5(2+) and Eu(H2O)9(3+) complexes, embedded in a shell of 7 and 8 PF6- anions, respectively. All studied UO2Cln(2-n) and EuCln(3-n) chloro complexes remain stable during the dynamics and coordinate additional H2O molecules in their first shell. UO2Cl4(2-) and EuCl6(3-) are surrounded by an "unsaturated" water shell, followed by a shell of BMI+ cations. According to an energy component analysis, the UO2Cl4(2-) and EuCl6(3-) species, intrinsically unstable toward dissociation, are more stable than their less halogenated analogues in the IL solution, due to the solvation forces. The different chloro species also interact better with the humid than with the dry IL, which hints at the importance of solvent humidity to improve their solubility. Humidity markedly modifies the local ion environment, with major consequences as far as their spectroscopic properties are concerned. We finally compare the aqueous interface of [BMI][PF6] and [OMI][PF6] ionic liquids, demonstrating the importance of imidazolium substituents (N-butyl versus N-octyl) to the nature of the interface and miscibility with water.

  12. Role of solvation in the energy stabilization inside the hydrophobic core of the protein rubredoxin.

    PubMed

    Riley, Kevin E; Merz, Kenneth M

    2006-08-17

    There are many forces that contribute to the stability of a protein; among these are dispersion interactions, hydrogen bonding, and solvation effects. In a recent work, Vondrasek et al. estimated the in vacuo stabilization energy of the hydrophobic core of the protein rubredoxin using high level ab initio methods (Vondrasek, J.; et al. J. Am. Chem. Soc. 2005, 127, 2615). In this work, we evaluate the effects of solvation on the stability of the hydrophobic core of this protein. Solvation calculations are made using the polarizable continuum method at the MP2/aug-cc-pVDZ level of theory. It is found that, in a protein-like environment (mimicked by a continuum solvent with a dielectric constant of approximately 4), the stability of rubredoxin's hydrophobic core is decreased by 40-50%. We also observed that the stabilization energy of the hydrophobic core is only slightly lower in a protein-like medium than in an aqueous one (DeltaGether-DeltaGwater approximately 1.0-3.5 kcal/mol).

  13. Conformational properties of trans-2-halo-acetoxycyclohexanes: 1H NMR, solvation and theoretical investigation

    NASA Astrophysics Data System (ADS)

    Freitas, Matheus P.; Tormena, Cláudio F.; Rittner, Roberto; Abraham, Raymond J.

    2005-01-01

    Conformational analyses of trans-2-halo-acetoxycyclohexanes have been performed through NMR, theoretical calculations and solvation theory. The solvent dependence of coupling constants analysed together with solvation parameters of the main calculated geometries allowed the determination of both the individual couplings and difference energies between the possible ax-ax and eq-eq conformations. For all the halo-compounds eq-eq is the most stable form in the vapour phase and in solution. The molar fractions ( naa) of the ax-ax conformer are 0.28, 0.30, 0.28 and 0.22 in the vapour phase for fluoro ( 1), chloro ( 2), bromo ( 3) and iodo ( 4) derivatives, respectively, decreasing to 0.06, 0.10, 0.12 and 0.12 in DMSO, calculated through MODELS and BESTFIT, using the solvation theory. The governing factors of these conformational equilibria are the classical steric and electrostatic interactions, as well as the ' gauche effect', especially for the fluoro compound. The acetoxy group effect has also been compared with previous results for the hydroxy and methoxy derivatives.

  14. Solvation-driven charge transfer and localization in metal complexes.

    PubMed

    Rondi, Ariana; Rodriguez, Yuseff; Feurer, Thomas; Cannizzo, Andrea

    2015-05-19

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

  15. Implicit and explicit contributions to statistical learning

    PubMed Central

    Batterink, Laura J.; Reber, Paul J.; Neville, Helen J.; Paller, Ken A.

    2015-01-01

    Statistical learning allows learners to detect regularities in the environment and appears to emerge automatically as a consequence of experience. Statistical learning paradigms bear many similarities to those of artificial grammar learning and other types of implicit learning. However, whether learning effects in statistical learning tasks are driven by implicit knowledge has not been thoroughly examined. The present study addressed this gap by examining the role of implicit and explicit knowledge within the context of a typical auditory statistical learning paradigm. Learners were exposed to a continuous stream of repeating nonsense words. Learning was tested (a) directly via a forced-choice recognition test combined with a remember/know procedure and (b) indirectly through a novel reaction time (RT) test. Behavior and brain potentials revealed statistical learning effects with both tests. On the recognition test, accurate responses were associated with subjective feelings of stronger recollection, and learned nonsense words relative to nonword foils elicited an enhanced late positive potential indicative of explicit knowledge. On the RT test, both RTs and P300 amplitudes differed as a function of syllable position, reflecting facilitation attributable to statistical learning. Explicit stimulus recognition did not correlate with RT or P300 effects on the RT test. These results provide evidence that explicit knowledge is accrued during statistical learning, while bringing out the possibility that dissociable implicit representations are acquired in parallel. The commonly used recognition measure primarily reflects explicit knowledge, and thus may underestimate the total amount of knowledge produced by statistical learning. Indirect measures may be more sensitive indices of learning, capturing knowledge above and beyond what is reflected by recognition accuracy. PMID:26034344

  16. Simulated Solvation of Organic Ions II: Study of Linear Alkylated Carboxylate Ions in Water Nanodrops and in Liquid Water. Propensity for Air/Water Interface and Convergence to Bulk Solvation Properties.

    PubMed

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

    2015-09-10

    We investigated the solvation of carboxylate ions from formate to hexanoate, in droplets of 50 to 1000 water molecules and neat water, by computations using standard molecular dynamics and sophisticated polarizable models. The carboxylate ions from methanoate to hexanoate show strong propensity for the air/water interface in small droplets. Only the ions larger than propanoate retain propensity for the interface in larger droplets, where their enthalpic stabilization by ion/water dispersion is reduced there by 3 kcal mol(-1) per CH2 group. This is compensated by entropy effects over +3.3 cal mol(-1) K(-1) per CH2 group. On the surface, the anionic headgroups are strongly oriented toward the aqueous core, while the hydrophobic alkyl chains are repelled into air and lose their structure-making effects. These results reproduce the structure-making effects of alkyl groups in solution, and suggest that the hydrocarbon chains of ionic headgroups and alkyl substituents solvate independently. Extrapolation to bulk solution using standard extrapolation schemes yields absolute carboxylate solvation energies. The results for formate and acetate yield a proton solvation enthalpy of about 270 kcal mol(-1), close to the experiment-based value. The largest carboxylate ions yield a value smaller by about 10 kcal mol(-1), which requires studies in much larger droplets. PMID:26287943

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  18. 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

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

    PubMed

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

    2013-04-28

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

  20. Solvated electrons at the atmospheric pressure plasma–water anodic interface

    NASA Astrophysics Data System (ADS)

    Gopalakrishnan, R.; Kawamura, E.; Lichtenberg, A. J.; Lieberman, M. A.; Graves, D. B.

    2016-07-01

    We present results from a particle-in-cell/Monte Carlo model of a dc discharge in argon at atmospheric pressure coupled with a fluid model of an aqueous electrolyte acting as anode to the plasma. The coupled models reveal the structure of the plasma–electrolyte interface and near-surface region, with a special emphasis on solvated or hydrated electrons. Results from the coupled models are in generally good agreement with the experimental results of Rumbach et al (2016 Nat. Commun. 6 7248). Electrons injected from the plasma into the water are solvated, then lost by reaction with water within about 10–20 nm from the surface. The major reaction products are OH‑ and H2. The solvated electron density profile is controlled by the injected electron current density and subsequent reactions with water, and is relatively independent of the external plasma electric field and the salt concentration in the aqueous electrolyte. Simulations of the effects of added scavenger compounds (H2O2, \\text{NO}2- , \\text{NO}2- and H+) on near-surface solvated electron density generally match the experimental results. The generation of near-surface OH‑ following electron-water decomposition in the presence of bulk acid creates a highly basic region (pH ~ 11) very near the surface. In the presence of bulk solution acidity, pH can vary from a very acidic pH 2 away from the surface to a very basic pH 11 over a distance of ~200 nm. High near-surface gradients in aqueous solution properties could strongly affect plasma-liquid applications and challenge theoretical understanding of this complex region.

  1. Solvated electrons at the atmospheric pressure plasma-water anodic interface

    NASA Astrophysics Data System (ADS)

    Gopalakrishnan, R.; Kawamura, E.; Lichtenberg, A. J.; Lieberman, M. A.; Graves, D. B.

    2016-07-01

    We present results from a particle-in-cell/Monte Carlo model of a dc discharge in argon at atmospheric pressure coupled with a fluid model of an aqueous electrolyte acting as anode to the plasma. The coupled models reveal the structure of the plasma-electrolyte interface and near-surface region, with a special emphasis on solvated or hydrated electrons. Results from the coupled models are in generally good agreement with the experimental results of Rumbach et al (2016 Nat. Commun. 6 7248). Electrons injected from the plasma into the water are solvated, then lost by reaction with water within about 10-20 nm from the surface. The major reaction products are OH- and H2. The solvated electron density profile is controlled by the injected electron current density and subsequent reactions with water, and is relatively independent of the external plasma electric field and the salt concentration in the aqueous electrolyte. Simulations of the effects of added scavenger compounds (H2O2, \\text{NO}2- , \\text{NO}2- and H+) on near-surface solvated electron density generally match the experimental results. The generation of near-surface OH- following electron-water decomposition in the presence of bulk acid creates a highly basic region (pH ~ 11) very near the surface. In the presence of bulk solution acidity, pH can vary from a very acidic pH 2 away from the surface to a very basic pH 11 over a distance of ~200 nm. High near-surface gradients in aqueous solution properties could strongly affect plasma-liquid applications and challenge theoretical understanding of this complex region.

  2. 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.

  3. Structure of Protonated Threonine Dimers in the Gas Phase: Salt-Bridged or Charge-Solvated?

    NASA Astrophysics Data System (ADS)

    Yin, Hong; Kong, Xianglei

    2015-09-01

    For homodimers of amino acids, their salt-bridged structures are gradually stabilized as the proton affinity of the component amino acid increases. Threonine has a proton affinity value located in the middle of the list of 20 natural amino acids. Thus, identifying whether the most stable isomer of protonated threonine dimer (Thr2H+) has a charge-solvated or salt-bridged structure is important and helpful for understanding the structures of other homodimers. By combining infrared photodissociation (IRPD) spectroscopy and theoretical calculations, the structures of Thr2H+ were investigated. Based on calculations at the M062X/6-311++G(d,p)//M062X/6-311++G(d,p) level, the most stable isomer of Thr2H+ was computed to be a charge-solvated structure, with an energy 3.87 kcal/mol lower than the most stable salt-bridged isomer. The predicted infrared spectrum is in good agreement with the experimental spectrum. To evaluate the temperature effect on the distribution of different isomers, the relative concentrations of the six isomers of Thr2H+ were calculated at different temperatures, according to their partition functions and enthalpies. The results show that the isomers are dominated by charge-solvated structures at a temperature of 300 K.

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

    PubMed

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

    2016-10-12

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

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

    PubMed

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

    2016-10-12

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

  7. 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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2016-08-25

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

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

    PubMed

    Matveev, Alexei; Li, Bo; Rösch, Notker

    2015-08-13

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

  12. 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

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

    DOE PAGES

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

    2015-09-16

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

  14. 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.

  15. 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.

  16. 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.

  17. Ionic solvation studied by image-charge reaction field method

    PubMed Central

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

    2011-01-01

    In a preceding paper [J. Chem. Phys. 131, 154103 (2009)], we introduced a new, hybrid explicit∕implicit method to treat electrostatic interactions in computer simulations, and tested its performance for liquid water. In this paper, we report further tests of this method, termed the image-charge solvation model (ICSM), in simulations of ions solvated in water. We find that our model can faithfully reproduce known solvation properties of sodium and chloride ions. The charging free energy of a single sodium ion is in excellent agreement with the estimates by other electrostatics methods, while offering much lower finite-size errors. Similarly, the potentials of mean force computed for Na–Cl, Na–Na, and Cl–Cl pairs closely reproduce those reported previously. Collectively, our results demonstrate the superior accuracy of the proposed ICSM method for simulations of mixed media. PMID:21280685

  18. Dependence of the benzophenone anion solvation on solvent structure

    SciTech Connect

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

    1992-12-10

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

  19. 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.

  20. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

    NASA Astrophysics Data System (ADS)

    Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.; Hünenberger, Philippe H.

    2013-11-01

    The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges -5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol-1) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB

  1. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

    SciTech Connect

    Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.; Hünenberger, Philippe H.

    2013-11-14

    The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges −5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol{sup −1}) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non

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

    SciTech Connect

    Not Available

    1993-04-13

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

  3. Generalized Born and Explicit Solvent Models for Free Energy Calculations in Organic Solvents: Cyclodextrin Dimerization.

    PubMed

    Zhang, Haiyang; Tan, Tianwei; van der Spoel, David

    2015-11-10

    Evaluation of solvation (binding) free energies with implicit solvent models in different dielectric environments for biological simulations as well as high throughput ligand screening remain challenging endeavors. In order to address how well implicit solvent models approximate explicit ones we examined four generalized Born models (GB(Still), GB(HCT), GB(OBC)I, and GB(OBC)II) for determining the dimerization free energy (ΔG(0)) of β-cyclodextrin monomers in 17 implicit solvents with dielectric constants (D) ranging from 5 to 80 and compared the results to previous free energy calculations with explicit solvents ( Zhang et al. J. Phys. Chem. B 2012 , 116 , 12684 - 12693 ). The comparison indicates that neglecting the environmental dependence of Born radii appears acceptable for such calculations involving cyclodextrin and that the GB(Still) and GB(OBC)I models yield a reasonable estimation of ΔG(0), although the details of binding are quite different from explicit solvents. Large discrepancies between implicit and explicit solvent models occur in high-dielectric media with strong hydrogen bond (HB) interruption properties. ΔG(0) with the GB models is shown to correlate strongly to 2(D-1)/(2D+1) (R(2) ∼ 0.90) in line with the Onsager reaction field ( Onsager J. Am. Chem. Soc. 1936 , 58 , 1486 - 1493 ) but to be very sensitive to D (D < 10) as well. Both high-dielectric environments where hydrogen bonds are of interest and low-dielectric media such as protein binding pockets and membrane interiors therefore need to be considered with caution in GB-based calculations. Finally, a literature analysis of Gibbs energy of solvation of small molecules in organic liquids shows that the Onsager relation does not hold for real molecules since the correlation between ΔG(0) and 2(D-1)/(2D+1) is low for most solutes. Interestingly, explicit solvent calculations of the solvation free energy ( Zhang et al. J. Chem. Inf. Model . 2015 , 55 , 1192 - 1201 ) reproduce the weak

  4. Interior and Interfacial Aqueous Solvation of Benzene Dicarboxylate Dianions and Their Methylated Analogues: A Combined Molecular Dynamics and Photoelectron Spectroscopy Study

    SciTech Connect

    Minofar, Babak; Vrbka, Lubos; Mucha, Martin; Jungwirth, Pavel; Yang, Xin; Wang, Xue B.; Fu, Youjun; Wang, Lai S.

    2005-06-16

    Aqueous solvation of benzene dicarboxylate dianions (BCD2-) was studied by means of photoelectron spectroscopy and molecular dynamics simulations. Photoelectron spectra of hydrated ortho-, and para-BCD2- with up to 25 water molecules were obtained. An even-odd effect was observed for the p-BCD2- system as a result of the alternate solvation of the two negative charges. However, the high polarizability of the benzene ring makes the two carboxylate groups interact with each other in p-BCD2-, suppressing the strength of this even-odd effect compared with the linear dicarboxylate dianions linked by an aliphatic chain. No even-odd effect was observed for the o-BCD2- system, because each solvent molecule can interact with the two carboxylate groups at the same time due to their proximity. For large solvated clusters, the spectral features of the solute decreased while the solvent features became dominant, suggesting that both o- and p-BCD2- are situated in the center of the solvated clusters. Molecular dynamics simulations with both non-polarizable and polarizable force fields confirmed that all three isomers (o-, m-, and p-BCD2-) solvate in the aqueous bulk. However, upon methylation the hydrophobic forces overwhelm electrostatic interactions and, as a result, the calculations predict that the tetra-methyl o-BCD2- is located at the water surface with the carboxylate groups anchored in the liquid and the methylated benzene ring tilted away from the aqueous phase.

  5. Enhanced fluorescence of [[5'-(4-hydroxyphenyl)[2,2'-bithiophen]-5-yl]methylene]-propanedinitrile (NIAD-4): solvation induced micro-viscosity enhancement.

    PubMed

    Hu, Jiangpu; Zhu, Huaning; Li, Yang; Wang, Xian; Ma, Renjun; Guo, Qianjin; Xia, Andong

    2016-07-28

    Excited state solvation plays a very important role in modulating the emission behavior of fluorophores upon excitation. Here, the solvation effects on the local micro-environment around a fluorophore are proposed by investigating the fantastic emission behavior of a novel amyloid fibril marker, NIAD-4, in different alcoholic and aprotic solvents. In alcoholic solvents, high solvent viscosity causes an obvious enhancement of fluorescence because of the restriction of torsion of NIAD-4, where the formation of a non-fluorescent twist intramolecular charge transfer (TICT) state is suppressed. In aprotic solvents, high solvent polarity leads to a remarkable redshift of the emission spectra suggesting strong solvation. Surprisingly, an abnormal fluorescence enhancement of NIAD-4 is observed with increasing solvent polarity of the aprotic solvents, whereas solvent viscosity plays little role in influencing the fluorescence intensity. We conclude that such an abnormal phenomenon is originated from a solvation induced micro-viscosity enhancement around the fluorophore upon excitation which restricts the torsion of NIAD-4. Femtosecond transient absorption results further prove such a micro-viscosity increasing mechanism. We believe that this solvation induced micro-viscosity enhancement effect on fluorescence could widely exist for most donor-π-acceptor (D-π-A) compounds in polar solvents, which should be carefully taken into consideration when probing the micro-viscosity in polar environments, especially in complex bioenvironments. PMID:27346590

  6. Solvent effects on the structures and vibrational features of zwitterionic dipeptides: L-diglycine and L-dialanine.

    PubMed

    Koyambo-Konzapa, Steve Jonathan; Minguirbara, Alain; Nsangou, Mama

    2015-08-01

    Calculations were done by applying the B3LYP/6-31++G(d) method on the zwitterionic L-diglycine and L-dialanine to study the solvent effects on their structures and vibrational features. Three models of solvation (implicit, explicit, and explicit in implicit) were used and the subsequent resulting values compared. Even though both dipeptides surrounded by 12 water molecules seem sufficient to stabilize their zwitterionic characters, notably to avoid the proton transfer between the backbone (N t H[Formula: see text], COO (-)) groups, the hybrid model of solvation (explicit in implicit noted 12W/Continuum) appears to be in better agreement with available IR and Raman experiments than explicit and implicit models. The harmonic vibrational modes derived from geometry optimization of L-diglycine and L-dialanine in 12W/Continuum, agree with the available IR and Raman experimental values within 1 % for L-diglycine and 2 % for L-dialanine, and they appear more accurate than those found using the explicit model (12W). Graphical Abstract DFT/6-31++G∗ Optimized structures of L-diglycine (top) and L-dialanine (bottom) surrounded by 12 water molecules all embedded in a continuum.

  7. Dielectric pressure in continuum electrostatic solvation of biomolecules.

    PubMed

    Cai, Qin; Ye, Xiang; Luo, Ray

    2012-12-01

    Continuum solvation representations based on the Poisson-Boltzmann equation have become widely accepted in biomolecular applications after years of basic research and development. Since analytical solution of the differential equation can be achieved only in a few specific cases with simple solute geometry, only numerical solution is possible for biomolecular applications. However, it is conceptually difficult to assign solvation forces in the numerical methods, limiting their applications into direct simulations of energy minimization and molecular dynamics. In this study a dielectric pressure formulation was derived from the general Maxwell stress tensor for continuum solvation of biomolecules modeled with the widely used abrupt-transitioned dielectrics. A charge-central strategy was then proposed to improve the numerical behavior of the computed pressure. An interesting observation is the highly similar charge-central formulations between the smooth-transition dielectric and the abrupt-transition dielectric models utilized in the biomolecular solvation treatments. The connections of the new formulation with both the Davis-McCammon and Gilson et al. approaches were further presented after applying the normal field approximation. The consistency was verified with the numerical tests on a realistic biomolecule. The numerical experiments on the tested biomolecule further indicate that the charge-central strategy combined with the normal field approximation not only improves the accuracy of the dielectric boundary force but also reduces its grid dependence for biomolecular applications. PMID:23093365

  8. 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.

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

    PubMed

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

    2016-09-01

    We compute the ion/water interaction energies of methylated ammonium cations and alkylated carboxylate anions solvated in large nanodroplets of 10 000 water molecules using 10 ns molecular dynamics simulations and an all-atom polarizable force-field approach. Together with our earlier results concerning the solvation of these organic ions in nanodroplets whose molecular sizes range from 50 to 1000, these new data allow us to discuss the reliability of extrapolating absolute single-ion bulk solvation energies from small ion/water droplets using common power-law functions of cluster size. We show that reliable estimates of these energies can be extrapolated from a small data set comprising the results of three droplets whose sizes are between 100 and 1000 using a basic power-law function of droplet size. This agrees with an earlier conclusion drawn from a model built within the mean spherical framework and paves the road toward a theoretical protocol to systematically compute the solvation energies of complex organic ions. PMID:27420562

  10. A theoretical investigation of gadolinium (III) solvation in molten salts

    NASA Astrophysics Data System (ADS)

    Hazebroucq, Sandrine; Picard, Gérard S.; Adamo, Carlo

    2005-06-01

    The solvation of lanthanides [here Gd(III)] in molten LiCl and KCl has been studied using a classical solvation approach, based on clusters of increasing size. In particular, density-functional calculations have been carried out on charged and neutral clusters, containing up to 35 chlorine halide molecules. A number of properties have been then evaluated and analyzed, including structural, vibrational, and thermochemical data. Special attention has also been devoted to the analysis of the local structure of the solvent surrounding the Gd3+ cation, a problem deeply investigated by experimentalists. Our results show that the charged clusters are not suitable to model the first solvation shell in such species, since their structures are strongly affected by the large electrostatic contribution. In contrast, more reliable simulations are obtained using the neutral clusters. In the latter, the coordination of Gd(III) in molten salts is computed to be 8 or 6, according to the salt LiCl or KCl. Furthermore, a good agreement is found with the experimental structural data and Raman spectra. Finally, preliminary results of potential interest for the estimation of solvation thermodynamics, a key parameter for exploiting molten salt chemistry, are reported for neutral clusters.

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

    PubMed

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

    2013-08-15

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

  12. The Complexity of Explicit Constructions

    NASA Astrophysics Data System (ADS)

    Santhanam, Rahul

    The existence of extremal combinatorial objects, such as Ramsey graphs and expanders, is often shown using the probabilistic method. It is folklore that pseudo-random generators can be used to obtain explicit constructions of these objects, if the test that the object is extremal can be implemented in polynomial time. In this talk, we pose several questions geared towards initiating a structural approach to the relationship between extremal combinatorics and computational complexity. One motivation for such an approach is to understand better why circuit lower bounds are hard. Another is to formalize connections between the two areas, so that progress in one leads automatically to progress in the other.

  13. Explicit solvent simulations of the aqueous oxidation potential and reorganization energy for neutral molecules: gas phase, linear solvent response, and non-linear response contributions.

    PubMed

    Guerard, Jennifer J; Tentscher, Peter R; Seijo, Marianne; Samuel Arey, J

    2015-06-14

    First principles simulations were used to predict aqueous one-electron oxidation potentials (Eox) and associated half-cell reorganization energies (λaq) for aniline, phenol, methoxybenzene, imidazole, and dimethylsulfide. We employed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations of the oxidized and reduced species in an explicit aqueous solvent, followed by EOM-IP-CCSD computations with effective fragment potentials for diabatic energy gaps of solvated clusters, and finally thermodynamic integration of the non-linear solvent response contribution using classical MD. A priori predicted Eox and λaq values exhibit mean absolute errors of 0.17 V and 0.06 eV, respectively, compared to experiment. We also disaggregate Eox into several well-defined free energy properties, including the gas phase adiabatic free energy of ionization (7.73 to 8.82 eV), the solvent-induced shift in the free energy of ionization due to linear solvent response (-2.01 to -2.73 eV), and the contribution from non-linear solvent response (-0.07 to -0.14 eV). The linear solvent response component is further apportioned into contributions from the solvent-induced shift in vertical ionization energy of the reduced species (ΔVIEaq) and the solvent-induced shift in negative vertical electron affinity of the ionized species (ΔNVEAaq). The simulated ΔVIEaq and ΔNVEAaq are found to contribute the principal sources of uncertainty in computational estimates of Eox and λaq. Trends in the magnitudes of disaggregated solvation properties are found to correlate with trends in structural and electronic features of the solute. Finally, conflicting approaches for evaluating the aqueous reorganization energy are contrasted and discussed, and concluding recommendations are given.

  14. Solvation free energy of the peptide group: its model dependence and implications for the additive-transfer free-energy model of protein stability.

    PubMed

    Tomar, Dheeraj S; Asthagiri, D; Weber, Valéry

    2013-09-17

    The group-additive decomposition of the unfolding free energy of a protein in an osmolyte solution relative to that in water poses a fundamental paradox: whereas the decomposition describes the experimental results rather well, theory suggests that a group-additive decomposition of free energies is, in general, not valid. In a step toward resolving this paradox, here we study the peptide-group transfer free energy. We calculate the vacuum-to-solvent (solvation) free energies of (Gly)n and cyclic diglycine (cGG) and analyze the data according to experimental protocol. The solvation free energies of (Gly)n are linear in n, suggesting group additivity. However, the slope interpreted as the free energy of a peptide unit differs from that for cGG scaled by a factor of half, emphasizing the context dependence of solvation. However, the water-to-osmolyte transfer free energies of the peptide unit are relatively independent of the peptide model, as observed experimentally. To understand these observations, a way to assess the contribution to the solvation free energy of solvent-mediated correlation between distinct groups is developed. We show that linearity of solvation free energy with n is a consequence of uniformity of the correlation contributions, with apparent group-additive behavior in the water-to-osmolyte transfer arising due to their cancellation. Implications for inferring molecular mechanisms of solvent effects on protein stability on the basis of the group-additive transfer model are suggested.

  15. 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.

  16. Evaluating effects of Everglades restoration on American crocodile populations in south Florida using a spatially-explicit, stage-based population model

    USGS Publications Warehouse

    Green, Timothy W.; Slone, Daniel H.; Swain, Eric D.; Cherkiss, Michael S.; Lohmann, Melinda; Mazzotti, Frank J.; Rice, Kenneth G.

    2014-01-01

    The distribution and abundance of the American crocodile (Crocodylus acutus) in the Florida Everglades is dependent on the timing, amount, and location of freshwater flow. One of the goals of the Comprehensive Everglades Restoration Plan (CERP) is to restore historic freshwater flows to American crocodile habitat throughout the Everglades. To predict the impacts on the crocodile population from planned restoration activities, we created a stage-based spatially explicit crocodile population model that incorporated regional hydrology models and American crocodile research and monitoring data. Growth and survival were influenced by salinity, water depth, and density-dependent interactions. A stage-structured spatial model was used with discrete spatial convolution to direct crocodiles toward attractive sources where conditions were favorable. The model predicted that CERP would have both positive and negative impacts on American crocodile growth, survival, and distribution. Overall, crocodile populations across south Florida were predicted to decrease approximately 3 % with the implementation of CERP compared to future conditions without restoration, but local increases up to 30 % occurred in the Joe Bay area near Taylor Slough, and local decreases up to 30 % occurred in the vicinity of Buttonwood Canal due to changes in salinity and freshwater flows.

  17. Intentional, explicit, systematic: Implementation and scale-up of effective practices for supporting student mental well-being in Ontario schools

    PubMed Central

    Short, Kathryn H.

    2016-01-01

    Increasingly, the potential for school mental health programming to enhance the well-being of children and youth is being recognized and realized. When evidence-based practices in mental health promotion and prevention are adopted in a whole school manner, students show positive social emotional and academic benefits. These findings have stimulated a proliferation of mental well-being programming for Canadian schools, with variability across offerings in terms of supporting evidence, costs and ease of implementation. In the absence of coordination and guidance, there has been uneven uptake of high-quality programming, resulting in a patchwork of sometimes competing efforts across our country. In order to build cohesive and sustainable evidence-based programming, intentional, explicit and systematic effort must be afforded to matters of implementation and scale-up. In Canada, School Mental Health ASSIST has been developed to provide leadership, implementation support and embeddable resources to the province of Ontario’s 72 school districts, and 5000 schools, with a view to ensuring long-term sustainability of best-in-class school mental health practices. Key elements for uptake and scale-up are described, with an implementation science lens and an emphasis on aspects that are generalizable across jurisdictions. PMID:27019639

  18. Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity

    NASA Astrophysics Data System (ADS)

    Grabowska, Joanna; Kuffel, Anna; Zielkiewicz, Jan

    2016-08-01

    Water molecules from the solvation shell of the ice-binding surface are considered important for the antifreeze proteins to perform their function properly. Herein, we discuss the problem whether the extent of changes of the mean properties of solvation water can be connected with the antifreeze activity of the protein. To this aim, the structure of solvation water of a type III antifreeze protein from Macrozoarces americanus (eel pout) is investigated. A wild type of the protein is used, along with its three mutants, with antifreeze activities equal to 54% or 10% of the activity of the native form. The solvation water of the ice-binding surface and the rest of the protein are analyzed separately. To characterize the structure of solvation shell, parameters describing radial and angular characteristics of the mutual arrangement of the molecules were employed. They take into account short-distance (first hydration shell) or long-distance (two solvation shells) effects. The obtained results and the comparison with the results obtained previously for a hyperactive antifreeze protein from Choristoneura fumiferana lead to the conclusion that the structure and amino acid composition of the active region of the protein evolved to achieve two goals. The first one is the modification of the properties of the solvation water. The second one is the geometrical adjustment of the protein surface to the specific crystallographic plane of ice. Both of these goals have to be achieved simultaneously in order for the protein to perform its function properly. However, they seem to be independent from one another in a sense that very small antifreeze activity does not imply that properties of water become different from the ones observed for the wild type. The proteins with significantly lower activity still modify the mean properties of solvation water in a right direction, in spite of the fact that the accuracy of the geometrical match with the ice lattice is lost because of the

  19. Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity.

    PubMed

    Grabowska, Joanna; Kuffel, Anna; Zielkiewicz, Jan

    2016-08-21

    Water molecules from the solvation shell of the ice-binding surface are considered important for the antifreeze proteins to perform their function properly. Herein, we discuss the problem whether the extent of changes of the mean properties of solvation water can be connected with the antifreeze activity of the protein. To this aim, the structure of solvation water of a type III antifreeze protein from Macrozoarces americanus (eel pout) is investigated. A wild type of the protein is used, along with its three mutants, with antifreeze activities equal to 54% or 10% of the activity of the native form. The solvation water of the ice-binding surface and the rest of the protein are analyzed separately. To characterize the structure of solvation shell, parameters describing radial and angular characteristics of the mutual arrangement of the molecules were employed. They take into account short-distance (first hydration shell) or long-distance (two solvation shells) effects. The obtained results and the comparison with the results obtained previously for a hyperactive antifreeze protein from Choristoneura fumiferana lead to the conclusion that the structure and amino acid composition of the active region of the protein evolved to achieve two goals. The first one is the modification of the properties of the solvation water. The second one is the geometrical adjustment of the protein surface to the specific crystallographic plane of ice. Both of these goals have to be achieved simultaneously in order for the protein to perform its function properly. However, they seem to be independent from one another in a sense that very small antifreeze activity does not imply that properties of water become different from the ones observed for the wild type. The proteins with significantly lower activity still modify the mean properties of solvation water in a right direction, in spite of the fact that the accuracy of the geometrical match with the ice lattice is lost because of the

  20. Understanding Models: An Explicit Path

    NASA Astrophysics Data System (ADS)

    Wade, P. D.

    2003-12-01

    Models consist of representations of the "real" world \\(Giere, 1988\\). Visual models, including 3-D representations, diagrams, images and photos are a dominant feature of science courses. However, the use and limitations of models is seldom explicitly taught. Results from a survey assessing students' 1. knowledge of what models are, 2. ability to understand what a model illustrates as well as describe its specific parts, and 3. ability to discuss the use and limitations \\(or distortions\\) of a model, suggest students' do not have a fundamental understanding of models. In an undergraduate Earth systems course and a science methods education course an explicit instructional approach is used which enhances students' abilities to understand and use models. The approach requires students to; 1. describe each component of a given model, 2. discuss what the model illustrates, 3. describe how the model is used and 4. discuss the limitations of the model. This approach aids the instructor in targeting specific areas of weakness in students' abilities to use models. Using this approach, students' abilities to understand and use models has increased. Additionally preservice teachers have an increased awareness that models can be misinterpreted by students which can lead to misconceptions.

  1. 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

  2. Explicit 3-D Hydrodynamic FEM Program

    2000-11-07

    DYNA3D is a nonlinear explicit finite element code for analyzing 3-D structures and solid continuum. The code is vectorized and available on several computer platforms. The element library includes continuum, shell, beam, truss and spring/damper elements to allow maximum flexibility in modeling physical problems. Many materials are available to represent a wide range of material behavior, including elasticity, plasticity, composites, thermal effects and rate dependence. In addition, DYNA3D has a sophisticated contact interface capability, includingmore » frictional sliding, single surface contact and automatic contact generation.« less

  3. 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

    2009-05-01

    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

  4. 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

    SciTech Connect

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

    2009-04-30

    We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the “D” stands for “density” to denote that the full solute electron density is used without defining partial atomic charges. “Continuum” denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where “universal” denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which 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

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

    PubMed

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

    2007-11-01

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

  6. Theory for the solvation of nonpolar solutes in water

    NASA Astrophysics Data System (ADS)

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

    2007-11-01

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

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

    PubMed

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

    2007-11-01

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

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

    PubMed Central

    Li, Bo; Zhao, Yanxiang

    2013-01-01

    Central in a variational implicit-solvent description of biomolecular solvation is an effective free-energy functional of the solute atomic positions and the solute-solvent interface (i.e., the dielectric boundary). The free-energy functional couples together the solute molecular mechanical interaction energy, the solute-solvent interfacial energy, the solute-solvent van der Waals interaction energy, and the electrostatic energy. In recent years, the sharp-interface version of the variational implicit-solvent model has been developed and used for numerical computations of molecular solvation. In this work, we propose a diffuse-interface version of the variational implicit-solvent model with solute molecular mechanics. We also analyze both the sharp-interface and diffuse-interface models. We prove the existence of free-energy minimizers and obtain their bounds. We also prove the convergence of the diffuse-interface model to the sharp-interface model in the sense of Γ-convergence. We further discuss properties of sharp-interface free-energy minimizers, the boundary conditions and the coupling of the Poisson–Boltzmann equation in the diffuse-interface model, and the convergence of forces from diffuse-interface to sharp-interface descriptions. Our analysis relies on the previous works on the problem of minimizing surface areas and on our observations on the coupling between solute molecular mechanical interactions with the continuum solvent. Our studies justify rigorously the self consistency of the proposed diffuse-interface variational models of implicit solvation. PMID:24058213

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  10. Disentangling Rheumatoid Arthritis Patients' Implicit and Explicit Attitudes toward Methotrexate.

    PubMed

    Linn, Annemiek J; Vandeberg, Lisa; Wennekers, Annemarie M; Vervloet, Marcia; van Dijk, Liset; van den Bemt, Bart J F

    2016-01-01

    Medication non-adherence is a major public health problem that has been termed an 'invisible epidemic.' Non-adherence is not only associated with negative clinical consequences but can also result in substantial healthcare costs. Up to now, effective adherence interventions are scarce and a more comprehensive model of adherence determinants is required to target the determinants for not taking the medication as prescribed. Current approaches only included explicit attitudes such as self-reported evaluations of medication as determinants, neglecting the role of associative processes that shape implicit attitudes. Implicit processes can predict daily behavior more accurately than explicit attitudes. Our aim is to assess explicit and implicit attitudes toward medication and explore the relation with beliefs, adherence and clinical (laboratory) outcomes in chronically ill patients. Fifty two Rheumatic Arthritis (RA) patients' attitudes toward Methotrexate (MTX) were explicitly (self-reported) and implicitly (Single-Category Implicit Association Test) assessed and related to the Beliefs about Medicine Questionnaire, the Compliance Questionnaire on Rheumatology and laboratory parameters [Erythrocyte Sedimentation Rate (ESR), C-Reactive Protein (CRP)]. Results show that explicit attitudes were positive and health-related. Implicit attitudes were, however, negative and sickness-related. Half of the patients displayed explicitly positive but implicitly negative attitudes. Explicit attitudes were positively related to ESR. A positive relationship between implicit attitudes and disease duration was observed. In this study, we have obtained evidence suggesting that the measurement of implicit attitudes and associations provides different information than explicit, self-reported attitudes toward medication. Since patients' implicit attitudes deviated from explicit attitudes, we can conclude that the relationship between implicit attitudes and medication adherence is worthwhile

  11. Disentangling Rheumatoid Arthritis Patients’ Implicit and Explicit Attitudes toward Methotrexate

    PubMed Central

    Linn, Annemiek J.; Vandeberg, Lisa; Wennekers, Annemarie M.; Vervloet, Marcia; van Dijk, Liset; van den Bemt, Bart J. F.

    2016-01-01

    Medication non-adherence is a major public health problem that has been termed an ‘invisible epidemic.’ Non-adherence is not only associated with negative clinical consequences but can also result in substantial healthcare costs. Up to now, effective adherence interventions are scarce and a more comprehensive model of adherence determinants is required to target the determinants for not taking the medication as prescribed. Current approaches only included explicit attitudes such as self-reported evaluations of medication as determinants, neglecting the role of associative processes that shape implicit attitudes. Implicit processes can predict daily behavior more accurately than explicit attitudes. Our aim is to assess explicit and implicit attitudes toward medication and explore the relation with beliefs, adherence and clinical (laboratory) outcomes in chronically ill patients. Fifty two Rheumatic Arthritis (RA) patients’ attitudes toward Methotrexate (MTX) were explicitly (self-reported) and implicitly (Single-Category Implicit Association Test) assessed and related to the Beliefs about Medicine Questionnaire, the Compliance Questionnaire on Rheumatology and laboratory parameters [Erythrocyte Sedimentation Rate (ESR), C-Reactive Protein (CRP)]. Results show that explicit attitudes were positive and health-related. Implicit attitudes were, however, negative and sickness-related. Half of the patients displayed explicitly positive but implicitly negative attitudes. Explicit attitudes were positively related to ESR. A positive relationship between implicit attitudes and disease duration was observed. In this study, we have obtained evidence suggesting that the measurement of implicit attitudes and associations provides different information than explicit, self-reported attitudes toward medication. Since patients’ implicit attitudes deviated from explicit attitudes, we can conclude that the relationship between implicit attitudes and medication adherence is

  12. Disentangling Rheumatoid Arthritis Patients' Implicit and Explicit Attitudes toward Methotrexate.

    PubMed

    Linn, Annemiek J; Vandeberg, Lisa; Wennekers, Annemarie M; Vervloet, Marcia; van Dijk, Liset; van den Bemt, Bart J F

    2016-01-01

    Medication non-adherence is a major public health problem that has been termed an 'invisible epidemic.' Non-adherence is not only associated with negative clinical consequences but can also result in substantial healthcare costs. Up to now, effective adherence interventions are scarce and a more comprehensive model of adherence determinants is required to target the determinants for not taking the medication as prescribed. Current approaches only included explicit attitudes such as self-reported evaluations of medication as determinants, neglecting the role of associative processes that shape implicit attitudes. Implicit processes can predict daily behavior more accurately than explicit attitudes. Our aim is to assess explicit and implicit attitudes toward medication and explore the relation with beliefs, adherence and clinical (laboratory) outcomes in chronically ill patients. Fifty two Rheumatic Arthritis (RA) patients' attitudes toward Methotrexate (MTX) were explicitly (self-reported) and implicitly (Single-Category Implicit Association Test) assessed and related to the Beliefs about Medicine Questionnaire, the Compliance Questionnaire on Rheumatology and laboratory parameters [Erythrocyte Sedimentation Rate (ESR), C-Reactive Protein (CRP)]. Results show that explicit attitudes were positive and health-related. Implicit attitudes were, however, negative and sickness-related. Half of the patients displayed explicitly positive but implicitly negative attitudes. Explicit attitudes were positively related to ESR. A positive relationship between implicit attitudes and disease duration was observed. In this study, we have obtained evidence suggesting that the measurement of implicit attitudes and associations provides different information than explicit, self-reported attitudes toward medication. Since patients' implicit attitudes deviated from explicit attitudes, we can conclude that the relationship between implicit attitudes and medication adherence is worthwhile

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

    PubMed

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

    2015-12-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  15. How does the solvation unveil AtO+ reactivity?

    PubMed

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

    2013-05-01

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

  16. Modeling Free Energies of Solvation in Olive Oil

    PubMed Central

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

    2009-01-01

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

  17. Differential geometry based solvation model I: Eulerian formulation

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

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

  18. Dragging of polarizable nanodroplets by distantly solvated ions.

    PubMed

    Wang, Boyang; Král, Petr

    2008-07-25

    We show by molecular dynamics simulations that ions intercalated in carbon and boron-nitride nanotubes can be solvated at distance in polarizable nanodroplets adsorbed on their surfaces. When the ions are driven in the nanotubes by electric fields, the adsorbed droplets are dragged together with them. We illustrate this phenomenon by dragging assemblies of 20-10,000 water molecules by individual Na+ and Cl- ions. This ion-facilitated dragging could be applied in molecular delivery, separation, and desalination.

  19. Solvated crystalline forms of nevirapine: thermoanalytical and spectroscopic studies.

    PubMed

    Chadha, Renu; Arora, Poonam; Saini, Anupam; Jain, Dharamvir Singh

    2010-09-01

    The study is aimed at exploring the utility of thermoanalytical methods in the solid-state characterization of various crystalline forms of nevirapine. The different forms obtained by recrystallization of nevirapine from various solvents were identified using differential scanning calorimetry and thermogravimetric analysis (TGA). The appearance of desolvation peak accompanied by weight loss in TGA indicated the formation of solvates: hemi-ethanolate (Form I), hemi-acetonitrilate (Form II), hemi-chloroformate (Form III), hemi-THF solvate (Form IV), mixed hemi-ethanolate hemi-hydrate (Form V), and hemi-toluenate (Form VI). The higher desolvation temperatures of all the solvates except toluenate than their respective boiling point indicate tighter binding of solvent. Emphasis has been laid on the determination of heat capacity and heat of solution utilizing microreaction calorimeter to further distinguish the various forms. The enthalpy of solution (ΔH(sol)), an indirect measure of the lattice energy of a solid, was well correlated with the crystallinity of all the solid forms obtained. The magnitude of ΔH(sol) was found to be -14.14 kJ/mol for Form I and -2.83 kJ/mol for Form V in phosphate buffer of pH 2, exhibiting maximum ease of molecular release from the lattice in Form I. The heat capacity for solvation (ΔC(p)) was found to be positive, providing information about the state of solvent molecules in the host lattice. The solubility and dissolution rate of the forms were also found to be in agreement with their enthalpy of solution. Form (I), being the most exothermic, was found to be the most soluble of all the forms.

  20. Solvation at nanoscale: Alkali-halides in water clusters

    SciTech Connect

    Partanen, Leena; Mikkelae, Mikko-Heikki; Huttula, Marko; Tchaplyguine, Maxim; Zhang Chaofan; Andersson, Tomas; Bjoerneholm, Olle

    2013-01-28

    The solvation of alkali-halides in water clusters at nanoscale is studied by photoelectron spectroscopy using synchrotron radiation. The Na 2p, K 3p, Cl 2p, Br 3d, and I 4d core level binding energies have been measured for salt-containing water clusters. The results have been compared to those of alkali halide clusters and the dilute aqueous salt solutions. It is found that the alkali halides dissolve in small water clusters as ions.

  1. Nitratotris(triphenyl­phosphine)copper(I) methanol solvate

    PubMed Central

    Steyl, Gideon

    2009-01-01

    The title compound, [Cu(NO3)(C18H15P)3]·CH3OH, is a methanol solvate derivative of nitratotris(triphenyl­phos­phine)copper(I). The complex crystallizes with three triphenyl­phosphine ligands coordinated to the copper centre, with an O—H⋯O hydrogen bond observed between the nitrate ligand and the methanol solvent mol­ecule. The coordination around the CuI centre is distorted tetrahedral. PMID:21582060

  2. Investigations of structure and dynamics of water solvation of the type I antifreeze protein

    NASA Astrophysics Data System (ADS)

    Cui, Jun; Battle, Keith; Wierzbicki, Andrzej; Madura, Jeffry D.

    We use molecular dynamics simulations to study the water structure and dynamics around the winter flounder antifreeze protein (AFP) and its two mutant forms in which the four key threonine residues of the winter flounder AFP are mutated to alanines and serines, respectively. The TIP4P-Ew water model is used to better describe the water interactions and water structure; all simulations are performed at 245.5 K, a temperature near the freezing point of the TIP4P-Ew water model. Analysis of structural and dynamic properties of the water around the threonines in the winter flounder AFP reveals that the water structure is ordered around the threonine residues, especially in the second-solvation shell. Alanine and serine mutations instead promote water hydration in the first-solvation shell. Also our calculations show that in the close vicinity of the threonine residues of the wild-type AFP, the mobility of water molecules is substantially decreased. A smaller effect is observed for the weakly active alanine-substituted mutant, and no effect is observed for the inactive serine-substituted mutant. The results of this study suggest that water ordering and immobilization play important roles in the recognition and adsorption of the antifreeze protein to ice.

  3. Computational observation of enhanced solvation of the hydroxyl radical with increased NaCl concentration

    SciTech Connect

    Wick, Collin D.; Dang, Liem X.

    2006-05-11

    Classical molecular dynamics simulations with many-body potentials were carried out to quantitatively determine the effect of NaCl salt concentration on the aqueous solvation and surface concentration of hydroxyl radicals. The potential of mean force technique was used to track the incremental free energy of the hydroxyl radical from the vapor, crossing the air-water interface into the aqueous bulk. Results showed increased NaCl salt concentration significantly enhanced hydroxyl radical solvation, which should significantly increase its accommodation on water droplets. This has been experimentally observed for ozone aqueous accommodation with increased NaI concentration, but to our knowledge, no experimental study has probed this for hydroxyl radicals. The origin for this effect was found to be very favorable hydroxyl radical-chloride ion interactions, being stronger than for water-chloride. This work was performed at Pacific Northwest National Laboratory (PNNL) under the auspices of the Division of Chemical Sciences, Office of Basic Energy Sciences, U.S. Department of Energy. Battelle operates PNNL for the Department of Energy.

  4. Anger enhances correspondence between implicit and explicit attitudes.

    PubMed

    Huntsinger, Jeffrey R

    2013-04-01

    The goal of the current research was to subject to empirical examination the idea that the experience of anger would narrow the separation between implicit and explicit attitudes. Specifically, the tendency of anger to promote a sense of certainty in one's point of view was predicted to enhance the subjective validity of implicit attitudes, and that this validation of implicit attitudes by anger should increase implicit-explicit attitude correspondence. Consistent with these predictions, across three experiments, anger, as compared with neutral emotion (Experiments 1-3) and sad emotion (Experiments 1-2), was found to increase implicit-explicit attitude correspondence. Appraisals of certainty, but not individual control, mediated the effect of anger on implicit-explicit correspondence (Experiment 3). More generally, these results imply that anger may play an essential, but until now overlooked, role in directing the interplay between spontaneous and deliberative aspects of the self.

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

    PubMed

    Carvalho, Nathalia F; Pliego, Josefredo R

    2015-10-28

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

  6. The role of sleep and practice in implicit and explicit motor learning

    PubMed Central

    Rieth, Cory A.; Cai, Denise J.; McDevitt, Elizabeth A.; Mednick, Sara C.

    2010-01-01

    Sleep is hypothesized to play a functional role in the consolidation of memory, with more robust findings for implicit, than explicit memory. Previous studies have observed improvements on an explicit motor task after a sleep period. We examined the role of massed practice and sleep on implicit and explicit learning within a motor task. Controlling for non-sleep factors (e.g. massed practice, circadian confounds) eliminated both explicit and implicit learning effects that have been attributed to sleep. PMID:20553972

  7. Materials Properties and Solvated Electron Dynamics of Isolated Nanoparticles and Nanodroplets Probed with Ultrafast Extreme Ultraviolet Beams.

    PubMed

    Ellis, Jennifer L; Hickstein, Daniel D; Xiong, Wei; Dollar, Franklin; Palm, Brett B; Keister, K Ellen; Dorney, Kevin M; Ding, Chengyuan; Fan, Tingting; Wilker, Molly B; Schnitzenbaumer, Kyle J; Dukovic, Gordana; Jimenez, Jose L; Kapteyn, Henry C; Murnane, Margaret M

    2016-02-18

    We present ultrafast photoemission measurements of isolated nanoparticles in vacuum using extreme ultraviolet (EUV) light produced through high harmonic generation. Surface-selective static EUV photoemission measurements were performed on nanoparticles with a wide array of compositions, ranging from ionic crystals to nanodroplets of organic material. We find that the total photoelectron yield varies greatly with nanoparticle composition and provides insight into material properties such as the electron mean free path and effective mass. Additionally, we conduct time-resolved photoelectron yield measurements of isolated oleylamine nanodroplets, observing that EUV photons can create solvated electrons in liquid nanodroplets. Using photoemission from a time-delayed 790 nm pulse, we observe that a solvated electron is produced in an excited state and subsequently relaxes to its ground state with a lifetime of 151 ± 31 fs. This work demonstrates that femotosecond EUV photoemission is a versatile surface-sensitive probe of the properties and ultrafast dynamics of isolated nanoparticles. PMID:26807653

  8. Two-photon-absorption DNA sensitization via solvated electron production: unraveling photochemical pathways by molecular modeling and simulation.

    PubMed

    Gattuso, Hugo; Dumont, Elise; Marazzi, Marco; Monari, Antonio

    2016-07-21

    DNA photosensitization is one of the physical processes behind photodynamic therapy techniques, i.e. the combined use of photoactive drugs and visible radiation for therapeutical purposes. In this contribution we report the analysis of the photophysical properties of a two-photon absorption dye together with its interaction with DNA. The linear and non-linear optical properties are modeled taking into account the complex environment including dynamic and vibrational effects. It is also clearly demonstrated that the excited state manifold may evolve toward spontaneous photoionization with the production of a solvated electron. In turn both the radical cation and the solvated electron may react with the DNA backbone to produce a strand break; hence we have characterized a phototherapeutic dye that absorbs in the infrared region and is able to work under hypoxidic conditions, i.e. a prodrug of great interest for the potential treatment of solid tumors. PMID:27345613

  9. Dynamics of solvation and rotational relaxation of Coumarin 153 in ionic liquid confined nanometer-sized microemulsions.

    PubMed

    Chakrabarty, Debdeep; Seth, Debabrata; Chakraborty, Anjan; Sarkar, Nilmoni

    2005-03-31

    The effects of confinement of the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate on solvation dynamics and rotational relaxation of Coumarin 153 (C-153) in Triton X-100/cyclohexane microemulsions have been explored using steady-state and picosecond time-resolved emission spectroscopy. The steady-state and rotational relaxation data indicate that C-153 molecules are incorporated in the core of the microemulsions. The average rotational relaxation time increases with increase in w ([bmim][BF(4)]/[TX-100]) values. The solvent relaxation in the core of the microemulsion occurs on two different time scales and is almost insensitive to the increase in w values. The solvent relaxation is retarded in the pool of the microemulsions compared to the neat solvent. Though, the retardation is very small compared to several-fold retardation of the solvation time of the conventional solvent inside the pool of the microemulsions. PMID:16851624

  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. The effect of a content-embedded explicit-reflective approach on inservice teachers' views and practices related to nature of science

    NASA Astrophysics Data System (ADS)

    Wahbeh, Nader A. K.

    The phrase "nature of science" has been used to refer to "the epistemology of science, science as a way of knowing, or the values and beliefs inherent to the development of scientific knowledge" (Lederman, Abd-El-Khalick, Bell, & Schwartz, 2002, p. 497). Despite the disagreement about specific definitions, some aspects of NOS are shared and considered non-controversial and accessible to K-12 students. These aspects are that scientific knowledge is: "tentative (subject to change); empirically-based (based on and/or derived from observations of the natural world); theory-laden; partially based on human inference, imagination and creativity; and socially and culturally embedded" (Abd-El-Khalick & Lederman, 2000b, p. 1063). Four other aspects of NOS that have been emphasized are the distinction between observation and inferences, the relationship between theories and laws, the myth of the scientific method, and the social dimension of scientific knowledge (Abd-El-Khalick, 1998; Akerson & Abd-El-Khalick, 2000). This study aimed to assess the influence of an explicit-reflective, metacognitive, content-embedded instructional approach undertaken from within a learning-as-conceptual change framework on inservice middle and high school science teachers' understandings of NOS. The study also aimed to examine whether this instructional approach would enable participant teachers to translate their NOS understandings into actual classroom practices, as well as document the factors that facilitate or hinder such translation. The study was guided by the following research questions: (a) What is the impact of the intervention on participant teachers' understandings of several target aspects of NOS? (b) What is the impact of the intervention on participant teachers' instructional planning and delivery related to NOS? (c) What factors mediate (i.e., enhance or impede) the translation of teachers' NOS understandings into instructional practice? The study used a pretest, posttest

  12. The effect of a content-embedded explicit-reflective approach on inservice teachers' views and practices related to nature of science

    NASA Astrophysics Data System (ADS)

    Wahbeh, Nader A. K.

    The phrase "nature of science" has been used to refer to "the epistemology of science, science as a way of knowing, or the values and beliefs inherent to the development of scientific knowledge" (Lederman, Abd-El-Khalick, Bell, & Schwartz, 2002, p. 497). Despite the disagreement about specific definitions, some aspects of NOS are shared and considered non-controversial and accessible to K-12 students. These aspects are that scientific knowledge is: "tentative (subject to change); empirically-based (based on and/or derived from observations of the natural world); theory-laden; partially based on human inference, imagination and creativity; and socially and culturally embedded" (Abd-El-Khalick & Lederman, 2000b, p. 1063). Four other aspects of NOS that have been emphasized are the distinction between observation and inferences, the relationship between theories and laws, the myth of the scientific method, and the social dimension of scientific knowledge (Abd-El-Khalick, 1998; Akerson & Abd-El-Khalick, 2000). This study aimed to assess the influence of an explicit-reflective, metacognitive, content-embedded instructional approach undertaken from within a learning-as-conceptual change framework on inservice middle and high school science teachers' understandings of NOS. The study also aimed to examine whether this instructional approach would enable participant teachers to translate their NOS understandings into actual classroom practices, as well as document the factors that facilitate or hinder such translation. The study was guided by the following research questions: (a) What is the impact of the intervention on participant teachers' understandings of several target aspects of NOS? (b) What is the impact of the intervention on participant teachers' instructional planning and delivery related to NOS? (c) What factors mediate (i.e., enhance or impede) the translation of teachers' NOS understandings into instructional practice? The study used a pretest, posttest

  13. Spatially explicit modelling of cholera epidemics

    NASA Astrophysics Data System (ADS)

    Finger, F.; Bertuzzo, E.; Mari, L.; Knox, A. C.; Gatto, M.; Rinaldo, A.

    2013-12-01

    Epidemiological models can provide crucial understanding about the dynamics of infectious diseases. Possible applications range from real-time forecasting and allocation of health care resources to testing alternative intervention mechanisms such as vaccines, antibiotics or the improvement of sanitary conditions. We apply a spatially explicit model to the cholera epidemic that struck Haiti in October 2010 and is still ongoing. The dynamics of susceptibles as well as symptomatic and asymptomatic infectives are modelled at the scale of local human communities. Dissemination of Vibrio cholerae through hydrological transport and human mobility along the road network is explicitly taken into account, as well as the effect of rainfall as a driver of increasing disease incidence. The model is calibrated using a dataset of reported cholera cases. We further model the long term impact of several types of interventions on the disease dynamics by varying parameters appropriately. Key epidemiological mechanisms and parameters which affect the efficiency of treatments such as antibiotics are identified. Our results lead to conclusions about the influence of different intervention strategies on the overall epidemiological dynamics.

  14. 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.

  15. Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies

    PubMed Central

    Bardhan, Jaydeep P.; Jungwirth, Pavel; Makowski, Lee

    2012-01-01

    Two mechanisms have been proposed to drive asymmetric solvent response to a solute charge: a static potential contribution similar to the liquid-vapor potential, and a steric contribution associated with a water molecule's structure and charge distribution. In this work, we use free-energy perturbation molecular-dynamics calculations in explicit water to show that these mechanisms act in complementary regimes; the large static potential (∼44 kJ/mol/e) dominates asymmetric response for deeply buried charges, and the steric contribution dominates for charges near the solute-solvent interface. Therefore, both mechanisms must be included in order to fully account for asymmetric solvation in general. Our calculations suggest that the steric contribution leads to a remarkable deviation from the popular “linear response” model in which the reaction potential changes linearly as a function of charge. In fact, the potential varies in a piecewise-linear fashion, i.e., with different proportionality constants depending on the sign of the charge. This discrepancy is significant even when the charge is completely buried, and holds for solutes larger than single atoms. Together, these mechanisms suggest that implicit-solvent models can be improved using a combination of affine response (an offset due to the static potential) and piecewise-linear response (due to the steric contribution). PMID:23020318

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

    PubMed

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

    2016-07-28

    Three-dimensional models for the aqueous solvation structures of chloride, bromide, and iodide are reported. K-edge extended X-ray absorption fine structure (EXAFS) and Minuit X-ray absorption near edge (MXAN) analyses found well-defined single shell solvation spheres for bromide and iodide. However, dissolved chloride proved structurally distinct, with two solvation shells needed to explain its strikingly different X-ray absorption near edge structure (XANES) spectrum. Final solvation models were as follows: iodide, 8 water molecules at 3.60 ± 0.13 Å and bromide, 8 water molecules at 3.40 ± 0.14 Å, while chloride solvation included 7 water molecules at 3.15 ± 0.10 Å, and a second shell of 7 water molecules at 4.14 ± 0.30 Å. Each of the three derived solvation shells is approximately uniformly disposed about the halides, with no global asymmetry. Time-dependent density functional theory calculations simulating the chloride XANES spectra following from alternative solvation spheres revealed surprising sensitivity of the electronic state to 6-, 7-, or 8-coordination, implying a strongly bounded phase space for the correct structure during an MXAN fit. MXAN analysis further showed that the asymmetric solvation predicted from molecular dynamics simulations using halide polarization can play no significant part in bulk solvation. Classical molecular dynamics used to explore chloride solvation found a 7-water solvation shell at 3.12 (-0.04/+0.3) Å, supporting the experimental result. These experiments provide the first fully three-dimensional structures presenting to atomic resolution the aqueous solvation spheres of the larger halide ions. PMID:27475372

  17. 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.

  18. Multidimensional infrared spectroscopy reveals the vibrational and solvation dynamics of isoniazid

    NASA Astrophysics Data System (ADS)

    Shaw, Daniel J.; Adamczyk, Katrin; Frederix, Pim W. J. M.; Simpson, Niall; Robb, Kirsty; Greetham, Gregory M.; Towrie, Michael; Parker, Anthony W.; Hoskisson, Paul A.; Hunt, Neil T.

    2015-06-01

    The results of infrared spectroscopic investigations into the band assignments, vibrational relaxation, and solvation dynamics of the common anti-tuberculosis treatment Isoniazid (INH) are reported. INH is known to inhibit InhA, a 2-trans-enoyl-acyl carrier protein reductase enzyme responsible for the maintenance of cell walls in Mycobacterium tuberculosis but as new drug-resistant strains of the bacterium appear, next-generation therapeutics will be essential to combat the rise of the disease. Small molecules such as INH offer the potential for use as a biomolecular marker through which ultrafast multidimensional spectroscopies can probe drug binding and so inform design strategies but a complete characterization of the spectroscopy and dynamics of INH in solution is required to inform such activity. Infrared absorption spectroscopy, in combination with density functional theory calculations, is used to assign the vibrational modes of INH in the 1400-1700 cm-1 region of the infrared spectrum while ultrafast multidimensional spectroscopy measurements determine the vibrational relaxation dynamics and the effects of solvation via spectral diffusion of the carbonyl stretching vibrational mode. These results are discussed in the context of previous linear spectroscopy studies on solid-phase INH and its usefulness as a biomolecular probe.

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

    PubMed

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

    2016-04-19

    Modern theories of the hydrophobic effect highlight its dependence on length scale, emphasizing the importance of interfaces in the vicinity of sizable hydrophobes. We recently showed that a faithful treatment of such nanoscale interfaces requires careful attention to the statistics of capillary waves, with significant quantitative implications for the calculation of solvation thermodynamics. Here, we show that a coarse-grained lattice model like that of Chandler [Chandler D (2005)Nature437(7059):640-647], when informed by this understanding, can capture a broad range of hydrophobic behaviors with striking accuracy. Specifically, we calculate probability distributions for microscopic density fluctuations that agree very well with results of atomistic simulations, even many SDs from the mean and even for probe volumes in highly heterogeneous environments. This accuracy is achieved without adjustment of free parameters, because the model is fully specified by well-known properties of liquid water. As examples of its utility, we compute the free-energy profile for a solute crossing the air-water interface, as well as the thermodynamic cost of evacuating the space between extended nanoscale surfaces. These calculations suggest that a highly reduced model for aqueous solvation can enable efficient multiscale modeling of spatial organization driven by hydrophobic and interfacial forces.

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

    PubMed

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

    2016-04-19

    Modern theories of the hydrophobic effect highlight its dependence on length scale, emphasizing the importance of interfaces in the vicinity of sizable hydrophobes. We recently showed that a faithful treatment of such nanoscale interfaces requires careful attention to the statistics of capillary waves, with significant quantitative implications for the calculation of solvation thermodynamics. Here, we show that a coarse-grained lattice model like that of Chandler [Chandler D (2005)Nature437(7059):640-647], when informed by this understanding, can capture a broad range of hydrophobic behaviors with striking accuracy. Specifically, we calculate probability distributions for microscopic density fluctuations that agree very well with results of atomistic simulations, even many SDs from the mean and even for probe volumes in highly heterogeneous environments. This accuracy is achieved without adjustment of free parameters, because the model is fully specified by well-known properties of liquid water. As examples of its utility, we compute the free-energy profile for a solute crossing the air-water interface, as well as the thermodynamic cost of evacuating the space between extended nanoscale surfaces. These calculations suggest that a highly reduced model for aqueous solvation can enable efficient multiscale modeling of spatial organization driven by hydrophobic and interfacial forces. PMID:26957607

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

    PubMed

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

    2016-08-23

    Oligoglycine is a backbone mimic for all proteins and is prevalent in the sequences of intrinsically disordered proteins. We have computed the absolute chemical potential of glycine oligomers at infinite dilution by simulation with the CHARMM36 and Amber ff12SB force fields. We performed a thermodynamic decomposition of the solvation free energy (ΔG(sol)) of Gly2-5 into enthalpic (ΔH(sol)) and entropic (ΔS(sol)) components as well as their van der Waals and electrostatic contributions. Gly2-5 was either constrained to a rigid/extended conformation or allowed to be completely flexible during simulations to assess the effects of flexibility on these thermodynamic quantities. For both rigid and flexible oligoglycine models, the decrease in ΔG(sol) with chain length is enthalpically driven with only weak entropic compensation. However, the apparent rates of decrease of ΔG(sol), ΔH(sol), ΔS(sol), and their elec and vdw components differ for the rigid and flexible models. Thus, we find solvation entropy does not drive aggregation for this system and may not explain the collapse of long oligoglycines. Additionally, both force fields yield very similar thermodynamic scaling relationships with respect to chain length despite both force fields generating different conformational ensembles of various oligoglycine chains. PMID:27558719

  4. 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.

  5. Dynamics of solvation and rotational relaxation in neutral Brij 35 and Brij 58 micelles

    NASA Astrophysics Data System (ADS)

    Chakrabarty, Debdeep; Hazra, Partha; Chakraborty, Anjan; Sarkar, Nilmoni

    2004-07-01

    Solvation dynamics of Coumarin 480 (C-480) and Coumarin 490 (C-490) in neutral polyoxyethylene (23) lauryl ether (Brij 35) and polyoxyethylene (20) cetyl ether (Brij 58) micelles is severely retarded compared to pure water. The solvation dynamics is biexponential in all these micelles. The fast component of the solvation dynamics arises due to the water molecules present in the palisade layer of the micelles. The slow nanosecond component in solvation dynamics may arise due to the hydrogen bonding of water molecules with the polar part of micelles. The rotational relaxations in all these micelles are bimodal and comprising of a picosecond and a nanosecond component.

  6. Lengthscale-Dependent Solvation and Density Fluctuations in n-Octane.

    PubMed

    Wu, Eugene; Garde, Shekhar

    2015-07-23

    Much attention has been focused on the solvation and density fluctuations in water over the past decade. These studies have brought to light interesting physical features of solvation in condensed media, especially the dependence of solvation on the solute lengthscale, which may be general to many fluids. Here, we focus on the lengthscale-dependent solvation and density fluctuations in n-octane, a simple organic liquid. Using extensive molecular simulations, we show a crossover in the solvation of solvophobic solutes with increasing size in n-octane, with the specifics of the crossover depending on the shape of the solute. Large lengthscale solvation, which is dominated by interface formation, emerges over subnanoscopic lengthscales. The crossover in n-octane occurs at smaller lengthscales than that in water. We connect the lengthscale of crossover to the range of attractive interactions in the fluid. The onset of the crossover is accompanied by the emergence of non-Gaussian tails in density fluctuations in solute shaped observation volumes. Simulations over a range of temperatures highlight a corresponding thermodynamic crossover in solvation. Qualitative similarities between lengthscale-dependent solvation in water, n-octane, and Lennard-Jones fluids highlight the generality of the underlying physics of solvation.

  7. Cybersex: regulating sexually explicit expression on the Internet.

    PubMed

    Cate, F H

    1996-01-01

    While the First Amendment restricts the power of the government to control access by adults to sexually explicit expression that is not obscene, the government may restrict access by children, provided that those restrictions do not limit adults to reading only "what is fit for children." Controlling access by children presents special problems in the context of broadcasting, because broadcast programming is accessible to children too young to read and because of the impossibility of segregating adults and children in the audience. The Supreme Court therefore permits the government to require "channeling" of sexually explicit programming to times when fewer unsupervised children are in the audience, to facilitate parental control over children's access to sexually explicit material. Although Internet content includes less than one percent of sexually explicit expression, that material has been the subject of intensive media and government attention. Much of that attention ignores (1) the high level of constitutional protection applicable to non-obscene, sexually explicit expression; (2) features of the Internet which facilitate controlling access by children to sexually explicit expression far more effectively than in broadcasting or print media; and (3) the First Amendment values served by permitting expression of all forms on the Internet. PMID:10160233

  8. Ultrafast studies of excess electrons in liquid acetonitrile: revisiting the solvated electron/solvent dimer anion equilibrium.

    PubMed

    Doan, Stephanie C; Schwartz, Benjamin J

    2013-04-25

    We examine the ultrafast relaxation dynamics of excess electrons injected into liquid acetonitrile using air- and water-free techniques and compare our results to previous work on this system [Xia, C. et al. J. Chem. Phys. 2002, 117, 8855]. Excess electrons in liquid acetonitrile take on two forms: a "traditional" solvated electron that absorbs in the near-IR, and a solvated molecular dimer anion that absorbs weakly in the visible. We find that excess electrons initially produced via charge-transfer-to-solvent excitation of iodide prefer to localize as solvated electrons, but that there is a subsequent equilibration to form the dimer anion on an ~80 ps time scale. The spectral signature of this interconversion between the two forms of the excess electron is a clear isosbestic point. The presence of the isosbestic point makes it possible to fully deconvolute the spectra of the two species. We find that solvated molecular anion absorbs quite weakly, with a maximum extinction coefficient of ~2000 M(-1)cm(-1). With the extinction coefficient of the dimer anion in hand, we are also able to determine the equilibrium constant for the two forms of excess electron, and find that the molecular anion is favored by a factor of ~4. We also find that relatively little geminate recombination takes place, and that the geminate recombination that does take place is essentially complete within the first 20 ps. Finally, we show that the presence of small amounts of water in the acetonitrile can have a fairly large effect on the observed spectral dynamics, explaining the differences between our results and those in previously published work.

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

    NASA Astrophysics Data System (ADS)

    Calvo, F.; Yurtsever, E.

    2016-08-01

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

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

    PubMed

    Calvo, F; Yurtsever, E

    2016-06-14

    This work theoretically examines the progressive coating of planar polycyclic aromatic hydrocarbon (PAH) molecules ranging from benzene to circumcoronene (C54H18) by para-hydrogen and ortho-deuterium. The coarse-grained Silvera-Goldman potential has been extended to model the interactions between hydrogen molecules and individual atoms of the PAH and parametrized against quantum chemical calculations for benzene-H2. Path-integral molecular dynamics simulations at 2 K were performed for increasingly large amounts of hydrogen coating the PAH up to the first solvation shell and beyond. From the simulations, various properties were determined such as the size of the first shell and its thickness as well as the solvation energy. The degree of delocalization was notably quantified from an energy landscape perspective, by monitoring the fluctuations among inherent structures sampled by the trajectories. Our results generally demonstrate a high degree of localization owing to relatively strong interactions between hydrogen and the PAH, and qualitatively minor isotopic effects. In the limit of large hydrogen amounts, the shell size and solvation energy both follow approximate linear relations with the numbers of carbon and hydrogen in the PAH. PMID:27306002

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

    NASA Astrophysics Data System (ADS)

    Calvo, F.; Yurtsever, E.

    2016-06-01

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

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

    PubMed

    Calvo, F; Yurtsever, E

    2016-08-28

    The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C60 (+) and C70 (+) are close to 49 and 51, respectively, and agree with mass spectrometry experiments. PMID:27586919

  13. Rationalizing the effects of modified electrostatic interactions in computer simulations: The dielectric self-consistent field method

    NASA Astrophysics Data System (ADS)

    Boresch, Stefan; Steinhauser, Othmar

    1999-11-01

    The dielectric self-consistent field method, a novel tool to study solvated systems based on continuum electrostatics, is introduced. It permits the qualitative and even semiquantitative calculation of orientational correlation functions, i.e., it gives insights into the orientational structure of a solute-solvent system. Further, modified Coulomb potentials and periodic boundary conditions can easily be integrated. One possible application is rapid, yet detailed methodological studies of the effects resulting from the various modified electrostatic interactions that are used regularly in computer simulations with explicit solvent molecules. As an example, we report the distance dependent Kirkwood g-factor and ion-dipole correlation functions of a solvated glycine zwitterion obtained with a simple cutoff, a shifted potential, two reaction field techniques, and Ewald summation. For the reaction fields and Ewald summation, conducting and adjusted dielectric boundary conditions are compared.

  14. Children's Acquisition and Use of the Control-of-Variables Strategy: Effects of Explicit and Implicit Instructional Guidance

    ERIC Educational Resources Information Center

    Lazonder, Ard W.; Egberink, Angelique

    2014-01-01

    Direct instruction is a proven effective method to strengthen children's ability to design unconfounded experiments using the control-of-variables strategy (CVS). Recent research suggests that task segmentation can also promote children's use of this strategy. The present study investigated this assumption by comparing the relative…

  15. Selective School Systems and Academic Self-Concept: How Explicit and Implicit School-Level Tracking Relate to the Big-Fish--Little-Pond Effect across Cultures

    ERIC Educational Resources Information Center

    Salchegger, Silvia

    2016-01-01

    A large body of research has demonstrated a big-fish--little-pond effect (BFLPE) by showing that equally able students have lower academic self-concepts in high-ability schools than in low-ability schools. Although the BFLPE generalizes across many countries, it varies significantly between countries. The reasons for this variation are still…

  16. Reporting transparency: making the ethical mandate explicit.

    PubMed

    Nicholls, Stuart G; Langan, Sinéad M; Benchimol, Eric I; Moher, David

    2016-03-16

    Improving the transparency and quality of reporting in biomedical research is considered ethically important; yet, this is often based on practical reasons such as the facilitation of peer review. Surprisingly, there has been little explicit discussion regarding the ethical obligations that underpin reporting guidelines. In this commentary, we suggest a number of ethical drivers for the improved reporting of research. These ethical drivers relate to researcher integrity as well as to the benefits derived from improved reporting such as the fair use of resources, minimizing risk of harms, and maximizing benefits. Despite their undoubted benefit to reporting completeness, questions remain regarding the extent to which reporting guidelines can influence processes beyond publication, including researcher integrity or the uptake of scientific research findings into policy or practice. Thus, we consider investigation on the effects of reporting guidelines an important step in providing evidence of their benefits.

  17. Reporting transparency: making the ethical mandate explicit.

    PubMed

    Nicholls, Stuart G; Langan, Sinéad M; Benchimol, Eric I; Moher, David

    2016-01-01

    Improving the transparency and quality of reporting in biomedical research is considered ethically important; yet, this is often based on practical reasons such as the facilitation of peer review. Surprisingly, there has been little explicit discussion regarding the ethical obligations that underpin reporting guidelines. In this commentary, we suggest a number of ethical drivers for the improved reporting of research. These ethical drivers relate to researcher integrity as well as to the benefits derived from improved reporting such as the fair use of resources, minimizing risk of harms, and maximizing benefits. Despite their undoubted benefit to reporting completeness, questions remain regarding the extent to which reporting guidelines can influence processes beyond publication, including researcher integrity or the uptake of scientific research findings into policy or practice. Thus, we consider investigation on the effects of reporting guidelines an important step in providing evidence of their benefits. PMID:26979591

  18. Partial atomic charges and their impact on the free energy of solvation.

    PubMed

    Jämbeck, Joakim P M; Mocci, Francesca; Lyubartsev, Alexander P; Laaksonen, Aatto

    2013-01-30

    Free energies of solvation (ΔG) in water and n-octanol have been computed for common drug molecules by molecular dynamics simulations with an additive fixed-charge force field. The impact of the electrostatic interactions was investigated by computing the partial atomic charges with four methods that all fit the charges from the quantum mechanically determined electrostatic potential (ESP). Due to the redistribution of electron density that occurs when molecules are transferred from gas phase to condensed phase, the polarization impact was also investigated. By computing the partial atomic charges with the solutes placed in a conductor-like continuum, the charges were effectively polarized to take the polarization effects into account. No polarization correction term or similar was considered, only the partial atomic charges. Results show that free energies are very sensitive to the choice of atomic charges and that ΔG can differ by several k(B)T depending on the charge computing method. Inclusion of polarization effects makes the solutes too hydrophilic with most methods and in vacuo charges make the solutes too hydrophobic. The restrained-ESP methods together with effectively polarized charges perform well in our test set and also when applied to a larger set of molecules. The effect of water models is also highlighted and shows that the conclusions drawn are valid for different three-point models. Partitioning between an aqueous and a hydrophobic phase is also described better if the two environment's polarization is taken into account, but again the results are sensitive to the charge calculation method. Overall, the results presented here show that effectively polarized charges can improve the description of solvating a drug-like molecule in a solvent and that the choice of partial atomic charges is crucial to ensure that molecular simulations produce reliable results.

  19. 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.

  20. 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