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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. Modeling aqueous solvation with semi-explicit assembly

    PubMed Central

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

    2011-01-01

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

  3. 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.

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

    PubMed

    White, Ronald P; Meirovitch, Hagai

    2006-01-01

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

  5. 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

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

    PubMed

    Wu, X W; Sung, S S

    1999-02-15

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

  7. 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.

  8. Infrared and vibrational CD spectra of partially solvated alpha-helices: DFT-based simulations with explicit solvent.

    PubMed

    Turner, David R; Kubelka, Jan

    2007-02-22

    Theoretical simulations are used to investigate the effects of aqueous solvent on the vibrational spectra of model alpha-helices, which are only partly exposed to solvent to mimic alpha-helices in proteins. Infrared absorption (IR) and vibrational circular dichroism (VCD) amide I' spectra for 15-amide alanine alpha-helices are simulated using density functional theory (DFT) calculations combined with the property transfer method. The solvent is modeled by explicit water molecules hydrogen bonded to the solvated amide groups. Simulated spectra for two partially solvated model alpha-helices, one corresponding to a more exposed and the other to a more buried structure, are compared to the fully solvated and unsolvated (gas phase) simulations. The dependence of the amide I spectra on the orientation of the partially solvated helix with respect to the solvent and effects of solvation on the amide I' of 13C isotopically substituted alpha-helices are also investigated. The partial exposure to solvent causes significant broadening of the amide I' bands due to differences in the vibrational frequencies of the explicitly solvated and unsolvated amide groups. The different degree of partial solvation is reflected primarily in the frequency shifts of the unsolvated (buried) amide group vibrations. Depending on which side of the alpha-helix is exposed to solvent, the simulated IR band-shapes exhibit significant changes, from broad and relatively featureless to distinctly split into two maxima. The simulated amide I' VCD band-shapes for the partially solvated alpha-helices parallel the broadening of the IR and exhibit more sign variation, but generally preserve the sign pattern characteristic of the alpha-helical structures and are much less dependent on the alpha-helix orientation with respect to the solvent. The simulated amide I' IR spectra for the model peptides with explicitly hydrogen-bonded water are consistent with the experimental data for small alpha-helical proteins

  9. 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.

  10. 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).

  11. 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.

  12. Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge.

    PubMed

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

    2014-03-01

    Here, we test a method, called semi-explicit assembly (SEA), that computes the solvation free energies of molecules in water in the SAMPL4 blind test challenge. SEA was developed with the intention of being as accurate as explicit-solvent models, but much faster to compute. It is accurate because it uses pre-simulations of simple spheres in explicit solvent to obtain structural and thermodynamic quantities, and it is fast because it parses solute free energies into regionally additive quantities. SAMPL4 provided us the opportunity to make new tests of SEA. Our tests here lead us to the following conclusions: (1) The newest version, called Field-SEA, which gives improved predictions for highly charged ions, is shown here to perform as well as the earlier versions (dipolar and quadrupolar SEA) on this broad blind SAMPL4 test set. (2) We find that both the past and present SEA models give solvation free energies that are as accurate as TIP3P. (3) Using a new approach for force field parameter optimization, we developed improved hydroxyl parameters that ensure consistency with neat-solvent dielectric constants, and found that they led to improved solvation free energies for hydroxyl-containing compounds in SAMPL4. We also learned that these hydroxyl parameters are not just fixing solvent exposed oxygens in a general sense, and therefore do not improve predictions for carbonyl or carboxylic-acid groups. Other such functional groups will need their own independent optimizations for potential improvements. Overall, these tests in SAMPL4 indicate that SEA is an accurate, general and fast new approach to computing solvation free energies. PMID:24474161

  13. 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

  14. Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble.

    PubMed

    Deighan, Michael; Bonomi, Massimiliano; Pfaendtner, Jim

    2012-07-10

    Herein, we report significant reduction in the cost of combined parallel tempering and metadynamics simulations (PTMetaD). The efficiency boost is achieved using the recently proposed well-tempered ensemble (WTE) algorithm. We studied the convergence of PTMetaD-WTE conformational sampling and free energy reconstruction of an explicitly solvated 20-residue tryptophan-cage protein (trp-cage). A set of PTMetaD-WTE simulations was compared to a corresponding standard PTMetaD simulation. The properties of PTMetaD-WTE and the convergence of the calculations were compared. The roles of the number of replicas, total simulation time, and adjustable WTE parameter γ were studied. PMID:26588950

  15. 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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  17. 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.

  18. DFT studies of carbohydrate solvation: II. MD-DFTr of a super-molecule complex of glucose, explicit waters, and an implicit solvent (COSMO)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    MD-DFTr studies are carried out on the super-molecule solvated complexes of glucose described in paper I. Included were ten explicit water molecules and an implicit solvation model, COSMO, superimposed upon the complex. Starting configurations were taken from DFTr optimized complexes resulting from ...

  19. 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.

  20. 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. PMID:25807150

  1. 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

  2. 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

  3. Surface protonation at the rutile (110) interface: explicit incorporation of solvation structure within the refined MUSIC model framework.

    PubMed

    Machesky, Michael L; Predota, Milan; Wesolowski, David J; Vlcek, Lukas; Cummings, Peter T; Rosenqvist, Jörgen; Ridley, Moira K; Kubicki, James D; Bandura, Andrei V; Kumar, Nitin; Sofo, Jorge O

    2008-11-01

    The detailed solvation structure at the (110) surface of rutile (alpha-TiO2) 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 A 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 degrees 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 pHznpc values agree to within 0.1 pH unit with those measured at all temperatures between 10 and 250 degrees C. A slightly smaller manual adjustment of the DFT-derived Ti-O surface bond lengths was sufficient to bring the predicted pHznpcvalue of the rutile (110) surface at 25 degrees 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 strength

  4. 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

  5. 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

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

    PubMed

    Yan, Zhiqiang; Wang, Jin

    2015-09-01

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

  7. 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. PMID:25076413

  8. Solvation of chromone using combined Discrete/SCRF models

    NASA Astrophysics Data System (ADS)

    Alemán, Carlos; Galembeck, Sergio E.

    1998-06-01

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

  9. Age effects on explicit and implicit memory

    PubMed Central

    Ward, Emma V.; Berry, Christopher J.; Shanks, David R.

    2013-01-01

    It is well-documented that explicit memory (e.g., recognition) declines with age. In contrast, many argue that implicit memory (e.g., priming) is preserved in healthy aging. For example, priming on tasks such as perceptual identification is often not statistically different in groups of young and older adults. Such observations are commonly taken as evidence for distinct explicit and implicit learning/memory systems. In this article we discuss several lines of evidence that challenge this view. We describe how patterns of differential age-related decline may arise from differences in the ways in which the two forms of memory are commonly measured, and review recent research suggesting that under improved measurement methods, implicit memory is not age-invariant. Formal computational models are of considerable utility in revealing the nature of underlying systems. We report the results of applying single and multiple-systems models to data on age effects in implicit and explicit memory. Model comparison clearly favors the single-system view. Implications for the memory systems debate are discussed. PMID:24065942

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

    NASA Astrophysics Data System (ADS)

    Weber, J. Mathias

    2015-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  12. 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…

  13. 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

  14. 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.

  15. 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

  16. 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.

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

    PubMed

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

    2013-12-27

    The electrostatic (ΔGel), van der Waals cavity-formation (ΔGvdw), and total (ΔG) solvation free energies for 10 alanine peptides ranging in length (n) from 1 to 10 monomers were calculated. The free energies were computed both with fixed, extended conformations of the peptides and again for some of the peptides without constraints. The solvation free energies, ΔGel, and components ΔGvdw, and ΔG, were found to be linear in n, with the slopes of the best-fit lines being γel, γvdw, and γ, respectively. Both γel and γ were negative for fixed and flexible peptides, and γvdw was negative for fixed peptides. That γvdw was negative was surprising, as experimental data on alkanes, theoretical models, and MD computations on small molecules and model systems generally suggest that γvdw should be positive. A negative γvdw seemingly contradicts the notion that ΔGvdw drives the initial collapse of the protein when it folds by favoring conformations with small surface areas. When we computed ΔGvdw for the flexible peptides, thereby allowing the peptides to assume natural ensembles of more compact conformations, γvdw was positive. Because most proteins do not assume extended conformations, a ΔGvdw that increases with increasing surface area may be typical for globular proteins. An alternative hypothesis is that the collapse is driven by intramolecular interactions. We find few intramolecular H-bonds but show that the intramolecular van der Waals interaction energy is more favorable for the flexible than for the extended peptides, seemingly favoring this hypothesis. The large fluctuations in the vdw energy may make attributing the collapse of the peptide to this intramolecular energy difficult. PMID:24328358

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

    PubMed Central

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

    2014-01-01

    The electrostatic (ΔGel), van der Waals cavity-formation (ΔGvdw), and total (ΔG) solvation free energies for 10 alanine peptides ranging in length (n) from 1 to 10 monomers were calculated. The free energies were computed both with fixed, extended conformations of the peptides and again for some of the peptides without constraints. The solvation free energies, ΔGel, and components ΔGvdw, and ΔG, were found to be linear in n, with the slopes of the best-fit lines being γel, γvdw, and γ, respectively. Both γel and γ were negative for fixed and flexible peptides, and γvdw was negative for fixed peptides. That γvdw was negative was surprising, as experimental data on alkanes, theoretical models, and MD computations on small molecules and model systems generally suggest that γvdw should be positive. A negative γvdw seemingly contradicts the notion that ΔGvdw drives the initial collapse of the protein when it folds by favoring conformations with small surface areas. When we computed ΔGvdw for the flexible peptides, thereby allowing the peptides to assume natural ensembles of more compact conformations, γvdw was positive. Because most proteins do not assume extended conformations, a ΔGvdw that increases with increasing surface area may be typical for globular proteins. An alternative hypothesis is that the collapse is driven by intramolecular interactions. We find few intramolecular h-bonds but show that the intramolecular van der Waal’s interaction energy is more favorable for the flexible than for the extended peptides, seemingly favoring this hypothesis. The large fluctuations in the vdw energy may make attributing the collapse of the peptide to this intramolecular energy difficult. PMID:24328358

  19. 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.

  20. 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…

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  2. 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.

  3. 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

  4. COMPUTER SIMULATIONS WITH EXPLICIT SOLVENT: Recent Progress in the Thermodynamic Decomposition of Free Energies and in Modeling Electrostatic Effects

    NASA Astrophysics Data System (ADS)

    Levy, Ronald M.; Gallicchio, Emilio

    1998-10-01

    This review focuses on recent progress in two areas in which computer simulations with explicit solvent are being applied: the thermodynamic decomposition of free energies, and modeling electrostatic effects. The computationally intensive nature of these simulations has been an obstacle to the systematic study of many problems in solvation thermodynamics, such as the decomposition of solvation and ligand binding free energies into component enthalpies and entropies. With the revolution in computer power continuing, these problems are ripe for study but require the judicious choice of algorithms and approximations. We provide a critical evaluation of several numerical approaches to the thermodynamic decomposition of free energies and summarize applications in the current literature. Progress in computer simulations with explicit solvent of charge perturbations in biomolecules was slow in the early 1990s because of the widespread use of truncated Coulomb potentials in these simulations, among other factors. Development of the sophisticated technology described in this review to handle the long-range electrostatic interactions has increased the predictive power of these simulations to the point where comparisons between explicit and continuum solvent models can reveal differences that have their true physical origin in the inherent molecularity of the surrounding medium.

  5. Effects of geometry and chemistry on hydrophobic solvation.

    PubMed

    Harris, Robert C; Pettitt, B Montgomery

    2014-10-14

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

  6. Effects of geometry and chemistry on hydrophobic solvation

    PubMed Central

    Harris, Robert C.; Pettitt, B. Montgomery

    2014-01-01

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

  7. Spin-State Energetics of Fe(III) and Ru(III) Aqua Complexes: Accurate ab Initio Calculations and Evidence for Huge Solvation Effects.

    PubMed

    Radoń, Mariusz; Gąssowska, Katarzyna; Szklarzewicz, Janusz; Broclawik, Ewa

    2016-04-12

    Aqua complexes of transition metals are useful models for understanding the electronic structure of metal-oxide species relevant in photocatalytic water splitting. Moreover, spin-forbidden d-d transitions of aqua complexes provide valuable experimental data of spin-state energetics, which can be used for benchmarking of computational methods. Here, low-energy spin states of Fe(III) and Ru(III) aqua complexes are studied with an array of DFT and high-level wave function methods (CASPT2, RASPT2, NEVPT2, CCSD(T)-F12, and other coupled cluster methods up to full CCSDT). The results from single-reference and multireference methods are cross-checked, and the amount of multireference character for both considered spin states of [Fe(H2O)6](3+) is carefully analyzed. In addition to small [M(H2O)6](3+) clusters (M = Fe, Ru), we also employ larger models [M(H2O)6·(H2O)12](3+), with explicit water molecules in the second coordination sphere, to describe the situation in aqueous solution. By comparing the results for both types of models, our calculations evidence large and systematic solvation effects on the spin-state energetics. It is found that, due to the interaction with hydrogen-bonded water molecules in the second coordination sphere, the first coordination sphere undergoes a noticeable contraction and deformation. In consequence, the presence of solvation shell affects the relative energies of spin states by as much as 3-4 × 10(3) cm(-1) (∼10 kcal/mol). Once this solvation effect is accounted for, the spin-state energetics from CCSD(T) and NEVPT2 calculations turn out to be in an excellent agreement with the experimental estimates, which was not the case for isolated [M(H2O)6](3+) species is gas phase. We thus postulate that significant discrepancies between theory and experimental data for [Fe(H2O)6](3+) that were previously reported in the literature may be plausibly resolved and attributed to the neglect of explicit solvation effects and also, to some extent, to

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

    PubMed Central

    England, Jeremy L.; Haran, Gilad

    2011-01-01

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

  9. 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.

  10. Highly effective configurational assignment using bisthioureas as chiral solvating agents in the presence of DABCO.

    PubMed

    Bian, Guangling; Fan, Hongjun; Huang, Huayin; Yang, Shiwei; Zong, Hua; Song, Ling; Yang, Genjin

    2015-03-20

    A highly effective (1)H NMR method for determining the absolute configurations of various chiral α-hydroxyl acids and their derivatives has been developed with the use of bisthioureas (R)-CSA 1 and (S)-CSA 1 as chiral solvating agents in the presence of DABCO, giving distinguishable proton signals with up to 0.66 ppm chemical shift nonequivalence. Computational modeling studies were performed with Gaussian09 to reveal the chiral recognition mechanism. PMID:25751415

  11. 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

  12. 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

  13. 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.

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

    PubMed

    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. PMID:27276970

  15. 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.

  16. Probing solvation effects at conical intersections by ultrafast photoelectron imaging

    NASA Astrophysics Data System (ADS)

    Soep, Benoit; Poisson, Lionel; Raffael, Kevin; Mestdagh, Jean Michel

    2007-03-01

    The electronic excitation of polyatomic molecules is generally followed by relaxation of the electronic energy to the ground state or to metastable, low lying states such as triplet states in hydrocarbons. It can be extremely rapid whenever conical intersections between the surfaces are at play, owing to their structural changes. Since, in general, relaxation is observed in condensed phases, it is essential to conduct the relevant experiments in the presence of a perturbing medium, here the surface of an argon cluster. We address the coupling of two excited configurations in a molecule possessing charge transfer intermediates thus prone to medium effects. We shall compare here the observation of the free and deposited molecule at the surface of argon clusters. The effect of the cluster and the possibility to record significant photoelectron spectra is thus described that represents an innovation for large systems. We made use of the anisotropy of the photoelectron angular distribution of the electrons to unravel the dynamics of the several excited configurations that are traversed during the electronic relaxation.

  17. 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

  18. 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. PMID:26542400

  19. 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

  20. Effective interactions between nanoparticles: Creating temperature-independent solvation environments for self-assembly.

    PubMed

    Yadav, Hari O S; Shrivastav, Gourav; Agarwal, Manish; Chakravarty, Charusita

    2016-06-28

    The extent to which solvent-mediated effective interactions between nanoparticles can be predicted based on structure and associated thermodynamic estimators for bulk solvents and for solvation of single and pairs of nanoparticles is studied here. As a test of the approach, we analyse the strategy for creating temperature-independent solvent environments using a series of homologous chain fluids as solvents, as suggested by an experimental paper [M. I. Bodnarchuk et al., J. Am. Chem. Soc. 132, 11967 (2010)]. Our conclusions are based on molecular dynamics simulations of Au140(SC10H21)62 nanoparticles in n-alkane solvents, specifically hexane, octane, decane and dodecane, using the TraPPE-UA potential to model the alkanes and alkylthiols. The 140-atom gold core of the nanocrystal is held rigid in a truncated octahedral geometry and the gold-thiolate interaction is modeled using a Morse potential. The experimental observation was that the structural and rheological properties of n-alkane solvents are constant over a temperature range determined by equivalent solvent vapour pressures. We show that this is a consequence of the fact that long chain alkane liquids behave to a good approximation as simple liquids formed by packing of monomeric methyl/methylene units. Over the corresponding temperature range (233-361 K), the solvation environment is approximately constant at the single and pair nanoparticle levels under good solvent conditions. However, quantitative variations of the order of 10%-20% do exist in various quantities, such as molar volume of solute at infinite dilution, entropy of solvation, and onset distance for soft repulsions. In the opposite limit of a poor solvent, represented by vacuum in this study, the effective interactions between nanoparticles are no longer temperature-independent with attractive interactions increasing by up to 50% on decreasing the temperature from 361 K to 290 K, accompanied by an increase in emergent anisotropy due to

  1. 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

  2. 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

  3. 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.

  4. Solvation force induced by short range, exact dissipative particle dynamics effective surfaces on a simple fluid and on polymer brushes.

    PubMed

    Goicochea, Armando Gama; Alarcón, Francisco

    2011-01-01

    The thermodynamic properties of a simple fluid confined by effective wall forces are calculated using Monte Carlo simulations in the grand canonical ensemble. The solvation force produced by polymer brushes of two different lengths is obtained also. For the particular type of model interactions used, known as the dissipative particle dynamics method, we find that it is possible to obtain an exact, simple expression for the effective force induced by a planar wall composed of identical particles that interact with those in the fluid. We show that despite the short range of all forces in the model, the solvation force can be finite at relatively large distances and therefore does not depend only on the range of the interparticle or solvent-surface forces. As for the polymer brushes, we find that the shape of the solvation force profiles is in fair agreement with scaling and self-consistent field theories. The applications and possible extensions of this work are discussed. PMID:21219016

  5. 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.

  6. 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

  7. A Density Functional Theory Evaluation of Hydrophobic Solvation: Ne, Ar and Kr in a 50-Water Cluster. Implications for the Hydrophobic Effect

    PubMed Central

    Kobko, Nadya; Marianski, Mateusz; Asensio, Amparo; Wieczorek, Robert; Dannenberg, J. J.

    2011-01-01

    The physical explanation for the hydrophobic effect has been the subject of disagreement. Physical organic chemists tend to use a explanation related to pressure, while many biochemists prefer an explanation that involves decreased entropy of the aqueous solvent. We present DFT calculations at the B3LYP/6-31G(d,p) and X3LYP/6-31G(d,p) levels on the solvation of three noble gases (Ne, Ar, and Kr) in clusters of 50 waters. Vibrational analyses show no substantial decreases in the vibrational entropies of the waters in any of the three clusters. The observed positive free energies of transfer from the gas phase or from nonpolar solvents to water appear to be due to the work needed to make a suitable hole in the aqueous solvent. We distinguish between hydrophobic solvations (explicitly studied here) and the hydrophobic effect that occurs when a solute (or transition state) can decrease its volume through conformational change (which is not possible for the noble gases). PMID:22666658

  8. Physical Modeling of Aqueous Solvation

    PubMed Central

    Fennell, Christopher J.

    2014-01-01

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

  9. Do Macromolecular Crowding Agents Exert Only an Excluded Volume Effect? A Protein Solvation Study.

    PubMed

    Mukherjee, Sanjib K; Gautam, Saurabh; Biswas, Saikat; Kundu, Jayanta; Chowdhury, Pramit K

    2015-11-01

    The effect of macromolecular crowding on protein structure and dynamics has mostly been explained on the basis of the excluded volume effect, its origin being entropic. In recent times a progressive shift in this view has been taking place with increasing emphasis on soft interactions that are enthalpic by nature. Using very low concentrations (1-10 g/L) of both synthetic (dextran- and poly(ethylene glycol) (PEG)-based) and protein (α-synuclein and myoglobin)-based crowders, we have shown that the solvation of probe molecule ANS (1-anilinonapthalene-8-sulfonate) bound to serum proteins bovine serum albumin (BSA) and human serum albumin (HSA) is significantly modulated in both a protein- and crowder-dependent fashion. Since under such conditions the effect of excluded volume is appreciably low, we propose that our observations are direct evidence of soft interactions between the macromolecular crowding agents used and the serum proteins. Moreover, our data reveal, that since at these low crowder concentrations major perturbations to the protein structure are unlikely to take place while minor perturbations might not be readily visible, protein solvation provides a unique spectral signature for capturing such local dynamics, thereby allowing one to decouple hard-sphere interactions from soft sphere ones. Furthermore, since fast fluctuations are known to play a major role in determining the functional characteristics of proteins and enzymes, our results suggest that such motions are prone to be modulated even when the cellular crowding conditions are quite relaxed. In other words, by the time the excluded volume effects come into the picture in the physiological milieu, modulations of functionally important protein motions that need a relatively lower activation energy have already taken place as a result of the aforementioned enthalpic (soft) interactions. PMID:26452170

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  11. Solvation effects are responsible for the reduced inhibitor affinity of some HIV-1 PR mutants.

    PubMed Central

    Sussman, F.; Villaverde, M. C.; Davis, A.

    1997-01-01

    The formulation of HIV-1 PR inhibitors as anti-viral drugs has been hindered by the appearance of protease strains that present drug resistance to these compounds. The mechanism by which the HIV-1 PR mutants lower their affinity for the inhibitor is not yet fully understood. We have applied a modified Poisson-Boltzmann method to the evaluation of the molecular interactions that contribute to the lowering of the inhibitor affinity to some polar mutants at position 82. These strains present drug resistance behavior and hence are ideally suited for these studies. Our results indicate that the reduction in binding affinity is due to the solvation effects that penalize the binding to the more polar mutants. The inhibitor binding ranking of the different mutants can be explained from the analysis of the different components of our free energy scoring function. PMID:9144773

  12. Solvation effects for polymers at an interface: a hybrid self-consistent field-density functional theory approach.

    PubMed

    Bryk, Paweł; MacDowell, Luis G

    2011-11-28

    Using polyatomic density functional theory of Kierlik and Rosinberg, we show that Wertheim's thermodynamic perturbation theory (TPT) incorporates solvation effects in a systematic, although simplified form. We derive two approximate solvation potentials, which require the knowledge of the correlation function in the reference unbonded fluid only. The theoretical predictions are tested against many-chain Monte Carlo simulations for moderate chain lengths. The predictions of the end-to-end distance in the bulk are in a reasonable agreement with simulations for the TPT(M-1) approximation, while the simpler TPT2_e approximation leads to the solvation potential that is shorter ranged and considerably less accurate. The resulting conformations are used in the subsequent self-consistent field theory calculations of hard-sphere polymers at a hard wall. While the incorporation of the solvation effects has little impact on the density profiles, the predictions of the components of the end-to-end distance vector as a function of the distance to the wall are much improved. PMID:22128953

  13. 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

  14. [Effects of color on implicit and explicit memory tests].

    PubMed

    Wippich, W; Mecklenbräuker, S; Baumann, R

    1994-01-01

    We report two experiments that explore why recent investigations of implicit memory did not find any effects of color information on test performance. The argument that previous failures to find effects of repetition priming were due to an arbitrary association between objects and colors was found to be wanting. To the contrary, both experiments showed no or small effects of repetition for objects paired with their prototypical colors. A second argument according to which subjects attend to the colors at encoding did not fare much better. More importantly, however, we found strong effects of repetition priming with a conceptual implicit memory measure, whereas previous research had relied exclusively on perceptual tests of implicit memory. In both experiments, the subjects were asked to choose a suitable color for each object at testing. No instructions about remembering the objects were given. The results demonstrated strong preferences for the previously seen colors in the color-choice task. Furthermore, this effect was present to the same extent with picture objects and with object names, corroborating the conceptual nature of the implicit memory measure. Finally, we observed many functional dissociations with explicit measures of memory for color information, demonstrating implicit use of memory in the conceptual choice-test for colors. PMID:7941623

  15. 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

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

    NASA Astrophysics Data System (ADS)

    Limmer, Krista; Williams, Kristen; Andzelm, Jan

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

  17. 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.

  18. 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.

  19. 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.

  20. Solvation forces between rough surfaces

    SciTech Connect

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

    1998-04-01

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

  1. 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

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

    NASA Astrophysics Data System (ADS)

    Jha, Abhishek K.; Freed, Karl F.

    2008-01-01

    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.

  3. Drug design for cardiovascular disease: the effect of solvation energy on Rac1-ligand interactions.

    PubMed

    Maggi, Norbert; Arrigo, Patrizio; Ruggiero, Carmelina

    2011-01-01

    'OMICS' techniques have deeply changed the drug discovery process. The availability of many different potential druggable genes, generated by these new techniques, have exploited the complexity of new lead compounds screening. 'Virtual screening', based on the integration of different analytical tools on high performance hardware platforms, has speeded up the search for new chemical entities suitable for experimental validation. Docking is a key step in the screening process. The aim of this paper is the evaluation of binding differences due to solvation. We have compared two commonly used software, one of which takes into account solvation, on a set of small molecules (Morpholines, flavonoids and imidazoles) which are able to target the RAC1 protein--a cardiovascular target. We have evaluated the degree of agreement between the two different programs using a machine learning approach combined with statistical test. Our analysis, on a sample of small molecules, has pointed out that 35% of the molecules seem to be sensitive to solvation. This result, even though quite preliminary, stresses the need to combine different algorithms to obtain a more reliable filtered set of ligands. PMID:22255029

  4. Production of solvated electrons

    NASA Technical Reports Server (NTRS)

    Thomas, J. K.

    1969-01-01

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

  5. Molecular Dynamics Simulations on Parallel Computers: a Study of Polar Versus Nonpolar Media Effects in Small Molecule Solvation.

    NASA Astrophysics Data System (ADS)

    Debolt, Stephen Edward

    Solvent effects were studied and described via molecular dynamics (MD) and free energy perturbation (FEP) simulations using the molecular mechanics program AMBER. The following specific topics were explored:. Polar solvents cause a blue shift of the rm nto pi^* transition band of simple alkyl carbonyl compounds. The ground- versus excited-state solvation effects responsible for the observed solvatochromism are described in terms of the molecular level details of solute-solvent interactions in several modeled solvents spanning the range from polar to nonpolar, including water, methanol, and carbon tetrachloride. The structure and dynamics of octanol media were studied to explore the question: "why is octanol/water media such a good biophase analog?". The formation of linear and cyclic polymers of hydrogen-bonded solvent molecules, micelle-like clusters, and the effects of saturating waters are described. Two small drug-sized molecules, benzene and phenol, were solvated in water-saturated octanol. The solute-solvent structure and dynamics were analysed. The difference in their partitioning free energies was calculated. MD and FEP calculations were adapted for parallel computation, increasing their "speed" or the time span accessible by a simulation. The non-cyclic polyether ionophore salinomycin was studied in methanol solvent via parallel FEP. The path of binding and release for a potassium ion was investigated by calculating the potential of mean force along the "exit vector".

  6. 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

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

    PubMed

    Qiao, Yu; Tu, Bin; Lu, Benzhuo

    2014-05-01

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

  8. The AGBNP2 Implicit Solvation Model

    PubMed Central

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

    2009-01-01

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

  9. 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…

  10. 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

  11. Accuracy of exchange-correlation functionals and effect of solvation on the surface energy of copper

    NASA Astrophysics Data System (ADS)

    Fishman, Matthew; Zhuang, Houlong L.; Mathew, Kiran; Dirschka, William; Hennig, Richard G.

    2013-06-01

    Surface energies are important for predicting the shapes of nanocrystals and describing the faceting and roughening of surfaces. Copper surfaces are of particular interest in recent years since they are the preferred surfaces for growing graphene using chemical vapor deposition. In this study we calculate the surface energies of copper for the three low-index facets (111), (100), and (110) and one high-index facet, (210), using density-functional theory with both the local-density approximation and various parametrizations of the generalized-gradient approximation to the exchange-correlation functional. To assess the accuracy of the different functionals, we obtain the average surface energies of an isotropic crystal using a broken-bond model. We use this method, which can be generalized to other crystal structures, to compare calculated surface energies to experimental surface energies for fcc crystals. We find that the recent exchange-correlation functionals AM05 and PBEsol are the most accurate functionals for calculating the surface energies of copper. To determine how solvents affect the surface energies of copper, we perform calculations using a continuum solvation model. We find that aqueous solvation changes the overall magnitude of the surface energies only slightly but leads to more isotropic surface energies.

  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. 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.

  14. 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

  15. 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.

  16. 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

  17. 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

  18. 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. PMID:25181254

  19. 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…

  20. The Instructional Effect of Stimulus-Explicitness in Facilitating Student Achievement of Varied Educational Objectives.

    ERIC Educational Resources Information Center

    Arnold, Thomas C.; Dwyer, Francis M.

    In order to investigate the relative effectiveness of specific media attributes on student performance on criterion tests, a comparison was made of the effectiveness of two levels of stimulus explicitness in visuals in facilitating student achievement on criterion tests of knowledge, comprehension, and total understanding. Subjects were 171…

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

    NASA Astrophysics Data System (ADS)

    Schmollngruber, Michael; Schröder, Christian; Steinhauser, Othmar

    2013-05-01

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

  2. Modeling effects of explicit and nonexplicit sexual stimuli on the sexual anxiety and behavior of women.

    PubMed

    Wishnoff, R

    1978-09-01

    This study focused on the specific effects of explicit and nonexplicit sexual stimuli on anxious, coitally inexperienced women. Using Bandura's social learning theory as the thoretical framework, the consequences of modeling behavior on an individual's response patterns were examined. Responses indicating sexual anxiety level, preferred sexual behavior, and manifest anxiety level were recorded. Forty-five women were selected based on their scores on the Short Manifest Anxiety Scale. The subjects were then randomly placed into three treatment groups: explicit, nonexplicit, and control. Analysis of the data revealed significant differences among the women in each of the three groups regarding sexual behavior. Sexual anxiety levels also differed between women in the explicit and control groups. Pre- and posttest manifest anxiety scores also showed a significant difference in the explicit-group women. It has been shown that anxious, coitally inexperienced women who are exposed to sexually explicit stimuli in a controlled situation will have lower sexual anxiety levels, have lowered manifest anxiety levels, and be more willing to participate in a greater variety of sexual behaviors under appropriate circumstances. The results of this study may aid those in the helping professions gain a better understanding of the effects sexual stimuli have on certain individuals. PMID:568923

  3. 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

  4. 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

  5. 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

  6. 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…

  7. The Effects of Explicit Teaching of Metastrategic Knowledge on Low- And High-Achieving Students

    ERIC Educational Resources Information Center

    Zohar, Anat; Peled, Bracha

    2008-01-01

    This study assessed the effects of explicit teaching of metastrategic knowledge (MSK) on gains of low-achieving (LA) and high-achieving (HA) 5th grade students (N=41). Gains in reasoning scores of students from the Experimental group (compared to students from the control group) were obtained on the strategic and on the metastrategic level. Gains…

  8. 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…

  9. 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…

  10. Effects of Explicit Timing on Elementary Students' Oral Reading Rates of Word Phrases

    ERIC Educational Resources Information Center

    Cates, Gary L.; Rhymer, Katrina N.

    2006-01-01

    An ABAB withdrawal design was used to investigate the effects of explicit timing on accurate oral reading rate of sight word phrases of four elementary students demonstrating difficulty with reading. During baseline the students were exposed to flash cards with sight word phrases and asked to read them out loud and were not made aware that they…

  11. 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…

  12. The Effect of Explicit Embedded Reflective Instruction on Nature of Science Understandings in Advanced Science Students

    ERIC Educational Resources Information Center

    Koksal, Mustafa Serdar; Cakiroglu, Jale; Geban, Omer

    2013-01-01

    The purpose of this study is to investigate the effectiveness of explicit-embedded-reflective (EER) instruction in nature of science (NOS) understandings of ninth-grade advanced science students. This study was conducted with 71 students, who were divided into three groups, by using non-equivalent quasi-experimental design. In the treatment…

  13. Effectiveness of Explicit and Constructivist Mathematics Instruction for Low-Achieving Students in the Netherlands

    ERIC Educational Resources Information Center

    Kroesbergen, Evelyn H.; Van Luit, Johannes E.H.; Maas, Cora J.M.

    2004-01-01

    In this study we compared the effects of smallgroup constructivist and explicit mathematics instruction in basic multiplication on low-achieving students' performance and motivation. A total of 265 students (aged 8-11 years) from 13 general and 11 special elementary schools for students with learning and/or behavior disorders participated in the…

  14. 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…

  15. 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…

  16. 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…

  17. Origin of Asymmetric Solvation Effects for Ions in Water and Organic Solvents Investigated Using Molecular Dynamics Simulations: The Swain Acity-Basity Scale Revisited.

    PubMed

    Reif, Maria M; Hünenberger, Philippe H

    2016-08-25

    The asymmetric solvation of ions can be defined as the tendency of a solvent to preferentially solvate anions over cations or cations over anions, at identical ionic charge magnitudes and effective sizes. Taking water as a reference, these effects are quantified experimentally for many solvents by the relative acity (A) and basity (B) parameters of the Swain scale. The goal of the present study is to investigate the asymmetric solvation of ions using molecular dynamics simulations, and to connect the results to this empirical scale. To this purpose, the charging free energies of alkali and halide ions, and of their hypothetical oppositely charged counterparts, are calculated in a variety of solvents. In a first set of calculations, artificial solvent models are considered that present either a charge or a shape asymmetry at the molecular level. The solvation asymmetry, probed by the difference in charging free energy between the two oppositely charged ions, is found to encompass a term quadratic in the ion charge, related to the different solvation structures around the anion and cation, and a term linear in the ion charge, related to the solvation structure around the uncharged ion-sized cavity. For these simple solvent models, the two terms are systematically counteracting each other, and it is argued that only the quadratic term should be retained when comparing the results of simulations involving physical solvents to experimental data. In a second set of calculations, 16 physical solvents are considered. The theoretical estimates for the acity A are found to correlate very well with the Swain parameters, whereas the correlation for B is very poor. Based on this observation, the Swain scale is reformulated into a new scale involving an asymmetry parameter Σ, positive for acitic solvents and negative for basitic ones, and a polarity parameter Π. This revised scale has the same predictive power as the original scale, but it characterizes asymmetry in an

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

    NASA Astrophysics Data System (ADS)

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

    2011-02-01

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

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

    PubMed

    Choi, Hwanho; Kang, Hongsuk; Park, Hwangseo

    2013-05-01

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

  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. Supramolecular effects in redox chemistry. Local solvation in basket-handle iron porphyrins containing an increasing number of secondary amide groups

    SciTech Connect

    Lexa, D.; Maillard, P.; Momenteau, M.; Saveant, J.M.

    1987-03-26

    Local solvation can be created by including dipolar groups in a molecular superstructure attached to a reacting center. Changes in reactivity of the latter ensue in a manner which is reminiscent of the modulation of the reactivity of the prosthetic groups by surrounding protein chains in enzymatic systems. Quite large effects can thus be obtained as shown by an electrochemical study of two redox reactions, Fe(II) + e/sup -/ in equilibrium Fe(I)/sup -/, Fe(I)/sup -/ + e/sup -/ in equilibrium Fe(0)/sup 2 -/, in a series of basket-handle iron prophyrins including an increasing number of secondary amide groups in the chains. The local solvation which results from the electrostatic interaction between the CONH dipoles and the negatively charged porphyrin centers is shown to build up as more and more CONH groups are included and to depend upon the distance between these groups and the reacting center.

  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. PMID:27042988

  3. 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.

  4. 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.

  5. The Effects of the Explicit Inquiry Routine on the Performance of Students with Learning Disabilities on One-Variable Equations

    ERIC Educational Resources Information Center

    Scheuermann, Amy M.; Deshler, Donald D.; Schumaker, Jean B.

    2009-01-01

    This study determined the effects of the Explicit Inquiry Routine (EIR), a teaching routine, on the math performance of 14 middle-school students with math learning disabilities. The routine integrates validated mathematical teaching practices from general education (inquiry, dialogue) and special education (intensive, explicit instruction) to…

  6. 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…

  7. 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.

  8. 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.

  9. Abnormal cerebral effective connectivity during explicit emotional processing in adults with autism spectrum disorder

    PubMed Central

    Fonlupt, Pierre; Hubert, Bénédicte; Tardif, Carole; Gepner, Bruno; Deruelle, Christine

    2008-01-01

    Several recent studies suggest that autism may result from abnormal communication between brain regions. We directly assessed this hypothesis by testing the presence of abnormalities in a model of the functional cerebral network engaged during explicit emotion processing in adults with high functioning autism or Asperger syndrome. Comparison of structural equation models revealed abnormal patterns of effective connectivity, with the prefrontal cortex as a key site of dysfunction. These findings provide evidence that abnormal long-range connectivity between structures of the ‘social brain’ could explain the socio-emotional troubles that characterize the autistic pathology. PMID:19015104

  10. Crossovers in supercooled solvation water: Effects of hydrophilic and hydrophobic interactions

    NASA Astrophysics Data System (ADS)

    Tatini Titantah, John; Karttunen, Mikko

    2015-05-01

    Systematic 8 ns ab initio molecular dynamics (AIMD) were performed to study the structure and dynamics of water in bulk and close to hydrophobic (CH3) and hydrophilic (carbonyl) groups of tetramethylurea (TMU). Dynamical behaviour showed two crossovers: The first around the hydrophobic group at TX =256 +/- 4 \\text{K} , and the second at 265+/- 5 \\text{K} related to the relative strengths of water-water and water-carbonyl hydrogen bonds (HBs). For bulk water, relaxation times appear to diverge at Tc = 213+/- 10 \\text{K} , rendering support to the liquid-liquid critical point hypothesis. To identify the effects due to the hydrophilic carbonyl group, systems of water with one methane molecule were used as references. Our findings are related to the structural and thermodynamic transitions reported for proteins in solution and may play a role in cold denaturation.

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

    PubMed

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

    2014-10-28

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

    Frach, Roland; Kast, Stefan M

    2014-12-11

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

  15. 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

  16. 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.

  17. 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

  18. 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

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

    PubMed

    Gaalswyk, Kari; Rowley, Christopher N

    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

  20. Quantifying solvated electrons' delocalization.

    PubMed

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

    2015-07-28

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

  1. 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.

  2. Explicit accounting of electronic effects on the Hugoniot of porous materials

    NASA Astrophysics Data System (ADS)

    Nayak, Bishnupriya; Menon, S. V. G.

    2016-03-01

    A generalized enthalpy based equation of state, which includes thermal electron excitations explicitly, is formulated from simple considerations. Its application to obtain Hugoniot of materials needs simultaneous evaluation of pressure-volume curve and temperature, the latter requiring solution of a differential equation. The errors involved in two recent papers [Huayun et al., J. Appl. Phys. 92, 5917 (2002); 92, 5924 (2002)], which employed this approach, are brought out and discussed. In addition to developing the correct set of equations, the present work also provides a numerical method to implement this approach. Constant pressure specific heat of ions and electrons and ionic enthalpy parameter, needed for applications, are calculated using a three component equation of state. The method is applied to porous Cu with different initial porosities. Comparison of results with experimental data shows good agreement. It is found that temperatures along the Hugoniot of porous materials are significantly modified due to electronic effects.

  3. 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.

  4. 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.

  5. 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.

  6. The Effects of Explicit Spelling Instruction in the Spanish EFL Classroom: Diagnosis, Development and Durability

    ERIC Educational Resources Information Center

    Canado, Maria Luisa Perez

    2006-01-01

    This paper aims to shed light on the explicit-implicit paradigm contention in connection with the foreign language area of English spelling. To this end, it frames the subject against the backdrop of the prolonged dispute between implicit, whole language, top-down, or whole-to-part approaches and explicit, traditional, bottom-up, or part-to-whole…

  7. Effect of Explicit and Implicit Instruction on Free Written Response Task Performance

    ERIC Educational Resources Information Center

    Andringa, Sible; de Glopper, Kees; Hacquebord, Hilde

    2011-01-01

    A classroom study was designed to test the hypothesis that explicit knowledge is used by second-language (L2) learners in a free written response task if that knowledge is present. Eighty-one 12-18-year-old learners of Dutch as an L2 took part in a computer-assisted language learning experiment receiving either explicit or implicit instruction…

  8. 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…

  9. 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…

  10. 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…

  11. 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

  12. Can explicit visual feedback of postural sway efface the effects of sensory manipulations on mediolateral balance performance?

    PubMed

    Cofré Lizama, L Eduardo; Pijnappels, Mirjam; Reeves, N Peter; Verschueren, Sabine M P; van Dieën, Jaap H

    2016-02-01

    Explicit visual feedback on postural sway is often used in balance assessment and training. However, up-weighting of visual information may mask impairments of other sensory systems. We therefore aimed to determine whether the effects of somatosensory, vestibular, and proprioceptive manipulations on mediolateral balance are reduced by explicit visual feedback on mediolateral sway of the body center of mass and by the presence of visual information. We manipulated sensory inputs of the somatosensory system by transcutaneous electric nerve stimulation on the feet soles (TENS) of the vestibular system by galvanic vestibular stimulation (GVS) and of the proprioceptive system by muscle-tendon vibration (VMS) of hip abductors. The effects of these manipulations on mediolateral sway were compared with a control condition without manipulation under three visual conditions: explicit feedback of sway of the body center of mass (FB), eyes open (EO), and eyes closed (EC). Mediolateral sway was quantified as the sum of energies in the power spectrum and as the energy at the dominant frequencies in each of the manipulation signals. Repeated-measures ANOVAs were used to test effects of each of the sensory manipulations, of visual conditions and their interaction. Overall, sensory manipulations increased body sway compared with the control conditions. Absence of normal visual information had no effect on sway, while explicit feedback reduced sway. Furthermore, interactions of visual information and sensory manipulation were found at specific dominant frequencies for GVS and VMS, with explicit feedback reducing the effects of the manipulations but not effacing these. PMID:26631143

  13. 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

  14. Clustering of metal atoms in organic media. II. Effect of support on nickel catalysts prepared by solvated metal atom dispersion (SMAD)

    SciTech Connect

    Matsuo, K.; Klabunde, K.J.

    1982-02-26

    Highly dispersed Ni/support catalysts were prepared from toluene-solvated nickel atoms (solvated metal atom dispersed or SMAD). Catalysts were prepared on MgO, Al/sub 2/O/sub 3/, SiO/sub 2/, and carbon, and their activities were tested for hydrogenolysis of methylcyclopentane, hydrogenation of toluene, dehydrogenation of isopropyl alcohol, and methanation of carbon monoxide. Conventional catalysts were also studied and compared with the SMAD systems. The effect of the support on SMAD catalyst activities was minimal for hydrogenolysis of methylcyclopentane, hydrogenation of toluene, and dehydration of isopropyl alcohol. However, conventional catalysts showed a significant effect of support when these reactions were studied. This difference between SMAD and conventional catalysts is attributed to the presence of an insulating layer of carbonaceous species between Ni and the support in the SMAD systems. Conversely, catalyst activity for methanation of carbon monoxide was significantly affected by support, especially MgO. This phenomenon reflects a synergistic effect of MgO when Ni is present, where CO can be adsorbed readily on MgO which apparently aids in the initial CO reduction step. The SMAD method in combination with high surface area supports yields highly dispersed catalysts with very small particle sizes. Carbon, a support with a particularly high surface area, allows formation of the smallest particle sizes, and this phenomenon is believed to indicate a direct dependency ofmetal particle size on the surface area of the support. The implications of this finding on the mechanism of particle formation are discussed, as well as the observation of optimum nickel particle size effects for the reactions studied. 5 figures, 4 tables.

  15. Effects of Intravenous Ketamine on Explicit and Implicit Measures of Suicidality in Treatment-Resistant Depression

    PubMed Central

    Price, Rebecca B.; Nock, Matthew K.; Charney, Dennis S.; Mathew, Sanjay J.

    2010-01-01

    Background Intravenous ketamine has shown rapid antidepressant effects in early trials, making it a potentially attractive candidate for depressed patients at imminent risk of suicide. The Implicit Association Test (IAT), a performance-based measure of association between two concepts, may have utility in suicide assessment. Methods Twenty-six patients with treatment-resistant depression were assessed for suicidality 2 hours prior to, and 24 hours following, a single subanesthetic dose of intravenous ketamine using the suicidality item of the Montgomery-Asberg Depression Rating Scale (MADRS-SI). Ten patients also completed IATs assessing implicit suicidal associations at comparable time points. In a second study, 9 patients received thrice-weekly ketamine infusions over a 12-day period. Results 24-hours after a single infusion, MADRS-SI scores were reduced by an average of 2.08 points on a 0–6 scale (p<.001; d=1.37), and 81% of patients received a rating of 0 or 1 post-infusion. Implicit associations between self- and escape-related words were also reduced following ketamine (p=.003; d=1.36), with reductions correlated across implicit and explicit measures. MADRS-SI reductions were sustained for 12 days by repeated-dose ketamine (2.9-point mean reduction; p<.001; d=2.42). Conclusions These preliminary findings support the premise that ketamine has rapid beneficial effects on suicidal cognition and warrants further study. PMID:19545857

  16. 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.

  17. 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.

  18. 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…

  19. The Effectiveness of a Skill Based Explicit Phonics Reading Program K-2 as Measured by Student Performance and Teacher Evaluation.

    ERIC Educational Resources Information Center

    Dakin, Alexandra B.

    This study focuses on the effectiveness and advantages of using an explicit phonics based reading program in kindergarten through second grade. The methods of decoding words that teachers introduce to the beginning readers must prove to be effective in introducing and building reading skills. Most recent studies have revisited and concurred with…

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

    PubMed Central

    Chen, Zhan; Wei, Guo-Wei

    2011-01-01

    to many other classic and quantum models. By using experimental data, we show that the present quantum formulation of our differential geometry based multiscale solvation model improves the prediction of our earlier models, and outperforms some explicit solvation model. PMID:22112067

  1. 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

  2. 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

  3. 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

  4. Anthropogenic Aerosol Effects on Sea Surface Temperatures: Mixed-Layer Ocean Experiments with Explicit Aerosol Representation

    NASA Astrophysics Data System (ADS)

    Dallafior, Tanja; Folini, Doris; Wild, Martin; Knutti, Reto

    2014-05-01

    Anthropogenic aerosols affect the Earth's radiative balance both through direct and indirect effects. These effects can lead to a reduction of the incoming solar radiation at the surface, i.e. dimming, which may lead to a change in sea surface temperatures (SST) or SST pattern. This, in turn, may affect precipitation patterns. The goal of the present work is to achieve an estimate of the equilibrium SST changes under anthropogenic aerosol forcing since industrialisation. We show preliminary results from mixed-layer ocean (MLO) experiments with explicit aerosol representation performed with ECHAM6-HAM. The (fixed) MLO heat flux into the deep ocean was derived from atmosphere only runs with fixed climatological SSTs (1961-1990 average) and present day (year 2000) aerosols and GHG burdens. Some experiments we repeated with an alternative MLO deep ocean heat flux (based on pre-industrial conditions) to test the robustness of our results with regard to this boundary condition. The maximum surface temperature responses towards anthropogenic aerosol and GHG forcing (separately and combined) were derived on a global and regional scale. The same set of experiments was performed with aerosol and GHG forcings representative of different decades over the past one and a half centuries. This allows to assess how SST patterns at equilibrium changed with changing aerosol (and GHG) forcing. Correlating SST responses with the change in downward clear-sky and all-sky shortwave radiation provides a first estimate of the response to anthropogenic aerosols. Our results show a clear contrast in hemispheric surface temperature response, as expected from the inter-hemispheric asymmetry of aerosol forcing The presented work is part of a project aiming at quantifying the effect of anthropogenic aerosol forcing on SSTs and the consequences for global precipitation patterns. Results from this study will serve as a starting point for further experiments involving a dynamic ocean model, which

  5. 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.

  6. 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. PMID:16834324

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

    PubMed Central

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

    2008-01-01

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

  8. Implicit and Explicit Attitudes Predict Smoking Cessation: Moderating Effects of Experienced Failure to Control Smoking and Plans to Quit

    PubMed Central

    Chassin, Laurie; Presson, Clark C.; Sherman, Steven J.; Seo, Dong-Chul; Macy, Jon

    2010-01-01

    The current study tested implicit and explicit attitudes as prospective predictors of smoking cessation in a Midwestern community sample of smokers. Results showed that the effects of attitudes significantly varied with levels of experienced failure to control smoking and plans to quit. Explicit attitudes significantly predicted later cessation among those with low (but not high or average) levels of experienced failure to control smoking. Conversely, however, implicit attitudes significantly predicted later cessation among those with high levels of experienced failure to control smoking, but only if they had a plan to quit. Because smoking cessation involves both controlled and automatic processes, interventions may need to consider attitude change interventions that focus on both implicit and explicit attitudes. PMID:21198227

  9. 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…

  10. Explicit Rap Music Lyrics and Attitudes toward Rape: The Perceived Effects on African American College Students' Attitudes.

    ERIC Educational Resources Information Center

    Wade, Bruce H.; Thomas-Gunnar, Cynthia A.

    1993-01-01

    Examines the effects of rap music on the attitudes and behaviors of students in historically black colleges. Interviews with 38 females indicate that they find explicit lyrics inappropriate and harmful to society, but they feel that rap music accurately represents some of the realities of gender relations between black males and females. (SLD)

  11. POTENTIAL EFFECTS OF A FOREST MANAGEMENT PLAN ON BACHMAN'S SPARROWS (AIMOPHILA AESTIVALIS): LINKING A SPATIALLY EXPLICIT MODEL WITH GIS

    EPA Science Inventory

    By combining a spatially explicit, individual-based population simulation model with a geographic information system, this study simulated the potential effects of a U.S. Forest management plan on the population dynamics of Bachman's Sparrow at the Savannah River Site, South Caro...

  12. Reexamining Effects of Form-Focused Instruction on L2 Pronunciation Development: The Role of Explicit Phonetic Information

    ERIC Educational Resources Information Center

    Saito, Kazuya

    2013-01-01

    The present study examines whether and to what degree providing explicit phonetic information (EI) at the beginning of form-focused instruction (FFI) on second language pronunciation can enhance the generalizability and magnitude of FFI effectiveness by increasing learners' ability to notice a new phone. Participants were 49 Japanese learners of…

  13. 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…

  14. Explicit Self-Regulated Strategy Development Versus Reciprocal Questioning: Effects on Expository Reading Comprehension Among Struggling Readers

    ERIC Educational Resources Information Center

    Mason, Linda H.

    2004-01-01

    The effects of 2 rigorous strategic approaches to reading comprehension for 32 5th-grade students who struggle with reading were investigated. The first approach, TWA (Think before reading, think While reading, think After reading), was taught following explicit self-regulated strategy development instructional procedures (K. R. Harris & S.…

  15. 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,…

  16. Collisional Family Formation and Scaling Laws: Effects of Porosity and Explicit Formation of Spinning Aggregates

    NASA Astrophysics Data System (ADS)

    Michel, Patrick; Jutzi, M.; Richardson, D. C.; Benz, W.

    2008-09-01

    Main belt asteroid families are the products of impact events. In recent years, we have been able for the first time to simulate the formation of families and reproduce their main properties. The fragmentation of the asteroid was computed using a 3D SPH hydrocode and the mutual gravitational interaction of the generated fragments was computed with a parallel N-body code (pkdgrav). In our previous simulations, all fragments during the gravitational phase were treated as spheres. We have improved our model by implementing a semi-rigid body approximation. The shapes and spins of the aggregates are preserved as clumps reaccumulate. We will present simulations of asteroid family formation including this explicit formation of spinning aggregates. Our model can provide some clues regarding the likely physical structure (surface, internal) of small bodies resulting from reaccumulation. Our earlier model of fragmentation was adapted to brittle materials with no porosity at microscales, limiting it to the study of families of S taxonomic type, believed to be composed of such material. Dark (C) type asteroids, Kuiper Belt objects and comets are believed to contain microporosity. We have extended our hydrocode to include the effect of porosity at a sub-resolution scale by adapting the so-called P-alpha model. A first validation at laboratory scale has been performed. We will show its application to dark-type family formation and to the characterization of the impact energy threshold for disruption (Q*D) of porous bodies as a function of their size. This work is supported by the ESA Advanced Concept Team (Ariadna study "NEO Encounter 2029"), the French Programme National de Planétologie, the Swiss National Science Foundation, NASA under Grant NNX08AM39G issued through the Office of Space Science, the NSF under Grant AST0708110, the cooperation program CNRS-JSPS 2008. We also thank the Mésocentre de Calcul-SIGAMM (Observatoire de la Côte d'Azur, France).

  17. 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…

  18. 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…

  19. Effects of Explicit Rules in Learning to Spell Open- and Closed-Syllable Words

    ERIC Educational Resources Information Center

    Hilte, Maartje; Reitsma, Pieter

    2011-01-01

    Second graders (N=222; 7.7 years of age) practiced with open- and closed-syllable words in a computer-assisted training program and appropriate spelling rules were either explicitly provided during practice or not. Also, children practiced either with a small set of exemplars or with a large set; the latter condition was expected to promote the…

  20. Structural effect of glyme-Li(+) salt solvate ionic liquids on the conformation of poly(ethylene oxide).

    PubMed

    Chen, Zhengfei; McDonald, Samila; Fitzgerald, Paul A; Warr, Gregory G; Atkin, Rob

    2016-06-01

    The conformation of 36 kDa polyethylene oxide (PEO) dissolved in three glyme-Li(+) solvate ionic liquids (SILs) has been investigated by small angle neutron scattering (SANS) and rheology as a function of concentration and compared to a previously studied SIL. The solvent quality of a SIL for PEO can be tuned by changing the glyme length and anion type. Thermogravimetric analysis (TGA) reveals that PEO is dissolved in the SILs through Li(+)-PEO coordinate bonds. All SILs (lithium triglyme bis(trifluoromethanesulfonyl)imide ([Li(G3)]TFSI), lithium tetraglyme bis(pentafluoroethanesulfonyl)imide ([Li(G4)]BETI), lithium tetraglyme perchlorate ([Li(G4)]ClO4) and the recently published [Li(G4)]TFSI) are found to be moderately good solvents for PEO but solvent quality decreases in the order [Li(G4)]TFSI ∼ [Li(G4)]BETI > [Li(G4)]ClO4 > [Li(G3)]TFSI due to decreased availability of Li(+) for PEO coordination. For the same glyme length, the solvent qualities of SILs with TFSI(-) and BETI(-) anions ([Li(G4)]TFSI and [Li(G4)]BETI) are very similar because they weakly coordinate with Li(+), which facilitates Li(+)-PEO interactions. [Li(G4)]ClO4 presents a poorer solvent environment for PEO than [Li(G4)]BETI because ClO4(-) binds more strongly to Li(+) and thereby hinders interactions with PEO. [Li(G3)]TFSI is the poorest PEO solvent of these SILs because G3 binds more strongly to Li(+) than G4. Rheological and radius of gyration (Rg) data as a function of PEO concentration show that the PEO overlap concentrations, c* and c**, are similar in the three SILs. PMID:27189677

  1. Single-Molecule Solvation-Shell Sensing

    NASA Astrophysics Data System (ADS)

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

    2009-02-01

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

  2. 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

  3. Solvation in supercritical water

    SciTech Connect

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

    1991-01-01

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

  4. 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

  5. Stress Effects on Working Memory, Explicit Memory, and Implicit Memory for Neutral and Emotional Stimuli in Healthy Men

    PubMed Central

    Luethi, Mathias; Meier, Beat; Sandi, Carmen

    2008-01-01

    Stress is a strong modulator of memory function. However, memory is not a unitary process and stress seems to exert different effects depending on the memory type under study. Here, we explored the impact of social stress on different aspects of human memory, including tests for explicit memory and working memory (for neutral materials), as well as implicit memory (perceptual priming, contextual priming and classical conditioning for emotional stimuli). A total of 35 young adult male students were randomly assigned to either the stress or the control group, with stress being induced by the Trier Social Stress Test (TSST). Salivary cortisol levels were assessed repeatedly throughout the experiment to validate stress effects. The results support previous evidence indicating complex effects of stress on different types of memory: A pronounced working memory deficit was associated with exposure to stress. No performance differences between groups of stressed and unstressed subjects were observed in verbal explicit memory (but note that learning and recall took place within 1 h and immediately following stress) or in implicit memory for neutral stimuli. Stress enhanced classical conditioning for negative but not positive stimuli. In addition, stress improved spatial explicit memory. These results reinforce the view that acute stress can be highly disruptive for working memory processing. They provide new evidence for the facilitating effects of stress on implicit memory for negative emotional materials. Our findings are discussed with respect to their potential relevance for psychiatric disorders, such as post traumatic stress disorder. PMID:19169362

  6. 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

  7. 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.

  8. 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

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

    NASA Astrophysics Data System (ADS)

    Yigit, Cemil; Heyda, Jan; Dzubiella, Joachim

    2015-08-01

    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. Solvation and kinetic isotope effects in H and D abstraction reactions from formate ions by D, H, and Mu atoms in aqueous solutions.

    SciTech Connect

    Lossack, A. M.; Roduner, E.; Bartels, D. M.; Chemistry; Univ. of Stuttgart

    2001-01-01

    Electron paramagnetic resonance free induction decay attenuation and muon spin rotation measurements were performed in the temperature range of liquid water for the reactions of the hydrogen isotopes D, H, and Mu with undeuterated and deuterated formate ions. Accurate rate constants were determined, and excellent Arrhenius behavior represented bywas found in all cases. Ab initio calculations at the MP2 and the QCISD level with the aug-cc-pvDZ basis set reveal that the reaction has no electronic barrier in the gas phase. This contrasts with quite sizeable activation energies observed in aqueous solution, and it suggests that the barrier is entirely solvent induced. Calculations at the above mentioned ab initio level using a polarized dielectric continuum for the solvated reaction system restore a realistic barrier and confirm this interpretation. It is shown that the solvent effect is a consequence of a pronounced change of polarization of the system along the reaction path. It may be more appropriate to describe the reaction as a consecutive electron-proton transfer rather than an H atom abstraction.

  11. 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

  12. The solvation structure of alprazolam.

    PubMed

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

    2016-08-10

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

  13. 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

  14. 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

  15. 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

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

    PubMed Central

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

    2011-01-01

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

  17. 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.

  18. 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. PMID:25494789

  19. Effect of Vapor Pressure Scheme on Multiday Evolution of SOA in an Explicit Model

    NASA Astrophysics Data System (ADS)

    Lee-Taylor, J.; Madronich, S.; Aumont, B.; Camredon, M.; Emmons, L. K.; Tyndall, G. S.; Valorso, R.

    2011-12-01

    Recent modeling of the evolution of Secondary Organic Aerosol (SOA) has led to the critically important prediction that SOA mass continues to increase for several days after emission of primary pollutants. This growth of organic aerosol in dispersing plumes originating from urban point sources has direct implications for regional aerosol radiative forcing. We investigate the robustness of predicted SOA mass growth downwind of Mexico City in the model GECKO-A (Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere), by assessing its sensitivity to the choice of vapor pressure prediction scheme. We also explore the implications for multi-day SOA mass growth of glassification / solidification of SOA constituents during aging. Finally we use output from the MOZART-4 chemical transport model to evaluate our results in the regional and global context.

  20. 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. PMID:25000374

  1. The effect of explicit, inquiry instruction on freshman college science majors' understanding of the nature of science

    NASA Astrophysics Data System (ADS)

    Kenyon, Lisa Orvik

    Reform efforts have placed strong emphasis on teaching practices that should help students learn about the nature of science. Researchers have examined two general instructional approaches, explicit and implicit, believed to be useful in teaching science. Of these two approaches, researchers emphasize explicit instruction as the more effective approach when enhancing students' views of the scientific endeavor (Abd-El-Khalick & Lederman, 2000; Bell, 2001; Billeh & Hasan, 1975; Carey & Stauss, 1968; Schwartz et al., 2000). Furthermore, recent studies (Schwartz et al ., 2000, 2001) indicate that teaching science inquiry through investigative activities and reflective discussions have demonstrated to be most effective for understanding science. The purpose of this study was to describe the effect of explicit, inquiry instruction on the understanding of freshman college science majors regarding the nature of science. Participants included 74 freshman college science majors, 50 students in the experimental group and 24 students in the control group. The experimental group was exposed to the treatment of the study, which took place in a Succeeding in Science course. The course content included explicit instruction on the nature of science, emphasizing scientific inquiry and the processes that scientists carry out in their work. The course reflected three aspects of inquiry-based science that are discussed in the Inquiry and the National Science Education Standards (2000) which are (1) to learn the principles and concepts of science; (2) to participate in scientific investigations; and (3) to reflect on the epistemology of science. The research design of this study used a pretest-posttest instrument, The Views of Nature of Science Questionnaire Form C (VNOS-C) (Lederman et al., 2001) and an essay paper at the end of the course to assess students' understanding about the nature of science. The results from the VNOS-C were analyzed using analysis of covariance in which the

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

    PubMed

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

    2014-08-12

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

  3. 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

  4. 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…

  5. 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.

  6. Trypsin-Ligand Binding Free Energies from Explicit and Implicit Solvent Simulations with Polarizable Potential

    PubMed Central

    Jiao, Dian; Zhang, Jiajing; Duke, Robert E.; Li, Guohui; Ren, Pengyu

    2009-01-01

    We have calculated the binding free energies of a series of benzamidine-like inhibitors to trypsin with a polarizable force field using both explicit and implicit solvent approaches. Free energy perturbation has been performed for the ligands in bulk water and in protein complex with molecular dynamics simulations. The calculated binding free energies are well within the accuracy of experimental measurement and the direction of change is predicted correctly in call cases. We analyzed the molecular dipole moments of the ligands in gas, water and protein environments. Neither binding affinity nor ligand solvation free energy in bulk water shows much dependence on the molecular dipole moments of the ligands. Substitution of the aromatic or the charged group in the ligand results in considerable change in the solvation energy in bulk water and protein whereas the binding affinity varies insignificantly due to cancellation. The effect of chemical modification on ligand charge distribution is mostly local. Replacing benzene with diazine has minimal impact on the atomic multipoles at the amidinium group. We have also utilized an implicit solvent based end-state approach to evaluate the binding free energies of these inhibitors. In this approach, the polarizable multipole model combined with Poisson-Boltzmann/surface area (PMPB/SA) provides the electrostatic interaction energy and the polar solvation free energy. Overall the relative binding free energies obtained from the PMPB/SA model are in good agreement with the experimental data. PMID:19399779

  7. 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. PMID:27236073

  8. 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

  9. 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

  10. 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

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

    PubMed

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

    2015-03-21

    The entropy of hydrophobic solvation has been explained as the result of ordered solvation structures, of hydrogen bonds, of the small size of the water molecule, of dispersion forces, and of solvent density fluctuations. We report a new approach to the calculation of the entropy of hydrophobic solvation, along with tests of and comparisons to several other methods. The methods are assessed in the light of the available thermodynamic and spectroscopic information on the effects of temperature on hydrophobic solvation. Five model hydrophobes in SPC/E water give benchmark solvation entropies via Widom's test-particle insertion method, and other methods and models are tested against these particle-insertion results. Entropies associated with distributions of tetrahedral order, of electric field, and of solvent dipole orientations are examined. We find these contributions are small compared to the benchmark particle-insertion entropy. Competitive with or better than other theories in accuracy, but with no free parameters, is the new estimate of the entropy contributed by correlations between dipole moments. Dipole correlations account for most of the hydrophobic solvation entropy for all models studied and capture the distinctive temperature dependence seen in thermodynamic and spectroscopic experiments. Entropies based on pair and many-body correlations in number density approach the correct magnitudes but fail to describe temperature and size dependences, respectively. Hydrogen-bond definitions and free energies that best reproduce entropies from simulations are reported, but it is difficult to choose one hydrogen bond model that fits a variety of experiments. The use of information theory, scaled-particle theory, and related methods is discussed briefly. Our results provide a test of the Frank-Evans hypothesis that the negative solvation entropy is due to structured water near the solute, complement the spectroscopic detection of that solvation structure by

  12. Lithium solvation in dimethyl sulfoxide-acetonitrile mixtures.

    PubMed

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

    2014-12-01

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

  13. 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.

  14. Lithium solvation in dimethyl sulfoxide-acetonitrile mixtures

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  15. 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.

  16. On the accuracy limits of orbital expansion methods: Explicit effects of k-functions on atomic and molecular energies

    NASA Astrophysics Data System (ADS)

    Valeev, Edward F.; Allen, Wesley D.; Hernandez, Rigoberto; Sherrill, C. David; Schaefer, Henry F.

    2003-05-01

    For selected first- and second-row atoms, correlation-optimized Gaussian k functions have been determined and used in the construction of septuple-ζ basis sets for the correlation-consistent cc-pVXZ and aug-cc-pVXZ series. Restricted Hartree-Fock (RHF) and second-order Møller-Plesset (MP2) total and pair energies were computed for H, N, O, F, S, H2, N2, HF, H2O, and (H2O)2 to demonstrate the consistency of the new septuple-ζ basis sets as extensions of the established (aug)-cc-pVXZ series. The pV7Z and aug-pV7Z sets were then employed in numerous extrapolation schemes on the test species to probe the accuracy limits of the conventional MP2 method vis-à-vis explicitly correlated (MP2-R12/A) benchmarks. For (singlet, triplet) pairs, (X+1/2)-n functional forms with n=(3, 5) proved best for extrapolations. The (mean abs. relative error, std. dev.) among the 73 singlet pair energies in the dataset is (1.96%, 0.54%) and (1.72%, 0.51%) for explicit computations with the pV7Z and aug-pV7Z basis sets, respectively, but only (0.07%, 0.09%) after two-point, 6Z/7Z extrapolations with the (X+1/2)-3 form. The effects of k functions on molecular relative energies were examined by application of the septuple-ζ basis sets to the barrier to linearity and the dimerization energy of water. In the former case, an inherent uncertainty in basis set extrapolations persists which is comparable in size to the error (≈20 cm-1) in explicit aug-pV7Z computations, revealing fundamental limits of orbital expansion methods in the domain of subchemical accuracy (0.1 kcal mol-1).

  17. 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

  18. 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

  19. 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.

  20. 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

  1. Affinity of HIV-1 antibody 2G12 with monosaccharides: a theoretical study based on explicit and implicit water models.

    PubMed

    Koyama, Yuka; Ueno-Noto, Kaori; Takano, Keiko

    2014-04-01

    In order to develop potential ligands to HIV-1 antibody 2G12 toward HIV-1 vaccine, binding mechanisms of the antibody 2G12 with the glycan ligand of D-mannose and D-fructose were theoretically examined. D-Fructose, whose molecular structure is slightly different from D-mannose, has experimentally shown to have stronger binding affinity to the antibody than that of D-mannose. To clarify the nature of D-fructose's higher binding affinity over D-mannose, we studied interaction between the monosaccharides and the antibody using ab initio fragment molecular orbital (FMO) method considering solvation effect as implicit model (FMO-PCM) as well as explicit water model. The calculated binding free energies of the glycans were qualitatively well consistent with the experimentally reported order of their affinities with the antibody 2G12. In addition, the FMO-PCM calculation elucidated the advantages of D-fructose over D-mannose in the solvation energy as well as the entropic contribution term obtained by MD simulations. The effects of explicit water molecules observed in the X-ray crystal structure were also scrutinized by means of FMO methods. Significant pair interaction energies among D-fructose, amino acids, and water molecules were uncovered, which indicated contributions from the water molecules to the strong binding ability of D-fructose to the antibody 2G12. These FMO calculation results of explicit water model as well as implicit water model indicated that the strong binding of D-fructose over D-mannose was due to the solvation effects on the D-fructose interaction energy. PMID:24583603

  2. 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.

  3. 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. PMID:26030450

  4. Effects of Explicit Subtraction Instruction on Fifth Grade Students with Learning Disabilities

    ERIC Educational Resources Information Center

    Ferreira, Danielle

    2009-01-01

    This study involved an investigation of the effects of strategy instruction integrated with the concrete-representational-abstract teaching sequence on students with learning disabilities. A multiple probe design across subjects with one replication was used in this study. Two sets of data were analyzed to determine effectiveness of the…

  5. 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…

  6. 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

  7. 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. PMID:26386396

  8. A new organized media: glycerol:N,N-dimethylformamide mixtures/AOT/n-heptane reversed micelles. The effect of confinement on preferential solvation.

    PubMed

    Durantini, Andrés M; Falcone, R Dario; Silber, Juana J; Correa, N Mariano

    2011-05-19

    In this work we investigate the behavior of the glycerol (GY):N,N-dimethylformamide (DMF) mixture in homogeneous and sodium 1,4-bis(2-ethylhexyl)sulfosuccinate (AOT)/n-heptane reversed micelles (RMs) media. To achieve this goal we have used the solvatochromic behavior of 1-methyl-8-oxyquinolinium betaine (QB) as an absorption probe, and dynamic light scattering (DLS). QB shows strong preferential solvation when it is dissolved in the GY:DMF mixture, and, as QB is a good hydrogen bond acceptor molecular probe, it is preferentially solvated by the GY-DMF hydrogen-bonded (H-bonded) species. On the other hand, when the GY:DMF mixture was investigated in AOT RMs, the results show that the mixture is encapsulated in the polar core of the AOT RMs. DLS confirms the formation of the GY:DMF/AOT/n-heptane RMs since an increase in the W(s)=([GY]+[DMF])/[AOT] values causes an increment in the RMs droplets sizes. The solvatochromic behavior of QB, which resides at the AOT RMs interface, shows that QB is mostly solvated by GY molecules, especially at low W(s) values. Thus, it seems that upon encapsulation inside the polar core of the AOT RMs, the GY-DMF interaction diminishes due to the strong AOT-GY interaction. (1)H NMR chemical shifts of GY and DMF measured in the different AOT RMs investigated shows that GY and DMF behave practically as noninteracting solvents inside the RMs. PMID:21517031

  9. 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

  10. Application of Roof-Shape Amines as Chiral Solvating Agents for Discrimination of Optically Active Acids by NMR Spectroscopy: Study of Match-Mismatch Effect and Crystal Structure of the Diastereomeric Salts.

    PubMed

    Gupta, Riddhi; Gonnade, Rajesh G; Bedekar, Ashutosh V

    2016-09-01

    Optically active roof-shape amines were prepared and scanned as chiral solvating agents to study molecular recognition of acids by NMR analysis. Three types of amines were studied to establish a match-mismatch effect for structurally diverse acid analytes. Single-crystal X-ray diffraction analysis was performed on the diastereomeric salts of roof-shape amines and both isomers of mandelic acid to establish molecular conformation and correlate the absolute configuration with the observed NMR shift. The present system also recognizes the two isomers of weakly acidic BINOL and its derivatives. PMID:27484455

  11. 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…

  12. 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,…

  13. 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.

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

    SciTech Connect

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

    1991-08-22

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

  15. 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.

  16. 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.

  17. 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.

  18. Why direct effects of predation complicate the social brain hypothesis: And how incorporation of explicit proximate behavioral mechanisms might help.

    PubMed

    van der Bijl, Wouter; Kolm, Niclas

    2016-06-01

    A growing number of studies have found that large brains may help animals survive by avoiding predation. These studies provide an alternative explanation for existing correlative evidence for one of the dominant hypotheses regarding the evolution of brain size in animals, the social brain hypothesis (SBH). The SBH proposes that social complexity is a major evolutionary driver of large brains. However, if predation both directly selects for large brains and higher levels of sociality, correlations between sociality and brain size may be spurious. We argue that tests of the SBH should take direct effects of predation into account, either by explicitly including them in comparative analyses or by pin-pointing the brain-behavior-fitness pathway through which the SBH operates. Existing data and theory on social behavior can then be used to identify precise candidate mechanisms and formulate new testable predictions. PMID:27174816

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

    PubMed

    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

  20. Lithium pinacolone enolate solvated by hexamethylphosphoramide.

    PubMed

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

    2015-06-17

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

  1. 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.

  2. Solvates of Dasatinib: Diversity and Isostructurality.

    PubMed

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

    2016-04-01

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

  3. Anthropogenic effects on global riverine sediment and water discharge - a spatially explicit analysis

    NASA Astrophysics Data System (ADS)

    Cohen, S.; Kettner, A. J.; Syvitski, J. P.

    2013-12-01

    Changes in global riverine water discharge and suspended sediment flux over a 50-year period, 1960-2010 are studied, applying a new version of the WBMsed (WBMsed v.2.0) global hydrological water balance model. A new floodplain component is introduced to better represent water and sediment dynamics during periods of overbank discharge. Validated against data from 16 globally distributed stations, WBMsed v.2.0 simulation results show considerable improvement over the original model. Anthropogenic impact on sediment and water discharge is evaluated by comparing global scale simulations with and without human drivers and parameters (agricultural land use, water intake form aquifers and rivers, sediment trapping in reservoirs, and human-induced soil erosion). The results show that, on average, global riverine sediment flux is reduced by approximately 25% by anthropogenic activities (almost exclusively due to trapping in reservoirs) while water discharge is reduced by about 2%. These results correspond to previous analysis by other research groups. Substantial global and intra-basin variability is observed (see Figure 1) for the first time. In some regions an opposite anthropogenic effect on sediment and water discharge was predicted (e.g. west Mississippi Basin, Rio Grande River, Indian subcontinent). We discuss the western part of the Mississippi Basin as an example of this intriguing anthropogenic impact. Figure 1. Percent change between disturbed and pristine simulations (with and without human footprint respectively) for sediment flux (top) and water discharge (bottom).

  4. 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…

  5. 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)

  6. Effect of solvation on induce-fit molecular recognition in supercritical fluid to organic crystals immobilized on a quartz crystal microbalance.

    PubMed

    Naito, M; Sasaki, Y; Dewa, T; Aoyama, Y; Okahata, Y

    2001-11-01

    The inclusion behavior of guest molecules to a solid apohost of an orthogonal anthracene-bis(resorcinol)tetraol (1) was investigated in supercritical carbon dioxide (scCO(2)) by using a 9 MHz quartz-crystal microbalance (QCM). Compound 1 forms crystals composed of molecular-sheet bound together by an extensive hydrogen-bonded network. The selective binding of gaseous ethyl acetate to the apohost-immobilized QCM in scCO(2) was observed, and the inclusion amount of ethyl acetate showed a drastic increase above a threshold concentration, [Guest](th) = 0.08 M, and the apparent Gibbs' free energy for the binding was DeltaG(app) = -1.3 kcal mol(-1). Similar selective bindings of ethyl acetate or ethanol had been observed in the gas phase and in water: [Guest](th) = 0.002 M with DeltaG(app) = -3.5 kcal mol(-1) and [Guest](th) = 0.5 M with DeltaG(app) = -0.41 kcal mol(-1), respectively. These values obtained in scCO(2) were intermediate between those in the gas and water phases. Since various physical properties (viscosity, density, polarity, diffusion constant, and solvation) of supercritical fluid are known to be intermediate between gas and liquid, these values clearly reflect the solvation behavior of guest molecules. Thus, the lower solvation of guest molecules indicates the lower threshold concentration and the larger binding energy in the following order: in air > in scCO(2) > in water. PMID:11686709

  7. Electronic absorption spectra and solvatochromic shifts by the vertical excitation model: solvated clusters and molecular dynamics sampling.

    PubMed

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

    2015-01-22

    A physically realistic treatment of solvatochromic shifts in liquid-phase electronic absorption spectra requires a proper account for various short- and long-range equilibrium and nonequilibrium solute-solvent interactions. The present article demonstrates that such a treatment can be accomplished using a mixed discrete-continuum approach based on the two-time-scale self-consistent state-specific vertical excitation model (called VEM) for electronic excitation in solution. We apply this mixed approach in combination with time-dependent density functional theory to compute UV/vis absorption spectra in solution for the n → π* ((1)A2) transition for acetone in methanol and in water, the π → π* ((1)A1) transition for para-nitroaniline (PNA) in methanol and in water, the n → π* ((1)B1) transition for pyridine in water, and the n → π* ((1)B1) transition for pyrimidine in water. Hydrogen bonding and first-solvation-shell-specific complexation are included by means of explicit solvent molecules, and solute-solvent dispersion is included by using the solvation model with state-specific polarizability (SMSSP). Geometries of microsolvated clusters were treated in two different ways, (i) using single liquid-phase global-minimum solute-solvent clusters containing up to two explicit solvent molecules and (ii) using solute-solvent cluster snapshots derived from molecular dynamics (MD) trajectories. The calculations in water involve using VEM/TDDFT excitation energies and oscillator strengths computed over 200 MD-derived solute-solvent clusters and convoluted with Gaussian functions. We also calculate ground- and excited-state dipole moments for interpretation. We find that inclusion of explicit solvent molecules generally improves the agreement with experiment and can be recommended as a way to include the effect of hydrogen bonding in solvatochromic shifts. PMID:25159827

  8. Continuum estimates of rotational dielectric friction and polar solvation

    SciTech Connect

    Maroncelli, M.

    1997-01-01

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

  9. 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. PMID:21279359

  10. 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

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

    PubMed

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

    2015-05-28

    We present a formulation of four-component relativistic self-consistent field (SCF) theory for a molecular solute described within the framework of the polarizable continuum model (PCM) for solvation. The linear response function for a four-component PCM-SCF state is also derived, as well as the explicit form of the additional contributions to the first-order response equations. The implementation of such a four-component PCM-SCF model, as carried out in a development version of the DIRAC program package, is documented. In particular, we present the newly developed application programming interface PCMSolver used in the actual implementation with DIRAC. To demonstrate the applicability of the approach, we present and analyze calculations of solvation effects on the geometries, electric dipole moments, and static electric dipole polarizabilities for the group 16 dihydrides H2X (X = O, S, Se, Te, Po). PMID:25412410

  12. Effects of Attention and Levels of Processing on Explicit and Implicit Memory Function with Interesting and Uninteresting Tasks in University Students

    NASA Astrophysics Data System (ADS)

    Mahdavian, Alireza; Kormi-Nouri, Reza

    This study aims to investigate the effect of attention and levels of processing on memory function and recalling words in two situations when students are interested in the subject and when they are not. This is an experimental study of 160 students conducted individually using a computer software. Results reveal focused attention, interest in the subject and deep processing caused the explicit memory to be at its highest level of functionality. On the contrary, shallow processing, divided attention and lack of interest in the subject plunged memory function into its lowest levels. Variables have different effects on attention, explicit and implicit memory. That is, interesting tasks with focused attention and deep processing have the highest effect on explicit memory in order. Also, interesting tasks, focused attention, respectively affect implicit memory. But level of processing does not affect implicit memory significantly.

  13. 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

  14. 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

  15. Variational approach for nonpolar solvation analysis

    PubMed Central

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

    2012-01-01

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

  16. Solvated Electrons on Metal Oxide Surfaces

    SciTech Connect

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

    2006-09-13

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

  17. 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.

  18. 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. PMID:18287007

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

    PubMed

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

    2012-02-23

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

  20. DFTr optimization and DFTr-MD studies of glucose, ten explicit water molecules enclosed by an implicit solvent, COSMO

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DFTr optimization studies are carried out on alpha/beta-glucose surrounded by ten explicit water molecules and the glucose/water super-molecule completely enclosed by an implicit solvation model, COSMO. Twenty one starting configurations of the explicit waters were first optimized empirically with t...

  1. Theoretical Characterization of Oxoanion, XOmn-, Solvation

    SciTech Connect

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

    2003-07-31

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

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

    PubMed

    Rana, Malay Kumar; Chandra, Amalendu

    2012-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Rana, Malay Kumar; Chandra, Amalendu

    2012-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-11-01

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

  5. Explicit Nature of Science and Argumentation Instruction in the Context of Socioscientific Issues: An effect on student learning and transfer

    NASA Astrophysics Data System (ADS)

    Khishfe, Rola

    2014-04-01

    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 learned in one socioscientific context into other similar contexts (familiar and unfamiliar). Participants were a total of 121 seventh grade students from two schools. The treatment involved an eight-week unit about the water usage and safety, which was taught by two teachers for two intact groups (Treatments I and II). Explicit NOS instruction was integrated for all groups. However, only the Treatment I groups had the additional explicit argumentation instruction. Participants were pre- and post-tested using an open-ended questionnaire and interviews about two socioscientific issues to assess their learning and transfer of argumentation skills and NOS understandings. Results showed improvements in the learning of argumentation practice and NOS understandings for Treatment I group participants. Similarly, there were improvements in the learning and transfer of NOS understandings for Treatment II group participants with only some improvements for the argumentation practice. Further, some of the Treatment I group participants made connections to argumentation when explicating their NOS understandings by the end of the study. Findings were discussed in light of classroom practice that utilizes an explicit approach, contextual approach, as well as an approach that integrates NOS and argumentation simultaneously.

  6. 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

  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. PMID:19048313

  8. 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

  9. Proton solvation in protic and aprotic solvents.

    PubMed

    Rossini, Emanuele; Knapp, Ernst-Walter

    2016-05-01

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

  10. The Effects of Explicit Feedback and Form--Meaning Processing on the Development of Pragmatic Proficiency in Consciousness-Raising Tasks

    ERIC Educational Resources Information Center

    Takimoto, Masahiro

    2006-01-01

    The present study evaluates the relative effectiveness of two types of input-based instruction, consciousness-raising instruction (the consciousness-raising task only) and consciousness-raising instruction with feedback (the consciousness-raising task + reactive explicit feedback) for teaching English polite requestive forms, involving 45 Japanese…

  11. The Effectiveness of Color Coding on Middle School Students' Ability To Differentiate Explicit from Implicit Information in Narrative and Expository Texts.

    ERIC Educational Resources Information Center

    Schraeder, Laura L.

    This study investigated the effectiveness of color coding, accomplished by highlighting, used to help students differentiate between exact meaning (explicit information) and implied meaning (implicit information) in both narrative (short story) and expository texts. Subjects were 78 sixth-grade students randomly enrolled in four language arts…

  12. 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…

  13. 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…

  14. The Effectiveness of a Highly Explicit, Teacher-Directed Strategy Instruction Routine: Changing the Writing Performance of Students with Learning Disabilities.

    ERIC Educational Resources Information Center

    Troia, Gary A.; Graham, Steve

    2002-01-01

    A study examined the effectiveness of a highly explicit, teacher-directed instructional routine used to teach three planning strategies to 20 fourth-fifth graders with learning disabilities. In comparison to peers who received process writing instruction, those taught goal setting, brainstorming, and organizing spent more time planning stories and…

  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. Polymorphs and Versatile Solvates of 7-Hydroxyisoflavone.

    PubMed

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

    2016-04-01

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

  17. Solvation dynamics in a protein surfactant complex

    NASA Astrophysics Data System (ADS)

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

    2003-08-01

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

  18. 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.

  19. 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

  20. 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,…

  1. Evaluating the Effects of a Systemic Intervention on First-Grade Teachers' Explicit Reading Instruction

    ERIC Educational Resources Information Center

    Nelson-Walker, Nancy J.; Fien, Hank; Kosty, Derek B.; Smolkowski, Keith; Smith, Jean Louise M.; Baker, Scott K.

    2013-01-01

    This article examines the efficacy of a multitiered systemic reading intervention for increasing the intensity and quality of explicit literacy instruction that teachers provide in first-grade classrooms. Schools ("j" = 16) were randomly assigned to the treatment or comparison condition. In both conditions, teachers ("i" = 42)…

  2. 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…

  3. 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.

  4. 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…

  5. 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…

  6. 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…

  7. Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation

    PubMed Central

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

    2014-01-01

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

  8. 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. 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.

  10. 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

  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. 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

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

    PubMed

    Deep, Shashank; Ahluwalia, J C

    2003-06-01

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

  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. Solvatochromism and the solvation structure of benzophenone.

    PubMed

    Elenewski, Justin E; Hackett, John C

    2013-06-14

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

  16. 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. PMID:15493239

  17. 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.

  18. 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

  19. 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

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2010-02-01

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

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

    PubMed Central

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

    2010-01-01

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

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

    SciTech Connect

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

    2010-02-14

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

  4. Femtosecond resolved solvation dynamics in polar solvents

    NASA Astrophysics Data System (ADS)

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

    1989-01-01

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

  5. 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…

  6. Sexual Priming, Gender Stereotyping, and Likelihood to Sexually Harass: Examining the Cognitive Effects of Playing a Sexually-Explicit Video Game.

    PubMed

    Yao, Mike Z; Mahood, Chad; Linz, Daniel

    2010-01-01

    The present study examines the short-term cognitive effects of playing a sexually explicit video game with female "objectification" content on male players. Seventy-four male students from a university in California, U.S. participated in a laboratory experiment. They were randomly assigned to play either a sexually-explicit game or one of two control games. Participants' cognitive accessibility to sexual and sexually objectifying thoughts was measured in a lexical decision task. A likelihood-to-sexually-harass scale was also administered. Results show that playing a video game with the theme of female "objectification" may prime thoughts related to sex, encourage men to view women as sex objects, and lead to self-reported tendencies to behave inappropriately towards women in social situations. PMID:20098511

  7. Roles of the scalar and vector components of the solvation effects on the vibrational properties of hydrogen- or halogen-bond accepting stretching modes.

    PubMed

    Torii, Hajime; Noge, Saori

    2016-04-21

    Solvation-induced vibrational frequency shifts and infrared (IR) intensity changes of the hydrogen- or halogen-bond accepting stretching modes, especially their dependence on the angular position of the hydrogen- or halogen-bond donating molecule, are examined theoretically. Calculations are carried out for some modes of hydrogen- or halogen-bonding molecular complexes, including the S[double bond, length as m-dash]O stretch of dimethyl sulfoxide-(13)C2H2O, the C[triple bond, length as m-dash]N stretch of acetonitrileH2O, and the amide I' mode of the N-methylacetamide-d1BrNC 1 : 1 complex. It is shown that, in all the example cases dealt with in this study, the frequency shift depends rather strongly on the hydrogen- or halogen-bond angle (e.g., S[double bond, length as m-dash]OH angle), with a larger low-frequency shift as the hydrogen or halogen bond becomes more bent, indicating the generality of the results obtained for the amide I' mode of the N-methylacetamide-d1(2)H2O 1 : 1 complex in a previous study. Contrary to our vague expectation, the frequency shift is not well correlated to the hydrogen- or halogen-bond distance or strength, but nevertheless, it is well reproduced by an electrostatic interaction model if it is carefully constructed by considering the scalar and vector components separately in a reasonable way. On the basis of this electrostatic interaction model, the reason why our vague expectation is not realized is clarified, and a unified understanding is achieved on the hydration-induced high-frequency shift of the C[triple bond, length as m-dash]N stretch and the low-frequency shifts of the S[double bond, length as m-dash]O stretch and amide I'. With regard to the IR intensity, it is shown that, in some of the example cases, it also has rather strong angular position dependence. The mechanism of the IR intensity changes is estimated by analyzing the dipole derivative vector, especially its angular relation with the hydrogen or halogen

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

    SciTech Connect

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

    2015-04-14

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

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

    PubMed

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

    2008-06-01

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

  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. Effects of solvation on the spin state of iron(III) in 2,8,12,18-tetrabutyl-3,7,13,17-tetramethyl-5,10-diazaporphyrinatoiron(III) chloride.

    PubMed

    Stuzhin, Pavel A; Nefedov, Sergei E; Kumeev, Roman S; Ul-Haq, Anwar; Minin, Vadim V; Ivanova, Svetlana S

    2010-06-01

    The chloroiron(III) complex of 2,8,12,18-tetrabutyl-3,7,13,17-tetramethyl-5,10-diazaporphyrin, [(Cl)FeMBDAP], was prepared and studied by X-ray crystallography and by solution (1)H NMR and UV-vis measurements. In the crystal structure of hemisolvate [(Cl)FeMBDAP] x 0.5CHCl(3), two nonequivalent [(Cl)FeMBDAP] units containing Fe1 and Fe2 are arranged in pi-dimers with considerable overlap on their concave sides. Axial chloride bonded to Fe2 is solvated by hydrogen bonding with CHCl(3). Parameters of the coordination pyramid have typical values for the spin-mixed (S = 3/2 / 5/2) Fe(III) complexes in the case of Fe1 and are characteristic for the pure intermediate-spin state for Fe2 (displacement from the (N(Pyr))(4) planes - 0.385 and 0.290 A and the average N(Pyr)-Fe bond lengths -1.992 and 1.954 A for Fe1 and Fe2, respectively). Effective magnetic moments in CHCl(3) and CH(2)Cl(2) capable of specific solvation of chloride by hydrogen bonding (4.5-4.6 micro(B) at 298 K) are indicative about mixed intermediate/high-spin state S = 3/2 / 5/2, with the S = 3/2 contribution increasing upon lowering of the temperature (4.02 micro(B) in CD(2)Cl(2) at 193 K). In nonsolvating CCl(4), C(6)D(6), and THF-d(8), the mu(eff) values are consistent with the predominantly high-spin state at ambient temperature (5.5-5.75 micro(B) at 298 K) and almost pure S = 5/2 state at low temperature (ca. 5.9 micro(B) in THF-d(8) below 270 K). Downfield isotropic shifts from 35 to 50 ppm are observed for alpha-alkyl protons and upfield shifts from -5 to -15 ppm for meso-CH protons, which is characteristic for the presence of the intermediate-spin state. The splitting of signals of the diastereotopic alpha-CH(2) protons is increased with growth of the S = 3/2 state contribution from 1.5 to 4 ppm in nonsolvating to 11 ppm in specifically solvating solvents at 298 K and further to 31 ppm at 193 K (in CD(2)Cl(2)). In the presence of DMSO addition and in methanol solution, the single CH(2) signal is

  12. Making Programming Knowledge Explicit.

    ERIC Educational Resources Information Center

    Navrat, Pavol; Rozinajova, Viera

    1993-01-01

    Addresses the question of how to write computer programs using explicit knowledge and rules-based systems. Highlights include the knowledge representation tool; the knowledge base on programming; and results of experiments that tested the system. Appendices include the set of rules for the experimental knowledge base and details of two…

  13. Electric Interfacial Layer of Modified Cellulose Nanocrystals in Aqueous Electrolyte Solution: Predictions by the Molecular Theory of Solvation.

    PubMed

    Lyubimova, Olga; Stoyanov, Stanislav R; Gusarov, Sergey; Kovalenko, Andriy

    2015-06-30

    The X-ray crystal structure-based models of Iα cellulose nanocrystals (CNC), both pristine and containing surface sulfate groups with negative charge 0-0.34 e/nm(2) produced by sulfuric acid hydrolysis of softwood pulp, feature a highly polarized "crystal-like" charge distribution. We perform sampling using molecular dynamics (MD) of the structural relaxation of neutral pristine and negatively charged sulfated CNC of various lengths in explicit water solvent and then employ the statistical mechanical 3D-RISM-KH molecular theory of solvation to evaluate the solvation structure and thermodynamics of the relaxed CNC in ambient aqueous NaCl solution at a concentration of 0.0-0.25 mol/kg. The MD sampling induces a right-hand twist in CNC and rearranges its initially ordered structure with a macrodipole of high-density charges at the opposite faces into small local spots of alternating charge at each face. This surface charge rearrangement observed for both neutral and charged CNC significantly affects the distribution of ions around CNC in aqueous electrolyte solution. The solvation free energy (SFE) of charged sulfated CNC has a minimum at a particular electrolyte concentration depending on the surface charge density, whereas the SFE of neutral CNC increases linearly with NaCl concentration. The SFE contribution from Na(+) counterions exhibits behavior similar to the NaCl concentration dependence of the whole SFE. An analysis of the 3D maps of Na(+) density distributions shows that these model CNC particles exhibit the behavior of charged nanocolloids in aqueous electrolyte solution: an increase in electrolyte concentration shrinks the electric interfacial layer and weakens the effective repulsion between charged CNC particles. The 3D-RISM-KH method readily treats solvent and electrolyte of a given nature and concentration to predict effective interactions between CNC particles in electrolyte solution. We provide CNC structural models and a modeling procedure for

  14. 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

  15. 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. PMID:23588797

  16. 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

  17. 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.

  18. Nonadiabatic dynamics of photoinduced proton-coupled electron transfer: comparison of explicit and implicit solvent simulations.

    PubMed

    Auer, Benjamin; Soudackov, Alexander V; Hammes-Schiffer, Sharon

    2012-07-01

    Theoretical approaches for simulating the ultrafast dynamics of photoinduced proton-coupled electron transfer (PCET) reactions in solution are developed and applied to a series of model systems. These processes are simulated by propagating nonadiabatic surface hopping trajectories on electron-proton vibronic surfaces that depend on the solute and solvent nuclear coordinates. The PCET system is represented by a four-state empirical valence bond model, and the solvent is treated either as explicit solvent molecules or as a dielectric continuum, in which case the solvent dynamics is described in terms of two collective solvent coordinates corresponding to the energy gaps associated with electron and proton transfer. The explicit solvent simulations reveal two distinct solvent relaxation time scales, where the faster time scale relaxation corresponds to librational motions of solvent molecules in the first solvation shell, and the slower time scale relaxation corresponds to the bulk solvent dielectric response. The charge transfer dynamics is strongly coupled to both the fast and slow time scale solvent dynamics. The dynamical multistate continuum theory is extended to include the effects of two solvent relaxation time scales, and the resulting coupled generalized Langevin equations depend on parameters that can be extracted from equilibrium molecular dynamics simulations. The implicit and explicit solvent approaches lead to qualitatively similar charge transfer and solvent dynamics for model PCET systems, suggesting that the implicit solvent treatment captures the essential elements of the nonequilibrium solvent dynamics for many systems. A combination of implicit and explicit solvent approaches will enable the investigation of photoinduced PCET processes in a variety of condensed phase systems. PMID:22651684

  19. 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

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

    PubMed

    Garcia-Ratés, Miquel; López, Núria

    2016-03-01

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

  1. Experimental and computational studies of polar solvation

    SciTech Connect

    Not Available

    1991-01-01

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

  2. 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.)

  3. FAST MOLECULAR SOLVATION ENERGETICS AND FORCE COMPUTATION.

    PubMed

    Bajaj, Chandrajit; Zhao, Wenqi

    2010-01-20

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

  4. Inertial solvation in femtosecond 2D spectra

    NASA Astrophysics Data System (ADS)

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

    2001-03-01

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

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

    PubMed

    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 the

  6. Methylene transfer or carbometalation? A theoretical study to determine the mechanism of lithium carbenoid-promoted cyclopropanation reactions in aggregation and solvation States.

    PubMed

    Ke, Zhuofeng; Zhao, Cunyuan; Phillips, David Lee

    2007-02-01

    Density functional theory calculations for the lithium carbenoid-promoted cyclopropanations in aggregation and solvation states are presented in order to investigate the controversy of the mechanistic dichotomy, that is, the methylene-transfer mechanism and the carbometalation mechanism. The methylene-transfer mechanism represents the reaction reality, whereas the carbometalation pathway does not appear to compete significantly with the methylene-transfer pathway and should be ruled out as a major factor. A simple model calculation for monomeric lithium carbenoid-promoted cyclopropanations with ethylene in the gas phase is not sufficient to reflect the reaction conditions accurately or to determine the reaction mechanism since its result is inconsistent with the experimental facts. The aggregated lithium carbenoids are the most probable reactive species in the reaction system. The calculated reaction barriers of the methylene-transfer pathways are 10.1 and 8.0 kcal/mol for the dimeric (LiCH2F)2 and tetrameric (LiCH2F)4 species, respectively, compared with the reaction barrier of 16.0 kcal/mol for the monomeric LiCH2F species. In contrast, the reaction barriers of the carbometalation pathways are 26.8 kcal/mol for the dimeric (LiCH2F)2 and 33.9 kcal/mol for the tetrameric (LiCH2F)4 species, compared with the reaction barrier of 12.5 kcal/mol for the monomeric LiCH2F species. The effects of solvation were investigated by explicit coordination of the solvent molecules to the lithium centers. This solvation effect is found to enhance the methylene-transfer pathway, while it is found to impede the carbometalation pathway instead. The combined effects of the aggregation and solvation lead to barriers to reaction in the range of 7.2-9.0 kcal/mol for lithium carbenoid-promoted cyclopropanation reactions along the methylene-transfer pathway. Our computational results are in good agreement with the experimental observations. PMID:17253804

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

    PubMed

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

    2016-03-15

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

  8. 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.

  9. 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.

  10. A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation.

    PubMed Central

    Young, M A; Ravishanker, G; Beveridge, D L

    1997-01-01

    We report the results of four new molecular dynamics (MD) simulations on the DNA duplex of sequence d(CGCGAATTCGCG)2, including explicit consideration of solvent water, and a sufficient number of Na+ counterions to provide electroneutrality to the system. Our simulations are configured particularly to characterize the latest MD models of DNA, and to provide a basis for examining the sensitivity of MD results to the treatment of boundary conditions, electrostatics, initial placement of solvent, and run lengths. The trajectories employ the AMBER 4.1 force field. The simulations use particle mesh Ewald summation for boundary conditions, and range in length from 500 ps to 5.0 ns. Analysis of the results is carried out by means of time series for conformationalm, helicoidal parameters, newly developed indices of DNA axis bending, and groove widths. The results support a dynamically stable model of B-DNA for d(CGCGAATTCGCG)2 over the entire length of the trajectory. The MD results are compared with corresponding crystallographic and NMR studies on the d(CGCGAATTCGCG)2 duplex, and placed in the context of observed behavior of B-DNA by comparisons with the complete crystallographic data base of B-form structures. The calculated distributions of mobile solvent molecules, both water and counterions, are displayed. The calculated solvent structure of the primary solvation shell is compared with the location of ordered solvent positions in the corresponding crystal structure. The results indicate that ordered solvent positions in crystals are roughly twice as structured as bulk water. Detailed analysis of the solvent dynamics reveals evidence of the incorporation of ions in the primary solvation of the minor groove B-form DNA. The idea of localized complexation of otherwise mobile counterions in electronegative pockets in the grooves of DNA helices introduces an additional source of sequence-dependent effects on local conformational, helicoidal, and morphological structure

  11. 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

  12. 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

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

    PubMed

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

    2013-03-21

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

  14. Parameter optimization in differential geometry based solvation models.

    PubMed

    Wang, Bao; Wei, G W

    2015-10-01

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

  15. 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

  16. The explicit token store

    SciTech Connect

    Culler, D.E. ); Papadopoulos, G.M. )

    1990-12-01

    This paper presents an unusually simple approach to dynamic dataflow execution, called the Explicit Token Store (ETS) architecture, and its current realization in Monsoon. The essence of dynamic dataflow execution is captured by a simple transition on state bits associated with storage local to a processor. Low-level storage management is performed by the compiler in assigning nodes to slots in an activation frame, rather than dynamically in hardware. The processor is simple, highly pipelined, and quite general. There is exactly one instruction executed for each action on the dataflow graph. Thus, the machine-oriented ETS model provides new insight into the real cost of direct execution of dataflow graphs.

  17. 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

  18. Ion solvation in aqueous and non-aqueous solvents

    NASA Astrophysics Data System (ADS)

    Arslanargin, Ayse

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

  19. Cells containing solvated electron lithium negative electrodes

    NASA Astrophysics Data System (ADS)

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

    1989-12-01

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

  20. Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation.

    PubMed

    Khandogin, Jana; Gregersen, Brent A; Thiel, Walter; York, Darrin M

    2005-05-19

    The present paper describes the extension of a recently developed smooth conductor-like screening model for solvation to a d-orbital semiempirical framework (MNDO/d-SCOSMO) with analytic gradients that can be used for geometry optimizations, transition state searches, and molecular dynamics simulations. The methodology is tested on the potential energy surfaces for separating ions and the dissociative phosphoryl transfer mechanism of methyl phosphate. The convergence behavior of the smooth COSMO method with respect to discretization level is examined and the numerical stability of the energy and gradient are compared to that from conventional COSMO calculations. The present method is further tested in applications to energy minimum and transition state geometry optimizations of neutral and charged metaphosphates, phosphates, and phosphoranes that are models for stationary points in transphosphorylation reaction pathways of enzymes and ribozymes. The results indicate that the smooth COSMO method greatly enhances the stability of quantum mechanical geometry optimization and transition state search calculations that would routinely fail with conventional solvation methods. The present MNDO/d-SCOSMO method has considerable computational advantages over hybrid quantum mechanical/molecular mechanical methods with explicit solvation, and represents a potentially useful tool in the arsenal of multi-scale quantum models used to study biochemical reactions. PMID:16852180

  1. Frequency Effects in Language Processing: A Review with Implications for Theories of Implicit and Explicit Language Acquisition.

    ERIC Educational Resources Information Center

    Ellis, Nick C.

    2002-01-01

    Shows how language processing is intimately tuned to input frequency. Examples are given of frequency effects in the processing of phonology, phonotactics, reading, spelling, lexis, morphosyntax, formulaic language, language comprehension, grammaticality, sentence production, and syntax. (Author/VWL)

  2. A Protein Solvation Model Based on Residue Burial.

    PubMed

    Ceres, Nicoletta; Pasi, Marco; Lavery, Richard

    2012-06-12

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

  3. Electrostatics of solvated systems in periodic boundary conditions

    NASA Astrophysics Data System (ADS)

    Andreussi, Oliviero; Marzari, Nicola

    2014-12-01

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

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

    PubMed

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

    2014-01-23

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

  5. 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

  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. PMID:16828533

  9. 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.

  10. Molecular hydrogen solvated in water - A computational study

    NASA Astrophysics Data System (ADS)

    Śmiechowski, Maciej

    2015-12-01

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

  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. 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

  13. Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects

    NASA Astrophysics Data System (ADS)

    Alakent, Burak; Camurdan, Mehmet C.; Doruker, Pemra

    2005-10-01

    Time series analysis tools are employed on the principal modes obtained from the Cα trajectories from two independent molecular-dynamics simulations of α-amylase inhibitor (tendamistat). Fluctuations inside an energy minimum (intraminimum motions), transitions between minima (interminimum motions), and relaxations in different hierarchical energy levels are investigated and compared with those encountered in vacuum by using different sampling window sizes and intervals. The low-frequency low-indexed mode relationship, established in vacuum, is also encountered in water, which shows the reliability of the important dynamics information offered by principal components analysis in water. It has been shown that examining a short data collection period (100ps) may result in a high population of overdamped modes, while some of the low-frequency oscillations (<10cm-1) can be captured in water by using a longer data collection period (1200ps). Simultaneous analysis of short and long sampling window sizes gives the following picture of the effect of water on protein dynamics. Water makes the protein lose its memory: future conformations are less dependent on previous conformations due to the lowering of energy barriers in hierarchical levels of the energy landscape. In short-time dynamics (<10ps), damping factors extracted from time series model parameters are lowered. For tendamistat, the friction coefficient in the Langevin equation is found to be around 40-60cm-1 for the low-indexed modes, compatible with literature. The fact that water has increased the friction and that on the other hand has lubrication effect at first sight contradicts. However, this comes about because water enhances the transitions between minima and forces the protein to reduce its already inherent inability to maintain oscillations observed in vacuum. Some of the frequencies lower than 10cm-1 are found to be overdamped, while those higher than 20cm-1 are slightly increased. As for the long

  14. Effects of Syntactic Complexity, Semantic Reversibility and Explicitness on Discourse Comprehension in Persons with Aphasia and in Healthy Controls

    PubMed Central

    Levy, Joshua; Hoover, Elizabeth; Waters, Gloria; Kiran, Swathi; Caplan, David; Berardino, Alex; Sandberg, Chaleece

    2012-01-01

    Purpose Prior studies of discourse comprehension have concluded that the deficits of persons with aphasia (PWA) in syntactically based comprehension of sentences in isolation are not predictive of deficits in comprehending sentences in discourse (Brookshire & Nicholas, 1984; Caplan & Evans, 1990). However, these studies used semantically constrained sentences in discourse, which do not require syntactic analysis to be understood. We developed a discourse task to assess the effect of syntactic complexity, among other factors, upon discourse comprehension. Method 38 PWA and 30 healthy control subjects were presented with passages that contained 2 – 3 semantically reversible sentences that were either syntactically simple or syntactically complex. The passages were presented auditorily and comprehension was assessed with the auditory and written presentation of four multiple-choice questions immediately following each passage. Results Passages with syntactically simple sentences were better understood than passages with syntactically complex sentences. Moreover, semantically constrained sentences were more likely to be accurately interpreted than semantically reversible sentences. Comprehension accuracy on our battery correlated positively with comprehension accuracy on an existing battery. Conclusions The results show that the presence of semantically reversible syntactically complex sentences in a passage affects comprehension of the passage in both PWA and neurologically healthy individuals. PMID:22355004

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

    SciTech Connect

    Chialvo, Ariel A

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

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

  17. Good and Poor Readers' Use of Explicitly Cued Graphic Aids.

    ERIC Educational Resources Information Center

    Reinking, David; And Others

    1988-01-01

    Investigates the effects of explicitly cuing graphic aids in accompanying text. Finds (1) explicit cuing increases attention to graphic aids and recall of information displayed in graphic aids, and (2) poor readers' comprehension of illustrated text is improved by explicit cuing of graphic aids. (RS)

  18. 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.

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

    PubMed

    van Noort, Paul

    2013-01-01

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

  20. 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. PMID:25849810

  1. Discovery of the glycogen phosphorylase-modulating activity of a resveratrol glucoside by using a virtual screening protocol optimized for solvation effects.

    PubMed

    Mavrokefalos, Nikolaos; Myrianthopoulos, Vassilios; Chajistamatiou, Aikaterini S; Chrysina, Evangelia D; Mikros, Emmanuel

    2015-04-01

    The identification of natural products that can modulate blood glucose levels is of great interest as it can possibly facilitate the utilization of mild interventions such as herbal medicine or functional foods in the treatment of chronic diseases like diabetes. One of the established drug targets for antihyperglycemic therapy is glycogen phosphorylase. To evaluate the glycogen phosphorylase inhibitory properties of an in-house compound collection consisting to a large extent of natural products, a stepwise virtual and experimental screening protocol was devised and implemented. The fact that the active site of glycogen phosphorylase is highly hydrated emphasized that a methodological aspect needed to be efficiently addressed prior to an in silico evaluation of the compound collection. The effect of water molecules on docking calculations was regarded as a key parameter in terms of virtual screening protocol optimization. Statistical analysis of 125 structures of glycogen phosphorylase and solvent mapping focusing on the active site hydration motif in combination with a retrospective screening revealed the importance of a set of 29 crystallographic water molecules for achieving high enrichment as to the discrimination between active compounds and inactive decoys. The scaling of Van der Waals radii of system atoms had an additional effect on screening performance. Having optimized the in silico protocol, a prospective evaluation of the in-house compound collection derived a set of 18 top-ranked natural products that were subsequently evaluated in vitro for their activity as glycogen phosphorylase inhibitors. Two phenolic glucosides with glycogen phosphorylase-modulating activity were identified, whereas the most potent compound affording mid-micromolar inhibition was a glucosidic derivative of resveratrol, a stilbene well-known for its wide range of biological activities. Results show the possible phytotherapeutic and nutraceutical potential of products common in

  2. Role of the central arginine R133 toward the ion selectivity of the phosphate specific channel OprP: effects of charge and solvation.

    PubMed

    Modi, Niraj; Bárcena-Uribarri, Iván; Bains, Manjeet; Benz, Roland; Hancock, Robert E W; Kleinekathöfer, Ulrich

    2013-08-20

    The outer membrane porin OprP of Pseudomonas aeruginosa forms a highly specific phosphate selective channel. This channel is responsible for the high-affinity uptake of phosphate ions into the periplasmic space of the bacteria. A detailed investigation of the structure-function relationship of OprP is inevitable to decipher the anion and phosphate selectivity of this porin in particular and to broaden the present understanding of the ion selectivity of different channels. To this end we investigated the role of the central arginine of OprP, R133, in terms of its effects in selectivity and ion transport properties of the pore. Electrophysiological bilayer measurements and free-energy molecular dynamics simulations were carried out to probe the transport of different ions through various R133 mutants. For these mutants, the change in phosphate binding specificity, ion conduction, and anion selectivity was determined and compared to previous molecular dynamic calculations and electrophysiological measurements with wild-type OprP. Molecular analysis revealed a rather particular role of arginine 133 and its charge, while at the same time this residue together with the network of other residues, namely, D94 and Y114, has the ability to dehydrate the permeating ion. These very specific features govern the ion selectivity of OprP. PMID:23875754

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

    PubMed

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

    2015-09-16

    The solvation of Li+ with 11 nonaqueous solvents commonly used as electrolytes for lithium batteries was studied. The solvation preferences of different solvents were compared by means of electrospray mass spectrometry and collision-induced dissociation. The relative strength of the solvent for the solvation of Li+ was determined. The Lewis acidity of the solvated Li+ cations was determined by the preferential solvation of the solvent in the solvation shell. The kinetics of the catalytic disproportionation of the O2•- depends on the relative Lewis acidity of the solvated Li+ ion. The impact of the solvated Li+ cation on the O2 redox reaction was also investigated. PMID:26301499

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

    PubMed Central

    Haranczyk, Maciej; Gutowski, Maciej; Warshel, Arieh

    2008-01-01

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

  5. 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.

  6. Partial solvation parameters and mixture thermodynamics.

    PubMed

    Panayiotou, Costas

    2012-06-21

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

  7. A connectionist approach to making the predictability of English orthography explicit to at-risk beginning readers: evidence for alternative, effective strategies.

    PubMed

    Berninger, V W; Abbott, R D; Brooksher, R; Lemos, Z; Ogier, S; Zook, D; Mostafapour, E

    2000-01-01

    A case is made (and illustrated with empirical data with children) for connectionist models that are not only computationally explicit but also instructionally explicit. First-graders (N = 128) at the bottom of their classes in reading (average 11.5 percentile on nationally normed tests) participated in a 3-layer intervention. In the first layer, kept constant for all treatment groups, the alphabet principle was taught, making functional spelling units and alternations explicit. In the second layer, which varied systematically across treatment groups, children received different kinds of tutor modeling in learning a set of words of varying spelling-sound predictability, using different connections between printed and spoken words, singly or in combination. In the third layer, also kept constant, children read and discussed illustrated books. Over the 4-month, 24-lesson intervention, all 7 treatment groups in the second layer improved more in word-specific learning than a contact control group that received phonological and orthographic awareness training without explicit instruction on orthographic-phonological connections. Of these 7, only 3 kinds of explicit modeling (whole word, letter-phoneme, and combined whole word and letter-phoneme) resulted in greater transfer to untrained words than the contact control or the other 4 kinds of explicit modeling. Results are discussed in reference to the controversy over whether dual route or connectionist models best account for the acquisition of reading. PMID:10955205

  8. Solvation of electrolytes and nonelectrolytes in aqueous solutions.

    PubMed

    Afanas'ev, V N

    2011-05-26

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  10. 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.

  11. 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…

  12. Solvation dynamics and rotational relaxation of coumarin 153 in mixed micelles of Triton X-100 and cationic gemini surfactants: effect of composition and spacer chain length of gemini surfactants.

    PubMed

    Sonu; Kumari, Sunita; Saha, Subit K

    2016-01-21

    Solvation dynamics and rotational relaxation of coumarin 153 (C-153) in mixed micelles of non-ionic surfactant, Triton X-100 and a series of cationic gemini surfactants, 12-s-12, 2Br with varying polymethylene spacer chain length (s = 3, 6, 8, 12) at different bulk mole fractions of a surfactant were studied. Studies were carried out by means of UV-Vis absorption, steady-state fluorescence and fluorescence anisotropy, time-resolved fluorescence and fluorescence anisotropy, and dynamic light scattering measurements. While micropolarity of the environment around C-153 in mixed micelles increased, the microviscosity decreased with increasing amount of a gemini surfactant. This is because the thickness of the Stern layer of micelles increases as a result of greater extent of penetration of water molecules. Solvation dynamics and rotational relaxation of C-153 become faster with increasing mole fraction of a gemini surfactant in the mixed micelles. Increasing the thickness of the Stern layer leads to an increase in the number of water molecules hydrogen bonded among themselves, resulting in an increase in polarity and microfluidity of the environment. At a given bulk mole fraction of a surfactant, the microviscosity of micelles decreases with increasing the spacer chain length of the gemini surfactant resulting in an increase in the rate of the rotational relaxation process. However, at a given bulk mole fraction of a surfactant, solvation dynamics becomes slower with increasing spacer chain length from s = 3 to 8 because of the increasing degree of counter ion dissociation. The slow rotational relaxation process is mainly due to the lateral diffusion of C-153 along the surface of the micelles. Rotationalmotion of the micelle as a whole is much slower than the lateral diffusion of C-153. PMID:26750436

  13. 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.

  14. 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

  15. 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

  16. A systematic study of chloride ion solvation in water using van der Waals inclusive hybrid density functional theory

    NASA Astrophysics Data System (ADS)

    Bankura, Arindam; Santra, Biswajit; DiStasio, Robert A., Jr.; Swartz, Charles W.; Klein, Michael L.; Wu, Xifan

    2015-09-01

    In this work, the solvation and electronic structure of the aqueous chloride ion solution was investigated using density functional theory (DFT) based ab initio molecular dynamics (AIMD). From an analysis of radial distribution functions, coordination numbers, and solvation structures, we found that exact exchange (Exx) and non-local van der Waals (vdW) interactions effectively weaken the interactions between the Cl- ion and the first solvation shell. With a Cl-O coordination number in excellent agreement with experiment, we found that most configurations generated with vdW-inclusive hybrid DFT exhibit sixfold coordinated distorted trigonal prism structures, which is indicative of a significantly disordered first solvation shell. By performing a series of band structure calculations on configurations generated from AIMD simulations with varying DFT potentials, we found that the solvated ion orbital energy levels (unlike the band structure of liquid water) strongly depend on the underlying molecular structures. In addition, these orbital energy levels were also significantly affected by the DFT functional employed for the electronic structure; as the fraction of Exx was increased, the gap between the highest occupied molecular orbital of Cl- and the valence band maximum of liquid water steadily increased towards the experimental value.

  17. 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

  18. Solvation and Cavity Occupation in Biomolecules

    PubMed Central

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

    2014-01-01

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

  19. 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. 3D-RISM-KH molecular theory of solvation and density functional theory investigation of the role of water in the aggregation of model asphaltenes.

    PubMed

    da Costa, L M; Hayaki, S; Stoyanov, S R; Gusarov, S; Tan, X; Gray, M R; Stryker, J M; Tykwinski, R; Carneiro, J Walkimar de M; Sato, H; Seidl, P R; Kovalenko, A

    2012-03-21

    We applied a multiscale modeling approach that involves the statistical-mechanical three-dimensional reference interaction site model with the Kovalenko-Hirata closure approximation (3D-RISM-KH molecular theory of solvation) as well as density functional theory (DFT) of electronic structure to study the role of water in aggregation of the asphaltene model compound 4,4'-bis(2-pyren-1-yl-ethyl)-2,2'-bipyridine (PBP) [X. Tan, H. Fenniri and M. R. Gray, Energy Fuels, 2008, 22, 715]. The solvation free energy and potential of mean force predicted by 3D-RISM-KH reveal favorable pathways for disaggregation of PBP dimers in pure versus water-saturated chloroform solvent. The water density distribution functions elucidate hydrogen bonding preferences and water bridge formation between PBP monomers. The ΔG(298) values of -5 to -7 kcal mol(-1) for transfer of water molecules in chloroform to a state interacting with PBP molecules are in agreement with experimental results. Geometry optimization and thermochemistry analysis of PBP dimers with and without water bridges using WB97Xd/6-31G(d,p) predict that both PBP dimerization and dimer stabilization by water bridges are spontaneous (ΔG(298) < 0). The (1)H NMR chemical shifts of PBP monomers and dimers predicted using the gauge-independent atomic orbital method and polarizable continuum model for solvation in chloroform are in an excellent agreement with the experimental results for dilute and concentrated PBP solutions in chloroform, respectively [X. Tan, H. Fenniri and M. R. Gray, Energy Fuels, 2009, 23, 3687]. The DFT calculations of PBP dimers with explicit water show that bridges containing 1-3 water molecules lead to stabilization of PBP dimers. Additional water molecules form hydrogen bonds with these bridges and de-shield the PBP protons, negating the effect of water on the (1)H(C3) NMR chemical shift of PBP, in agreement with experiment. The ΔG(298) results show that hydrogen bonding to water and water

  4. 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 ...

  5. 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.

  6. 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.

  7. 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.

  8. Computational 17O-NMR spectroscopy of organic acids and peracids: comparison of solvation models.

    PubMed

    Baggioli, Alberto; Crescenzi, Orlando; Field, Martin J; Castiglione, Franca; Raos, Guido

    2013-01-28

    We examine several computational strategies for the prediction of the (17)O-NMR shielding constants for a selection of organic acids and peracids in aqueous solution. In particular, we consider water (the solvent and reference for the chemical shifts), hydrogen peroxide, acetic acid, lactic acid and peracetic acid. First of all, we demonstrate that the PBE0 density functional in combination with the 6-311+G(d,p) basis set provides an excellent compromise between computational cost and accuracy in the calculation of the shielding constants. Next, we move on to the problem of the solvent representation. Our results confirm the shortcomings of the Polarizable Continuum Model (PCM) in the description of systems susceptible to strong hydrogen bonding interactions, while at the same time they demonstrate its usefulness within a molecular-continuum approach, whereby PCM is applied to describe the solvation of the solute surrounded by some explicit solvent molecules. We examine different models of the solvation shells, sampling their configurations using both energy minimizations of finite clusters and molecular dynamics simulations of bulk systems. Hybrid molecular dynamics simulations, in which the solute is described at the PM6 semiempirical level and the solvent by the TIP3P model, prove to be a promising sampling method for medium-to-large sized systems. The roles of solvent shell size and structure are also briefly discussed. PMID:23223608

  9. Surface of active polarons: A semiexplicit solvation method for biomolecular dynamics

    NASA Astrophysics Data System (ADS)

    Kimura, S. Roy; Brower, Richard C.; Zhang, Chao; Sugimori, Masamichi

    2000-05-01

    We present a strategy for solvating biomolecules in molecular dynamics or Monte Carlo simulations. The method employs a thin layer (often monomolecular) of explicit water with additional external forces representing the electrostatics, pressure, fluctuations, and dissipations caused by the neglected bulk. Long-range electrostatic corrections are supplied through a set of variable surface charges (polarons) that recreates the mean reaction field (or dielectric properties) of an infinite solvent. We refer to this "fictitious" boundary layer as a "surface of active polarons" (or SOAP). Test simulations of the solvation free energies of 15 amino acid analogs and nine ions are in good agreement with experiment (correlation coefficients: 0.995 and 1.000, respectively) despite the use of unaltered published force-fields with only one adjustable parameter. Dynamical capabilities of SOAP are illustrated by application to a six residue peptide with a stable conformation (SYPFDV), as well as a flexible nine residue HIV-1 gp120 peptide (TLTSCNTSV from PDB 1hhg). Future extensions, calibrations, and applications are discussed briefly.

  10. Potentials of Mean Force Between Rigid Solvated Polymers

    SciTech Connect

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

    1999-09-29

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

  11. 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

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

    PubMed

    Kar, Parimal; Lipowsky, Reinhard; Knecht, Volker

    2013-05-16

    highlights that structural inspection alone is not sufficient for identifying the key contributions to binding affinities and affinity changes for the design of drugs but that solvation effects must be taken into account. A detailed understanding of the molecular forces governing binding and drug resistance might assist in the design of new inhibitors against HIV-1 PR variants that are resistant against current drugs. PMID:23614718

  13. A New Tabu-Search-Based Algorithm for Solvation of Proteins.

    PubMed

    Grebner, Christoph; Kästner, Johannes; Thiel, Walter; Engels, Bernd

    2013-01-01

    The proper description of explicit water shells is of enormous importance for all-atom calculations. We propose a new approach for the setup of water shells around proteins based on Tabu-Search global optimization and compare its efficiency with standard molecular dynamics protocols using the chignolin protein as a test case. Both algorithms generate reasonable water shells, but the new approach provides solvated systems with an increased water-enzyme interaction and offers further advantages. It enables a stepwise buildup of the solvent shell, so that the more important inner part can be prepared more carefully. It also allows the generation of solute structures which can be biased either toward the (experimental) starting structure or the underlying theoretical model, i.e., the employed force field. PMID:26589073

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

    NASA Astrophysics Data System (ADS)

    Shirota, Hideaki; Castner, Edward W.

    2000-02-01

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed

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

    2012-07-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-07-01

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

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

    PubMed Central

    2016-01-01

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

  19. 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.

  20. Mode coupling theory analysis of electrolyte solutions: Time dependent diffusion, intermediate scattering function, and ion solvation dynamics

    NASA Astrophysics Data System (ADS)

    Roy, Susmita; Yashonath, Subramanian; Bagchi, Biman

    2015-03-01

    A self-consistent mode coupling theory (MCT) with microscopic inputs of equilibrium pair correlation functions is developed to analyze electrolyte dynamics. We apply the theory to calculate concentration dependence of (i) time dependent ion diffusion, (ii) intermediate scattering function of the constituent ions, and (iii) ion solvation dynamics in electrolyte solution. Brownian dynamics with implicit water molecules and molecular dynamics method with explicit water are used to check the theoretical predictions. The time dependence of ionic self-diffusion coefficient and the corresponding intermediate scattering function evaluated from our MCT approach show quantitative agreement with early experimental and present Brownian dynamic simulation results. With increasing concentration, the dispersion of electrolyte friction is found to occur at increasingly higher frequency, due to the faster relaxation of the ion atmosphere. The wave number dependence of intermediate scattering function, F(k, t), exhibits markedly different relaxation dynamics at different length scales. At small wave numbers, we find the emergence of a step-like relaxation, indicating the presence of both fast and slow time scales in the system. Such behavior allows an intriguing analogy with temperature dependent relaxation dynamics of supercooled liquids. We find that solvation dynamics of a tagged ion exhibits a power law decay at long times—the decay can also be fitted to a stretched exponential form. The emergence of the power law in solvation dynamics has been tested by carrying out long Brownian dynamics simulations with varying ionic concentrations. The solvation time correlation and ion-ion intermediate scattering function indeed exhibit highly interesting, non-trivial dynamical behavior at intermediate to longer times that require further experimental and theoretical studies.

  1. 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.

  2. 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

  3. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  5. 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.

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

    PubMed

    Andreussi, Oliviero; Dabo, Ismaila; Marzari, Nicola

    2012-02-14

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

  7. Band offsets across solid-liquid interfaces from continuum solvation methods

    NASA Astrophysics Data System (ADS)

    Sundararaman, Ravishankar; Ping, Yuan; Galli, Giulia A.; Goddard, William A., III

    2015-03-01

    The band edge positions of photo-electrodes relative to water redox potentials play an important role in determining the efficiency of the photo-electrochemical cell. Direct theoretical calculations of solid-liquid interfaces are expensive and simplified models are desirable for rapid theoretical screening of new materials. However, traditional solvation models are extensively fit to describe organic solutes and hence extrapolate poorly to highly-polar inorganic surfaces. We develop minimally-empirical continuum solvation models suitable for treating such surfaces and present theoretical predictions of the band positions of rutile TiO2 (110) and WO3 (001) surfaces in water. We obtain non-negligible solvation effects ~ 1-2 eV, in good agreement with experimental results. This material is based upon work performed by the Joint Center for Artificial Photosynthesis, a DOE Energy Innovation Hub, supported through the Office of Science of the U.S. Department of Energy under Award Number DE-SC0004993.

  8. Wavelength Dependence of UV Photoemission from Solvated Electrons in Bulk Water, Methanol, and Ethanol.

    PubMed

    Yamamoto, Yo-ichi; Karashima, Shutaro; Adachi, Shunsuke; Suzuki, Toshinori

    2016-03-01

    We have measured the wavelength dependence (340-215 nm) of one-photon photoemission from the ground electronic state of solvated electrons in bulk water, methanol, and ethanol. In every case, the vertical electron binding energy (VBE) gradually increased with photon energy, indicating that the photoelectron kinetic energy diminishes as a result of electron-vibration inelastic scattering prior to emission from the liquid surface. In contrast, the VBE of the Rydberg electron in DABCO (1,4-diazabicyclo[2,2,2]octane), which has a surface-excess density, revealed no clear wavelength dependence. These results suggest that the solvated electrons are created predominantly in the bulk and that VBEs measured using UV photoemission spectroscopy of liquids generally require energy corrections to account for inelastic scattering effects. From the wavelength dependence, we have re-estimated the VBEs of solvated electrons in bulk water, methanol, and ethanol to be 3.3, 3.1, and 3.1 eV, respectively. Hydrated electrons were also identified by photoemission spectroscopy using 90 nm radiation. PMID:26836447

  9. 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).

  10. Solvent effects on isotope effects: methyl cation as a model system.

    PubMed

    Wilson, Philippe B; Weaver, Paul J; Greig, Ian R; Williams, Ian H

    2015-01-22

    The isotopic sensitivity (CH3(+) vs CD3(+)) of the equilibrium between the methyl cation in vacuum and in solution has been investigated. Two alternative options for describing the shape of the solute cavity within the widely used polarized continuum model for implicit solvation were compared; the UFF and UA0 methods give equilibrium isotope effects (EIEs) that vary as a function of the dielectric constant in opposite directions. The same isotope effect was also obtained as the average over 40 structures from a hybrid quantum mechanical/molecular mechanical molecular dynamics simulation for the methyl cation explicitly solvated by many water molecules; the inverse value of the EIE agrees with UFF but not UA0. The opposing trends may be satisfactorily explained in terms of the different degrees of exposure of the atomic charges to the dielectric continuum in cavities of different shapes. PMID:25010417

  11. 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

  12. 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

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

    SciTech Connect

    Matyushov, Dmitry V.

    2009-06-21

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

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

    PubMed

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

    2016-08-25

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

  15. 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

  16. 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

  17. 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

    PubMed Central

    Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.; Hünenberger, Philippe H.

    2013-01-01

    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

  18. 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

  19. 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.

  20. 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.

  1. 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.

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

    DOE PAGESBeta

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

    2015-09-16

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

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

    PubMed

    Boyer, Robert D; Bryan, Richard L

    2012-03-29

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

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    Katoh, Ryuzi

    2009-11-01

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

  6. Solvated electrons formed in methanol cluster in ethane

    SciTech Connect

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

    2000-03-09

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

  7. 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.

  8. Learning to (dis)like: The effect of evaluative conditioning with tastes and faces on odor valence assessed by implicit and explicit measurements.

    PubMed

    van den Bosch, I; van Delft, J M; de Wijk, R A; de Graaf, C; Boesveldt, S

    2015-11-01

    Evaluative conditioning may be an important mechanism for learning food preferences and aversions; however, in both real life and experimental settings it has not been consistently successful. The current study aimed to gain more insight into which underlying factors may contribute to a successful outcome of olfactory evaluative conditioning. Two groups of 18 participants came in on three consecutive days, and were repeatedly exposed to four novel, neutral odors (CS) coupled to varying disliked, neutral, liked, or no stimuli (taste and/or pictures, US), following a 50% reinforcement schedule, leading to 40 odor presentations per session. Liking ratings, as well as changes in the autonomic nervous system were assessed before, during and after conditioning. We were able to induce negative, but not positive, affective changes by pairing neutral odors with tastes and pictures differing in valence. Negative as well as multimodal stimuli appear to be more potent US, since they may be considered more salient. Lastly, results of the current study imply that heart rate is responsive to changes in valence of olfactory stimuli, and perhaps even more sensitive than explicit ratings of liking. PMID:26300468

  9. 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

  10. 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.

  11. 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.

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

    PubMed

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

    2005-01-01

    We have used molecular dynamics simulations to study the structural, dynamical, and thermodynamical properties of ions in water clusters. Careful evaluations of the free energy, internal energy, and entropy are used to address controversial or unresolved issues, related to the underlying physical cause of surface solvation, and the basic assumptions that go with it. Our main conclusions are the following. (i) The main cause of surface solvation of a single ion in a water cluster is both water and ion polarization, coupled to the charge and size of the ion. Interestingly, the total energy of the ion increases near the cluster surface, while the total energy of water decreases. Also, our analysis clearly shows that the cause of surface solvation is not the size of the total water dipole (unless this is too small). (ii) The entropic contribution is the same order of magnitude as the energetic contribution, and therefore cannot be neglected for quantitative results. (iii) A pure energetic analysis can give a qualitative description of the ion position at room temperature. (iv) We have observed surface solvation of a large positive iodinelike ion in a polarizable water cluster, but not in a nonpolarizable water cluster. PMID:15638604

  13. Electron solvation in aqueous reverse micelles: Equilibrium properties

    NASA Astrophysics Data System (ADS)

    Laria, Daniel; Kapral, Raymond

    2002-10-01

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

  14. 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

  15. 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

  16. 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.

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

    PubMed Central

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

    1999-01-01

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

  18. Explicit 3-D Hydrodynamic FEM Program

    Energy Science and Technology Software Center (ESTSC)

    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

  19. Explicit 3-D Hydrodynamic FEM Program

    SciTech Connect

    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, including frictional sliding, single surface contact and automatic contact generation.

  20. 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

  1. Implicit and Explicit Learning of Languages.

    ERIC Educational Resources Information Center

    McDermott, James E.

    1999-01-01

    Discusses theoretical and practical issues connected with implicit and explicit learning of languages. Explicit learning is knowledge expressed in the form of rules or definitions; implicit knowledge can be inferred to exist because of observed performance but cannot be clearly described. Hypothesizes why explicit learning can lead to implicit…

  2. 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

  3. 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.

  4. Prediction of Complex Aerodynamic Flows with Explicit Algebraic Stress Models

    NASA Technical Reports Server (NTRS)

    Abid, Ridha; Morrison, Joseph H.; Gatski, Thomas B.; Speziale, Charles G.

    1996-01-01

    An explicit algebraic stress equation, developed by Gatski and Speziale, is used in the framework of K-epsilon formulation to predict complex aerodynamic turbulent flows. The nonequilibrium effects are modeled through coefficients that depend nonlinearly on both rotational and irrotational strains. The proposed model was implemented in the ISAAC Navier-Stokes code. Comparisons with the experimental data are presented which clearly demonstrate that explicit algebraic stress models can predict the correct response to nonequilibrium flow.

  5. 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.

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

    PubMed

    Li, Bo; Zhao, Yanxiang

    2013-01-01

    Central in a variational implicit-solvent description of biomolecular solvation is an effective free-energy functional of the solute atomic positions and the solute-solvent interface (i.e., the dielectric boundary). The free-energy functional couples together the solute molecular mechanical interaction energy, the solute-solvent interfacial energy, the solute-solvent van der Waals interaction energy, and the electrostatic energy. In recent years, the sharp-interface version of the variational implicit-solvent model has been developed and used for numerical computations of molecular solvation. In this work, we propose a diffuse-interface version of the variational implicit-solvent model with solute molecular mechanics. We also analyze both the sharp-interface and diffuse-interface models. We prove the existence of free-energy minimizers and obtain their bounds. We also prove the convergence of the diffuse-interface model to the sharp-interface model in the sense of Γ-convergence. We further discuss properties of sharp-interface free-energy minimizers, the boundary conditions and the coupling of the Poisson-Boltzmann equation in the diffuse-interface model, and the convergence of forces from diffuse-interface to sharp-interface descriptions. Our analysis relies on the previous works on the problem of minimizing surface areas and on our observations on the coupling between solute molecular mechanical interactions with the continuum solvent. Our studies justify rigorously the self consistency of the proposed diffuse-interface variational models of implicit solvation. PMID:24058213

  7. 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

  8. 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

  9. 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

  10. 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

  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. 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.

  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. PMID:26723595

  14. Lewis base mediated efficient synthesis and solvation-like host-guest chemistry of covalent organic framework-1.

    PubMed

    Kalidindi, Suresh Babu; Wiktor, Christian; Ramakrishnan, Ayyappan; Weßing, Jana; Schneemann, Andreas; Van Tendeloo, Gustaaf; Fischer, Roland A

    2013-01-18

    N-Lewis base mediated room temperature synthesis of covalent organic frameworks (COFs) starting from a solution of building blocks instead of partially soluble building blocks was developed. This protocol shifts COF synthetic chemistry from sealed tubes to open beakers. Non-conventional inclusion compounds of COF-1 were obtained by vapor phase infiltration of ferrocene and azobenzene, and solvation like effects were established. PMID:23208512

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

    PubMed

    Kaur, Harveen; Koley, Somnath; Ghosh, Subhadip

    2014-06-26

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

  16. Local Control Mechanisms of Implicit and Explicit Conflicts.

    PubMed

    Zhao, Liang; Bai, Yang; Ma, Jie; Wang, Yonghui

    2015-01-01

    Congruency sequence effects are observed when the congruency effects following incongruent trials are smaller than those following congruent trials. It is typically assumed that such flexible adjustments are evidence of cognitively controlled dynamic modulations. The present study investigated whether cognitive control acts locally or globally when implicit and explicit conflicts exist simultaneously within a system. The implicit SNARC task and explicit Simon task were combined in a single task. The results showed that congruency effects of one type (e.g., SNARC effect) were only smaller following an incongruent trial of the same type (e.g., SNARC effect), but not when following an incongruent trial of the other type (e.g., Simon effect). These results indicate the operation of local control mechanisms triggered by implicit and explicit conflicts. PMID:25516007

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

    NASA Astrophysics Data System (ADS)

    McConnell, Harden

    2010-05-01

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

  18. 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

  19. How does the solvation unveil AtO+ reactivity?

    PubMed

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

    2013-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  1. 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.

  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. Hydroxide Solvation and Transport in Anion Exchange Membranes.

    PubMed

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

    2016-01-27

    Understanding hydroxide solvation and transport in anion exchange membranes (AEMs) can provide important insight into the design principles of these new membranes. To accurately model hydroxide solvation and transport, we developed a new multiscale reactive molecular dynamics model for hydroxide in aqueous solution, which was then subsequently modified for an AEM material. With this model, we investigated the hydroxide solvation structure and transport mechanism in the membrane. We found that a relatively even separation of the rigid side chains produces a continuous overlapping region for hydroxide transport that is made up of the first hydration shell of the tethered cationic groups. Our results show that hydroxide has a significant preference for this overlapping region, transporting through it and between the AEM side chains with substantial contributions from both vehicular (standard diffusion) and Grotthuss (proton hopping) mechanisms. Comparison of the AEM with common proton exchange membranes (PEMs) showed that the excess charge is less delocalized in the AEM than the PEMs, which is correlated with a higher free energy barrier for proton transfer reactions. The vehicular mechanism also contributes considerably more than the Grotthuss mechanism for hydroxide transport in the AEM, while our previous studies of PEM systems showed a larger contribution from the Grotthuss mechanism than the vehicular mechanism for proton transport. The activation energy barrier for hydroxide diffusion in the AEM is greater than that for proton diffusion in PEMs, implying a more significant enhancement of ion transport in the AEM at elevated temperatures. PMID:26716727

  4. 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.

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

    PubMed

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

    2004-12-01

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

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

    PubMed

    Carvalho, Nathalia F; Pliego, Josefredo R

    2015-10-28

    Absolute single-ion solvation free energy is a very useful property for understanding solution phase chemistry. The real solvation free energy of an ion depends on its interaction with the solvent molecules and on the net potential inside the solute cavity. The tetraphenyl arsonium-tetraphenyl borate (TATB) assumption as well as the cluster-continuum quasichemical theory (CC-QCT) approach for Li(+) solvation allows access to a solvation scale excluding the net potential. We have determined this free energy scale investigating the solvation of the lithium ion in water (H2O), acetonitrile (CH3CN) and dimethyl sulfoxide (DMSO) solvents via the CC-QCT approach. Our calculations at the MP2 and MP4 levels with basis sets up to the QZVPP+diff quality, and including solvation of the clusters and solvent molecules by the dielectric continuum SMD method, predict the solvation free energy of Li(+) as -116.1, -120.6 and -123.6 kcal mol(-1) in H2O, CH3CN and DMSO solvents, respectively (1 mol L(-1) standard state). These values are compatible with the solvation free energy of the proton of -253.4, -253.2 and -261.1 kcal mol(-1) in H2O, CH3CN and DMSO solvents, respectively. Deviations from the experimental TATB scale are only 1.3 kcal mol(-1) in H2O and 1.8 kcal mol(-1) in DMSO solvents. However, in the case of CH3CN, the deviation reaches a value of 9.2 kcal mol(-1). The present study suggests that the experimental TATB scale is inconsistent for CH3CN. A total of 125 values of the solvation free energy of ions in these three solvents were obtained. These new data should be useful for the development of theoretical solvation models. PMID:26395146

  7. A molecular dynamics computer simulation study of room-temperature ionic liquids. I. Equilibrium solvation structure and free energetics

    NASA Astrophysics Data System (ADS)

    Shim, Y.; Choi, M. Y.; Kim, Hyung J.

    2005-01-01

    Solvation in 1-ethyl-3-methylmidazolium chloride and in 1-ethyl-3-methylimidazolium hexafluorophosphate near equilibrium is investigated via molecular dynamics computer simulations with diatomic and benzenelike molecules employed as probe solutes. It is found that electrostriction plays an important role in both solvation structure and free energetics. The angular and radial distributions of cations and anions become more structured and their densities near the solute become enhanced as the solute charge separation grows. Due to the enhancement in structural rigidity induced by electrostriction, the force constant associated with solvent configuration fluctuations relevant to charge shift and transfer processes is also found to increase. The effective polarity and reorganization free energies of these ionic liquids are analyzed and compared with those of highly polar acetonitrile. Their screening behavior of electric charges is also investigated.

  8. 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

  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. 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

  11. 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…

  12. 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…

  13. 3DRISM Multigrid Algorithm for Fast Solvation Free Energy Calculations.

    PubMed

    Sergiievskyi, Volodymyr P; Fedorov, Maxim V

    2012-06-12

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

  14. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  16. 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. 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.

  18. 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

  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. PMID:26957607

  20. Multidimensional infrared spectroscopy reveals the vibrational and solvation dynamics of isoniazid.

    PubMed

    Shaw, Daniel J; Adamczyk, Katrin; Frederix, Pim W J M; Simpson, Niall; Robb, Kirsty; Greetham, Gregory M; Towrie, Michael; Parker, Anthony W; Hoskisson, Paul A; Hunt, Neil T

    2015-06-01

    The results of infrared spectroscopic investigations into the band assignments, vibrational relaxation, and solvation dynamics of the common anti-tuberculosis treatment Isoniazid (INH) are reported. INH is known to inhibit InhA, a 2-trans-enoyl-acyl carrier protein reductase enzyme responsible for the maintenance of cell walls in Mycobacterium tuberculosis but as new drug-resistant strains of the bacterium appear, next-generation therapeutics will be essential to combat the rise of the disease. Small molecules such as INH offer the potential for use as a biomolecular marker through which ultrafast multidimensional spectroscopies can probe drug binding and so inform design strategies but a complete characterization of the spectroscopy and dynamics of INH in solution is required to inform such activity. Infrared absorption spectroscopy, in combination with density functional theory calculations, is used to assign the vibrational modes of INH in the 1400-1700 cm(-1) region of the infrared spectrum while ultrafast multidimensional spectroscopy measurements determine the vibrational relaxation dynamics and the effects of solvation via spectral diffusion of the carbonyl stretching vibrational mode. These results are discussed in the context of previous linear spectroscopy studies on solid-phase INH and its usefulness as a biomolecular probe. PMID:26049421

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

    We apply our recently developed generalized Flory-Huggins (FH) type theory for the competitive solvation of polymers by two mixed solvents to explain general trends in the variation of phase boundaries and solvent quality (quantified by the second osmotic virial coefficient B 2 ) with solvent composition. The complexity of the theoretically predicted miscibility patterns for these ternary mixtures arises from the competitive association between the polymer and the solvents and from the interplay of these associative interactions with the weak van der Waals interactions between all components of the mixture. The main focus here lies in determining the influence of the free energy parameters for polymer-solvent association (solvation) and the effective FH interaction parameters {χαβ} (driving phase separation) on the phase boundaries (specifically the spinodals), the second osmotic virial coefficient B 2 , and the relation between the positions of the spinodal curves and the theta temperatures at which B 2 vanishes. Our classification of the predicted miscibility patterns is relevant to numerous applications of ternary polymer solutions in industrial formulations and the use of mixed solvent systems for polymer characterization, such as chromatographic separation where mixed solvents are commonly employed. A favorable comparison of B 2 with experimental data for poly(methyl methacrylate)/acetonitrile/methanol (or 1-propanol) solutions only partially supports the validity of our theoretical predictions due to the lack of enough experimental data and the neglect of the self and mutual association of the solvents.

  3. Influence of Large-Scale Advective Cooling and Moistening Effects on the Quasi-Equilibrium Behavior of Explicitly Simulated Cumulus Ensembles.

    NASA Astrophysics Data System (ADS)

    Xu, Kuan-Man; Randall, David A.

    1998-03-01

    The influence of large-scale advective cooling and/or moistening on the quasi-equilibrium behavior of simulated, tropical oceanic cumulus ensembles is examined in this study. Two sensitivity simulations are performed by imposing time varying/invariant large-scale advective cooling effects and time invariant/varying large-scale advective moistening effects. The results are compared with a control simulation performed with both large-scale advective cooling and moistening effects that are time varying.It is found that the generalized convective available potential energy (GCAPE) tendency is almost one order of magnitude smaller than the GCAPE production in all simulations. This indicates that the quasi-equilibrium assumption of Arakawa and Schubert is well justified. The higher-order behavior of quasi-equilibrium cumulus ensemble is then examined. It is found that the GCAPE variations are nearly equally contributed by temperature and water vapor variations in the control simulation. In the sensitivity simulations, they are mainly contributed by the temperature (water vapor) variations even though the imposed large-scale advective cooling (moistening) is time invariant. A significant finding of this study is that there is a negative lag correlation between GCAPE and the intensity of cumulus convection. The lag corresponding to the largest negative correlation ranges from 1 to 5 h in various simulations. The existence of a negative correlation and the maximum lag of a few hours is independent of the character and period of the imposed large-scale advective forcing. The maximum lag can be interpreted as the adjustment timescale from disequilibrium to quasi-equilibrium states in the presence of time-varying large-scale forcing.

  4. 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

  5. On thermohydrologic conditions near high-level nuclear wastes emplaced in partially saturated fractured tuff: 1. Simulation studies with explicit consideration of fracture effects

    NASA Astrophysics Data System (ADS)

    Pruess, K.; Wang, J. S. Y.; Tsang, Y. W.

    1990-06-01

    We have performed modeling studies on the simultaneous transport of heat, liquid water, vapor, and air in partially saturated, fractured porous rock. Formation parameters were chosen as representative of the potential nuclear waste repository site in the Topopah Spring unit of the Yucca Mountain tuffs. The presence of fractures makes the transport problem very complex, both in terms of flow geometry and physics. The numerical simulator used for our flow calculations takes into account most of the physical effects believed to be important in multiphase fluid and heat flow. It has provisions for handling the extreme nonlinearities that arise in phase transitions, component disappearances, and capillary discontinuities at fracture faces. We model a region around an infinite linear string of nuclear waste canisters, taking into account both the discrete fractures and the porous matrix. Thermohydrologic conditions in the vicinity of the waste packages are found to depend strongly on relative permeability and capillary pressure characteristics of the fractures, which are unknown at the present time. If liquid held on the rough walls of drained fractures is assumed to be mobile, strong heat pipe effects are predicted. Under these conditions the host rock will remain in two-phase conditions right up to the emplacement hole, and formation temperatures will peak near 100°C. If it is assumed that liquid cannot move along drained fractures, the region surrounding the waste packages is predicted to dry up, and formation temperatures will rise beyond 200°C. A substantial fraction of waste heat can be removed if emplacement holes are left open and ventilated, as opposed to backfilled and sealed emplacement conditions. Comparing our model predictions with observations from in situ heater experiments reported by Zimmerman and coworkers, some intriguing similarities are noted. However, for a quantitative evaluation, additional carefully controlled laboratory and field experiments

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. Estimating geocenter motion and barystatic sea-level variability from GRACE observations with explicit consideration of self-attraction and loading effects

    NASA Astrophysics Data System (ADS)

    Bergmann-Wolf, I.; Dobslaw, H.

    2015-12-01

    Estimating global barystatic sea-level variations from monthly mean gravity fields delivered by the Gravity Recovery and Climate Experiment (GRACE) satellite mission requires additional information about geocenter motion. These variations are not available directly due to the mission implementation in the CM-frame and are represented by the degree-1 terms of the spherical harmonics expansion. Global degree-1 estimates can be determined with the method of Swenson et al. (2008) from ocean mass variability, the geometry of the global land-sea distribution, and GRACE data of higher degrees and orders. Consequently, a recursive relation between the derivation of ocean mass variations from GRACE data and the introduction of geocenter motion into GRACE data exists.In this contribution, we will present a recent improvement to the processing strategy described in Bergmann-Wolf et al. (2014) by introducing a non-homogeneous distribution of global ocean mass variations in the geocenter motion determination strategy, which is due to the effects of loading and self-attraction induced by mass redistributions at the surface. A comparison of different GRACE-based oceanographic products (barystatic signal for both the global oceans and individual basins; barotropic transport variations of major ocean currents) with degree-1 terms estimated with a homogeneous and non-homogeneous ocean mass representation will be discussed, and differences in noise levels in most recent GRACE solutions from GFZ (RL05a), CSR, and JPL (both RL05) and their consequences for the application of this method will be discussed.

  11. Parallel Explicit and Implicit Control of Reaching

    PubMed Central

    Mazzoni, Pietro; Wexler, Nancy S.

    2009-01-01

    Background Human movement can be guided automatically (implicit control) or attentively (explicit control). Explicit control may be engaged when learning a new movement, while implicit control enables simultaneous execution of multiple actions. Explicit and implicit control can often be assigned arbitrarily: we can simultaneously drive a car and tune the radio, seamlessly allocating implicit or explicit control to either action. This flexibility suggests that sensorimotor signals, including those that encode spatially overlapping perception and behavior, can be accurately segregated to explicit and implicit control processes. Methodology/Principal Findings We tested human subjects' ability to segregate sensorimotor signals to parallel control processes by requiring dual (explicit and implicit) control of the same reaching movement and testing for interference between these processes. Healthy control subjects were able to engage dual explicit and implicit motor control without degradation of performance compared to explicit or implicit control alone. We then asked whether segregation of explicit and implicit motor control can be selectively disrupted by studying dual-control performance in subjects with no clinically manifest neurologic deficits in the presymptomatic stage of Huntington's disease (HD). These subjects performed successfully under either explicit or implicit control alone, but were impaired in the dual-control condition. Conclusion/Significance The human nervous system can exert dual control on a single action, and is therefore able to accurately segregate sensorimotor signals to explicit and implicit control. The impairment observed in the presymptomatic stage of HD points to a possible crucial contribution of the striatum to the segregation of sensorimotor signals to multiple control processes. PMID:19847295

  12. Estimating geocenter motion and barystatic sea-level variability from GRACE observations with explicit consideration of self-attraction and loading effects

    NASA Astrophysics Data System (ADS)

    Bergmann-Wolf, Inga; Dobslaw, Henryk

    2016-04-01

    Estimating global barystatic sea-level variations from monthly mean gravity fields delivered by the Gravity Recovery and Climate Experiment (GRACE) satellite mission requires additional information about geocenter motion. These variations are not available directly due to the mission implementation in the CM-frame and are represented by the degree-1 terms of the spherical harmonics expansion. Global degree-1 estimates can be determined with the method of Swenson et al. (2008) from ocean mass variability, the geometry of the global land-sea distribution, and GRACE data of higher degrees and orders. Consequently, a recursive relation between the derivation of ocean mass variations from GRACE data and the introduction of geocenter motion into GRACE data exists. In this contribution, we will present a recent improvement to the processing strategy described in Bergmann-Wolf et al. (2014) by introducing a non-homogeneous distribution of global ocean mass variations in the geocenter motion determination strategy, which is due to the effects of loading and self-attraction induced by mass redistributions at the surface. A comparison of different GRACE-based oceanographic products (barystatic signal for both the global oceans and individual basins; barotropic transport variations of major ocean currents) with degree-1 terms estimated with a homogeneous and non-homogeneous ocean mass representation will be discussed, and differences in noise levels in most recent GRACE solutions from GFZ (RL05a), CSR, and JPL (both RL05) and their consequences for the application of this method will be discussed. Swenson, S., D. Chambers and J. Wahr (2008), Estimating geocenter variations from a combination of GRACE and ocean model output, J. Geophys. Res., 113, B08410 Bergmann-Wolf, I., L. Zhang and H. Dobslaw (2014), Global Eustatic Sea-Level Variations for the Approximation of Geocenter Motion from GRACE, J. Geod. Sci., 4, 37-48

  13. The Intergenerational Transmission of Implicit and Explicit Attitudes Toward Smoking

    PubMed Central

    Sherman, Steven J.; Chassin, Laurie; Presson, Clark; Seo, Dong-Chul; Macy, Jonathan T.

    2009-01-01

    This study examined the intergenerational transmission of implicit and explicit attitudes toward smoking, as well as the role of these attitudes in adolescents’ smoking initiation. There was evidence of intergenerational transmission of implicit attitudes. Mothers who had more positive implicit attitudes had children with more positive implicit attitudes. In turn, these positive implicit attitudes of adolescents predicted their smoking initiation 18-months later. Moreover, these effects were obtained above and beyond the effects of explicit attitudes. These findings provide the first evidence that the intergenerational transmission of implicit cognition may play a role in the intergenerational transmission of an addictive behavior. PMID:20126293

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

    PubMed

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

    2008-11-27

    of each pair of probes (of similar pK(a)) to solvent acidity is the same, provided that solute-solvent hydrogen-bonding is not seriously affected by steric crowding (as in case of RB). We show, for the first time, that the response to solvent dipolarity/polarizability is linearly correlated to the dipole moment of the probes. The successive introduction of bromine atoms in MePM (to give MePMBr, then MePMBr(2)) leads to the following linear decrease: pK(a) in water, length of the phenolate oxygen-carbon bond, length of the central ethylenic bond, susceptibility to solvent acidity, and susceptibility to solvent dipolarity/polarizability. Thus studying the solvation of probes whose molecular structures are varied systematically produces a wealth of information on the effect of solute structure on its solvation. The results of solvation of the present probes were employed in order to test the goodness of fit of two independent sets of solvent solvatochromic parameters. PMID:18973380

  15. Implicit and Explicit Exercise and Sedentary Identity

    ERIC Educational Resources Information Center

    Berry, Tanya R.; Strachan, Shaelyn M.

    2012-01-01

    We examined the relationship between implicit and explicit "exerciser" and "sedentary" self-identity when activated by stereotypes. Undergraduate participants (N = 141) wrote essays about university students who either liked to exercise or engage in sedentary activities. This was followed by an implicit identity task and an explicit measure of…

  16. Thinking Styles in Implicit and Explicit Learning

    ERIC Educational Resources Information Center

    Xie, Qiuzhi; Gao, Xiangping; King, Ronnel B.

    2013-01-01

    This study investigated whether individual differences in thinking styles influence explicit and implicit learning. Eighty-seven university students in China participated in this study. Results indicated that performance in the explicit learning condition was positively associated with Type I thinking styles (i.e. legislative and liberal styles)…

  17. A hybrid explicit solution technique for quasi-static transients

    SciTech Connect

    Sauve, R.G.; Metzger, D.R.

    1996-12-01

    In certain instances, such as in the modeling of manufacturing process, undesirable dynamic effects may accompany the use of an explicit transient solution, while the use of full dynamic relaxation is inefficient for this class of problem due to critical damping. In this paper, an approach that merges the salient features of dynamic relaxation with those of the fully explicit solution, is presented. The key objective of the method is the removal of unwanted dynamic (e.g., inertial) effects, while providing for a transient kinematic loading history. This work focuses on the development of an adaptive mass algorithm consistent with specified damping and time step for use within the framework of explicit time integration. The paper describes the hybrid solution formulation and the implementation of the proposed algorithm. Applications include an experimental punch test used for material characterization and a rolled joint expansion manufacturing process used for installation of tubes in steam generators, both involving three-dimensional finite deformation.

  18. Multibody correlations in the hydrophobic solvation of glycine peptides

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  19. Multibody correlations in the hydrophobic solvation of glycine peptides

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-12-14

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