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Sample records for explicit solvation effects

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    NASA Astrophysics Data System (ADS)

    Williams, Michael; Schwartz, Steven

    2015-03-01

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

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

    PubMed

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

    2015-11-28

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

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

    SciTech Connect

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

    2009-05-01

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

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

    PubMed

    Turner, David R; Kubelka, Jan

    2007-02-22

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

  6. A comparative VCD study of methyl mandelate in methanol, dimethyl sulfoxide, and chloroform: explicit and implicit solvation models.

    PubMed

    Poopari, Mohammad Reza; Dezhahang, Zahra; Xu, Yunjie

    2013-02-07

    Vibrational absorption (VA) and vibrational circular dichroism (VCD) spectra of methyl mandelate, a prototype chiral molecule, in a series of organic solvents, namely methanol (MeOH-d(4)), dimethyl sulfoxide (DMSO-d(6)), and chloroform (CDCl(3)), have been measured in the finger print region from 1800 to 1150 cm(-1). Implicit solvation models in the form of polarizable continuum model and explicit solvation models have been employed independently and simultaneously. The goal is to evaluate their efficiencies in dealing with solvent effects in each solution and to establish a general strategy to adequately account for effects of solvents. Molecular dynamics (MD) simulation and radial distribution function analysis have been performed to aid the construction of the explicit solvation models. Initial geometry searches have been carried out at the B3LYP/6-31G(d) level for the methyl mandelate monomer and its explicit 1 : 1 and 1 : 2 solute-solvent hydrogen-bonded complexes. B3LYP/cc-pVTZ has been used for all the final geometry optimizations, the vibrational frequency, VA and VCD intensity, and optical rotation dispersion (ORD) calculations. The results show that inclusion of solvent explicitly and implicitly at the same time has significant impacts on the appearance of the VA and VCD spectra, and is crucial for reliable spectral assignments when solvents are capable of hydrogen-bonding interactions with solutes. When no strong solvent-solute hydrogen-bonding interactions in the case of chloroform are expected, the gas phase monomer model is adequate for spectral interpretation, while inclusion of implicit solvation improves the frequency agreement with experiment. ORD spectra of methyl mandelate in the aforementioned solvents at different concentrations under 5 excitation wavelengths have also been measured. The comparison between the calculated and the experimental ORD spectra supports the conclusions drawn from the VA and VCD investigations.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Arias, Tomas

    2015-03-01

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

  9. Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

    We report here a test of the Semi-Explicit Assembly (SEA) model in the solvation free energy category of the SAMPL3 blind prediction event (summer 2011). We tested how dependent the SEA results are on the chosen force field by performing calculations with both the General Amber and OPLS force fields. We compared our SEA results with full molecular dynamics simulations in explicit solvent. Of the 20 submissions, our SEA/OPLS results gave the second smallest RMS errors in free energies compared to experiments. SEA gives results that are very similar to those of its underlying force field and explicit solvent model. Hence, while the SEA water modeling approach is much faster than explicit solvent simulations, its predictions appear to be just as accurate.

  10. 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.

  11. Solvation!

    SciTech Connect

    Adamovic, Ivana

    2004-01-01

    This dissertation consists of two closely related parts: theory development and coding of correlation effects in a model potential for solvation, and study of solvent effects on chemical reactions and processes. The effective fragment potential (EFP) method has been re-parameterized, using density functional theory (DFT), more specifically, the B3LYP functional. The DFT based EFP method includes short-range correlation effects; hence it is a first step in incorporating the treatment of correlation in the EFP solvation model. In addition, the gradient of the charge penetration term in the EFP model was derived and coded. The new method has been implemented in the electronic structure code GAMESS and is in use. Formulas for the dynamic dipole polarizability, C6 dispersion coefficient and dispersion energy were derived and coded as a part of a treatment of the dispersion interactions in the general solvation model, EFP2. Preliminary results are in good agreement with experimental and other theoretical data. The DFT based EFP (EFP1/DFT) method was used in the study of microsolvation effects on the SN2 substitution reaction, between chloride and methyl bromide. Changes in the central barrier, for several lowest lying isomers of the systems with one, two, three and four waters, were studied using second order perturbation theory (MP2), DFT and mixed quantum mechanics (QM)/(EFP1/DFT) methods. EFP1/DFT is found to reproduce QM results with high accuracy, at just a fraction of the cost. Molecular structures and potential energy surfaces for IHI- • Arn (n=1-7) were studied using the MP2 method. Experimentally observed trends in the structural arrangement of the Ar atoms were explained through the analysis of the geometrical parameters and three-dimensional MP2 molecular electrostatic potentials.

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

    PubMed

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

    2015-06-09

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

  13. 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...

  14. 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...

  15. Elastic energy storage in an unmineralized collagen type I molecular model with explicit solvation and water infiltration.

    PubMed

    Kwansa, Albert L; Freeman, Joseph W

    2010-02-21

    Collagen type I is a structural protein that provides tensile strength to tendons and ligaments. Type I collagen molecules form collagen fibers, which are viscoelastic and can therefore store energy elastically via molecular elongation and dissipate viscous energy through molecular rearrangement and fibrillar slippage. The ability to store elastic energy is important for the resiliency of tendons and ligaments, which must be able to deform and revert to their initial lengths with changes in load. In an earlier paper by one of the present authors, molecular modeling was used to investigate the role of mineralization upon elastic energy storage in collagen type I. Their collagen model showed a similar trend to their experimental data but with an over-estimation of elastic energy storage. Their simulations were conducted in vacuum and employed a distance-dependent dielectric function. In this study, we performed a re-evaluation of Freeman and Silver's model data incorporating the effects of explicit solvation and water infiltration, in order to determine whether the model data could be improved with a more accurate representation of the solvent and osmotic effects. We observed an average decrease in the model's elastic energy storage of 45.1%+/-6.9% in closer proximity to Freeman and Silver's experimental data. This suggests that although the distance-dependent dielectric implicit solvation approach was favored for its increased speed and decreased computational requirements, an explicit representation of water may be necessary to more accurately model solvent interactions in this particular system. In this paper, we discuss the collagen model described by Freeman and Silver, the present model building approach, the application of the present model to that of Freeman and Silver, and additional assumptions and limitations.

  16. 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 ...

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

    NASA Astrophysics Data System (ADS)

    Omelyan, Igor; Kovalenko, Andriy

    2013-12-01

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

  19. Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules

    NASA Astrophysics Data System (ADS)

    Brini, Emiliano; Paranahewage, S. Shanaka; Fennell, Christopher J.; Dill, Ken A.

    2016-11-01

    We describe here some tests we made in the SAMPL5 communal event of `Semi-Explicit Assembly' (SEA), a recent method for computing solvation free energies. We combined the prospective tests of SAMPL5 with followup retrospective calculations, to improve two technical aspects of the field variant of SEA. First, SEA uses an approximate analytical surface around the solute on which a water potential is computed. We have improved and simplified the mathematical model of that surface. Second, some of the solutes in SAMPL5 were large enough to need a way to treat solvating waters interacting with `buried atoms', i.e. interior atoms of the solute. We improved SEA with a buried-atom correction. We also compare SEA to Thermodynamic Integration molecular dynamics simulations, so that we can sort out force field errors.

  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.

  1. Probing the role of interfacial waters in protein-DNA recognition using a hybrid implicit/explicit solvation model.

    PubMed

    Li, Shen; Bradley, Philip

    2013-08-01

    When proteins bind to their DNA target sites, ordered water molecules are often present at the protein-DNA interface bridging protein and DNA through hydrogen bonds. What is the role of these ordered interfacial waters? Are they important determinants of the specificity of DNA sequence recognition, or do they act in binding in a primarily nonspecific manner, by improving packing of the interface, shielding unfavorable electrostatic interactions, and solvating unsatisfied polar groups that are inaccessible to bulk solvent? When modeling details of structure and binding preferences, can fully implicit solvent models be fruitfully applied to protein-DNA interfaces, or must the individualistic properties of these interfacial waters be accounted for? To address these questions, we have developed a hybrid implicit/explicit solvation model that specifically accounts for the locations and orientations of small numbers of DNA-bound water molecules, while treating the majority of the solvent implicitly. Comparing the performance of this model with that of its fully implicit counterpart, we find that explicit treatment of interfacial waters results in a modest but significant improvement in protein side-chain placement and DNA sequence recovery. Base-by-base comparison of the performance of the two models highlights DNA sequence positions whose recognition may be dependent on interfacial water. Our study offers large-scale statistical evidence for the role of ordered water for protein-DNA recognition, together with detailed examination of several well-characterized systems. In addition, our approach provides a template for modeling explicit water molecules at interfaces that should be extensible to other systems.

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

    PubMed

    Habershon, Scott

    2014-05-21

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

  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

    2008-11-04

    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. 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

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

    PubMed Central

    Singh, Nidhi; Warshel, Arieh

    2009-01-01

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

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

    PubMed Central

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

    2010-01-01

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

  7. 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.

  8. 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…

  9. Conformational distributions of N-acetyl-L-cysteine in aqueous solutions: a combined implicit and explicit solvation treatment of VA and VCD spectra.

    PubMed

    Poopari, Mohammad Reza; Dezhahang, Zahra; Yang, Guochun; Xu, Yunjie

    2012-06-18

    The conformational distributions of N-acetyl-L-cysteine (NALC) in aqueous solutions at several representative pH values are investigated using vibrational absorption (VA), UV/Vis, and vibrational circular dichroism (VCD) spectroscopy, together with DFT and molecular dynamics (MD) simulations. The experimental VA and UV/Vis spectra of NALC in water are obtained under strongly acid, neutral, and strongly basic conditions, as well as the VCD spectrum at pH 7 in D(2)O. Extensive searches are carried out to locate the most stable conformers of the protonated, neutral, deprotonated, and doubly deprotonated NALC species at the B3LYP/6-311++G(d,p) level. The inclusion of the polarizable continuum model (PCM) modifies the geometries and the relative stabilities of the conformers noticeably. The simulated PCM VA spectra show significantly better agreement with the experimental data than the gas-phase ones, thus allowing assignment of the conformational distributions and dominant species under each experimental condition. To further properly account for the discrepancies noted between the experimental and simulated VCD spectra, PCM and the explicit solvent model are utilized. MD simulations are used to aid the modelling of the NALC-(water)(N) clusters. The geometry optimization, harmonic frequency calculations, and VA and VCD intensities are computed for the NALC-(water)(3,4) clusters at the B3LYP/6-311++G(d,p) level without and with the PCM. The inclusion of both explicit and implicit solvation models at the same time provides a decisively better agreement between theory and experiment and therefore conclusive information about the conformational distributions of NALC in water and hydrogen-bonding interactions between NALC and water molecules.

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

    PubMed

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

    2016-12-21

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

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

    PubMed

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

    2003-10-07

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

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

    PubMed

    Periyasamy, Ganga; Remacle, F

    2009-08-01

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

  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.

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

    NASA Astrophysics Data System (ADS)

    Nandi, Nilashis; Roy, Srabani; Bagchi, Biman

    1995-01-01

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

  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. 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…

  18. 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.

  19. The effect of explicit financial incentives on physician behavior.

    PubMed

    Armour, B S; Pitts, M M; Maclean, R; Cangialose, C; Kishel, M; Imai, H; Etchason, J

    2001-05-28

    Managed care organizations use explicit financial incentives to influence physicians' use of resources. This has contributed to concerns regarding conflicts of interest for physicians and adverse effects on the quality of patient care. In light of recent publicized legislative and legal battles about this issue, we reviewed the literature and analyzed studies that examine the effect of these explicit financial incentives on the behavior of physicians. The method used to undertake the literature review followed the approach set forth in the Cochrane Collaboration handbook. Our literature review revealed a paucity of data on the effect of explicit financial incentives. Based on this limited evidence, explicit incentives that place individual physicians at financial risk appear to be effective in reducing physician resource use. However, the empirical evidence regarding the effectiveness of bonus payments on physician resource use is mixed. Similarly, our review revealed mixed effects of the influence of explicit financial incentives on the quality of patient care. The effect of explicit financial incentives on physician behavior is complicated by a lack of understanding of the incentive structure by the managed care organization and the physician. The lack of a universally acceptable definition of quality renders it important that future researchers identify the term explicitly.

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

    PubMed Central

    Vagenende, Vincent; Trout, Bernhardt L.

    2012-01-01

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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

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

    PubMed Central

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

    2016-01-01

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

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    Kalyuzhnyi, Yuriy V.; Vlachy, Vojko

    2016-06-01

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

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

    SciTech Connect

    Mata-Segreda, J.F.

    1988-08-31

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

  7. Finite-size effect on the charging free energy of protein in explicit solvent.

    PubMed

    Ekimoto, Toru; Matubayasi, Nobuyuki; Ikeguchi, Mitsunori

    2015-01-13

    The finite-size effect in periodic system is examined for the charging free energy of protein in explicit solvent over a variety of charged states. The key to the finite-size correction is the self-energy, which is defined as the interaction energy of the solute with its own periodic images and the neutralizing background. By employing the thermodynamic-integration method with systematically varied sizes of the unit cell of molecular dynamics (MD) simulations, we show for ubiquitin that the self-energy corrects the finite-size effect on the charging free energy within 1 kcal/mol at total charges of -5e, -1e, neutral, and +1e and within 5 kcal/mol even for a highly charged state with +8e. We then sought the additional correction from the solvation effect using the numerical solution to the Poisson equation of the protein with implicit solvent. This correction reduces the cell-size dependence of the charging free energy at +8e to 3 kcal/mol and is well expressed as the self-energy divided by the dielectric constant of solvent water.

  8. 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

  9. 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.

  10. 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

  11. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  13. The effects of charge transfer on the aqueous solvation of ions

    SciTech Connect

    Soniat, Marielle; Rick, Steven W.

    2012-07-28

    Ab initio-based charge partitioning of ionic systems results in ions with non-integer charges. This charge-transfer (CT) effect alters both short- and long-range interactions. Until recently, the effects of CT have been mostly neglected in molecular dynamics (MD) simulations. The method presented in this paper for including charge transfer between ions and water is consistent with ab initio charge partitioning and does not add significant time to the simulation. The ions of sodium, potassium, and chloride are parameterized to reproduce dimer properties and aqueous structures. The average charges of the ions from MD simulations (0.900, 0.919, and -0.775 for Na{sup +}, K{sup +}, and Cl{sup -}, respectively) are consistent with quantum calculations. The hydration free energies calculated for these ions are in agreement with experimental estimates, which shows that the interactions are described accurately. The ions also have diffusion constants in good agreement with experiment. Inclusion of CT results in interesting properties for the waters in the first solvation shell of the ions. For all ions studied, the first shell waters acquire a partial negative charge, due to the difference between water-water and water-ion charge-transfer amounts. CT also reduces asymmetry in the solvation shell of the chloride anion, which could have important consequences for the behavior of chloride near the air-water interface.

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  15. Effects of Preferential Solvation Revealed by Time-Resolved Magnetic Field Effects.

    PubMed

    Pham, Van Thi Bich; Hoang, Hao Minh; Grampp, Günter; Kattnig, Daniel Rudolf

    2017-03-06

    External magnetic fields can impact recombination yields of photo-induced electron transfer reactions by affecting the spin dynamics in transient, spin-correlated radical pair intermediates. For exciplex-forming donor-acceptor systems, this magnetic field effect (MFE) can be investigated sensitively by studying the delayed recombination fluorescence. Here, we investigate the effect of preferential solvation in micro-heterogeneous solvent mixtures on the radical pair dynamics of the system 9,10-dimethylanthracene (fluorophore) / N,N-dimethylaniline (quencher) by means of time-resolved magnetic field effect (TR-MFE) measurements, wherein the exciplex emission is recorded in the absence and the presence of an external magnetic field using Time-Correlated Single Photon Counting (TCSPC). In micro-heterogeneous environments, the MFE of the exciplex emission occurs on a faster timescale than in iso-dielectric homogeneous solvents. In addition, the local polarity reported by the exciplex is enhanced compared to homogeneous solvent mixtures of the same macroscopic permittivity. Detailed analyses of the TR-MFE reveal that the quenching reaction directly yielding the radical ion pair is favored in micro-heterogeneous environments. This is in stark contrast to homogeneous media, for which the MFE predominantly involves direct formation of the exciplex, its subsequent dissociation to the magneto-sensitive radical pair, and re-encounters. These observations provide evidence for polar micro-domains and enhanced caging, which are shown to have a significant impact on the reaction dynamics in micro-heterogeneous binary solvents.

  16. Effects of Preferential Solvation Revealed by Time-Resolved Magnetic Field Effects

    PubMed Central

    2017-01-01

    External magnetic fields can impact recombination yields of photoinduced electron transfer reactions by affecting the spin dynamics in transient, spin-correlated radical pair intermediates. For exciplex-forming donor–acceptor systems, this magnetic field effect (MFE) can be investigated sensitively by studying the delayed recombination fluorescence. Here, we investigate the effect of preferential solvation in microheterogeneous solvent mixtures on the radical pair dynamics of the system 9,10-dimethylanthracene (fluorophore)/N,N-dimethylaniline (quencher) by means of time-resolved magnetic field effect (TR-MFE) measurements, wherein the exciplex emission is recorded in the absence and the presence of an external magnetic field using time-correlated single photon counting (TCSPC). In microheterogeneous environments, the MFE of the exciplex emission occurs on a faster time scale than in iso-dielectric homogeneous solvents. In addition, the local polarity reported by the exciplex is enhanced compared to homogeneous solvent mixtures of the same macroscopic permittivity. Detailed analyses of the TR-MFE reveal that the quenching reaction directly yielding the radical ion pair is favored in microheterogeneous environments. This is in stark contrast to homogeneous media, for which the MFE predominantly involves direct formation of the exciplex, its subsequent dissociation to the magneto-sensitive radical pair, and re-encounters. These observations provide evidence for polar microdomains and enhanced caging, which are shown to have a significant impact on the reaction dynamics in microheterogeneous binary solvents. PMID:28263599

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

    PubMed

    Goicochea, Armando Gama; Alarcón, Francisco

    2011-01-07

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

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

    PubMed

    Liu, Lijun; Nakamura, Issei

    2017-04-03

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

  19. 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

  20. Solvent effects on IR and VCD spectra of helical peptides: DFT-based static spectral simulations with explicit water.

    PubMed

    Kubelka, Jan; Huang, Rong; Keiderling, Timothy A

    2005-04-28

    Simulations of IR and VCD spectra are carried out for model alpha-helical, 3(10)-helical, and 3(1)-helical (polyProII-like) oligopeptides, with up to 21 amide groups, and including explicit consideration of effects of directly hydrogen-bonded solvent (water). Parameters used were obtained from ab initio density functional theory (DFT) computations of force field, atomic polar and axial tensors for oligopeptides of 5 to 7 amides, whose structures were constrained in (phi,psi) to target the secondary structure type but otherwise fully optimized. By comparison with experimental data as well as with calculations for identical but isolated (gas phase) peptides, the computed effects of an inner shell of aqueous solvent on the vibrational spectra of helical oligopeptides are illustrated. The interaction with solvent causes significant frequency shifts of the amide bands, but only minor changes in the characteristic IR intensity distributions and splittings and the VCD band shapes. Better agreement with experimental band shapes is achieved for the alpha-helical amide I' (N-deuterated) VCD by inclusion of explicit solvent in the calculations. Some improvements are also observed in theoretical VCD predictions for 13C labeled alpha-helical peptides when solvated models are used. However, the qualitative isotopic splitting patterns are preserved and just shifted in frequency due to consistent, solvent independent interamide coupling constants. The critical match of experiment and theory for relative positions of transitions in peptides with specifically separated 13C=O labels, including and neglecting solvent, confirms the stability of the coupling interactions. Despite these solvation effects, the calculated VCD band shape of the amide I mode is shown to be a reliable conformational probe, since it remains basically insensitive to frequency shifts caused by environment. Thus theoretical VCD simulations, even vacuum calculations, are shown to provide useful spectral

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

    PubMed

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

    2017-02-15

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

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

    PubMed

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

    2013-02-28

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

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

    PubMed

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

    2015-10-14

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

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  6. 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

    2015-11-05

    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.

  7. 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

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

    PubMed Central

    Jha, Abhishek K; Freed, Karl F

    2009-01-01

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

  9. Simple and exact approach to the electronic polarization effect on the solvation free energy: formulation for quantum-mechanical/molecular-mechanical system and its applications to aqueous solutions.

    PubMed

    Takahashi, Hideaki; Omi, Atsushi; Morita, Akihiro; Matubayasi, Nobuyuki

    2012-06-07

    We present a simple and exact numerical approach to compute the free energy contribution δμ in solvation due to the electron density polarization and fluctuation of a quantum-mechanical solute in the quantum-mechanical/molecular-mechanical (QM/MM) simulation combined with the theory of the energy representation (QM/MM-ER). Since the electron density fluctuation is responsible for the many-body QM-MM interactions, the standard version of the energy representation method cannot be applied directly. Instead of decomposing the QM-MM polarization energy into the pairwise additive and non-additive contributions, we take sum of the polarization energies in the QM-MM interaction and adopt it as a new energy coordinate for the method of energy representation. Then, it is demonstrated that the free energy δμ can be exactly formulated in terms of the energy distribution functions for the solution and reference systems with respect to this energy coordinate. The benchmark tests were performed to examine the numerical efficiency of the method with respect to the changes in the individual properties of the solvent and the solute. Explicitly, we computed the solvation free energy of a QM water molecule in ambient and supercritical water, and also the free-energy change associated with the isomerization reaction of glycine from neutral to zwitterionic structure in aqueous solution. In all the systems examined, it was demonstrated that the computed free energy δμ agrees with the experimental value, irrespective of the choice of the reference electron density of the QM solute. The present method was also applied to a prototype reaction of adenosine 5'-triphosphate hydrolysis where the effect of the electron density fluctuation is substantial due to the excess charge. It was demonstrated that the experimental free energy of the reaction has been accurately reproduced with the present approach.

  10. DFT Study of Hydrogen-Bonding Interaction, Solvation Effect, and Electric-Field Effect on Raman Spectra of Hydrated Proton.

    PubMed

    Pang, Ran; Yu, Li-Juan; Zhang, Meng; Tian, Zhong-Qun; Wu, De-Yin

    2016-10-12

    Strong hydrogen-bonding interaction and Raman spectra of hydrated proton have been investigated using hybrid density functional theory method B3LYP. The solvation model of density (SMD) approach is employed in the present calculation to simulate hydrated protons in aqueous solution. Focusing on the different hydrogen-bonded Eigen-water and Zundel-water interactions, we present a better assignment of Raman signals of hydrated proton on the basis of vibrational analysis in different environments. Our results showed that B3LYP calculations could give a good prediction for characteristic vibrational frequencies of Eigen and Zundel isomers in liquid phase. The O-H stretching vibrational frequencies from Eigen and Zundel units are very sensitive to hydrogen-bonding interaction with solvent water molecules. Moreover, the solvation effect and the external electric-field effect lead to the proton deviating from the central position of Zundel structure and finally resulting in a transition to Eigen one in aqueous solution. Furthermore, by combining theoretical prediction and Raman scattering theory, we calculate absolute Raman intensities of characteristic signals based on the polarizability tensor derivatives of hydrated proton clusters. This is very helpful to infer the microstructure of hydrated protons in aqueous solution by using Raman measurements.

  11. 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.

  12. Preferential solvation of polyvinylacetate (PVA) in water-ethanol mixtures and its effect on the permeability properties of PVA-membranes

    SciTech Connect

    Neidlinger, H.H.

    1985-05-01

    The preferential interaction of polyvinylacetate (PVA) with one of the solvent components in water-ethanol mixtures has been investigated by the method of equilibrium dialysis, evaluated by differential refractometry. It has been found that at a 1:1 molar ratio of water-ethanol there occurs an inversion point of preferential solvation. The overall solvation was determined from intrinsic viscosity and equilibrium swelling measurements. Its plot versus the composition of the binary solvent has a maximum that practically coincides with the inversion point of the preferential solvation. These results are compared with those obtained from pervaporation studies carried out on PVA-membranes in the same solvent system, and they are discussed in terms of the existence of special interaction phenomena due to hydrogen bonding effects. It can be concluded that for the system investigated preferential solvation parameters help to understand, but do not necessarily predict, membrane permselectivity. 12 refs., 14 figs., 2 tabs.

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

    PubMed

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

    2014-12-26

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

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

    SciTech Connect

    Walewski, Łukasz Forbert, Harald; Marx, Dominik

    2014-04-14

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

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

    PubMed

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

    2000-07-01

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

  16. Differential Age Effects for Implicit and Explicit Conceptual Associative Memory

    PubMed Central

    Dew, Ilana T. Z.; Giovanello, Kelly S.

    2010-01-01

    Older adults show disproportionate declines in explicit memory for associative relative to item information. However, the source of these declines is still uncertain. One explanation is a generalized impairment in the processing of associative information. A second explanation is a more specialized impairment in the strategic, effortful recollection of associative information, leaving less effortful forms of associative retrieval preserved. Assessing implicit memory of new associations is a way to distinguish between these viewpoints. To date, mixed findings have emerged from studies of associative priming in aging. One factor that may account for the variability is whether the manipulations inadvertently involve strategic, explicit processes. In 2 experiments we present a novel paradigm of conceptual associative priming in which subjects make speeded associative judgments about unrelated objects. Using a size classification task, Experiment 1 showed equivalent associative priming between young and older adults. Experiment 2 generalized the results of Experiment 1 to an inside/outside classification task, while replicating the typical age-related impairment in associative but not item recognition. Taken together, the findings support the viewpoint that older adults can incidentally encode and retrieve new meaningful associations despite difficulty with the intentional recollection of the same information. PMID:21077717

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

    PubMed

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

    2016-10-11

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

  18. 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.

  19. Force field development for actinyl ions via quantum mechanical calculations: an approach to account for many body solvation effects.

    PubMed

    Rai, Neeraj; Tiwari, Surya P; Maginn, Edward J

    2012-09-06

    Advances in computational algorithms and methodologies make it possible to use highly accurate quantum mechanical calculations to develop force fields (pair-wise additive intermolecular potentials) for condensed phase simulations. Despite these advances, this approach faces numerous hurdles for the case of actinyl ions, AcO2(n+) (high-oxidation-state actinide dioxo cations), mainly due to the complex electronic structure resulting from an interplay of s, p, d, and f valence orbitals. Traditional methods use a pair of molecules (“dimer”) to generate a potential energy surface (PES) for force field parametrization based on the assumption that many body polarization effects are negligible. We show that this is a poor approximation for aqueous phase uranyl ions and present an alternative approach for the development of actinyl ion force fields that includes important many body solvation effects. Force fields are developed for the UO2(2+) ion with the SPC/Fw, TIP3P, TIP4P, and TIP5P water models and are validated by carrying out detailed molecular simulations on the uranyl aqua ion, one of the most characterized actinide systems. It is shown that the force fields faithfully reproduce available experimental structural data and hydration free energies. Failure to account for solvation effects when generating PES leads to overbinding between UO2(2+) and water, resulting in incorrect hydration free energies and coordination numbers. A detailed analysis of arrangement of water molecules in the first and second solvation shell of UO2(2+) is presented. The use of a simple functional form involving the sum of Lennard-Jones + Coulomb potentials makes the new force field compatible with a large number of available molecular simulation engines and common force fields.

  20. Solvent density effects on the solvation behavior and configurational structure of bare and passivated 38-atom gold nanoparticle in supercritical ethane.

    PubMed

    Lal, Moti; Plummer, Martin; Smith, William

    2006-10-26

    In exploring the effects of solvent density on the mode and the degree of solvation of the bare and passivated 38-atom gold particle in supercritical ethane, we have extended the molecular dynamics simulations of the system, reported previously,(34) to cover a range of isotherms in the T > T(c) regime, where T(c) is the critical temperature of the solvent. Consonant with our previous observations, the modes of solvation of the bare and the passivated particle, deduced from the radial distribution of the solvent about the metal core center of mass, are found to be vastly different from each other at all solvent densities: while the molecules solvating the bare particle form a well-defined, two-region layer around it, those solvating the passivated particle are loosely dispersed in the passivating layer. For the bare particle, the degree of solvation (vartheta) as a function of solvent density passes through a maximum occurring in the close vicinity of the critical point, consistent with our previous results and in agreement with Debenedetti's theoretical analysis,(22,23) which predicts a solvation enhancement effect in the critical region for systems where the unlike solvent/solute interaction is much stronger than the solvent/solvent interaction. Taking the degree of solvation (vartheta) as a measure of solvent quality, we have investigated how the solvent quality would vary along the solvent-density isotherms. In the solvent-density regime rho > rho(c), the solvent quality is found to be a decreasing function of the density as a result of progressive dominance of the excluded volume effect over the attractive particle/solvent interactions. The particle/solvent affinity is greatly reduced in the presence of the passivating layer, resulting in considerable shrinkage of the good-solvent-quality domain in the supercritical regime. The solvent environment and the presence of the passivating chains produce significant disorder in the equilibrium structure assumed by the

  1. Production of solvated electrons

    NASA Technical Reports Server (NTRS)

    Thomas, J. K.

    1969-01-01

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

  2. Effect of Explicit Language Learning Strategy Instruction on Language-Test and Self-Assessment Scores

    ERIC Educational Resources Information Center

    Jurkovic, Violeta

    2010-01-01

    The present article reports on the findings of a study that explored the effect of explicit language learning strategy instruction on the development of English as a foreign language within a higher education setting in mixed language ability groups. The research results indicate that explicit language learning strategy instruction that aimed at…

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

    ERIC Educational Resources Information Center

    Pesco, Diane; Devlin, Christine

    2015-01-01

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

  4. 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

  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. Rough dependence upon initial data exemplified by explicit solutions and the effect of viscosity

    NASA Astrophysics Data System (ADS)

    Li, Y. Charles

    2017-03-01

    In this article, we present some interesting non-steady explicit solutions to the 2D Euler and Navier–Stokes equations. Explicit calculations on the explicit solutions show that Navier–Stokes (and Euler) equations have the novel property of rough dependence upon initial data in contrast to the sensitive dependence upon initial data found in chaos. Through the explicit calculations, we are able to obtain a lower bound on the norm of the Fréchet derivative of the solution operator at the explicit solutions to the Navier–Stokes equations. The lower bound approaches infinity as the Reynolds number approaches infinity. For Euler equations, this lower bound is indeed infinity. The rough dependence property in the inviscid case is closely related to the theorem of Cauchy. The viscous effect on the theorem of Cauchy and the rough dependence property is also studied.

  7. 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

  8. 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…

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

    SciTech Connect

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

    1992-06-01

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

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

    SciTech Connect

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

    1992-06-01

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

  11. Effect of partial atomic charges on the calculated free energy of solvation of poly(vinyl alcohol) in selected solvents.

    PubMed

    Noorjahan, Abolfazl; Choi, Phillip

    2015-03-01

    It is well-known that properties of poly(vinyl alcohol) (PVA) in the pure and solution states depend largely on the hydrogen bonding networks formed. In the context of molecular simulation, such networks are handled through the Coulombic interactions. Therefore, a good set of partial atom charges (PACs) for simulations involving PVA is highly desirable. In this work, we calculated the PACs for PVA using a few commonly used population analysis schemes with a hope to identify an accurate set of PACs for PVA monomers. To evaluate the quality of the calculated parameters, we have benchmarked their predictions for free energy of solvation (FES) in selected solvents by molecular dynamics simulations against the ab initio calculated values. Selected solvents were water, ethanol and benzene as they covered a range of size and polarity. Also, PVA with different tacticities were used to capture their effect on the calculated FESs. Based on our results, neither PACs nor FESs are affected by the chain tacticity. While PACs predicted by the Merz-Singh-Kollman scheme were close to original values in the OPLS-AA force field in way that no significant difference in properties of pure PVA was observed, free energy of solvation calculated using such PACs showed greater agreement with ab initio calculated values than those calculated by OPLS-AA (and all other schemes used in this work) in all three solvents considered.

  12. Brief Report: Effects of Subtle and Explicit Health Messages on Food Choice

    PubMed Central

    Wagner, Heather; Howland, Maryhope; Mann, Traci

    2014-01-01

    Objective Explicitly—as opposed to subtly—labeling a food healthy may inadvertently license people to indulge, imply that the food tastes bad, or lead to reactance. We investigated the effects of explicit and subtle health messages on individuals’ food selection in two field studies. Methods We manipulated the signs on healthy foods such that they explicitly stated that the food was healthy, subtly suggested it with an image, or did not mention health. As participants, attendees at academic conferences, approached registration tables, research assistants recorded the number and type of snacks individuals chose. Results Participants were more likely to choose the healthy food when it was labeled with the subtle health message than when it was labeled with the explicit health message, which itself was not more effective than the control message. Conclusion Subtle messages may be more useful than explicit health messages in encouraging individuals to make a healthy snack choice. PMID:24467259

  13. 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.

  14. 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.

  15. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations.

    PubMed

    Dixit, Surjit B; Mezei, Mihaly; Beveridge, David L

    2012-07-01

    Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute-solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interact more strongly with water molecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning's counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 A from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general, the

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

    PubMed

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

    2017-03-27

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

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

    PubMed

    Gounder, Rajamani; Iglesia, Enrique

    2013-05-04

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

  19. Combined QM/MM Molecular Dynamics Study on a Condensed-Phase SN2 Reaction at Nitrogen:  The Effect of Explicitly Including Solvent Polarization.

    PubMed

    Geerke, Daan P; Thiel, Stephan; Thiel, Walter; van Gunsteren, Wilfred F

    2007-07-01

    In a previous combined QM/MM molecular dynamics (MD) study from our laboratory on the identity SN2 reaction between a chloride anion and an amino chloride in liquid dimethyl ether (DME), an increase in the free energy activation barrier was observed in the condensed phase when compared to the gas-phase activation energy. Here we reproduce these findings, but when comparing the condensed-phase potential of mean force (PMF) with the free energy profile in the gas phase (obtained from Monte Carlo simulations), we observe a smaller solvent effect on the activation barrier of the reaction. In a next step, we introduce an explicit description of electronic polarization in the MM (solvent) part of the system. A polarizable force field for liquid DME was developed based on the charge-on-spring (COS) model, which was calibrated to reproduce thermodynamic properties of the nonpolarizable model in classical MD simulations. The COS model was implemented into the MNDO/GROMOS interface in a special version of the QM/MM software ChemShell, which was used to investigate the effect of solvent polarization on the free energy profile of the reaction under study. A higher activation barrier was obtained using the polarizable solvent model than with the nonpolarizable force field, due to a better solvation of and a stronger polarization of solvent molecules around the separate reactants. The obtained PMFs were subjected to an energy-entropy decomposition of the relative solvation free energies of the reactant complex along the reaction coordinate, to investigate in a quantitative manner whether the solvent (polarization) effects are mainly due to favorable QM-MM (energetic) interactions.

  20. Pulse radiolysis study of ion-species effects on the solvated electron in alkylammonium ionic liquids

    NASA Astrophysics Data System (ADS)

    Kondoh, Takafumi; Asano, Akira; Yang, Jinfeng; Norizawa, Kimihiro; Takahashi, Kenji; Taguchi, Mitsumasa; Nagaishi, Ryuji; Katoh, Ryuzi; Yoshida, Yoichi

    2009-12-01

    The spectra and kinetic behavior of solvated electrons (e sol-) in alkyl ammonium ionic liquids (ILs), i.e. N,N-diethyl-N-methyl-N-(2-methoxyethyl)ammonium bis(trifluoromethanesulfonyl)imide (DEMMA-TFSI), N,N-diethyl-N-methyl-N-(2-methoxyethyl)ammonium tetrafluoroborate (DEMMA-BF 4), N,N,N-trimethyl-N-propylammonium bis(trifluoromethanesulfonyl)imide (TMPA-TFSI), N-methyl-N-propylpiperidinium bis(trifluoromethanesulfonyl)imide (PP13-TFSI), N-methyl-N-propylpyrrolidinium bis(trifluoromethanesulfonyl)imide (P13-TFSI), and N-methyl-N-butylpyrrolidinium bis(trifluoromethanesulfonyl)imide (P14-TFSI) were investigated by the pulse radiolysis method. The e sol- in each of the ammonium ILs has an absorption peak at 1100 nm, with molar absorption coefficients of 1.5-2.3×10 4 dm 3 mol -1 cm -1. The e sol- decayed by first order with a rate constant of 1.4-6.4×10 6 s -1. The reaction rate constant of the solvated electron with pyrene (Py) was 1.5-3.5×10 8 dm 3 mol -1 s -1 in the various ILs. These values were about one order of magnitude higher than the diffusion-controlled limits calculated from measured viscosities. The radiolytic yields ( G-value) of the e sol- were 0.8-1.7×10 -7 mol J -1. The formation rate constant of e sol- in DEMMA-TFSI was 3.9×10 10 s -1. The dry electron (e dry-) in DEMMA-TFSI reacts with Py with a rate constant of 7.9×10 11 dm 3 mol -1 s -1, three orders of magnitude higher than that of the e sol- reactions. The G-value of the e sol- in the picosecond time region is 1.2×10 -7 mol J -1. The capture of e dry- by scavengers was found to be very fast in ILs.

  1. 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…

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

    NASA Astrophysics Data System (ADS)

    Lemler, Paul M.; Vaccaro, Patrick

    2016-06-01

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

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

    PubMed

    Zachmann, Martin; Mathias, Gerald; Antes, Iris

    2015-06-08

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

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

    ERIC Educational Resources Information Center

    Colovic-Markovic, Jelena

    2012-01-01

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

  5. 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…

  6. 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

  7. The Effects of Obesity-Related Health Messages on Explicit and Implicit Weight Bias.

    PubMed

    Rudolph, Almut; Hilbert, Anja

    2016-01-01

    The pervasiveness of explicit and implicit weight bias (WB) defined as negative stereotypes and prejudice regarding one's weight has been observed among individuals of all weight categories. As a source of WB, health messages have been discussed due to reinforcing stigmatizing notions. The present study sought to investigate whether health messages (i.e., eat healthy, become physically active) have the potential to increase explicit and implicit WB. Participants (N = 144) from the community were randomized to either an experimental group (EG) or a control group (CG). While the EG was presented with health messages, the CG was presented with neutral information. Before and after manipulation, participants completed measures of explicit and implicit WB. Paired samples t-test revealed no differences in explicit WB after manipulation, however, a small effect decrease of implicit WB in the EG but not in the CG was found. This study provided evidence that health messages might have differential impact to change WB. According to dual-model approaches, explicit and implicit WB tap into two different information processing systems, and thus were differentially affected by health messages. Brief exposure to health messages might have the potential to contribute to health behavior and to mitigate implicit WB.

  8. The Effects of Obesity-Related Health Messages on Explicit and Implicit Weight Bias

    PubMed Central

    Rudolph, Almut; Hilbert, Anja

    2017-01-01

    The pervasiveness of explicit and implicit weight bias (WB) defined as negative stereotypes and prejudice regarding one’s weight has been observed among individuals of all weight categories. As a source of WB, health messages have been discussed due to reinforcing stigmatizing notions. The present study sought to investigate whether health messages (i.e., eat healthy, become physically active) have the potential to increase explicit and implicit WB. Participants (N = 144) from the community were randomized to either an experimental group (EG) or a control group (CG). While the EG was presented with health messages, the CG was presented with neutral information. Before and after manipulation, participants completed measures of explicit and implicit WB. Paired samples t-test revealed no differences in explicit WB after manipulation, however, a small effect decrease of implicit WB in the EG but not in the CG was found. This study provided evidence that health messages might have differential impact to change WB. According to dual-model approaches, explicit and implicit WB tap into two different information processing systems, and thus were differentially affected by health messages. Brief exposure to health messages might have the potential to contribute to health behavior and to mitigate implicit WB. PMID:28123375

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

    ERIC Educational Resources Information Center

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

    2005-01-01

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

  10. 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…

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

    ERIC Educational Resources Information Center

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

    2001-01-01

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

  12. 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…

  13. 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…

  14. 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…

  15. 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…

  16. Examining the Effectiveness of Explicit Instruction of Vocabulary Learning Strategies with Japanese EFL University Students

    ERIC Educational Resources Information Center

    Mizumoto, Atsushi; Takeuchi, Osamu

    2009-01-01

    This study examined the effectiveness of explicit instruction of vocabulary learning strategies (VLSs) over a 10-week semester with a group of 146 female EFL learners from two Japanese universities. A vocabulary test and questionnaires on VLSs and motivation were administered at the beginning of the course. The learners were divided into two…

  17. Anion Solvation in Carbonate-Based Electrolytes

    SciTech Connect

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

    2015-11-16

    The correlation between Li+ solvation and interphasial chemistry on anodes firmly established in Li-ion batteries, the effect of cation–solvent interaction has gone beyond bulk thermodynamic and transport properties and become an essential element that determines the reversibility of electrochemistry and kinetics of Li-ion intercalation chemistries. Now, most studies are dedicated to the solvation of Li+, and the solvation of anions in carbonate-based electrolytes and its possible effect on the electrochemical stability of such electrolytes remains little understood. Moreover, as a mirror effort to prior Li+ solvation studies, this work focuses on the interactions between carbonate-based solvents and two anions (hexafluorophosphate, PF6–, and tetrafluoroborate, BF4–) that are most frequently used in Li-ion batteries. The possible correlation between such interaction and the interphasial chemistry on cathode surface is also explored.

  18. Anion Solvation in Carbonate-Based Electrolytes

    DOE PAGES

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

    2015-11-16

    The correlation between Li+ solvation and interphasial chemistry on anodes firmly established in Li-ion batteries, the effect of cation–solvent interaction has gone beyond bulk thermodynamic and transport properties and become an essential element that determines the reversibility of electrochemistry and kinetics of Li-ion intercalation chemistries. Now, most studies are dedicated to the solvation of Li+, and the solvation of anions in carbonate-based electrolytes and its possible effect on the electrochemical stability of such electrolytes remains little understood. Moreover, as a mirror effort to prior Li+ solvation studies, this work focuses on the interactions between carbonate-based solvents and two anions (hexafluorophosphate,more » PF6–, and tetrafluoroborate, BF4–) that are most frequently used in Li-ion batteries. The possible correlation between such interaction and the interphasial chemistry on cathode surface is also explored.« less

  19. 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.

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

    PubMed

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

    2011-02-07

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

  1. Theory and simulation of explicit solvent effects on protein folding in vitro and in vivo

    NASA Astrophysics Data System (ADS)

    England, Jeremy L.

    The aim of this work is to develop theoretical tools for understanding what happens to water that is confined in amphipathic cavities, and for testing the consequences of this understanding for protein folding in vitro and in vivo. We begin in the first chapter with a brief review of the theoretical and simulation literature on the hydrophobic effect and the aqueous solvation of charged species that also puts forward a simple theoretical framework within which various solvation phenomena reported in past studies may be unified. Subsequently, in the second chapter we also review past computational and theoretical work on the specific question of how chaperonin complexes assist the folding of their substrates. With the context set, we turn in Chapter 3 to the case of an open system with water trapped between hydrophobic plates that experiences a uniform electric field normal to and between the plates. Classic bulk theory of electrostriction in polarizable fluids tells us that the electric field should cause an increase in local water density as it rises, yet some simulations have suggested the opposite. We present a mean-field Potts model we have developed to explain this discrepancy, and show how such a simple, coarse-grained lattice description can capture the fundamental consequences of the fact that external electric fields can frustrate the hydrogen bond network in confined water. Chapter 4 continues to pursue the issue of solvent evacuation between hydrophobic plates, but focuses on the impact of chemical denaturants on hydrophobic effects using molecular dynamics simulations of hydrophobic dewetting. We find that while urea and guanidinium have similar qualitative effects at the bulk level, they seem to differ in the microscopic mechanism by which they denature proteins, although both inhibit the onset of dewetting. Lastly, Chapters 5 and 6 examine the potential importance of solvent-mediated forces to protein folding in vivo. Chapter 5 develops a Landau

  2. 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

    2015-01-02

    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.

  3. Comparison of Solvation Effects on CO2 Capture with Aqueous Amine Solutions and Amine-Functionalized Ionic Liquids.

    PubMed

    Yamada, Hidetaka

    2016-10-13

    Amines are the most widely utilized chemicals for postcombustion CO2 capture, because the reversible reactions between amines and CO2 through their moderate interaction allow effective "catch and release". Usually, CO2 is dissolved in the form of an anion such as carbamate or bicarbonate. Therefore, the reaction energy diagram is potentially governed to a large extent by the polarity of the surrounding solvent. Herein, we compared aqueous amine solutions and amine-functionalized ionic liquids by investigating their dielectric constants and performing an intrinsic reaction coordinate analysis of the CO2 absorption process. Quantum mechanical calculations at the CCSD(T)/6-311++G(d,p)//B3LYP/6-311++G(d,p) level within the continuum solvation model (SMD/IEF-PCM) revealed contrasting dependencies of C-N bond formation on the dielectric constant in those solutions. Amines react with CO2 on an energy surface that is significantly affected by the dielectric constant in conventional aqueous amine solutions, whereas amine-functionalized anions and CO2 form stable C-N bonds with a comparatively lower activation energy regardless of the dielectric constant.

  4. 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.

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

    PubMed

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

    2010-11-01

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

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

    PubMed Central

    Østvik, Leni; Eikeseth, Svein; Klintwall, Lars

    2012-01-01

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

  7. Neutral transition metal hydrides as acids in hydrogen bonding and proton transfer: media polarity and specific solvation effects.

    PubMed

    Levina, Vladislava A; Filippov, Oleg A; Gutsul, Evgenii I; Belkova, Natalia V; Epstein, Lina M; Lledos, Agusti; Shubina, Elena S

    2010-08-18

    Structural, spectroscopic, and electronic features of weak hydrogen-bonded complexes of CpM(CO)(3)H (M = Mo (1a), W (1b)) hydrides with organic bases (phosphine oxides R(3)PO (R = n-C(8)H(17), NMe(2)), amines NMe(3), NEt(3), and pyridine) are determined experimentally (variable temperature IR) and computationally (DFT/M05). The intermediacy of these complexes in reversible proton transfer is shown, and the thermodynamic parameters (DeltaH degrees , DeltaS degrees ) of each reaction step are determined in hexane. Assignment of the product ion pair structure is made with the help of the frequency calculations. The solvent effects were studied experimentally using IR spectroscopy in CH(2)Cl(2), THF, and CH(3)CN and computationally using conductor-like polarizable continuum model (CPCM) calculations. This complementary approach reveals the particular importance of specific solvation for the hydrogen-bond formation step. The strength of the hydrogen bond between hydrides 1 and the model bases is similar to that of the M-H...X hydrogen bond between 1 and THF (X = O) or CH(3)CN (X = N) or between CH(2)Cl(2) and the same bases. The latter competitive weak interactions lower the activities of both the hydrides and the bases in the proton transfer reaction. In this way, these secondary effects shift the proton transfer equilibrium and lead to the counterintuitive hampering of proton transfer upon solvent change from hexane to moderately polar CH(2)Cl(2) or THF.

  8. 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.

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

    SciTech Connect

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

    2004-01-01

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

  10. Effect of the solvatation shell exchange on the formation of malvidin-3-O-glucoside-ellagic acid complexes.

    PubMed

    Kunsagi-Maté, Sandor; Ortmann, Erika; Kollar, Laszló; Nikfardjam, Martin Pour

    2007-10-11

    The interaction of malvidin-3-O-glucoside with ellagic acid was studied in aqueous solutions in dependence of the ethanol content of the samples. The results show significant changes of the thermodynamic parameters when the ethanol content exceeds 8%vol. The quantum chemical calculations and the solvent relaxation measurements validate that the solvatation shell of the malvidin-ellagic acid complexes changes from water to ethanol around this critical alcoholic concentration. The change of the solvate shell is accompanied by increasing copigmentation; i.e., higher "multi-sandwich" complexes are formed. According to the considerable role of this interaction (namely copigmentation) in the formation of color in red wines, our results have several consequences for the winemaking process with regard to the stabilization of wine color.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-03-01

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

  13. Dielectric and thermal effects on the optical properties of natural dyes: a case study on solvated cyanin.

    PubMed

    Malcıoğlu, Osman Bariş; Calzolari, Arrigo; Gebauer, Ralph; Varsano, Daniele; Baroni, Stefano

    2011-10-05

    The optical properties of the flavylium state of the cyanin dye are simulated numerically by combining Car-Parrinello molecular dynamics and linear-response time-dependent density functional theory calculations. The spectrum of the dye calculated in the gas phase is characterized by two peaks in the yellow and in the blue (green and violet), using a GGA-PBE (hybrid-B3LYP) DFT functional, which would bring about a greenish (bright orange) color incompatible with the dark purple hue 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 the molecular distortions induced by thermal fluctuations.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2006-08-01

    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 control 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. However, we also show how our method for p Ka prediction could be improved using ab initio molecular dynamics simulations of solvated surfaces.

  16. Solvent Effects on Oxygen-17 Chemical Shifts in Amides. Quantitative Linear Solvation Shift Relationships

    NASA Astrophysics Data System (ADS)

    Díez, Ernesto; Fabián, Jesús San; Gerothanassis, Ioannis P.; Esteban, Angel L.; Abboud, José-Luis M.; Contreras, Ruben H.; de Kowalewski, Dora G.

    1997-01-01

    A multiple-linear-regression analysis (MLRA) has been carried out using the Kamlet-Abboud-Taft (KAT) solvatochromic parameters in order to elucidate and quantify the solvent effects on the17O chemical shifts ofN-methylformamide (NMF),N,N-dimethylformamide (DMF),N-methylacetamide (NMA), andN,N-dimethylacetamide (DMA). The chemical shifts of the four molecules show the same dependence (in ppm) on the solvent polarity-polarizability, i.e., -22π*. The influence of the solvent hydrogen-bond-donor (HBD) acidities is slightly larger for the acetamides NMA and DMA, i.e., -48α, than for the formamides NMF and DMF, i.e., -42α. The influence of the solvent hydrogen-bond-acceptor (HBA) basicities is negligible for the nonprotic molecules DMF and DMA but significant for the protic molecules NMF and NMA, i.e., -9β. The effect of substituting the N-H hydrogen by a methyl group amounts to -5.9 ppm in NMF and 5.4 ppm in NMA. The effect of substituting the O=C-H hydrogen amounts to 5.5 ppm in NMF and 16.8 ppm in DMF. The model of specific hydration sites of amides by I. P. Gerothanassis and C. Vakka [J. Org. Chem.59,2341 (1994)] is settled in a more quantitative basis and the model by M. I. Burgar, T. E. St. Amour, and D. Fiat [J. Phys. Chem.85,502 (1981)] is critically evaluated.17O hydration shifts have been calculated for formamide (FOR) by the ab initio LORG method at the 6-31G* level. For a formamide surrounded by the four in-plane molecules of water in the first hydration shell, the calculated17O shift change due to the four hydrogen bonds, -83.2 ppm, is smaller than the empirical hydration shift, -100 ppm. The17O shift change from each out-of-plane water molecule hydrogen-bonded to the amide oxygen is -18.0 ppm. These LORG results support the conclusion that no more than four water molecules are hydrogen-bonded to the amide oxygen in formamide.

  17. 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

  18. 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.

  19. 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

  20. Conformation of a Lennard-Jones polymer in explicit solvent

    NASA Astrophysics Data System (ADS)

    Ye, Yuting; Taylor, Mark

    2012-04-01

    The conformation of a polymer chain is 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 chain can be formally mapped to an exact n-body solvation potential. These potentials map the chain-solvent system to a single chain, thereby dramatically reducing the computational complexity of the polymer chain-in-solvent problem. We have recently shown that a pair-decomposition of this n-body potential is valid for short Lennard-Jones (LJ) chains in explicit LJ solvent [1]. Here we use these short chain results to construct solvation potentials for long chains. We present results for the size and intramolecular structure of LJ chains up to length n=400 in LJ solvent at state points spanning the solvent phase diagram (including vapor, liquid, and super-critical regions). In comparison with simulation results for the corresponding full chain-in-solvent system, our solvation potential approach is found to be quantitatively accurate for a wide range of solvent conditions and chain lengths.[4pt] [1] M.P. Taylor and S.R. Adhikari, J. Chem. Phys. 135, 044903 (2011).

  1. Conformation of a Lennard-Jones polymer in explicit solvent

    NASA Astrophysics Data System (ADS)

    Ye, Yuting; Taylor, Mark

    2011-10-01

    The conformation of a polymer chain is 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 chain can be formally mapped to an exact n-body solvation potential. These potentials map the chain-solvent system to a single chain, thereby dramatically reducing the computational complexity of the polymer chain-in-solvent problem. We have recently shown that a pair-decomposition of this n-body potential is valid for short Lennard-Jones (LJ) chains in explicit LJ solvent [1]. Here we use these short chain results to construct solvation potentials for long chains. We present results for the size and intramolecular structure of LJ chains up to length n=400 in LJ solvent at state points spanning the solvent phase diagram (including vapor, liquid, and super-critical regions). In comparison with simulation results for the corresponding full chain-in-solvent system, our solvation potential approach is found to be quantitatively accurate for a wide range of solvent conditions and chain lengths.[4pt] [1] M.P. Taylor and S.R. Adhikari, J. Chem. Phys. 135, 044903 (2011).

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

    PubMed

    Wang, Zhi-Xiang; Duan, Yong

    2004-11-15

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

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

    PubMed

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

    2006-11-01

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

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

    PubMed

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

    2015-02-10

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

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

    PubMed Central

    2015-01-01

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

  6. Working memory moderates the effect of the integrative process of implicit and explicit autonomous motivation on academic achievement.

    PubMed

    Gareau, Alexandre; Gaudreau, Patrick

    2017-03-10

    In previous research, autonomous motivation (AM) has been found to be associated with school achievement, but the relation has been largely heterogeneous across studies. AM has typically been assessed with explicit measures such as self-report questionnaires. Recent self-determination theory (SDT) research has suggested that converging implicit and explicit measures can be taken to characterize the integrative process in SDT. Drawing from dual-process theories, we contended that explicit AM is likely to promote school achievement when it is part of an integrated cognitive system that combines easily accessible mental representations (i.e., implicit AM) and efficient executive functioning. A sample of 272 university students completed a questionnaire and a lexical decision task to assess their explicit and implicit AM, respectively, and they also completed working memory capacity measures. Grades were obtained at the end of the semester to examine the short-term prospective effect of implicit and explicit AM, working memory, and their interaction. Results of moderation analyses have provided support for a synergistic interaction in which the association between explicit AM and academic achievement was positive and significant only for individuals with high level of implicit AM. Moreover, working memory was moderating the synergistic effect of explicit and implicit AM. Explicit AM was positively associated with academic achievement for students with average-to-high levels of working memory capacity, but only if their motivation operated synergistically with high implicit AM. The integrative process thus seems to hold better proprieties for achievement than the sole effect of explicit AM. Implications for SDT are outlined.

  7. 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.

  8. Drastic Compensation of Electronic and Solvation Effects on ATP Hydrolysis Revealed through Large-Scale QM/MM Simulations Combined with a Theory of Solutions.

    PubMed

    Takahashi, Hideaki; Umino, Satoru; Miki, Yuji; Ishizuka, Ryosuke; Maeda, Shu; Morita, Akihiro; Suzuki, Makoto; Matubayasi, Nobuyuki

    2017-03-16

    Hydrolysis of adenosine triphosphate (ATP) is the "energy source" for a variety of biochemical processes. In the present work, we address key features of ATP hydrolysis: the relatively moderate value (about -10 kcal/mol) of the standard free energy, ΔGhyd, of reaction and the insensitivity of ΔGhyd to the number of excess electrons on ATP. We conducted quantum mechanical/molecular mechanical simulation combined with the energy-representation theory of solutions to analyze the electronic-state and solvation contributions to ΔGhyd. It was revealed that the electronic-state contribution in ΔGhyd is largely negative (favorable) upon hydrolysis, due to the reduction of electrostatic repulsion accompanying the breakage of the P-O bond. In contrast, the solvation effect was found to be strongly more favorable on the reactant side. Thus, we showed that a drastic compensation of the two opposite effects takes place, leading to the modest value of ΔGhyd at each number of excess electrons examined. The computational analyses were also conducted for pyrophosphate ions (PPi), and the parallelism between the ATP and PPi hydrolyses was confirmed. Classical molecular dynamics simulation was further carried out to discuss the effect of the solvent environment; the insensitivity of ΔGhyd to the number of excess electrons was seen to hold in solvent water and ethanol.

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

    PubMed

    Sharma, Ity; Kaminski, George A

    2012-11-15

    We have computed pK(a) values for 11 substituted phenol compounds using the continuum Fuzzy-Border (FB) solvation model. Hydration energies for 40 other compounds, including alkanes, alkenes, alkynes, ketones, amines, alcohols, ethers, aromatics, amides, heterocycles, thiols, sulfides, and acids have been calculated. The overall average unsigned error in the calculated acidity constant values was equal to 0.41 pH units and the average error in the solvation energies was 0.076 kcal/mol. We have also reproduced pK(a) values of propanoic and butanoic acids within about 0.1 pH units from the experimental values by fitting the solvation parameters for carboxylate ion carbon and oxygen atoms. The FB model combines two distinguishing features. First, it limits the amount of noise which is common in numerical treatment of continuum solvation models by using fixed-position grid points. Second, it uses either second- or first-order approximation for the solvent polarization, depending on a particular implementation. These approximations are similar to those used for solute and explicit solvent fast polarization treatment which we developed previously. This article describes results of using the first-order technique. This approximation places the presented methodology between the Generalized Born and Poisson-Boltzmann continuum solvation models with respect to their accuracy of reproducing the many-body effects in modeling a continuum solvent.

  10. 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.

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

    PubMed

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

    2010-10-28

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

  12. Spatially explicit cholera model: effects of population, water resources and health conditions distributions.

    NASA Astrophysics Data System (ADS)

    Bertuzzo, E.; Casagrandi, R.; Gatto, M.; Rodriguez-Iturbe, I.; Rinaldo, A.

    2009-04-01

    Cholera epidemics are still a major public health concern to date in many areas of the world. In order to understand and forecast cholera outbreaks, one of the most important factors is the role played by the environmental matrix in which the disease spreads. The environmental matrix is constituted by different human communities and their interconnections. Each community is characterized by its spatial position, population size, water resources availability and hygiene conditions. By implementing a spatially explicit cholera model we seek the effects on epidemic dynamics of: i) the topology and metrics of the pathogens pathways that connect different communities; ii) the spatial distribution of the population size; and iii) the spatial distributions of water resources and public health conditions, and how they vary with population size. We further extend the model by deriving the speed of propagation of traveling fronts in the case of uniformly distributed systems for different topologies: one and two dimensional lattices and river networks. The derivation of the spreading celerity proves instrumental in establishing the overall conditions for the relevance of spatially explicit models. The conditions are sought by comparison between spreading and disease timescales. Consider a cholera epidemic that starts from a point and spreads throughout a finite size system, it is possible to identify two different timescales: i) the spreading timescale, that is the time needed for the disease to spread and involve all the communities in the system; and ii) the epidemic timescale, defined by the duration of the epidemic in a single community. While the latter mainly depends on biological factors, the former is controlled also by the geometry of the environmental matrix. If the epidemics timescales are comparable or larger than pathogens' spreading timescales, one expects that the spatial variability does not play a role and the system may be approximated by a well

  13. Solvation and Reaction in Ionic Liquids

    SciTech Connect

    Maroncelli, Mark

    2010-10-15

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

  14. 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.

  15. 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…

  16. 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…

  17. 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…

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

    SciTech Connect

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

    2016-07-01

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

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

    DOE PAGES

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

    2016-07-01

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

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

    PubMed

    Boda, Dezső; Henderson, Douglas; Gillespie, Dirk

    2013-08-07

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

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

    NASA Astrophysics Data System (ADS)

    Pandey, Ras; Farmer, Barry

    2015-03-01

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

  2. A Comparison of the Effects of Implicit and Explicit Corrective Feedback on Learners` Performance in Tailor-Made Tests

    NASA Astrophysics Data System (ADS)

    Dabaghi, Azizollah

    The study investigated the effects of correction of learners` grammatical errors on acquisition. Specifically, it compared the effects of manner of correction (explicit versus implicit correction). It also investigated the relative effects of explicit and implicit correction of morphological versus syntactic features and correction of developmental early versus developmental late features. Data were collected from 56 intermediate level Iranian students of English Each participant was required to read and then retell a written text in their own words during an oral interview. During or following the interview the researcher corrected the participants on their grammatical errors implicitly (using recasts) or explicitly. Individualised tests focusing on the corrected errors were constructed and administered. Statistical analyses were conducted on the scores the participants received on their individualised tests. Results showed that the participants who received explicit correction gained significantly higher scores than those who received implicit correction. Analyses of the interactions between independent variables showed that explicit correction was more effective for the acquisition of developmental early features and implicit correction was more effective for the acquisition of developmental late features.

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

    PubMed

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

    2014-11-01

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

  4. Analysis of solute-solvent interactions in the fragment molecular orbital method interfaced with effective fragment potentials: theory and application to a solvated griffithsin-carbohydrate complex.

    PubMed

    Nagata, Takeshi; Fedorov, Dmitri G; Sawada, Toshihiko; Kitaura, Kazuo

    2012-09-13

    Based on the proposed new expression of the polarization energy for the fragment molecular orbital (FMO) method interfaced with effective fragment potentials (EFPs), we develop an analysis of the solute(FMO)-solvent(EFP) interactions by defining individual fragment contributions for both solute and solvent. The obtained components are compared to all-electron calculations where water is treated as FMO fragments in the pair interaction energy decomposition analysis. The new energy expression is shown to be accurate, and the developed energy analysis is applied to the solvated griffithsin-carbohydrate complex. The details of the ligand recognition are revealed in the context with their interplay with the solvent effects. Tyr residue fragments are shown to reduce the desolvation penalty for Asp, which strongly binds the ligand.

  5. 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.

  6. 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.

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

    PubMed

    Chen, Zhan; Wei, Guo-Wei

    2011-11-21

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

  8. 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…

  9. 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…

  10. 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.

  11. The effects of sexually explicit material use on romantic relationship dynamics.

    PubMed

    Minarcik, Jenny; Wetterneck, Chad T; Short, Mary B

    2016-12-01

    Background and aims Pornography use has become increasingly common. Studies have shown that individuals who use sexually explicit materials (SEMs) report negative effects (Schneider, 2000b). However, Bridges (2008b) found that couples who use SEM together have higher relationship satisfaction than those who use SEM independently. A further investigation into various types of SEM use in relationships may highlight how SEM is related to various areas of couple satisfaction. Thus, the purpose of the current study is to examine the impact of SEM use related to different relationship dynamics. Methods The current study included a college and Internet sample of 296 participants divided into groups based upon the SEM use in relationships (i.e., SEM alone, SEM use with partner, and no SEM use). Results There were significant differences between groups in relationship satisfaction [F(2, 252) = 3.69, p = .026], intimacy [F(2, 252) = 7.95, p = <.001], and commitment [F(2, 252) = 5.30, p = .006]. Post-hoc analyses revealed additional differences in relationship satisfaction [t(174) = 2.13, p = .035] and intimacy [t(174) = 2.76, p = .006] based on the frequency of SEM use. Discussion Further exploration of the SEM use function in couples will provide greater understanding of its role in romantic relationships.

  12. The adsorption of xyloglucan on cellulose: effects of explicit water and side chain variation.

    PubMed

    Zhang, Qiong; Brumer, Harry; Ågren, Hans; Tu, Yaoquan

    2011-11-29

    The interaction between para-crystalline cellulose and the cross-linking glycan xyloglucan (XG) plays a central role for the strength and extensibility of plant cell walls. The coating of XGs on cellulose surfaces is believed to be one of the most probable interaction patterns. In this work, the effects of explicit water and side chain variation on the adsorption of XGs on cellulose are investigated by means of atomistic molecular dynamics simulations. The adsorption properties are studied in detail for three XGs on cellulose Iβ 1-10 surface in aqueous environment, namely GXXXGXXXG, GXXLGXXXG, and GXXFGXXXG, which differ in the length and composition of one side chain. Our work shows that when water molecules are included in the theoretical model, the total interaction energies between the adsorbed XGs and cellulose are considerably smaller than in vacuo. Furthermore, in water environment the van der Waals interactions prevail over the electrostatic interactions in the adsorption. Variation in one side chain does not have significant influence on the interaction energy and the binding affinity, but does affect the equilibrium structural properties of the adsorbed XGs to facilitate the interaction between both the backbone and the side chain residues with the cellulose surface. Together, this analysis provides new insights into the nature of the XG-cellulose interaction, which helps to further refine current molecular models of the composite plant cell wall.

  13. The effects of sexually explicit material use on romantic relationship dynamics

    PubMed Central

    Minarcik, Jenny; Wetterneck, Chad T.; Short, MARY B.

    2016-01-01

    Background and aims Pornography use has become increasingly common. Studies have shown that individuals who use sexually explicit materials (SEMs) report negative effects (Schneider, 2000b). However, Bridges (2008b) found that couples who use SEM together have higher relationship satisfaction than those who use SEM independently. A further investigation into various types of SEM use in relationships may highlight how SEM is related to various areas of couple satisfaction. Thus, the purpose of the current study is to examine the impact of SEM use related to different relationship dynamics. Methods The current study included a college and Internet sample of 296 participants divided into groups based upon the SEM use in relationships (i.e., SEM alone, SEM use with partner, and no SEM use). Results There were significant differences between groups in relationship satisfaction [F(2, 252) = 3.69, p = .026], intimacy [F(2, 252) = 7.95, p = <.001], and commitment [F(2, 252) = 5.30, p = .006]. Post-hoc analyses revealed additional differences in relationship satisfaction [t(174) = 2.13, p = .035] and intimacy [t(174) = 2.76, p = .006] based on the frequency of SEM use. Discussion Further exploration of the SEM use function in couples will provide greater understanding of its role in romantic relationships. PMID:27784182

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

    PubMed Central

    Wang, Xiao; Peng, Jian

    2016-01-01

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

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

    PubMed

    Wang, Xiao; Peng, Jian

    2016-01-01

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

  16. An explicit surface-potential-based MOSFET model incorporating the quantum mechanical effects

    NASA Astrophysics Data System (ADS)

    Basu, Dipanjan; Dutta, Aloke K.

    2006-07-01

    An explicit surface-potential-based MOSFET model has been proposed in this work here, which takes into account the quantum mechanical effects that arise in deep-submicron MOSFETs. The coupled Schrödinger's and Poisson's equations have been solved by using a variational wave function approach, as proposed by Fang and Howard. The resulting surface potential model is analytical, technology mapped, and completely continuous over the entire range of operation. The surface potential and the inversion charge density calculated using the proposed model show good match with the results of the numerical simulations obtained from a self-consistent Schrödinger-Poisson solver for a wide range of substrate doping and oxide thickness. The simulated values of the drain current match closely with the experimental results published elsewhere. The device small-signal parameters, e.g., transconductance, output conductance, etc., pass the standard benchmark tests suggested by Suyama and Tsividis qualitatively, thereby validating the approach of the model presented.

  17. Effects of isomer coexistence and solvent-induced core switching in the photodissociation of bare and solvated (CS{sub 2}){sub 2}{sup -} anions

    SciTech Connect

    Habteyes, Terefe; Velarde, Luis; Sanov, Andrei

    2009-03-28

    The photodissociation of the (CS{sub 2}){sub 2}{sup -} dimer anion, known to exist in the form of several electronic and structural isomers, has been investigated at 532, 355, and 266 nm. The observed anionic fragments are CS{sub 2}{sup -} and C{sub 2}S{sub 2}{sup -} at 532 nm, and C{sub 2}S{sub 2}{sup -}, CS{sub 2}{sup -}, CS{sub 3}{sup -}, S{sub 2}{sup -}, and S{sup -} at 355 and 266 nm. In addition to the photon energy, the fractional yields of the photofragments depend on the ion source conditions and solvation of the dimer anion. Specifically, the (C{sub 2}S{sub 2}{sup -}+S{sub 2}{sup -})/CS{sub 2}{sup -} product ratio is significantly higher when (CS{sub 2}){sub 2}{sup -} is formed in the presence of water in the precursor gas mixture, even though the parent anion itself does not include H{sub 2}O. On the other hand, an abrupt decrease in the above product ratio is observed upon the addition of solvent molecules (CS{sub 2} or H{sub 2}O) to the (CS{sub 2}){sub 2}{sup -} anion. Since the variation of this product ratio exhibits positive correlation with the relative intensity of the photoelectron band assigned to the C{sub 2v}({sup 2}B{sub 1}) covalent structure of C{sub 2}S{sub 4}{sup -} by Habteyes et al.[J. Phys. Chem. A 112, 10134 (2008)], this structure is suggested as the primary origin of the C{sub 2}S{sub 2}{sup -} and S{sub 2}{sup -} photoproducts. The switching of the fragmentation yield from C{sub 2}S{sub 2}{sup -} and S{sub 2}{sup -} to other products upon solvation is ascribed to the diminished presence of the C{sub 2v}({sup 2}B{sub 1}) dimer-anion structure relative to the CS{sub 2}{sup -} based clusters. This population shift is attributed to the more effective solvation of the latter. The CS{sub 2}{sup -} based clusters are suggested as the origin of the S{sup -} photoproduct, while CS{sub 3}{sup -} is formed through the secondary S{sup -}+CS{sub 2} intracluster association reaction.

  18. 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

  19. 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.

  20. Effects of explicit convection on global land-atmosphere coupling in the superparameterized CAM

    NASA Astrophysics Data System (ADS)

    Sun, Jian; Pritchard, Michael S.

    2016-09-01

    Conventional global climate models are prone to producing unrealistic land-atmosphere coupling signals. 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 in the Community Atmosphere Model (SPCAM) v3.5, focusing on both the terrestrial segment (i.e., soil moisture and surface turbulent fluxes interaction) and atmospheric segment (i.e., surface turbulent fluxes and precipitation interaction) in the water pathway of the land-atmosphere feedback loop. At daily timescales, SPCAM produces stronger uncoupled terrestrial signals (negative sign) over tropical rainforests in wet seasons, reduces the terrestrial coupling strength in the Central Great Plain in American, and reverses the coupling sign (from negative to positive) over India in the boreal summer season—all favorable improvements relative to reanalysis-forced land modeling. Analysis of the triggering feedback strength (TFS) and amplification feedback strength (AFS) shows that SPCAM favorably reproduces the observed geographic patterns of these indices over North America, with the probability of afternoon precipitation enhanced by high evaporative fraction along the eastern United States and Mexico, while conventional CAM does not capture this signal. We introduce a new diagnostic called the Planetary Boundary Layer (PBL) Feedback Strength (PFS), which reveals that SPCAM exhibits a tight connection between the responses of the lifting condensation level, the PBL height, and the rainfall triggering to surface turbulent fluxes; a triggering disconnect is found in CAM.

  1. Explicit solvent effects on the visible absorption spectrum of a photosynthetic pigment: Chlorophyll-c 2 in methanol

    NASA Astrophysics Data System (ADS)

    Jaramillo, Paula; Coutinho, Kaline; Cabral, Benedito J. C.; Canuto, Sylvio

    2011-11-01

    The explicit solvent effects on the light absorption properties of a photosynthetic pigment are analyzed from a combined study using Monte Carlo simulation and quantum mechanical Density-Functional Theory calculations. The case considered is chlorophyll-c2 in methanol and excellent results are obtained for both position and intensities in the entire visible region. Explicit solvent molecules are essential for describing the absorption spectrum. Analysis is also made of the coordination of the Mg atom, the influence of solute-solvent hydrogen bonds, the existence and location of dark states for internal conversion mechanisms and the adequacy of the four-state model for classifying the transitions.

  2. Photoinduced intramolecular charge transfer in push-pull polyenes: effects of solvation, electron-donor group, and polyenic chain length.

    PubMed

    Akemann, Walther; Laage, Damien; Plaza, Pascal; Martin, Monique M; Blanchard-Desce, Mireille

    2008-01-17

    Subpicosecond absorption spectroscopy is used to characterize the primary photoinduced processes in a class of push-pull polyenes bearing a julolidine end group as the electron donor and a diethylthiobarbituric acid end group as the electron acceptor. The excited-state decay time and relaxation pathway have been studied for four polyenes of increasing chain length (n = 2-5 double bonds) in aprotic solvents of different solvation time, polarity, and viscosity. Intramolecular charge transfer (ICT) leading to a transient state of cyanine-like structure (fully conjugated with no bond length alternation) is observed in all polar solvents at a solvent dependent rate, but the reaction is not observed in cyclohexane, a nonpolar solvent. In polar solvents, the reaction time increases with the average solvation time but remains slightly larger, except in the viscous solvent triacetin. These facts are interpreted as an indication that both solvent reorganization and internal restructuring are involved in the ICT-state formation. The observed photodynamics resemble those we previously found for another class of polyenes bearing a dibutylaniline group as the donor, including a similar charge-transfer rate in spite of the larger electron donor character of the julolidine group. This observation brings further support to the proposal that an intramolecular coordinate is involved in the charge-transfer reaction, possibly a torsional motion of the donor end group. On the other hand, relaxation of the ICT state leads to cis-trans isomerization or crossing to the triplet state, depending on the length of the polyenic chain. In dioxane, tetrahydrofuran, and triacetin, the ICT state of the shorter chains (n = 2, 3) relaxes to the isomer with a viscosity-dependent rate, while that of the longer ones (n = 4, 5) leads to the triplet state with a viscosity-independent rate, as expected. In acetonitrile, the ICT-state lifetime is generally much shorter. A change from photoisomerization to

  3. [Effects of imagery instructions on false memories produced on implicit and explicit memory tests].

    PubMed

    Tajika, Hidetsugu; Hamajima, Hideki

    2002-10-01

    In two experiments, we investigated whether the Deese-Roediger-McDermott paradigm using implicit and explicit memory tests would produce critical lure (CL) words. Participants studied lists of semantic associates (e.g., newspaper, book, write) to induce memories for CL words (e.g., read). Afterwards, participants participated in implicit and explicit memory tests in each experiment. The level of priming of the CL words was quite high and similar to that of the presented words when participants were instructed to image the interword relation on lists during study. Participants explicitly recognized many CL words as having been presented on the lists in Experiment 1 and recalled many CL words in Experiment 2. The results are discussed in light of Underwood's (1965) implicit associative response hypothesis.

  4. Effects of the stress of marathon running on implicit and explicit memory.

    PubMed

    Eich, Teal S; Metcalfe, Janet

    2009-06-01

    We tested the idea that real-world situations, such as the highly strenuous exercise involved in marathon running, that impose extreme physical demands on an individual may result in neurohormonal changes that alter the functioning of memory. Marathon runners were given implicit and explicit memory tasks before or immediately after they completed a marathon. Runners tested immediately upon completing the marathon showed impairment in the explicit memory task but enhancement in the implicit memory task. This postmarathon impairment in explicit memory is similar to that seen with amnesic patients with organic brain damage. However, no previous studies have shown a simultaneous enhancement in the implicit memory task, as shown by the marathon runners in the present study. This study indicates that human memory functioning can be dynamically altered by such activities as marathon running, in which hundreds of thousands of healthy normal individuals routinely partake.

  5. 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…

  6. Effects of Explicit Instruction and Self-Directed Video Prompting on Text Comprehension of Students with Autism Spectrum Disorder

    ERIC Educational Resources Information Center

    Sartini, Emily Claire

    2016-01-01

    The purpose of this study was to investigate the effects of explicit instruction combined with video prompting to teach text comprehension skills to students with autism spectrum disorder. Participants included 4 elementary school students with autism. A multiple probe across participants design was used to evaluate the intervention's…

  7. The Effect of Explicit Instruction versus Exposure Only on ESL Learners' Ability to Recognize, Use and Recall Phrasal Verbs

    ERIC Educational Resources Information Center

    Magnusson, Julina A.; Graham, C. Ray

    2011-01-01

    This study examines the effects of explicit instruction and exposure only on ESL students' ability to recognize, use and recall phrasal verbs. Subjects included 55 intermediate-level ESL students in reading classes at an intensive English program. Thirty-seven idiomatic phrasal verbs were divided into two lists. In a repeated measures design, one…

  8. The Effect of Explicit Affective Strategy Training on Iranian EFL Learners' Oral Language Proficiency and Anxiety Reduction

    ERIC Educational Resources Information Center

    Mostafavi, Fatemeh; Vahdany, Fereidoon

    2016-01-01

    The current study aimed at investigating the possible effects of explicit teaching of affective strategies on Iranian EFL learners' oral language proficiency and the extent of their anxiety in EFL classroom. First, PET test was administered to a total number of 120 female third grade high school EFL students. Then, 60 participants whose score fell…

  9. 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)

  10. 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,…

  11. Polaron theory of electrons solvated in molten salts

    NASA Astrophysics Data System (ADS)

    Malescio, G.; Parrinello, M.

    1987-01-01

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

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

    PubMed

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

    2014-06-19

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

  13. Dissociable effects of the implicit and explicit memory systems on learning control of reaching.

    PubMed

    Hwang, Eun Jung; Smith, Maurice A; Shadmehr, Reza

    2006-08-01

    Adaptive control of reaching depends on internal models that associate states in which the limb experienced a force perturbation with motor commands that can compensate for it. Limb state can be sensed via both vision and proprioception. However, adaptation of reaching in novel dynamics results in generalization in the intrinsic coordinates of the limb, suggesting that the proprioceptive states in which the limb was perturbed dominate representation of limb state. To test this hypothesis, we considered a task where position of the hand during a reach was correlated with patterns of force perturbation. This correlation could be sensed via vision, proprioception, or both. As predicted, when the correlations could be sensed only via proprioception, learning was significantly better as compared to when the correlations could only be sensed through vision. We found that learning with visual correlations resulted in subjects who could verbally describe the patterns of perturbations but this awareness was never observed in subjects who learned the task with only proprioceptive correlations. We manipulated the relative values of the visual and proprioceptive parameters and found that the probability of becoming aware strongly depended on the correlations that subjects could visually observe. In all conditions, aware subjects demonstrated a small but significant advantage in their ability to adapt their motor commands. Proprioceptive correlations produced an internal model that strongly influenced reaching performance yet did not lead to awareness. Visual correlations strongly increased the probability of becoming aware, yet had a much smaller but still significant effect on reaching performance. Therefore, practice resulted in acquisition of both implicit and explicit internal models.

  14. 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.

  15. 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)…

  16. 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…

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

    ERIC Educational Resources Information Center

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

    1998-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  19. 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…

  20. Exposure to Graphic Warning Labels on Cigarette Packages: Effects on Implicit and Explicit Attitudes toward Smoking among Young Adults

    PubMed Central

    Macy, Jonathan T.; Chassin, Laurie; Presson, Clark C.; Yeung, Ellen

    2015-01-01

    Objective Test the effect of exposure to the U.S. Food and Drug Administration’s proposed graphic images with text warning statements for cigarette packages on implicit and explicit attitudes toward smoking. Design and methods A two-session web-based study was conducted with 2192 young adults 18–25 years old. During session one, demographics, smoking behavior, and baseline implicit and explicit attitudes were assessed. Session two, completed on average 18 days later, contained random assignment to viewing one of three sets of cigarette packages, graphic images with text warnings, text warnings only, or current U.S Surgeon General’s text warnings. Participants then completed post-exposure measures of implicit and explicit attitudes. ANCOVAs tested the effect of condition on the outcomes, controlling for baseline attitudes. Results Smokers who viewed packages with graphic images plus text warnings demonstrated more negative implicit attitudes compared to smokers in the other conditions (p=.004). For the entire sample, explicit attitudes were more negative for those who viewed graphic images plus text warnings compared to those who viewed current U.S. Surgeon General’s text warnings (p=.014), but there was no difference compared to those who viewed text-only warnings. Conclusion Graphic health warnings on cigarette packages can influence young adult smokers’ implicit attitudes toward smoking. PMID:26442992

  1. Pupil Dilation to Explicit and Non-Explicit Sexual Stimuli.

    PubMed

    Watts, Tuesday M; Holmes, Luke; Savin-Williams, Ritch C; Rieger, Gerulf

    2017-01-01

    Pupil dilation to explicit sexual stimuli (footage of naked and aroused men or women) can elicit sex and sexual orientation differences in sexual response. If similar patterns were replicated with non-explicit sexual stimuli (footage of dressed men and women), then pupil dilation could be indicative of automatic sexual response in fully noninvasive designs. We examined this in 325 men and women with varied sexual orientations to determine whether dilation patterns to non-explicit sexual stimuli resembled those to explicit sexual stimuli depicting the same sex or other sex. Sexual orientation differences in pupil dilation to non-explicit sexual stimuli mirrored those to explicit sexual stimuli. However, the relationship of dilation to non-explicit sexual stimuli with dilation to corresponding explicit sexual stimuli was modest, and effect magnitudes were smaller with non-explicit sexual stimuli than explicit sexual stimuli. The prediction that sexual orientation differences in pupil dilation are larger in men than in women was confirmed with explicit sexual stimuli but not with non-explicit sexual stimuli.

  2. 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.

  3. Electron trapping in polar-solvated zeolites.

    PubMed

    Ellison, Eric H

    2005-11-03

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

  4. Macroscopic model for solvated ion dynamics

    NASA Astrophysics Data System (ADS)

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

    1980-02-01

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

  5. Solvation Energetics of Biomolecules

    NASA Astrophysics Data System (ADS)

    Williams, Evan

    2002-03-01

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

  6. 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

  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. 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.

  9. 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

  10. 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

  11. Reactivity of transition metal solvates

    NASA Astrophysics Data System (ADS)

    Berezin, Boris D.

    1991-09-01

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

  12. Flecainide acetate acetic acid solvates.

    PubMed

    Veldre, Kaspars; Actiņs, Andris; Eglite, Zane

    2011-02-01

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

  13. 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.

  14. Explicit solutions for effective four- and five-loop QCD running coupling

    NASA Astrophysics Data System (ADS)

    Cvetič, Gorazd; Kondrashuk, Igor

    2011-12-01

    We start with the explicit solution, in terms of the Lambert W function, of the renormalization group equation (RGE) for the gauge coupling in the supersymmetric Yang-Mills theory described by the well-known NSVZ β-function. We then construct a class of β-functions for which the RGE can be solved in terms of the Lambert W function. These β-functions are expressed in terms of a function which is a truncated Laurent series in the inverse u of the gauge coupling a ≡ α/π. The parameters in the Laurent series can be adjusted so that the first coefficients of the Taylor expansion of the β-function in the gauge coupling a reproduce the four-loop or five-loop QCD (or SQCD) β-function.

  15. 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.

  16. 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.

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

    ERIC Educational Resources Information Center

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

    2011-01-01

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

  18. 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

  19. Preparation of cerium halide solvate complexes

    SciTech Connect

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

    2013-08-06

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

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

    PubMed

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

    2011-06-17

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

  1. What Should Be Explicit in Explicit Grammar Instruction?

    ERIC Educational Resources Information Center

    Nagai, Noriko; Ayano, Seiki; Okada, Keiko; Nakanishi, Takayuki

    2015-01-01

    This article proposes an approach to explicit grammar instruction that seeks to develop metalinguistic knowledge of the L2 and raise L2 learners' awareness of their L1, which is crucial for the success of second language acquisition (Ellis 1997, 2002). If explicit instruction is more effective than implicit instruction (Norris and Ortega 2000),…

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    SciTech Connect

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

    2015-03-21

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

  4. 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.

  5. 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.

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

    PubMed Central

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

    2013-01-01

    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

  7. Generality of solvation effects on the hydrolysis rates of phosphate monoesters and their possible relevance to enzymatic catalysis.

    PubMed

    Grzyska, Piotr K; Czyryca, Przemyslaw G; Golightly, Justin; Small, Kelly; Larsen, Paul; Hoff, Richard H; Hengge, Alvan C

    2002-02-22

    Previous work by Kirby and co-workers revealed a significant acceleration of the rate of hydrolysis of p-nitrophenyl phosphate by added dipolar solvents such as DMSO. Activation parameters and kinetic isotope effects have been measured to ascertain the origin of this effect. The generality of this phenomenon was examined with a series of esters with more basic leaving groups. Computational analyses of the effects of desolvation of dianionic phosphate monoesters were carried out, and the possible effect of the transfer from water to the active site of alkaline phosphatase was modeled. The results are consistent with a desolvation-induced weakening of the P-O ester bond in the ground state. Other aryl phosphate esters show similar rate accelerations at high fractions of DMSO, but phenyl and methyl phosphates do not, and their hydrolysis reactions are actually slowed by these conditions.

  8. 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.

  9. 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.

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

    PubMed

    Bilsel, Mustafa; Arkin, Handan

    2010-05-01

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

  11. Residue length and solvation model dependency of elastinlike polypeptides

    NASA Astrophysics Data System (ADS)

    Bilsel, Mustafa; Arkin, Handan

    2010-05-01

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

  12. 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.

  13. Effect of organic solvents on Li+ ion solvation and transport in ionic liquid electrolytes: a molecular dynamics simulation study.

    PubMed

    Li, Zhe; Borodin, Oleg; Smith, Grant D; Bedrov, Dmitry

    2015-02-19

    Molecular dynamics simulations of N-methyl-N-propylpyrrolidinium (pyr13) bis(trifluoromethanesulfonyl)imide (Ntf2) ionic liquid [pyr13][Ntf2] doped with [Li][Ntf2] salt and mixed with acetonitrile (AN) and ethylene carbonate (EC) organic solvents were conducted using polarizable force field. Structural and transport properties of ionic liquid electrolytes (ILEs) with 20 and 40 mol % of organic solvents have been investigated and compared to properties of neat ILEs. Addition of AN and EC solvents to ILEs resulted in the partial displacement of the Ntf2 anions from the Li(+) first coordination shell by EC and AN and shifting the Li-Ntf2 coordination from bidentate to monodentate. The presence of organic solvents in ILE has increased the ion mobility, with the largest effect observed for the Li(+) cation. The Li(+) conductivity has doubled with addition of 40 mol % of AN. The Li(+)-N(Ntf2) residence times were dramatically reduced with addition of solvents, indicating an increasing contribution from structural diffusion of the Li(+) cations.

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

    ERIC Educational Resources Information Center

    Burrows, Lance; Holsworth, Michael

    2016-01-01

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

  15. The Effects of Task Explicitness to Communicate on the Expressiveness of Children's Drawings of Different Topics

    ERIC Educational Resources Information Center

    Burkitt, Esther

    2017-01-01

    Effects of asking children to communicate through their drawings have been investigated using animate rather than inanimate drawing topics. The present study investigated the impact of a communication context on children's drawings of topics with contrasting animism. Three hundred and twenty-two children, 156 boys and 166 girls aged 6-11 years…

  16. 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,…

  17. 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…

  18. Explicit Prewriting Instruction: Effect on Writing Quality of Adolescents with Learning Disabilities

    ERIC Educational Resources Information Center

    Sundeen, Todd H.

    2012-01-01

    Many students with learning disabilities struggle with the writing process throughout their school years. As students approach graduation, effective communication though writing becomes more critical. Writing is a skill that can directly impact the quality of life for older students preparing to graduate and progress to college, a career, or…

  19. 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.

  20. 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

  1. Explicit demonstration of the role of Marangoni effect in the breakup of nanoscale liquid filaments

    NASA Astrophysics Data System (ADS)

    Seric, Ivana; Mahady, Kyle; Afkhami, Shahriar; Hartnett, Chris; Fowlkes, Jason; Rack, Philip; Kondic, Lou

    2016-11-01

    We consider a breakup of bi-metal filaments deposited on a solid substrate. These filaments are exposed to laser irradiation and, while in the liquid phase, evolve by a process resembling breakup of a liquid jet governed by the Rayleigh-Plateau instability. The novel element is that the Marangoni effect, resulting from a different surface tension of the two metals from which the filament is built, is crucial in understanding the instability development. In particular, Marangoni effect may lead to the inversion of the breakup process, producing droplets at the locations where according to the Rayleigh-Plateau theory dry spots would be expected. We present experimental results carried out with Cu-Ni filaments, as well as direct numerical simulations based on a novel algorithm that includes variable surface tension in a Volume-of-Fluid based Navier-Stokes solver. These results suggest the possibility of using Marangoni effect for the purpose of self- and directed-assembly on the nanoscale. Supported by the NSF Grant No. CBET-1604351.

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

    PubMed Central

    Bastien, Renaud; Douady, Stéphane; Moulia, Bruno

    2014-01-01

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

  3. 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 learned in…

  4. Comparing spatially explicit ecological and social values for natural areas to identify effective conservation strategies.

    PubMed

    Bryan, Brett Anthony; Raymond, Christopher Mark; Crossman, Neville David; King, Darran

    2011-02-01

    Consideration of the social values people assign to relatively undisturbed native ecosystems is critical for the success of science-based conservation plans. We used an interview process to identify and map social values assigned to 31 ecosystem services provided by natural areas in an agricultural landscape in southern Australia. We then modeled the spatial distribution of 12 components of ecological value commonly used in setting spatial conservation priorities. We used the analytical hierarchy process to weight these components and used multiattribute utility theory to combine them into a single spatial layer of ecological value. Social values assigned to natural areas were negatively correlated with ecological values overall, but were positively correlated with some components of ecological value. In terms of the spatial distribution of values, people valued protected areas, whereas those natural areas underrepresented in the reserve system were of higher ecological value. The habitats of threatened animal species were assigned both high ecological value and high social value. Only small areas were assigned both high ecological value and high social value in the study area, whereas large areas of high ecological value were of low social value, and vice versa. We used the assigned ecological and social values to identify different conservation strategies (e.g., information sharing, community engagement, incentive payments) that may be effective for specific areas. We suggest that consideration of both ecological and social values in selection of conservation strategies can enhance the success of science-based conservation planning.

  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. Explicit continuous charge-based compact model for long channel heavily doped surrounding-gate MOSFETs incorporating interface traps and quantum effects

    NASA Astrophysics Data System (ADS)

    Hamzah, Afiq; Hamid, Fatimah A.; Ismail, Razali

    2016-12-01

    An explicit solution for long-channel surrounding-gate (SRG) MOSFETs is presented from intrinsic to heavily doped body including the effects of interface traps and fixed oxide charges. The solution is based on the core SRGMOSFETs model of the Unified Charge Control Model (UCCM) for heavily doped conditions. The UCCM model of highly doped SRGMOSFETs is derived to obtain the exact equivalent expression as in the undoped case. Taking advantage of the undoped explicit charge-based expression, the asymptotic limits for below threshold and above threshold have been redefined to include the effect of trap states for heavily doped cases. After solving the asymptotic limits, an explicit mobile charge expression is obtained which includes the trap state effects. The explicit mobile charge model shows very good agreement with respect to numerical simulation over practical terminal voltages, doping concentration, geometry effects, and trap state effects due to the fixed oxide charges and interface traps. Then, the drain current is obtained using the Pao-Sah's dual integral, which is expressed as a function of inversion charge densities at the source/drain ends. The drain current agreed well with the implicit solution and numerical simulation for all regions of operation without employing any empirical parameters. A comparison with previous explicit models has been conducted to verify the competency of the proposed model with the doping concentration of 1× {10}19 {{cm}}-3, as the proposed model has better advantages in terms of its simplicity and accuracy at a higher doping concentration.

  7. 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.}

  8. 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

  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.

  10. Dissociation between arithmetic relatedness and distance effects is modulated by task properties: an ERP study comparing explicit vs. implicit arithmetic processing.

    PubMed

    Avancini, Chiara; Galfano, Giovanni; Szűcs, Dénes

    2014-12-01

    Event-related potential (ERP) studies have detected several characteristic consecutive amplitude modulations in both implicit and explicit mental arithmetic tasks. Implicit tasks typically focused on the arithmetic relatedness effect (in which performance is affected by semantic associations between numbers) while explicit tasks focused on the distance effect (in which performance is affected by the numerical difference of to-be-compared numbers). Both task types elicit morphologically similar ERP waves which were explained in functionally similar terms. However, to date, the relationship between these tasks has not been investigated explicitly and systematically. In order to fill this gap, here we examined whether ERP effects and their underlying cognitive processes in implicit and explicit mental arithmetic tasks differ from each other. The same group of participants performed both an implicit number-matching task (in which arithmetic knowledge is task-irrelevant) and an explicit arithmetic-verification task (in which arithmetic knowledge is task-relevant). 129-channel ERP data differed substantially between tasks. In the number-matching task, the arithmetic relatedness effect appeared as a negativity over left-frontal electrodes whereas the distance effect was more prominent over right centro-parietal electrodes. In the verification task, all probe types elicited similar N2b waves over right fronto-central electrodes and typical centro-parietal N400 effects over central electrodes. The distance effect appeared as an early-rising, long-lasting left parietal negativity. We suggest that ERP effects in the implicit task reflect access to semantic memory networks and to magnitude discrimination, respectively. In contrast, effects of expectation violation are more prominent in explicit tasks and may mask more delicate cognitive processes.

  11. Explicit expressions describing elastic properties and buckling load of BN nanosheets due to the effects of vacancy defects

    NASA Astrophysics Data System (ADS)

    Sarvi, Z.; Asgari, M.; Shariyat, M.; Googarchin, H. Saeidi

    2015-12-01

    In this study, effects of the presence of vacancy defects in a hexagonal nanosheet on Young's modulus, effective Poisson's ratio, buckling loads and buckling modes, regardless of its constituent atoms, have been studied. Explicit expressions are proposed in order to define these characteristics considering a defect distribution term as a modifying parameter. Molecular structural mechanics concepts and FEM simulation are utilized in order to obtain these expressions and results. Different sizes and shapes of defects as well as random distribution of vacancies have been considered. The results for perfect Boron Nitride, Silicon Carbide and graphene nanosheet as well as defected Boron Nitride nanosheets are in a good agreement with those available in literature. Linear degradation behavior of Young's modulus and linear increase of effective Poisson's ratio in terms of defects distribution are observed in obtained results. A second order behavior is also observed in decreasing buckling load in terms of increasing vacancy distribution. Moreover, buckling mode characteristics due to the percentage of defects distribution has been investigated.

  12. Structural and thermodynamic investigations on the aggregation and folding of acylphosphatase by molecular dynamics simulations and solvation free energy analysis.

    PubMed

    Chong, Song-Ho; Lee, Chewook; Kang, Guipeun; Park, Mirae; Ham, Sihyun

    2011-05-11

    Protein engineering method to study the mutation effects on muscle acylphosphatase (AcP) has been actively applied to describe kinetics and thermodynamics associated with AcP aggregation as well as folding processes. Despite the extensive mutation experiments, the molecular origin and the structural motifs for aggregation and folding kinetics as well as thermodynamics of AcP have not been rationalized at the atomic resolution. To this end, we have investigated the mutation effects on the structures and thermodynamics for the aggregation and folding of AcP by using the combination of fully atomistic, explicit-water molecular dynamics simulations, and three-dimensional reference interaction site model theory. The results indicate that the A30G mutant with the fastest experimental aggregation rate displays considerably decreased α1-helical contents as well as disrupted hydrophobic core compared to the wild-type AcP. Increased solvation free energy as well as hydrophobicity upon A30G mutation is achieved due to the dehydration of hydrophilic side chains in the disrupted α1-helix region of A30G. In contrast, the Y91Q mutant with the slowest aggregation rate shows a non-native H-bonding network spanning the mutation site to hydrophobic core and α1-helix region, which rigidifies the native state protein conformation with the enhanced α1-helicity. Furthermore, Y91Q exhibits decreased solvation free energy and hydrophobicity compared to wild type due to more exposed and solvated hydrophilic side chains in the α1-region. On the other hand, the experimentally observed slower folding rates in both mutants are accompanied by decreased helicity in α2-helix upon mutation. We here provide the atomic-level structures and thermodynamic quantities of AcP mutants and rationalize the structural origin for the changes that occur upon introduction of those mutations along the AcP aggregation and folding processes.

  13. Path integral molecular dynamics combined with discrete-variable-representation approach: the effect of solvation structures on vibrational spectra of Cl 2 in helium clusters

    NASA Astrophysics Data System (ADS)

    Takayanagi, Toshiyuki; Shiga, Motoyuki

    2002-08-01

    The structures and vibrational frequencies of Cl 2-helium clusters have been studied using the path integral molecular dynamics method combined with the discrete-variable-representation approach. It is found that the Cl 2-helium clusters form clear shell structures comprised of rings around the Cl 2 bond. The vibrational frequencies calculated show a monotonically increasing red shift with an increase in cluster size. It can be concluded that the first solvation shell and its density around T-shaped configurations play the most important role in the observed frequency shifts.

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

    PubMed

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

    2015-05-28

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

  15. 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...

  16. 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.

  17. Effects of achievement goal striving on well-being: the moderating role of the explicit achievement motive.

    PubMed

    Job, Veronika; Langens, Thomas A; Brandstätter, Veronika

    2009-08-01

    This research is based on the theoretical conception of motives and goals as distinct motivational concepts. Previous research has demonstrated that discrepancies between implicit motives and goals have negative consequences for well-being. The authors have extended these findings to the explicit motive system, with four studies investigating the moderating role of the explicit achievement motive on the relationship between achievement goal striving and well-being. In line with their expectations, achievement goal striving was accompanied by high positive affect (Studies 1 and 2) and a high number of positive affective experiences (Study 3) only when the explicit achievement motive was high. Longitudinal Study 4 showed that the interaction between the explicit achievement motive and achievement goal commitment predicts changes in subjective well-being and health measured over a 3-month period.

  18. 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

  19. 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

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

    PubMed

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

    2015-05-07

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

  1. 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

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

    PubMed

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

    2010-06-01

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

  3. 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…

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

    ERIC Educational Resources Information Center

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

    2010-01-01

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

  5. 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 pre-service…

  6. Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model.

    PubMed Central

    Williams, D J; Hall, K B

    1999-01-01

    Three unrestrained stochastic dynamics simulations have been carried out on the RNA hairpin GGAC[UUCG] GUCC, using the AMBER94 force field (Cornell et al., 1995. J. Am. Chem. Soc. 117:5179-5197) in MacroModel 5.5 (Mohamadi et al., 1990. J. Comp. Chem. 11:440-467) and either the GB/SA continuum solvation model (Still et al., 1990. J. Am. Chem. Soc. 112:6127-6129) or a linear distance-dependent dielectric (1/R) treatment. The linear distance-dependent treatment results in severe distortion of the nucleic acid structure, restriction of all hydroxyl dihedrals, and collapse of the counterion atmosphere over the course of a 5-ns simulation. An additional vacuum simulation without counterions shows somewhat improved behavior. In contrast, the two GB/SA simulations (1.149 and 3.060 ns in length) give average structures within 1.2 A of the initial NMR structure and in excellent agreement with results of an earlier explicit solvent simulation (Miller and Kollman, 1997. J. Mol. Biol. 270:436-450). In a 3-ns GB/SA simulation starting with the incorrect UUCG tetraloop structure (Cheong et al., 1990. Nature. 346:680-682), this loop conformation converts to the correct loop geometry (Allain and Varani, 1995. J. Mol. Biol. 250:333-353), suggesting enhanced sampling relative to the previous explicit solvent simulation. Thermodynamic effects of 2'-deoxyribose substitutions of loop nucleotides were experimentally determined and are found to correlate with the fraction of time the ribose 2'-OH is hydrogen bonded and the distribution of the hydroxyl dihedral is observed in the GB/SA simulations. The GB/SA simulations thus appear to faithfully represent structural features of the RNA without the computational expense of explicit solvent. PMID:10354444

  7. 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…

  8. 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…

  9. The Effect of Explicit vs. Implicit Instruction on the Learnability of English Consonant Clusters by Iranian Learners of English

    ERIC Educational Resources Information Center

    Khanbeiki, Ruhollah; Abdolmanafi-Rokni, Seyed Jalal

    2015-01-01

    The present study was aimed at providing the English teachers across Iran with a good and fruitful method of teaching pronunciation. To this end, sixty female intermediate EFL learners were put in three different but equivalent groups of 20 based on the results of a pronunciation pre-test. One of the groups received explicit instruction including…

  10. 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…

  11. Interference Effect of Prior Explicit Information on Motor Sequence Learning in Relapsing-Remitting Multiple Sclerosis Patients

    PubMed Central

    Zahiri, Nahid; Abollahi, Iraj; Nabavi, Seyed Massood; Ehsani, Fatemeh; Arab, Amir Masoud; Shaw, Ina; Shariat, Ardalan; Shaw, Brandon S; Dastoorpoor, Maryam; Danaee, Mahmoud; Sangelaji, Bahram

    2017-01-01

    Background Multiple sclerosis (MS) is the most widespread disabling neurological condition in young adults around the world. The purpose of this study was to investigate the impact of explicit information (EI) on motor-sequence learning in MS patients. Methods Thirty patients with relapsing-remitting MS (RRMS), age: 29.5 (SD = 5.6) years and 30 healthy gender-, age-, and education-matched control group participants, age: 28.8 (SD = 6.0) years, were recruited for this study. The participants in the healthy group were then randomly assigned into an EI (n = 15) group and a no-EI (n = 15) group. Similarly, the participants in the control group were then randomly assigned into EI (n = 15) and no-EI (n = 15) groups. The participants performed a serial reaction time (SRT) task and reaction times. A retention test was performed after 48 hours. Results All participants reduced their reaction times across acquisition (MS group: 46.4 (SD = 3.3) minutes, P < 0.001, and healthy group: 39.4 (SD = 3.3) minutes, P < 0.001). The findings for the within-participants effect of repeated measures of time were significant (F(5.06, 283.7) = 71.33. P < 0.001). These results indicate that the interaction between group and time was significant (F(5.06, 283.7) = 6.44. P < 0.001), which indicated that the reaction time in both groups was significantly changed between the MS and healthy groups across times (B1 to B10). The main effect of the group (MS and healthy) (F(1, 56) = 22.78. P < 0.001) and also the main effect of no-EI vs EI (F(1, 56) = 4.71. P < 0.001) were significant. Conclusion This study demonstrated that that RRMS patients are capable of learning new skills, but the provision of EI prior to physical practice is deleterious to implicit learning. It is sufficient to educate MS patients on the aim and general content of the training and only to provide feedback at the end of the rehabilitative session. PMID:28381930

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  14. Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases.

    PubMed

    Abel, Robert; Salam, Noeris K; Shelley, John; Farid, Ramy; Friesner, Richard A; Sherman, Woody

    2011-06-06

    The prevention of blood coagulation is important in treating thromboembolic disorders, and several serine proteases involved in the coagulation cascade have been classified as pharmaceutically relevant. Whereas structure-based drug design has contributed to the development of some serine protease inhibitors, traditional computational methods have not been able to fully describe structure-activity relationships (SAR). Here, we study the SAR for a number of serine proteases by using a method that calculates the thermodynamic properties (enthalpy and entropy) of the water that solvates the active site. We show that the displacement of water from specific subpockets (such as S1-4 and the ester binding pocket) of the active site by the ligand can govern potency, especially for cases in which small chemical changes (i.e., a methyl group or halogen) result in a substantial increase in potency. Furthermore, we describe how relative binding free energies can be estimated by combining the water displacement energy with complementary terms from an implicit solvent molecular mechanics description binding.

  15. Solvation and electrostatic model for specific electrolyte adsorption

    NASA Astrophysics Data System (ADS)

    Sahai, Nita; Sverjensky, Dimitri A.

    1997-07-01

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

  16. Different Effects of Implicit and Explicit Motor Sequence Learning on Latency of Motor Evoked Potential Evoked by Transcranial Magnetic Stimulation on the Primary Motor Cortex

    PubMed Central

    Hirano, Masato; Kubota, Shinji; Koizume, Yoshiki; Tanaka, Shinya; Funase, Kozo

    2017-01-01

    Motor training induces plastic changes in the primary motor cortex (M1). However, it is unclear whether and how the latency of motor-evoked potentials (MEP) and MEP amplitude are affected by implicit and/or explicit motor learning. Here, we investigated the changes in M1 excitability and MEP latency induced by implicit and explicit motor learning. The subjects performed a serial reaction time task (SRTT) with their five fingers. In this task, visual cues were lit up sequentially along with a predetermined order. Through training, the subjects learned the order of sequence implicitly and explicitly. Before and after the SRTT, we recorded MEP at 25 stimulation points around the hot spot for the flexor pollicis brevis (FPB) muscle. Although no changes in MEP amplitude were observed in either session, we found increases in MEP latency and changes in histogram of MEP latency after implicit learning. Our results suggest that reorganization across the motor cortices occurs during the acquisition of implicit knowledge. In contrast, acquisition of explicit knowledge does not appear to induce the reorganization based on the measures we recorded. The fact that the above mentioned increases in MEP latency occurred without any alterations in MEP amplitude suggests that learning has different effects on different physiological signals. In conclusion, our results propose that analyzing a combination of some indices of M1 excitability, such as MEP amplitude and MEP latency, is encouraged in order to understand plasticity across motor cortices. PMID:28101014

  17. Different Effects of Implicit and Explicit Motor Sequence Learning on Latency of Motor Evoked Potential Evoked by Transcranial Magnetic Stimulation on the Primary Motor Cortex.

    PubMed

    Hirano, Masato; Kubota, Shinji; Koizume, Yoshiki; Tanaka, Shinya; Funase, Kozo

    2016-01-01

    Motor training induces plastic changes in the primary motor cortex (M1). However, it is unclear whether and how the latency of motor-evoked potentials (MEP) and MEP amplitude are affected by implicit and/or explicit motor learning. Here, we investigated the changes in M1 excitability and MEP latency induced by implicit and explicit motor learning. The subjects performed a serial reaction time task (SRTT) with their five fingers. In this task, visual cues were lit up sequentially along with a predetermined order. Through training, the subjects learned the order of sequence implicitly and explicitly. Before and after the SRTT, we recorded MEP at 25 stimulation points around the hot spot for the flexor pollicis brevis (FPB) muscle. Although no changes in MEP amplitude were observed in either session, we found increases in MEP latency and changes in histogram of MEP latency after implicit learning. Our results suggest that reorganization across the motor cortices occurs during the acquisition of implicit knowledge. In contrast, acquisition of explicit knowledge does not appear to induce the reorganization based on the measures we recorded. The fact that the above mentioned increases in MEP latency occurred without any alterations in MEP amplitude suggests that learning has different effects on different physiological signals. In conclusion, our results propose that analyzing a combination of some indices of M1 excitability, such as MEP amplitude and MEP latency, is encouraged in order to understand plasticity across motor cortices.

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

    SciTech Connect

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

    1995-11-30

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

  19. 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.

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

    PubMed Central

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

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Jeschke, Steffen; Wiemhöfer, Hans-Dieter

    2016-03-01

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

  2. 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.

  3. 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.

  4. 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…

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

    PubMed

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

    2017-05-01

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

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

    NASA Astrophysics Data System (ADS)

    Jeon, Jonggu; Kim, Hyung J.

    2003-10-01

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

  7. 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

  8. 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

  9. Water-enhanced solvation of organics

    SciTech Connect

    Lee, Jane H.

    1993-07-01

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

  10. 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.

  11. Explicit feedback to enhance the effect of an interim assessment: a cross-over study on learning effect and gender difference.

    PubMed

    Olde Bekkink, Marleen; Donders, Rogier; van Muijen, Goos N P; de Waal, Rob M W; Ruiter, Dirk J

    2012-11-01

    In a previous study we demonstrated by a prospective controlled design that an interim assessment during an ongoing small group work (SGW) session resulted in a higher score in the course examination. As this reflects the so-called testing effect, which is supposed to be enhanced by feedback, we investigated whether feedback following an interim assessment would have an effect on the score of the course exam, and whether the effect is influenced by the gender of the student. During a General Pathology bachelor course all 386 (bio) medical students took an interim assessment on the topics cell damage (first week) and tumour pathology (fourth week). The intervention consisted of immediate detailed oral feedback on the content of the questions of the interim assessment by the tutor, including the rationale of the correct and incorrect answers. It concerned a prospective randomized study using a cross-over design. Outcome measures were: (1) the difference in the normalized scores (1-10) of the course examination multiple choice questions related to the two topics, (2) effect of gender, and (3) gender-specific scores on formal examination. The effect of feedback was estimated as half the difference in the outcome between the two conditions. Mixed-model analysis was used whereby the SGW group was taken as the study target. The scores of the questions on cell damage amounted to 7.70 (SD 1.59) in the group without and 7.78 (SD 1.39) in the group with feedback, and 6.73 (SD 1.51) and 6.77 (SD 1.60), respectively, for those on tumour pathology. No statistically significant effect of feedback was found: 0.02 on a scale of 1-10 (95 % CI: -0.20; 0.25). There were no significant interactions of feedback with gender. Female students scored 0.43 points higher on the formal examination in comparison with their male colleagues. No additional effect of immediate explicit feedback following an interim assessment during an SGW session in an ongoing bachelor course could be

  12. Aqueous solvation dynamics at metal oxide surfaces.

    PubMed

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

    2006-04-20

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

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

    PubMed

    Oliveira, Ivan P; Martínez, Leandro

    2016-08-21

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

  14. Solvation Effects on S K-edge XAS Spectra of Fe-S Proteins: Normal and Inverse Effects on WT and Mutant Rubredoxin

    PubMed Central

    Sun, Ning; Dey, Abhishek; Xiao, Zhiguang; Wedd, Anthony G.; Hodgson, Keith O.; Hedman, Britt; Solomon, Edward I.

    2010-01-01

    S K-edge X-ray Absorption Spectroscopy (XAS) was performed on wild type Cp rubredoxin and its Cys->Ser mutants in both solution and lyophilized forms. For wild type rubredoxin and for the mutants where an interior cysteine residue (C6 or C39) is substituted by serine, a normal solvent effect is observed, that is, the S covalency increases upon lyophilization. For the mutants where a solvent accessible surface cysteine residue is substituted by serine, the S covalency decreases upon lyophilization which is an inverse solvent effect. Density functional theory (DFT) calculations reproduce these experimental results and show that the normal solvent effect reflects the covalency decrease due to solvent H-bonding to the surface thiolates and that the inverse solvent effect results from the covalency compensation from the interior thiolates. With respect to the Cys->Ser substitution, the S covalency decreases. Calculations indicate that the stronger bonding interaction of the alkoxide with the Fe relative to that of thiolate increases the energy of the Fe d orbitals and reduces their bonding interaction with the remaining cysteines. The solvent effects support a surface solvent tuning contribution to electron transfer and the Cys->Ser result provides an explanation for the change in properties of related iron-sulfur sites with this mutation. PMID:20726554

  15. 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

  16. 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.

  17. 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

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

    NASA Astrophysics Data System (ADS)

    Kumar, P. V.; Maroncelli, M.

    1995-08-01

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

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

    PubMed

    Huang, WenJuan; Blinov, Nikolay; Kovalenko, Andriy

    2015-04-30

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

  20. 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.

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

    PubMed Central

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

    2013-01-01

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

  2. 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.

  3. 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.

  4. 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.)

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

    NASA Astrophysics Data System (ADS)

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

    1999-10-01

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

  6. Conformational simulations of aqueous solvated alpha-conotoxin GI and its single disulfide analogues using a polarizable force field model.

    PubMed

    Jiang, Nan; Ma, Jing

    2008-10-09

    The solution conformation of alpha-conotoxin GI and its two single disulfide analogues are simulated using a polarizable force field in combination with the molecular fragmentation quantum chemical calculation. The polarizability is explicitly described by allowing the partial charges and fragment dipole moments to be variables, with values coming from the linear-scaling energy-based molecular fragmentation calculations at the B3LYP/6-31G(d) level. In comparison with the full quantum chemical calculations, the fragmentation approaches can yield precise ground-state energies, dipole moments, and static polarizabilities for peptides. The B3LYP/6-31G(d) charges and fragment-centered dipole moments are introduced in calculations of electrostatic terms in both AmberFF03 and OPLS force fields. Our test calculations on the gas-phase glucagon (PDB code: 1gcn) and solvated alpha-conotoxin GI (PDB code: 1not) demonstrate that the present polarization model is capable of describing the structural properties (such as the relative conformational energies, intramolecular hydrogen bonds, and disulfide bonds) with accuracy comparable to some other polarizable force fields (ABEEM/MM and OPLS-PFF) and the quantum mechanics/molecular mechanics (QM/MM) hybrid model. The employment of fragment-centered dipole moments in calculations of dipole-dipole interactions can save computational time in comparison with those polarization models using atom-centered dipole moments without much loss of accuracy. The molecular dynamics simulations using the polarizable force field demonstrate that two single disulfide GI analogues are more flexible and less structured than the native alpha-conotoxin GI, in agreement with NMR experiments. The polarization effect is important in simulations of the folding/unfolding process of solvated proteins.

  7. 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.

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

    PubMed Central

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

    2016-01-01

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

  9. CO2 solvation free energy using quasi-chemical theory

    NASA Astrophysics Data System (ADS)

    Jiao, Dian; Rempe, Susan B.

    2011-06-01

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

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

    PubMed

    Rane, Kaustubh; van der Vegt, Nico F A

    2016-03-21

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

  11. Effects of standard and explicit cognitive bias modification and computer-administered cognitive-behaviour therapy on cognitive biases and social anxiety☆

    PubMed Central

    Mobini, Sirous; Mackintosh, Bundy; Illingworth, Jo; Gega, Lina; Langdon, Peter; Hoppitt, Laura

    2014-01-01

    Background and objectives This study examines the effects of a single session of Cognitive Bias Modification to induce positive Interpretative bias (CBM-I) using standard or explicit instructions and an analogue of computer-administered CBT (c-CBT) program on modifying cognitive biases and social anxiety. Methods A sample of 76 volunteers with social anxiety attended a research site. At both pre- and post-test, participants completed two computer-administered tests of interpretative and attentional biases and a self-report measure of social anxiety. Participants in the training conditions completed a single session of either standard or explicit CBM-I positive training and a c-CBT program. Participants in the Control (no training) condition completed a CBM-I neutral task matched the active CBM-I intervention in format and duration but did not encourage positive disambiguation of socially ambiguous or threatening scenarios. Results Participants in both CBM-I programs (either standard or explicit instructions) and the c-CBT condition exhibited more positive interpretations of ambiguous social scenarios at post-test and one-week follow-up as compared to the Control condition. Moreover, the results showed that CBM-I and c-CBT, to some extent, changed negative attention biases in a positive direction. Furthermore, the results showed that both CBM-I training conditions and c-CBT reduced social anxiety symptoms at one-week follow-up. Limitations This study used a single session of CBM-I training, however multi-sessions intervention might result in more endurable positive CBM-I changes. Conclusions A computerised single session of CBM-I and an analogue of c-CBT program reduced negative interpretative biases and social anxiety. PMID:24412966

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    PubMed

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

    2012-08-14

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

  14. Evaluation of non-Fourier heat waves influenced by nonlinear/linear boundary effects employing an explicit architecture and controlled stabilization

    NASA Technical Reports Server (NTRS)

    Tamma, Kumar K.; Namburu, Raju R.; Glass, David E.

    1990-01-01

    The present paper is concerned with the problem of heat waves in solids, where, the heat transport due to conduction occurs as propagating thermal disturbances which are transmitted at finite but high speeds. Starting from the general heat flux model of the Jeffrey's-type, and subsequent formulations leading to the Cattaneo-type heat flux model, an evaluation of the heat transport behavior is described for models influenced by non-Fourier effects and subjected to general nonlinear/linear boundary conditions. An explicit time-integration architecture is employed which effectively provides not only accurate representations of the relaxation effects and general boundary conditions but also seeks to provide an understanding of the representative thermal behavior and heat transport mechanisms for a variety of physical situations.

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

    PubMed

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

    2017-02-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2009-08-04

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

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

    SciTech Connect

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

    1994-05-01

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

  20. Effect of interaction with coesite silica on the conformation of Cecropin P1 using explicit solvent molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Wu, Xiaoyu; Chang, Hector; Mello, Charlene; Nagarajan, Ramanathan; Narsimhan, Ganesan

    2013-01-01

    Explicit solvent molecular dynamics (MD) simulation was carried out for the antimicrobial peptides (i) Cecropin P1 and C-terminus cysteine modified Cecropin P1 (Cecropin P1 C) in solution, (ii) Cecropin P1 and Cecropin P1 C adsorbed onto coesite -Si - O - and Si - O - H surfaces, and (iii) Cecropin P1 C tethered to coesite -Si - O - surface with either (PEO)3 or (PEO)6 linker. Low energy structures for Cecropin P1 and Cecropin P1 C in solution consists of two regions of high α helix probability with a sharp bend, consistent with the available structures of other antimicrobial peptides. The structure of Cecropin P1 C at low ionic strength of 0.02 M exhibits two regions of high α helix probability (residues AKKLEN and EGI) whereas at higher ionic strength of 0.12 M, the molecule was more compact and had three regions of higher α helix probability (residues TAKKLENSA, ISE, and AIQG) with an increase in α helical content from 15.6% to 18.7% as a result of shielding of electrostatic interactions. In the presence of Cecropin P1 C in the vicinity of -Si - O - surface, there is a shift in the location of two peaks in H - O - H density profile to larger distances (2.95 Å and 7.38 Å compared to 2.82 Å and 4.88 Å in the absence of peptide) with attenuated peak intensity. This attenuation is found to be more pronounced for the first peak. H-bond density profile in the vicinity of -Si - O - surface exhibited a single peak in the presence of Cecropin P1 C (at 2.9 Å) which was only slightly different from the profile in the absence of polypeptide (2.82 Å) thus indicating that Cecropin P1 C is not able to break the H-bond formed by the silica surface. The α helix probability for different residues of adsorbed Cecropin P1 C on -Si - O - surface is not significantly different from that of Cecropin P1 C in solution at low ionic strength of 0.02 M whereas there is a decrease in the probability in the second (residues ISE) and third (residues AIQG) α helical regions at

  1. Parameter optimization in differential geometry based solvation models

    PubMed Central

    Wang, Bao; Wei, G. W.

    2015-01-01

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

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

    PubMed

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

    2015-05-21

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-11-01

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

  4. Preferential Solvation of an Asymmetric Redox Molecule

    SciTech Connect

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

    2016-12-15

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

  5. Implicit sequence learning with competing explicit cues.

    PubMed

    Jiménez, L; Méndez, C

    2001-05-01

    Previous research has shown that the expression of implicit sequence learning is eliminated in a choice reaction time task when an explicit cue allows participants to accurately predict the next stimulus (Cleeremans, 1997), but that two contingencies predicting the same outcome can be learned and expressed simultaneously when both of them remain implicit (Jiménez & Méndez, 1999). Two experiments tested the hypothesis that it is the deliberate use of explicit knowledge that produces the inhibitory effects over the expression of implicit sequence learning. However, the results of these experiments do not support this hypothesis, rather showing that implicit learning is acquired and expressed regardless of the influence of explicit knowledge. These results are interpreted as reinforcing the thesis about the automatic nature of both the acquisition and the expression of implicit sequence learning. The contradictory results reported by Cleeremans are attributed to a floor effect derived from the use of a special type of explicit cue.

  6. 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.

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

    PubMed

    Takahashi, Hideaki; Suzuoka, Daiki; Morita, Akihiro

    2015-03-10

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

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

    PubMed

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

    2009-06-01

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

  9. 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

  10. 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.

  11. 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.

  12. Solvent effects on chemical processes. I: Solubility of aromatic and heterocyclic compounds in binary aqueous-organic solvents.

    PubMed

    Khossravi, D; Connors, K A

    1992-04-01

    The standard free energy change (delta G0) for equilibrium dissolution in binary solvent mixtures is written as a sum of effects arising from solvent-solvent interactions (the general medium effect), solvent-solute interactions (the solvation effect), and solute-solute interactions (the intersolute effect). The general medium effect is given by gA gamma, where g is a curvature correction factor to the surface tension (gamma) and A is the molecular cavity surface area. A new feature is the definition of gamma to be that value appropriate to the equilibrium mean solvation shell composition. The solvation effect is modeled by stoichiometric stepwise competitive equilibria between the two solvent components for the solute. The intersolute effect includes the crystal energy and solution phase interactions. In this work, water was solvent component 1, and various miscible organic cosolvents served as solvent component 2. Relating all data to the fully aqueous solution gives an explicit expression for delta M delta G0, the solvent effect on the free energy change, as a function of the mole fractions x1 and x2. This function is a binding isotherm. Nonlinear regression leads (for a two-step solvation scheme) to estimates of the solvation exchange constants K1 and K2 and the parameter gA. This relationship was applied to 44 systems comprising combinations of 31 solutes and eight organic cosolvents. Curve fits were good to excellent, and most of the parameter estimates had physically reasonable magnitudes.

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

    PubMed

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

    2016-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Roy, Srabani; Bagchi, Biman

    1993-07-01

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

  15. Explicit solutions to an effective Gross-Pitaevskii equation: One-dimensional Bose-Einstein condensate in specific traps

    SciTech Connect

    Kengne, E.; Liu, X. X.; Liu, W. M.; Malomed, B. A.; Chui, S. T.

    2008-02-15

    An effective Gross-Pitaevskii equation, which describes the dynamics of quasi-one-dimensional Bose-Einstein condensates in specific potential traps, is considered, and new families of exact solutions are reported, which include periodic and solitary waves. The solutions are applied to the description of BEC patterns trapped in optical-lattice potentials.

  16. 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…

  17. The Effect of Bimodal Input on Implicit and Explicit Memory: An Investigation into the Benefits of Within-Language Subtitling.

    ERIC Educational Resources Information Center

    Bird, Stephen A.; Williams, John N.

    2002-01-01

    Two experiments examined the effect of single-modality (sound or text) and bimodal (sound and text) presentation on word meaning, as measured by both improvements in spoken word recognition efficiency and recognition memory. Both native and nonnative speakers of English were tested. Concludes simultaneous text presentation can aid novel word…

  18. 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…

  19. 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

  20. Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field.

    PubMed

    Shivakumar, Devleena; Williams, Joshua; Wu, Yujie; Damm, Wolfgang; Shelley, John; Sherman, Woody

    2010-05-11

    The accurate prediction of protein-ligand binding free energies is a primary objective in computer-aided drug design. The solvation free energy of a small molecule provides a surrogate to the desolvation of the ligand in the thermodynamic process of protein-ligand binding. Here, we use explicit solvent molecular dynamics free energy perturbation to predict the absolute solvation free energies of a set of 239 small molecules, spanning diverse chemical functional groups commonly found in drugs and drug-like molecules. We also compare the performance of absolute solvation free energies obtained using the OPLS_2005 force field with two other commonly used small molecule force fields-general AMBER force field (GAFF) with AM1-BCC charges and CHARMm-MSI with CHelpG charges. Using the OPLS_2005 force field, we obtain high correlation with experimental solvation free energies (R(2) = 0.94) and low average unsigned errors for a majority of the functional groups compared to AM1-BCC/GAFF or CHelpG/CHARMm-MSI. However, OPLS_2005 has errors of over 1.3 kcal/mol for certain classes of polar compounds. We show that predictions on these compound classes can be improved by using a semiempirical charge assignment method with an implicit bond charge correction.

  1. Quantum mechanical continuum solvation models for ionic liquids.

    PubMed

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

    2012-08-02

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

  2. Sleep enhances explicit recollection in recognition memory.

    PubMed

    Drosopoulos, Spyridon; Wagner, Ullrich; Born, Jan

    2005-01-01

    Recognition memory is considered to be supported by two different memory processes, i.e., the explicit recollection of information about a previous event and an implicit process of recognition based on an acontextual sense of familiarity. Both types of memory supposedly rely on distinct memory systems. Sleep is known to enhance the consolidation of memories, with the different sleep stages affecting different types of memory. In the present study, we used the process-dissociation procedure to compare the effects of sleep on estimates of explicit (recollection) and implicit (familiarity) memory formation on a word-list discrimination task. Subjects studied two lists of words before a 3-h retention interval of sleep or wakefulness, and recognition was tested afterward. The retention intervals were positioned either in the early night when sleep is dominated by slow-wave sleep (SWS), or in the late night, when sleep is dominated by REM sleep. Sleep enhanced explicit recognition memory, as compared with wakefulness (P < 0.05), whereas familiarity was not affected by sleep. Moreover, explicit recognition was particularly enhanced after sleep in the early-night retention interval, and especially when the words were presented with the same contextual features as during learning, i.e., in the same font (P < 0.05). The data indicate that in a task that allows separating the contribution of explicit and implicit memory, sleep particularly supports explicit memory formation. The mechanism of this effect appears to be linked to SWS.

  3. Association and not semantic relationships elicit the N400 effect: electrophysiological evidence from an explicit language comprehension task.

    PubMed

    Rhodes, Sinéad M; Donaldson, David I

    2008-01-01

    Language comprehension studies have identified the N400, an event-related potential (ERP) correlate of the processing of meaning, modulation of which is typically assumed to reflect the activation of semantic information. However, N400 studies of conscious language processing have not clearly distinguished between meaning derived from a semantic relationship and meaning extracted through association. We independently manipulated the presence of associative and semantic relationships while examining the N400 effect. Participants were asked to read and remember visually presented word pairs that shared an association (traffic-jam), an association+semantic relationship (lemon-orange), a semantic relationship alone (cereal-bread), or were unrelated (beard-tower). Modulation of the N400 (relative to unrelated word pairs) was observed for association and association+semantic word pairs but not for those that only shared a semantic relationship.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. Solvation of CO2 in water: effect of RuBP on CO2 concentration in bundle sheath of C4 plants.

    PubMed

    Sadhukhan, Tumpa; Latif, Iqbal A; Datta, Sambhu N

    2014-07-24

    An understanding of the temperature-dependence of solubility of carbon dioxide (CO2) in water is important for many industrial processes. Voluminous work has been done by both quantum chemical methods and molecular dynamics (MD) simulations on the interaction between CO2 and water, but a quantitative evaluation of solubility remains elusive. In this work, we have approached the problem by considering quantum chemically calculated total energies and thermal energies, and incorporating the effects of mixing, hydrogen bonding, and phonon modes. An overall equation relating the calculated free energy and entropy of mixing with the gas-solution equilibrium constant has been derived. This equation has been iteratively solved to obtain the solubility as functions of temperature and dielectric constant. The calculated solubility versus temperature plot excellently matches the observed plot. Solubility has been shown to increase with dielectric constant, for example, by addition of electrolytes. We have also found that at the experimentally reported concentration of enzyme RuBP in bundle sheath cells of chloroplast in C4 green plants, the concentration of CO2 can effectively increase by as much as a factor of 7.1-38.5. This stands in agreement with the observed effective rise in concentration by as much as 10 times.

  9. An Explicit Nonlinear Mapping for Manifold Learning.

    PubMed

    Qiao, Hong; Zhang, Peng; Wang, Di; Zhang, Bo

    2013-02-01

    Manifold learning is a hot research topic in the held of computer science and has many applications in the real world. A main drawback of manifold learning methods is, however, that there are no explicit mappings from the input data manifold to the output embedding. This prohibits the application of manifold learning methods in many practical problems such as classification and target detection. Previously, in order to provide explicit mappings for manifold learning methods, many methods have been proposed to get an approximate explicit representation mapping with the assumption that there exists a linear projection between the high-dimensional data samples and their low-dimensional embedding. However, this linearity assumption may be too restrictive. In this paper, an explicit nonlinear mapping is proposed for manifold learning, based on the assumption that there exists a polynomial mapping between the high-dimensional data samples and their low-dimensional representations. As far as we know, this is the hrst time that an explicit nonlinear mapping for manifold learning is given. In particular, we apply this to the method of locally linear embedding and derive an explicit nonlinear manifold learning algorithm, which is named neighborhood preserving polynomial embedding. Experimental results on both synthetic and real-world data show that the proposed mapping is much more effective in preserving the local neighborhood information and the nonlinear geometry of the high-dimensional data samples than previous work.

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

    PubMed

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

    2010-10-14

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

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

    NASA Astrophysics Data System (ADS)

    Montgomery Pettitt, B.

    2008-03-01

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

  12. Stepwise Solvation Effects on the Excited States of a Weakly Coupled Bichromophore: 1,2-DIPHENOXYETHANE-(H_{2}O)_N (N=2-4) Clusters

    NASA Astrophysics Data System (ADS)

    Walsh, Patrick S.; Buchanan, Evan G.; Gord, Joseph R.; Zwier, Timothy S.

    2013-06-01

    1,2-Diphenoxyethane (DPOE) is a prototypical flexible bichromophore which was shown to consist of two conformers in the gas phase with the first two excited states split by 1 cm^{-1} or less. Last year, we reported on the remarkable effects of asymmetric binding of a single H_{2}O molecule to DPOE, localizing the electronic excitation, and producing OH stretch IR spectra that report on the mixed electronic character of the excited state vibronic levels. Here, we extend that work to DPOE-(H_2O)_n clusters with n=2-4 with the goal of seeing how the degree of asymmetry and electronic coupling evolve as the number of water molecules bound to DPOE increases. Ground state IR spectra in the OH stretch region (3300-3750 cm^{-1}) sensitively probe the H-bonding networks present in the clusters. In the excited states, the stepwise addition of water molecules significantly changes the solvent-induced splitting of the excited states. Excited state IR spectroscopy is used to identify the (nominal) S_{1} and S_{2} origins, and to track the degree of S_{1}/S_{2} character via the OH stretch transitions observed. The spectra provide novel insight to the way in which solvent molecules redistribute the electronic energy as the density of intermolecular vibrational modes grows with cluster size. E. G. Buchanan, et al., J. Phys. Chem. A, submitted E. G. Buchanan, et al., 67^{th International Symposium on Molecular Spectroscopy}, 2012, WG08

  13. Frequency Dependent Non- Thermal Effects of Oscillating Electric Fields in the Microwave Region on the Properties of a Solvated Lysozyme System: A Molecular Dynamics Study

    PubMed Central

    Floros, Stelios; Liakopoulou-Kyriakides, Maria; Karatasos, Kostas

    2017-01-01

    The use of microwaves in every day’s applications raises issues regarding the non thermal biological effects of microwaves. In this work we employ molecular dynamics simulations to advance further the dielectric studies of protein solutions in the case of lysozyme, taking into consideration possible frequency dependent changes in the structural and dynamic properties of the system upon application of electric field in the microwave region. The obtained dielectric spectra are identical with those derived in our previous work using the Fröhlich-Kirkwood approach in the framework of the linear response theory. Noticeable structural changes in the protein have been observed only at frequencies near its absorption maximum. Concerning Cα position fluctuations, different frequencies affected different regions of the protein sequence. Furthermore, the influence of the field on the kinetics of protein-water as well as on the water-water hydrogen bonds in the first hydration shell has been studied; an extension of the Luzar-Chandler kinetic model was deemed necessary for a better fit of the applied field results and for the estimation of more accurate hydrogen bond lifetime values. PMID:28129348

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

    NASA Astrophysics Data System (ADS)

    Su, Zemin; Maroncelli, Mark

    2006-04-01

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

  15. Solvation effects on the electronic structure of 4-N, N-dimethylaminobenzonitrile: Mixing of the local ππ* and charge-transfer states

    NASA Astrophysics Data System (ADS)

    Shang, Quan-yuan; Bernstein, Elliot R.

    1992-07-01

    The effect of polar solvents acetonitrile and water on the electronic excited states of 4-N, N-dimethylaminobenzonitrile (DMABN) is studied through the optical spectroscopy of small clusters of DMABN/solvent. The clusters are created in a supersonic jet expansion. The results of mass resolved excitation spectroscopy (MRES), fluorescence excitation (FE), dispersed emission (DE), and photodepletion studies demonstrate that the solvent molecule can bind to DMABN at two distinct sites for the one-to-one cluster. Both DMABN (H2O)1 clusters generate small blue shifts for the S1←S0 cluster transition and evidence low-energy vibronic structure nearly identical to that found for the bare molecule. The DMABN (CH3CN)1 clusters behave quite differently. One cluster geometry induces a small blue shift of the S1←S0 electronic transition with little change in its vibronic structure and intensity pattern. We suggest this binding site involves the cyano end of the DMABN molecule. The second cluster geometry induces a large red shift (˜1000 cm-1) and significant broadening (>103 cm-1) of the lowest-energy transition. This red shifted transition is associated with a charge-transfer transition within the DMABN molecule lowered in energy due to the acetonitrile coordination with the DMABN aromatic ring. The lowering of the charge-transfer state in DMABN (CH3CN)n, n=1,...,5 clusters is supported by the following data: long wavelength emission from clusters with broad red shifted absorption; distinct lifetimes for emission at 350 nm (4.6 ns) and 400 nm (6.0 ns); broad red shifted absorption for one geometry of the DMABN (CH3CN)1 cluster. These results support the idea that the charge-transfer transition in DMABN is stabilized by short-range dipole-dipole interactions between DMABN and polar nonhydrogen bonding solvents.

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

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

    PubMed Central

    Muniz, Heloisa S.

    2017-01-01

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

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

    PubMed

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

    2006-11-30

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  1. 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…

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

    PubMed

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

    2004-08-02

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

  3. Consequences of the Hawkmoth Effect: Explicit subjective judgements about uncertain model-system relationships improve policy relevance of climate model output

    NASA Astrophysics Data System (ADS)

    Thompson, E. L.; Smith, L. A.

    2013-12-01

    The Earth's climate is a complex many-dimensional dynamical system with feedbacks, nonlinearities, and long time scale internal variability. The Hawkmoth Effect is a description of structural instability in dynamical systems (sensitivity to the mathematical structure of a model), analogous to the manner in which the better-known Butterfly Effect describes dynamical instability (sensitivity to initial conditions). The Hawkmoth Effect can be paraphrased in the following way: "You can be arbitrarily close to the correct equations (model structure), but still not be close to the correct solutions (future trajectories)". Here we illustrate the possible consequences for model-based climate research, drawing together a number of observations about modelling, data assimilation, climate model calibration, and numerical solution of partial differential equations. We contrast and then synthesise this with the statistical/stochastic modelling viewpoint and the sophisticated Bayesian frameworks that have been proposed to interpret model output. We conclude that the primary uncertainties in long term climate projections may well be the implicit subjective assumptions that dynamical modelling is appropriate and adequate for the predictive task, and that the Hawkmoth Effect will not be experienced. Good Bayesian practice involves quantification of such prior assumptions. The likelihood that model runs are adequate for predictive purpose will vary with the space and time scales of the task, and is necessarily quantified outside the limitations of the modelling framework; thus, intermodel diversity alone may not be informative about the probability of adequacy, nor about the timescales on which this assumption may become invalid. Intuition based on the underlying physics of the situation is, fortunately, likely to be of use, and expert elicitation frameworks exist for quantifying such judgements. Acknowledging and explicitly incorporating these subjective probabilities into research

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

    PubMed

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

    1992-10-20

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

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

    PubMed Central

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

    2015-01-01

    The photophysics and photochemistry of water-solvated guanine monophosphate (GMP) are here characterized by means of a multireference quantum-chemical/molecular mechanics theoretical approach (CASPT2//CASSCF/AMBER) in order to elucidate the main photo-processes occurring upon UV-light irradiation. The effect of the solvent and of the phosphate group on the energetics and structural features of this system are evaluated for the first time employing high-level ab initio methods and thoroughly compared to those in vacuo previously reported in the literature and to the experimental evidence to assess to which extent they influence the photoinduced mechanisms. Solvated electronic excitation energies of solvated GMP at the Franck-Condon (FC) region show a red shift for the ππ* La and Lb states, whereas the energy of the oxygen lone-pair nπ* state is blue-shifted. The main photoinduced decay route is promoted through a ring-puckering motion along the bright lowest-lying La state toward a conical intersection (CI) with the ground state, involving a very shallow stationary point along the minimum energy pathway in contrast to the barrierless profile found in gas-phase, the point being placed at the end of the minimum energy path (MEP) thus endorsing its ultrafast deactivation in accordance with time-resolved transient and photoelectron spectroscopy experiments. The role of the nπ* state in the solvated system is severely diminished as the crossings with the initially populated La state and also with the Lb state are placed too high energetically to partake prominently in the deactivation photo-process. The proposed mechanism present in solvated and in vacuo DNA/RNA chromophores validates the intrinsic photostability mechanism through CI-mediated non-radiative processes accompanying the bright excited-state population toward the ground state and subsequent relaxation back to the FC region. PMID:25941671

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. Brain Networks of Explicit and Implicit Learning

    PubMed Central

    Yang, Jing; Li, Ping

    2012-01-01

    Are explicit versus implicit learning mechanisms reflected in the brain as distinct neural structures, as previous research indicates, or are they distinguished by brain networks that involve overlapping systems with differential connectivity? In this functional MRI study we examined the neural correlates of explicit and implicit learning of artificial grammar sequences. Using effective connectivity analyses we found that brain networks of different connectivity underlie the two types of learning: while both processes involve activation in a set of cortical and subcortical structures, explicit learners engage a network that uses the insula as a key mediator whereas implicit learners evoke a direct frontal-striatal network. Individual differences in working memory also differentially impact the two types of sequence learning. PMID:22952624

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

    SciTech Connect

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

    1996-06-13

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

  13. Nonperiodic boundary conditions for solvated systems.

    PubMed

    Petraglio, Gabriele; Ceccarelli, Matteo; Parrinello, Michele

    2005-07-22

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

  14. Domain decomposition for implicit solvation models.

    PubMed

    Cancès, Eric; Maday, Yvon; Stamm, Benjamin

    2013-08-07

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

  15. 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…

  16. 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…

  17. 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

  18. 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.

  19. Solvation of lithium ion in dimethoxyethane and propylene carbonate

    NASA Astrophysics Data System (ADS)

    Chaban, Vitaly

    2015-07-01

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

  20. 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,…

  1. 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…

  2. 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.

  3. 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.

  4. Does explicit expectation really affect preparation?

    PubMed

    Umbach, Valentin J; Schwager, Sabine; Frensch, Peter A; Gaschler, Robert

    2012-01-01

    Expectation enables preparation for an upcoming event and supports performance if the anticipated situation occurs, as manifested in behavioral effects (e.g., decreased RT). However, demonstrating coincidence between expectation and preparation is not sufficient for attributing a causal role to the former. The content of explicit expectation may simply reflect the present preparation state. We targeted this issue by experimentally teasing apart demands for preparation and explicit expectations. Expectations often originate from our experience: we expect that events occurring with a high frequency in the past are more likely to occur again. In addition to expectation, other task demands can feed into action preparation. In four experiments, frequency-based expectation was pitted against a selective response deadline. In a three-choice reaction time task, participants responded to stimuli that appeared with varying frequency (60, 30, 10%). Trial-by-trial stimulus expectations were either captured via verbal predictions or induced by visual cues. Predictions as well as response times quickly conformed to the variation in stimulus frequency. After two (of five) experimental blocks we forced participants by selective time pressure to respond faster to a less frequent stimulus. Therefore, participants had to prepare for one stimulus (medium frequency) while often explicitly expecting a different one (high frequency). Response times for the less frequent stimulus decreased immediately, while explicit expectations continued to indicate the (unchanged) presentation frequencies. Explicit expectations were thus not just reflecting preparation. In fact, participants responded faster when the stimulus matched the trial-wise expectations, even when task demands discouraged their use. In conclusion, we argue that explicit expectation feeds into preparatory processes instead of being a mere by-product.

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

    ERIC Educational Resources Information Center

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

    2016-01-01

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

  6. 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 ...

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

    PubMed

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

    2011-10-21

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

  8. Nonexponential Solvation Dynamics of Simple Liquids and Mixtures

    DTIC Science & Technology

    1991-05-06

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

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

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

    PubMed

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

    2011-09-18

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

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

    SciTech Connect

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

    2012-06-07

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

  12. 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

  13. 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

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

    PubMed

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

    2008-03-20

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

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

    PubMed

    Johansson, Anna C V; Lindahl, Erik

    2006-12-15

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

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

    PubMed

    Oviedo, M Belén; Wong, Bryan M

    2016-04-12

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

  17. 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.

  18. 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.

  19. 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

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

    PubMed

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

    2008-11-25

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

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

    PubMed

    Yang, Pei-Kun

    2013-12-31

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

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

    NASA Astrophysics Data System (ADS)

    Mukherji, Debashish; Kremer, Kurt

    2013-03-01

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

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

    PubMed

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

    2015-02-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

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

    PubMed

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

    2014-08-12

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

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

    PubMed

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

    2016-10-05

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

  7. 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).

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

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

    PubMed

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

    2008-12-02

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

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

    PubMed

    Martin, Daniel R; Matyushov, Dmitry V

    2012-10-28

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

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

    PubMed Central

    2012-01-01

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

  12. Effects of thalamic hemorrhagic lesions on explicit and implicit learning during the acquisition and retrieval phases in an animal model of central post-stroke pain.

    PubMed

    Wang, Cheng Chung; Shih, Hsi-Chien; Shyu, Bai Chuang; Huang, Andrew Chih Wei

    2017-01-15

    Hemorrhagic stroke has many symptoms, including central pain, learning and memory impairments, motor deficits, language problems, emotional disturbances, and social maladjustment. Lesions of the ventral basal complex (VBC) of the thalamus elicit thermal and mechanical hyperalgesia, forming an animal model of central post-stroke pain (CPSP). However, no research has yet examined the involvement of learning and memory in CPSP using an animal model. The present study examined whether VBC lesions affect motor function, conditioned place preference (CPP; implicit memory), and spatial learning (explicit memory) in the acquisition and retrieval phases. The results showed that rats with VBC lesions exhibited thermal hyperalgesia in the acquisition and retrieval phases, indicating that these lesions can induce CPSP. During these phases, the rats with VBC lesions exhibited enhanced (morphine-induced) CPP learning. These lesions did not affect the rats' total distance travelled, time spent, or velocity in the spatial learning tasks. The lesions also did not affect motor function in the rotarod task. Altogether, VBC lesions resulted in CPSP and facilitated CPP (implicit memory). However, the lesions did not affect spatial learning (explicit memory) or motor function. The relationship between CPSP and learning and memory is important for patients who suffer from such central pain. The implications of the present study may provide insights into helping reduce CPSP and its associated symptoms.

  13. 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.

  14. Study of preferential solvation of 2,6-diaminoanthraquinone in binary mixtures by absorption and fluorescence studies

    NASA Astrophysics Data System (ADS)

    Sasirekha, V.; Ramakrishnan, V.

    2008-08-01

    The role of solute-solvent and solvent-solvent interaction on the preferential solvation characteristics of 2,6-diaminoanthraquinone (DAAQ) has been analysed by monitoring the optical absorption and fluorescence emission spectra. Binary mixtures consist of dimethylformamide (DMF)-ethanol (EtOH), DMF-dimelthylsulfoxide (DMSO), benzene (BZ)-DMF and acetonitrile (ACN)-DMF. The optical absorption spectra maximum and emission spectra maximum of DAAQ show the changes with varying the solvents and change in the composition in the case of binary mixtures. Non-ideal solvation characteristics are observed in all binary mixtures. It is found that at certain concentrations two mixed solvents interact to form a common structure with a ν12 (wave number in cm -1) value not always intermediate ( ν1 and ν2) between the values of the solvents mixed. Synergistic effect is observed in the case of DMF-EtOH mixtures. The preferential solvation parameters local mole fraction X2L, solvation index δS2, exchange constant K12 are calculated in all binary mixtures expect in the case of DMF-BZ mixture and DMF-EtOH mixture in the ground state. We have also monitored excitation wavelength effect on the probe molecule in aprotic polar and protic polar solvents.

  15. 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

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

    SciTech Connect

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

    2009-01-06

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

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

    NASA Astrophysics Data System (ADS)

    Golmohammadi, Hassan; Dashtbozorgi, Zahra

    2016-09-01

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

  18. 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.

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

    DOE PAGES

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

    2015-09-16

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

  20. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

    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

  1. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

    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

  2. Solvation model induced structural changes in peptides. A quantum chemical study on Ramachandran surfaces and conformers of alanine diamide using the polarizable continuum model.

    PubMed

    Hudáky, Ilona; Hudáky, Péter; Perczel, András

    2004-09-01

    Potential energy surfaces of the model peptide HCO-L-Ala-NH2 were calculated using polarizable continuum model (PCM) for the description of aqueous solution at RHF/3-21G, RHF/6-31+G(d), and B3LYP/6-31+G(d) levels of theory. Energy minima were optimized at all three levels as well as at B3LYP/PCM/6-311++G(d,p) level of theory. Results were correlated to experimental data of protein structures retrieved from PDB SELECT. It is concluded that alanine residues of proteins are modeled better by PCM results than by gas-phase calculations on the alanine diamide model (frequently called alanine dipeptide model). The currently available version of the PCM model implemented in Gaussian 03 provides a reasonable alternative to anticipate solvation effects without the computational costs of introducing explicit solvent molecules into the model system. Frequencies calculated at RHF/PCM/6-31+G(d) and B3LYP/PCM/6-31+G(d) levels of theory show high correlation; thus, RHF results have their own merit.

  3. 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.

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

    PubMed

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

    2006-12-28

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

  5. Explicit-water molecular dynamics study of a short-chain 3,3 ionene in solutions with sodium halides

    NASA Astrophysics Data System (ADS)

    Druchok, M.; Vlachy, V.; Dill, K. A.

    2009-04-01

    Ionenes are alkyl polymer chains in which hydrophobic groups are separated by ionic charges. They are useful for studying the properties of water as a solvent because they demonstrate a sufficiently complex combination of hydrophobicity, charge interactions, and specific-ion effects that some properties cannot be predicted by implicit-solvation theories. On the other hand, they are simple enough that their molecular structures can be varied and controlled in systematic experiments. In particular, implicit-solvent models predict that all such solutes will have negative enthalpies of dilution, whereas experiments show that enthalpies of dilution are positive for the chaotropic counterions. Here, we study ionenes that are short chains (six monomer units) in solutions of different counterions, with sodium as the coion by molecular dynamics simulations in explicit water. We explore the pair distributions of various atoms within the system at three different temperatures: T =278, 298, and 318 K. We find (i) that the molecular dynamics simulations are consistent with the experimental trends for the osmotic coefficients and enthalpies of dilution, (ii) that the fluorine-nitrogen and fluorine-carbon correlations decrease with decreasing temperature, (iii) while the opposite behavior is found for iodine ions, and (iv) that in the counterion-Na+ pair distributions, too, fluorine ions behave oppositely to iodine ions upon temperature increase.

  6. Second-harmonic generation of solvated molecules using multiconfigurational self-consistent-field quadratic response theory and the polarizable continuum model

    NASA Astrophysics Data System (ADS)

    Frediani, Luca; Ågren, Hans; Ferrighi, Lara; Ruud, Kenneth

    2005-10-01

    We present the first implementation of the quadratic response function for multiconfigurational self-consistent-field wave functions of solvated molecules described by a polarizable continuum model employing a molecule-shaped cavity. We apply the methodology to the first hyperpolarizability β and, in particular, the second-harmonic generation process for a series of conjugated push-pull oligomers, as well as for para-nitroaniline. The effect of solvation on the dispersion of the hyperpolarizability and the change in the hyperpolarizability for increasing chain length of the oligomers in vacuum and in solution is considered. The effect of a correlated description is analyzed by comparing the Hartree-Fock hyperpolarizabilities to the multiconfigurational self-consistent-field hyperpolarizabilities. The effect of geometry relaxation in the solvent on the properties of the solvated molecules are also investigated.

  7. Enhanced fluorescence of [[5'-(4-hydroxyphenyl)[2,2'-bithiophen]-5-yl]methylene]-propanedinitrile (NIAD-4): solvation induced micro-viscosity enhancement.

    PubMed

    Hu, Jiangpu; Zhu, Huaning; Li, Yang; Wang, Xian; Ma, Renjun; Guo, Qianjin; Xia, Andong

    2016-07-28

    Excited state solvation plays a very important role in modulating the emission behavior of fluorophores upon excitation. Here, the solvation effects on the local micro-environment around a fluorophore are proposed by investigating the fantastic emission behavior of a novel amyloid fibril marker, NIAD-4, in different alcoholic and aprotic solvents. In alcoholic solvents, high solvent viscosity causes an obvious enhancement of fluorescence because of the restriction of torsion of NIAD-4, where the formation of a non-fluorescent twist intramolecular charge transfer (TICT) state is suppressed. In aprotic solvents, high solvent polarity leads to a remarkable redshift of the emission spectra suggesting strong solvation. Surprisingly, an abnormal fluorescence enhancement of NIAD-4 is observed with increasing solvent polarity of the aprotic solvents, whereas solvent viscosity plays little role in influencing the fluorescence intensity. We conclude that such an abnormal phenomenon is originated from a solvation induced micro-viscosity enhancement around the fluorophore upon excitation which restricts the torsion of NIAD-4. Femtosecond transient absorption results further prove such a micro-viscosity increasing mechanism. We believe that this solvation induced micro-viscosity enhancement effect on fluorescence could widely exist for most donor-π-acceptor (D-π-A) compounds in polar solvents, which should be carefully taken into consideration when probing the micro-viscosity in polar environments, especially in complex bioenvironments.

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

    PubMed

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

    2016-09-08

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

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. Computational solvation dynamics of oxyquinolinium betaine linked to trehalose

    NASA Astrophysics Data System (ADS)

    Heid, Esther; Schröder, Christian

    2016-10-01

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

  14. 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.

  15. Explicit solvent simulations of the aqueous oxidation potential and reorganization energy for neutral molecules: gas phase, linear solvent response, and non-linear response contributions.

    PubMed

    Guerard, Jennifer J; Tentscher, Peter R; Seijo, Marianne; Samuel Arey, J

    2015-06-14

    First principles simulations were used to predict aqueous one-electron oxidation potentials (Eox) and associated half-cell reorganization energies (λaq) for aniline, phenol, methoxybenzene, imidazole, and dimethylsulfide. We employed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations of the oxidized and reduced species in an explicit aqueous solvent, followed by EOM-IP-CCSD computations with effective fragment potentials for diabatic energy gaps of solvated clusters, and finally thermodynamic integration of the non-linear solvent response contribution using classical MD. A priori predicted Eox and λaq values exhibit mean absolute errors of 0.17 V and 0.06 eV, respectively, compared to experiment. We also disaggregate Eox into several well-defined free energy properties, including the gas phase adiabatic free energy of ionization (7.73 to 8.82 eV), the solvent-induced shift in the free energy of ionization due to linear solvent response (-2.01 to -2.73 eV), and the contribution from non-linear solvent response (-0.07 to -0.14 eV). The linear solvent response component is further apportioned into contributions from the solvent-induced shift in vertical ionization energy of the reduced species (ΔVIEaq) and the solvent-induced shift in negative vertical electron affinity of the ionized species (ΔNVEAaq). The simulated ΔVIEaq and ΔNVEAaq are found to contribute the principal sources of uncertainty in computational estimates of Eox and λaq. Trends in the magnitudes of disaggregated solvation properties are found to correlate with trends in structural and electronic features of the solute. Finally, conflicting approaches for evaluating the aqueous reorganization energy are contrasted and discussed, and concluding recommendations are given.

  16. 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…

  17. Solvation free energy of the peptide group: its model dependence and implications for the additive-transfer free-energy model of protein stability.

    PubMed

    Tomar, Dheeraj S; Asthagiri, D; Weber, Valéry

    2013-09-17

    The group-additive decomposition of the unfolding free energy of a protein in an osmolyte solution relative to that in water poses a fundamental paradox: whereas the decomposition describes the experimental results rather well, theory suggests that a group-additive decomposition of free energies is, in general, not valid. In a step toward resolving this paradox, here we study the peptide-group transfer free energy. We calculate the vacuum-to-solvent (solvation) free energies of (Gly)n and cyclic diglycine (cGG) and analyze the data according to experimental protocol. The solvation free energies of (Gly)n are linear in n, suggesting group additivity. However, the slope interpreted as the free energy of a peptide unit differs from that for cGG scaled by a factor of half, emphasizing the context dependence of solvation. However, the water-to-osmolyte transfer free energies of the peptide unit are relatively independent of the peptide model, as observed experimentally. To understand these observations, a way to assess the contribution to the solvation free energy of solvent-mediated correlation between distinct groups is developed. We show that linearity of solvation free energy with n is a consequence of uniformity of the correlation contributions, with apparent group-additive behavior in the water-to-osmolyte transfer arising due to their cancellation. Implications for inferring molecular mechanisms of solvent effects on protein stability on the basis of the group-additive transfer model are suggested.

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    PubMed

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

    2016-09-21

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

  20. NMR-based simulation studies of Pf1 coat protein in explicit membranes.

    PubMed

    Cheng, Xi; Jo, Sunhwan; Marassi, Francesca M; Im, Wonpil

    2013-08-06

    As time- and ensemble-averaged measures, NMR observables contain information about both protein structure and dynamics. This work represents a computational study to extract such information for membrane proteins from orientation-dependent NMR observables: solid-state NMR chemical shift anisotropy and dipolar coupling, and solution NMR residual dipolar coupling. We have performed NMR-restrained molecular dynamics simulations to refine the structure of the membrane-bound form of Pf1 coat protein in explicit lipid bilayers using the recently measured chemical shift anisotropy, dipolar coupling, and residual dipolar coupling data. From the simulations, we have characterized detailed protein-lipid interactions and explored the dynamics. All simulations are stable and the NMR restraints are well satisfied. The C-terminal transmembrane (TM) domain of Pf1 finds its optimal position in the membrane quickly (within 6 ns), illustrating efficient solvation of TM domains in explicit bilayer environments. Such rapid convergence also leads to well-converged interaction patterns between the TM helix and the membrane, which clearly show the interactions of interfacial membrane-anchoring residues with the lipids. For the N-terminal periplasmic helix of Pf1, we identify a stable, albeit dynamic, helix orientation parallel to the membrane surface that satisfies the amphiphatic nature of the helix in an explicit lipid bilayer. Such detailed information cannot be obtained solely from NMR observables. Therefore, the present simulations illustrate the usefulness of NMR-restrained MD refinement of membrane protein structure in explicit membranes.

  1. 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

  2. Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity

    NASA Astrophysics Data System (ADS)

    Grabowska, Joanna; Kuffel, Anna; Zielkiewicz, Jan

    2016-08-01

    Water molecules from the solvation shell of the ice-binding surface are considered important for the antifreeze proteins to perform their function properly. Herein, we discuss the problem whether the extent of changes of the mean properties of solvation water can be connected with the antifreeze activity of the protein. To this aim, the structure of solvation water of a type III antifreeze protein from Macrozoarces americanus (eel pout) is investigated. A wild type of the protein is used, along with its three mutants, with antifreeze activities equal to 54% or 10% of the activity of the native form. The solvation water of the ice-binding surface and the rest of the protein are analyzed separately. To characterize the structure of solvation shell, parameters describing radial and angular characteristics of the mutual arrangement of the molecules were employed. They take into account short-distance (first hydration shell) or long-distance (two solvation shells) effects. The obtained results and the comparison with the results obtained previously for a hyperactive antifreeze protein from Choristoneura fumiferana lead to the conclusion that the structure and amino acid composition of the active region of the protein evolved to achieve two goals. The first one is the modification of the properties of the solvation water. The second one is the geometrical adjustment of the protein surface to the specific crystallographic plane of ice. Both of these goals have to be achieved simultaneously in order for the protein to perform its function properly. However, they seem to be independent from one another in a sense that very small antifreeze activity does not imply that properties of water become different from the ones observed for the wild type. The proteins with significantly lower activity still modify the mean properties of solvation water in a right direction, in spite of the fact that the accuracy of the geometrical match with the ice lattice is lost because of the

  3. Photoelectron Spectroscopy of Rare-Gas Solvated Nucleobase Anions

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

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

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

    PubMed

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

    2009-05-07

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

  5. A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge

    NASA Astrophysics Data System (ADS)

    Pal, Rajat Kumar; Haider, Kamran; Kaur, Divya; Flynn, William; Xia, Junchao; Levy, Ronald M.; Taran, Tetiana; Wickstrom, Lauren; Kurtzman, Tom; Gallicchio, Emilio

    2017-01-01

    As part of the SAMPL5 blinded experiment, we computed the absolute binding free energies of 22 host-guest complexes employing a novel approach based on the BEDAM single-decoupling alchemical free energy protocol with parallel replica exchange conformational sampling and the AGBNP2 implicit solvation model specifically customized to treat the effect of water displacement as modeled by the Hydration Site Analysis method with explicit solvation. Initial predictions were affected by the lack of treatment of ionic charge screening, which is very significant for these highly charged hosts, and resulted in poor relative ranking of negatively versus positively charged guests. Binding free energies obtained with Debye-Hückel treatment of salt effects were in good agreement with experimental measurements. Water displacement effects contributed favorably and very significantly to the observed binding affinities; without it, the modeling predictions would have grossly underestimated binding. The work validates the implicit/explicit solvation approach employed here and it shows that comprehensive physical models can be effective at predicting binding affinities of molecular complexes requiring accurate treatment of conformational dynamics and hydration.

  6. Modeling solvation contributions to conformational free energy changes of biomolecules using a potential of mean force expansion

    SciTech Connect

    Pellegrini, M.; Doniach, S.

    1995-08-15

    The standard free energy perturbation (FEP) techniques for the calculation of conformational free energy changes of a solvated biomolecule involve long molecular dynamics (MD) simulations. We have developed a method for performing the same calculations many orders of magnitude faster. We model the average solvent density around a solute as the product of the relevant solute--solvent correlation functions (CF), following the work of Garcia, Hummer, and Soumpasis. We calculate the CF`s by running Monte Carlo simulations of a single solute atom in a box of explicit water molecules and also angular dependent CF`s for selected pairs of solute atoms. We then build the water shell around a larger solute (e.g., alanine dipeptide) by taking the product of the appropriate CF`s. Using FEP techniques we are able to calculate free energy changes as we rotate the dihedral angles of the alanine dipeptide and we find they are in close agreement with the MD results. We also compute the potential of mean force as a function of distance between two solvated methanes and calculate the contribution of the solvent to the free energy change that results from rotating {ital n}-butane about its dihedral angle. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

  7. 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.

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

    PubMed

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

    2008-05-28

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

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

    PubMed Central

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

    2015-01-01

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

  10. 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

  11. The Absorption Spectrum of an Electron Solvated in Sodalite

    DTIC Science & Technology

    1992-05-15

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

  12. On the solvation of L-aspartic acid

    NASA Astrophysics Data System (ADS)

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

    2004-01-01

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

  13. Implicit and explicit representations of hand position in tool use.

    PubMed

    Rand, Miya K; Heuer, Herbert

    2013-01-01

    Understanding the interactions of visual and proprioceptive information in tool use is important as it is the basis for learning of the tool's kinematic transformation and thus skilled performance. This study investigated how the CNS combines seen cursor positions and felt hand positions under a visuo-motor rotation paradigm. Young and older adult participants performed aiming movements on a digitizer while looking at rotated visual feedback on a monitor. After each movement, they judged either the proprioceptively sensed hand direction or the visually sensed cursor direction. We identified asymmetric mutual biases with a strong visual dominance. Furthermore, we found a number of differences between explicit and implicit judgments of hand directions. The explicit judgments had considerably larger variability than the implicit judgments. The bias toward the cursor direction for the explicit judgments was about twice as strong as for the implicit judgments. The individual biases of explicit and implicit judgments were uncorrelated. Biases of these judgments exhibited opposite sequential effects. Moreover, age-related changes were also different between these judgments. The judgment variability was decreased and the bias toward the cursor direction was increased with increasing age only for the explicit judgments. These results indicate distinct explicit and implicit neural representations of hand direction, similar to the notion of distinct visual systems.

  14. 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.

  15. Hydroxide Solvation and Transport in Anion Exchange Membranes

    SciTech Connect

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

    2016-01-27

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

  16. 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.

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

    PubMed

    Scalmani, Giovanni; Frisch, Michael J

    2010-03-21

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

  18. 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.

  19. 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.

  20. Energetic and structural consequences of desolvation/solvation barriers to protein folding/unfolding assessed from experimental unfolding rates.

    PubMed

    Rodriguez-Larrea, David; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M

    2006-09-01

    Theoretical work has suggested the existence of solvation/desolvation barriers in protein folding/unfolding processes. We propose that the energetic and structural consequences of such barriers for the folding transition state can be assessed from experimental unfolding rates using well-established structure-energetics relationships. For a set of proteins of size within the 60-130 number-of-residues range, we find energetic effects associated to solvation/desolvation on the order of 10(2) kJ/mol. This supports that the folding transition states may be characterized by large networks of water-unsatisfied, broken internal contacts. In terms of buried surface, we estimate the typical network size to be on the order of several thousands of A2, or approximately 50% of the total change in accessible surface area upon unfolding. The analyses reported here thus suggest a clear structural picture for the different energetic balance of native and folding transition states.

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

    NASA Astrophysics Data System (ADS)

    Komath, Sneha Sudha; Bagchi, Biman

    1993-06-01

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

  2. Solvation shell structure of cyclooctylpyranone in water solvent and its comparative structure, dynamics and dipole moment in HIV protease.

    PubMed

    Arul Murugan, N; Chandra Jha, Prakash; Agren, Hans

    2009-08-14

    We have investigated the solvation structure for cyclooctylpyranone (COP) in water solvent using force-field molecular dynamics (MD) and Car-Parrinello mixed quantum mechanics-molecular mechanics (CPMD) calculations. The MD calculations show that in water solvent COP can exist in two conformational states which differ with respect to the relative orientations of the three rings, namely phenyl, pyranone and cyclooctane. We report the existence of strong orientational preference for the water molecule in the first solvation shell and the orientational preference disappears for solvent molecules beyond the first solvation shell. In order to investigate the confinement effect on the structure, dynamics, charge distribution and dipole moment of COP, we have carried out MD and CPMD calculations for COP within HIV type-1 protease (PR). Interestingly, we do not see any conformational transitions for COP within the protein cavity and it remains as a single conformer. We do see a remarkable effect of confinement on few other torsional degrees of freedom such as gg to tg conformational shift for the propyl group of COP. However, the methyl group rotational dynamics remains similar in the water solvent and in the protein environment. Also, within the protein cavity, the COP molecule is more polarized when compared to water solvent. Static ab initio electronic structure calculations were performed on the COP molecule with varying torsional angle in order to investigate the angle dependence of the molecular volume and energy.

  3. Performance analysis of junctionless double gate VeSFET considering the effects of thermal variation - An explicit 2D analytical model

    NASA Astrophysics Data System (ADS)

    Chaudhary, Tarun; Khanna, Gargi

    2017-03-01

    The purpose of this paper is to explore junctionless double gate vertical slit field effect transistor (JLDG VeSFET) with reduced short channel effects and to develop an analytical threshold voltage model for the device considering the impact of thermal variations for the very first time. The model has been derived by solving 2D Poisson's equation and the effects of variation in temperature on various electrical parameters of the device such as Rout, drain current, mobility, subthreshold slope and DIBL has been studied and described in the paper. The model provides a deep physical insight of the device behavior and is also very helpful in contributing to the design space exploration for JLDG VeSFET. The proposed model is verified with simulative analysis at different radii of the device and it has been observed that there is a good agreement between the analytical model and simulation results.

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  5. 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.

  6. 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…

  7. 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…

  8. 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.

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

    PubMed

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

    2015-11-21

    We apply our recently developed generalized Flory-Huggins (FH) type theory for the competitive solvation of polymers by two mixed solvents to explain general trends in the variation of phase boundaries and solvent quality (quantified by the second osmotic virial coefficient B2) with solvent composition. The complexity of the theoretically predicted miscibility patterns for these ternary mixtures arises from the competitive association between the polymer and the solvents and from the interplay of these associative interactions with the weak van der Waals interactions between all components of the mixture. The main focus here lies in determining the influence of the free energy parameters for polymer-solvent association (solvation) and the effective FH interaction parameters {χαβ} (driving phase separation) on the phase boundaries (specifically the spinodals), the second osmotic virial coefficient B2, and the relation between the positions of the spinodal curves and the theta temperatures at which B2 vanishes. Our classification of the predicted miscibility patterns is relevant to numerous applications of ternary polymer solutions in industrial formulations and the use of mixed solvent systems for polymer characterization, such as chromatographic separation where mixed solvents are commonly employed. A favorable comparison of B2 with experimental data for poly(methyl methacrylate)/acetonitrile/methanol (or 1-propanol) solutions only partially supports the validity of our theoretical predictions due to the lack of enough experimental data and the neglect of the self and mutual association of the solvents.

  10. 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.

  11. 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.

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

    PubMed

    Smyth, Maeve; Kohanoff, Jorge

    2012-06-06

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2006-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1999-10-01

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

  16. Ultrafast studies of excess electrons in liquid acetonitrile: revisiting the solvated electron/solvent dimer anion equilibrium.

    PubMed

    Doan, Stephanie C; Schwartz, Benjamin J

    2013-04-25

    We examine the ultrafast relaxation dynamics of excess electrons injected into liquid acetonitrile using air- and water-free techniques and compare our results to previous work on this system [Xia, C. et al. J. Chem. Phys. 2002, 117, 8855]. Excess electrons in liquid acetonitrile take on two forms: a "traditional" solvated electron that absorbs in the near-IR, and a solvated molecular dimer anion that absorbs weakly in the visible. We find that excess electrons initially produced via charge-transfer-to-solvent excitation of iodide prefer to localize as solvated electrons, but that there is a subsequent equilibration to form the dimer anion on an ~80 ps time scale. The spectral signature of this interconversion between the two forms of the excess electron is a clear isosbestic point. The presence of the isosbestic point makes it possible to fully deconvolute the spectra of the two species. We find that solvated molecular anion absorbs quite weakly, with a maximum extinction coefficient of ~2000 M(-1)cm(-1). With the extinction coefficient of the dimer anion in hand, we are also able to determine the equilibrium constant for the two forms of excess electron, and find that the molecular anion is favored by a factor of ~4. We also find that relatively little geminate recombination takes place, and that the geminate recombination that does take place is essentially complete within the first 20 ps. Finally, we show that the presence of small amounts of water in the acetonitrile can have a fairly large effect on the observed spectral dynamics, explaining the differences between our results and those in previously published work.

  17. Development of Implicit and Explicit Category Learning

    ERIC Educational Resources Information Center

    Huang-Pollock, Cynthia L.; Maddox, W. Todd; Karalunas, Sarah L.

    2011-01-01

    We present two studies that examined developmental differences in the implicit and explicit acquisition of category knowledge. College-attending adults consistently outperformed school-age children on two separate information-integration paradigms due to children's more frequent use of an explicit rule-based strategy. Accuracy rates were also…

  18. 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…

  19. 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)…

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

    NASA Astrophysics Data System (ADS)

    Calvo, F.; Yurtsever, E.

    2016-08-01

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

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

    PubMed

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

    2008-01-01

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

  2. A study of the effect of attenuation curvature on molecular correlation energies by introducing an explicit cutoff radius into two-electron integrals.

    PubMed

    Dutoi, Anthony D; Head-Gordon, Martin

    2008-03-13

    We present a new attenuator function that can be applied to the Coulomb operator. Similar to the popular erf(omegar) attenuator, the function [erf(omega(r + r0)) + erf(omega(r - r0))]/2 divides the Coulomb potential into a singular short-range piece and a non-singular long-range piece. In our attenuator, omega controls the sharpness of the short-range/long-range division at r0. With r0 = 0, this reduces to erf(omegar), but the additional parameter allows more flexible adjustment of the potential, for physical and/or computational reasons. We present some illustrative results for a truncated MP2 method, where mean field effects are handled exactly and correlation is treated locally. This study indicates, somewhat expectedly, that the slope and curvature of the attenuated potential are more important than its value (a trivial constant may always be added to a potential). However, there are some surprising features of the data that suggest what bounds need to be put on the curvature of the attenuated potential in order to achieve reasonable physics. Conveniently, we find that our attenuator form has the ability to preserve the curvature of the Coulomb potential almost exactly at short range, allowing for the truncation of long-range interactions while preserving the local physics very well. The molecular integrals for the resultant operator can be done analytically over Gaussian basis functions, and the extensive algebraic manipulations necessary to evaluate them stably are shown.

  3. 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.

  4. 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

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

    NASA Astrophysics Data System (ADS)

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

    2005-11-01

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

  6. 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.

  7. Multibody correlations in the hydrophobic solvation of glycine peptides

    SciTech Connect

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

    2014-12-14

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

  8. 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.

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

    PubMed

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

    2010-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Carlacci, Louis

    1998-03-01

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

  11. Differential geometry based solvation model I: Eulerian formulation

    PubMed Central

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

    2010-01-01

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

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

    PubMed

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

    2015-04-07

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

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

    SciTech Connect

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

    2007-09-11

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

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

    PubMed Central

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

    2005-01-01

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

  15. Comment on ``Analysis of optimal velocity model with explicit delay''

    NASA Astrophysics Data System (ADS)

    Davis, L. C.

    2002-09-01

    The effect of including an explicit delay time (due to driver reaction) on the optimal velocity model is studied. For a platoon of vehicles to avoid collisions, many-vehicle simulations demonstrate that delay times must be well below the critical delay time determined by a linear analysis for the response of a single vehicle. Safe platoons require rather small delay times, substantially smaller than typical reaction times of drivers. The present results do not support the conclusion of Bando et al. [M. Bando, K. Hasebe, K. Nakanishi, and A. Nakayama, Phys. Rev. E 58, 5429 (1998)] that explicit delay plays no essential role.

  16. Comment on "Analysis of optimal velocity model with explicit delay".

    PubMed

    Davis, L C

    2002-09-01

    The effect of including an explicit delay time (due to driver reaction) on the optimal velocity model is studied. For a platoon of vehicles to avoid collisions, many-vehicle simulations demonstrate that delay times must be well below the critical delay time determined by a linear analysis for the response of a single vehicle. Safe platoons require rather small delay times, substantially smaller than typical reaction times of drivers. The present results do not support the conclusion of Bando et al. [M. Bando, K. Hasebe, K. Nakanishi, and A. Nakayama, Phys. Rev. E 58, 5429 (1998)] that explicit delay plays no essential role.

  17. Interfacial solvation and excited state photophysical properties of 7-aminocoumarins at silica/liquid interfaces

    NASA Astrophysics Data System (ADS)

    Roy, Debjani

    The properties of solutes adsorbed at interfaces can be very different compared to bulk solution limits. This thesis examines how polar, hydrophilic silica surfaces and different solvents systematically change a solute's equilibrium and dynamic solvation environment at solid/liquid interfaces. The primary tools used in these studies are steady state fluorescence spectroscopy and time correlated single photon counting (TCSPC) --a fluorescence method capable resolving fluorescence emission on the picosecond timescale. To sample adsorbed solutes, TCSPC experiments were carried out in total internal reflection (TIR) geometry. These studies used total of six different 7-aminocoumarin dyes to isolate the effects of molecular and electronic structure on solute photophysical behavior. Fluorescence lifetimes measured in the TIR geometry are compared to the lifetimes of coumarins in bulk solution using different solvents to infer interfacial polarity and excited state solute conformation and dynamics. Steady state emission experiments measuring the behavior of the coumarins adsorbed at silica surfaces from bulk methanol solutions show that all coumarins had a similar affinity DeltaG ads ˜ - 25-30 kJ/mole. Despite these similar adsorption energetics solute structure had a very pronounced effect on the tendency of solutes to aggregate and form multilayers. Our finding suggests that hydrogen bonding donating properties of the silica surface plays a dominant role in determining the interfacial behavior of these solutes. The silica surface also had pronounced effects on the time dependent emission of some solutes. In particular, the strong hydrogen bond donating properties of the silica surface inhibit formation of a planar, charge transfer state through hydrogen bond donation to the solute's amine group. A consequence of this interaction is that the time dependent emission from solutes adsorbed at the surface appears to be more similar to emission from solutes in nonpolar

  18. Understanding the Role of Solvation Forces on the Preferential Attachment of Nanoparticles in Liquid

    SciTech Connect

    Welch, David A.; Woehl, Taylor J.; Park, Chiwoo; Faller, Roland; Evans, James E.; Browning, Nigel D.

    2016-01-20

    Optimization of colloidal nanoparticle synthesis techniques requires an understanding of underlying particle growth mechanisms. Non-classical growth mechanisms are particularly important as they affect nanoparticle size and shape distributions which in turn influence functional properties. For example, preferential attachment of nanoparticles is known to lead to the formation of mesocrystals, although the formation mechanism is currently not well understood. Here we employ in situ liquid cell scanning transmission electron microscopy (STEM) and steered molecular dynamics (SMD) simulations to demonstrate that the experimentally observed preference for end-to-end attachment of silver nanorods is a result of weaker solvation forces occurring at rod ends. SMD reveals that when the side of a nanorod approaches another rod, perturbation in the surface bound water at the nanorod surface creates significant energy barriers to attachment. Additionally, rod morphology (i.e. facet shape) effects can explain the majority of the side attachment effects that are observed experimentally.

  19. Understanding the Role of Solvation Forces on the Preferential Attachment of Nanoparticles in Liquid

    SciTech Connect

    Welch, David A.; Woehl, Taylor J.; Park, Chiwoo; Faller, Roland; Evans, James E.; Browning, Nigel D.

    2015-11-20

    We discuss optimization of colloidal nanoparticle synthesis techniques, which requires an understanding of underlying particle growth mechanisms. Nonclassical growth mechanisms are particularly important as they affect nanoparticle size and shape distributions, which in turn influence functional properties. For example, preferential attachment of nanoparticles is known to lead to the formation of mesocrystals, although the formation mechanism is currently not well-understood. Here we employ in situ liquid cell scanning transmission electron microscopy and steered molecular dynamics (SMD) simulations to demonstrate that the experimentally observed preference for end-to-end attachment of silver nanorods is a result of weaker solvation forces occurring at rod ends. In conclusion, SMD reveals that when the side of a nanorod approaches another rod, perturbation in the surface-bound water at the nanorod surface creates significant energy barriers to attachment. Additionally, rod morphology (i.e., facet shape) effects can explain the majority of the side attachment effects that are observed experimentally.

  20. Solvated calcium ions in charged silica nanopores

    NASA Astrophysics Data System (ADS)

    Bonnaud, Patrick A.; Coasne, Benoît; Pellenq, Roland J.-M.

    2012-08-01

    Hydroxyl surface density in porous silica drops down to nearly zero when the pH of the confined aqueous solution is greater than 10.5. To study such extreme conditions, we developed a model of slit silica nanopores where all the hydrogen atoms of the hydroxylated surface are removed and the negative charge of the resulting oxygen dangling bonds is compensated by Ca2+ counterions. We employed grand canonical Monte Carlo and molecular dynamics simulations to address how the Ca2+ counterions affect the thermodynamics, structure, and dynamics of confined water. While most of the Ca2+ counterions arrange themselves according to the so-called "Stern layer," no diffuse layer is observed. The presence of Ca2+ counterions affects the pore filling for strong confinement where the surface effects are large. At full loading, no significant changes are observed in the layering of the first two adsorbed water layers compared to nanopores with fully hydroxylated surfaces. However, the water structure and water orientational ordering with respect to the surface is much more disturbed. Due to the super hydrophilicity of the Ca2+-silica nanopores, water dynamics is slowed down and vicinal water molecules stick to the pore surface over longer times than in the case of hydroxylated silica surfaces. These findings, which suggest the breakdown of the linear Poisson-Boltzmann theory, provide important information about the properties of nanoconfined electrolytes upon extreme conditions where the surface charge and ion concentration are large.