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Sample records for explicit solvation effects

  1. Explicit solvation effects on the conventional resonance model for protonated imine, carbonyl, and thiocarbonyl compounds

    NASA Astrophysics Data System (ADS)

    Braïda, Benoît; Hiberty, Philippe C.

    The conventional resonance model describes carbonyls, imines, and thiocarbonyls, as well as their protonated analogues, by a superposition of two valence bond structures. Ab initio Breathing-Orbital Valence Bond computations on formaldehyde, formimine, and thioformaldehyde as well as their protonated forms are performed to directly quantify the weights of their valence bond structures. Following a gas phase study that showed that protonation significantly increases the weight of the carbenic form relative to the π polar-covalent bonded form (Braida, et al., Org Lett, 2008, 10, 1951), the present work estimates the influence of a polar protic solvent, modelized by water. Solvation effects are modeled explicitly by performing VB calculations on supersystems made of the organic substrate surrounded by four water molecules. It is shown that protonation significantly increases the polarity of the C=X π bond in all three cases (X = O, NH, S) in solvated phase, in line with the known acceleration of nucleophilic additions on these compounds by acidic catalysis. Moreover, solvation significantly enhances the polarity of the C=X π bond in the protonated forms of formaldehyde and thioformaldehyde, but has practically no effect on the C=X π bond of protonated formimine.

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    NASA Astrophysics Data System (ADS)

    Williams, Michael; Schwartz, Steven

    2015-03-01

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

  4. Solvation energies of the proton in ammonia explicitly versus temperature

    NASA Astrophysics Data System (ADS)

    Malloum, Alhadji; Fifen, Jean Jules; Dhaouadi, Zoubeida; Engo, Serge Guy Nana; Jaidane, Nejm-Eddine

    2017-04-01

    We provide in this work, the absolute solvation enthalpies and the absolute solvation free energies of the proton in ammonia explicitly versus temperature. As a result, the absolute solvation free energy of the proton remains quite constant for temperatures below 200 K. Above this temperature, it increases as a linear function of the temperature: Δ Ga m(H+,T ) =-1265.832 +0.210 T . This indicates that a temperature change of 100 K would induce a solvation free energy change of 21 kJ mol-1. Thus, ignoring this free energy change would lead to a bad description of hydrogen bonds and an unacceptable error higher than 3.7 pKa units. However, the absolute solvation enthalpy of the proton in ammonia is not significantly affected by a temperature change and, the room temperature value is -1217 kJ mol-1. The change of the solvation enthalpy is only within 3 kJ mol-1 for a temperature change up to 200 K.

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

    PubMed

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

    2015-11-28

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

  6. 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.

  7. 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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Arias, Tomas

    2015-03-01

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

  11. 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.

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

    PubMed

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

    2014-03-01

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

  13. 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.

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

    SciTech Connect

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

    2009-01-01

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

  15. Connecting Free Energy Surfaces in Implicit and Explicit Solvent: an Efficient Method to Compute Conformational and Solvation Free Energies

    PubMed Central

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

    2015-01-01

    The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions and protein-ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibration on rugged landscapes containing multiple basins separated by barriers. In many cases, implicit solvent models can be used to significantly speed up the conformational sampling; however, implicit solvent simulations do not fully capture the effects of a molecular solvent, and this can lead to loss of accuracy in the estimated free energies. Here we introduce a new approach to compute free energy changes in which the molecular details of explicit solvent simulations are retained while also taking advantage of the speed of the implicit solvent simulations. In this approach, the slow equilibration in explicit solvent, due to the long waiting times before barrier crossing, is avoided by using a thermodynamic cycle which connects the free energy basins in implicit solvent and explicit solvent using a localized decoupling scheme. We test this method by computing conformational free energy differences and solvation free energies of the model system alanine dipeptide in water. The free energy changes between basins in explicit solvent calculated using fully explicit solvent paths agree with the corresponding free energy differences obtained using the implicit/explicit thermodynamic cycle to within 0.3 kcal/mol out of ~3 kcal/mol at only ~8 % of the computational cost. We note that WHAM methods can be used to further improve the efficiency and accuracy of the explicit/implicit thermodynamic cycle. PMID:26236174

  16. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    USDA-ARS?s Scientific Manuscript database

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

  19. 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. (c) 2009 Elsevier Ltd. All rights reserved.

  20. 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.

  1. 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.

  2. Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics.

    PubMed

    Khuntawee, Wasinee; Kunaseth, Manaschai; Rungnim, Chompoonut; Intagorn, Suradej; Wolschann, Peter; Kungwan, Nawee; Rungrotmongkol, Thanyada; Hannongbua, Supot

    2017-04-24

    Large ring cyclodextrins have become increasingly important for drug delivery applications. In this work, we have performed replica-exchange molecular dynamics simulations using both implicit and explicit water solvation models to study the conformational diversity of iota-cyclodextrin containing 14 α-1,4 glycosidic linked d-glucopyranose units (CD14). The new quantifiable calculation methods are proposed to analyze the openness, bending, and twisted conformation of CD14 in terms of circularity, biplanar angle, and one-directional conformation (ODC). CD14 in GB implicit water model (Igb5) was found mostly in an opened conformation with average circularity of 0.39 ± 0.16 and a slight bend with average biplanar angle of 145.5 ± 16.0°. In contrast, CD14 in TIP3P explicit water solvation is significantly twisted with average circularity of 0.16 ± 0.10, while 29.1% are ODCs. In addition, classification of CD14 conformations using a Gaussian mixture model (GMM) shows that 85.0% of all CD14 in implicit water at 300 K correspond to the elliptical conformation, in contrast to 82.3% in twisted form in explicit water. GMM clustering also reveals minority conformations of CD14 such as the 8-shape, boat-form, and twisted conformations. This work provides fundamental insights into CD14 conformation, influence of solvation models, and also proposes new quantifiable analysis techniques for molecular conformation studies in the future.

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

    USDA-ARS?s Scientific Manuscript database

    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 ...

  4. Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation.

    PubMed

    Komeiji, Yuto; Ishikawa, Takeshi; Mochizuki, Yuji; Yamataka, Hiroshi; Nakano, Tatsuya

    2009-01-15

    Fragment Molecular Orbital based-Molecular Dynamics (FMO-MD, Komeiji et al., Chem Phys Lett 2003, 372, 342) is an ab initio MD method suitable for large molecular systems. Here, FMO-MD was implemented to conduct full quantum simulations of chemical reactions in explicit solvation. Several FMO-MD simulations were performed for a sphere of water to find a suitable simulation protocol. It was found that annealing of the initial configuration by a classical MD brought the subsequent FMO-MD trajectory to faster stabilization, and also that use of bond constraint in the FMO-MD heating stage effectively reduced the computation time. Then, the blue moon ensemble method (Sprik and Ciccotti, J Chem Phys 1998, 109, 7737) was implemented and was tested by calculating free energy profiles of the Menschutkin reaction (H3N + CH3Cl --> +H3NCH3 + Cl-) in the presence and absence of the solvent water via FMO-MD. The obtained free energy profiles were consistent with the Hammond postulate in that stabilization of the product by the solvent, namely hydration of Cl-, shifted the transition state to the reactant-side. Based on these FMO-MD results, plans for further improvement of the method are discussed. Copyright 2008 Wiley Periodicals, Inc.

  5. 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.

  6. Comparison of Implicit and Explicit Solvent Models for the Calculation of Solvation Free Energy in Organic Solvents.

    PubMed

    Zhang, Jin; Zhang, Haiyang; Wu, Tao; Wang, Qi; van der Spoel, David

    2017-03-14

    Quantitative prediction of physical properties of liquids is important for many applications. Computational methods based on either explicit or implicit solvent models can be used to approximate thermodynamics properties of liquids. Here, we evaluate the predictive power of implicit solvent models for solvation free energy of organic molecules in organic solvents. We compared the results calculated with four generalized Born (GB) models (GB(Still), GB(HCT), GB(OBC)I, and GB(OBC)II), the Poisson-Boltzmann (PB) model, and the density-based solvent model SMD with previous solvation free energy calculations (Zhang et al. J. Chem. Inf. 2015, 55, 1192-1201) and experimental data. The comparison indicates that both PB and GB give poor agreement with explicit solvent calculations and even worse agreement with experiments (root-mean-square deviation ≈ 15 kJ/mol). The main problem seems to be the prediction of the apolar contribution, which should include the solvent entropy. The quantum mechanical-based SMD model gives significantly better agreement with experimental data than do PB or GB, but it is not as good as explicit solvent calculation results. The dielectric constant ε of the solvent is found to be a powerful predictor for the polar contribution to the free energy in implicit models; however, the Onsager relation may not hold for realistic solvent, as suggested by explicit solvent and SMD calculations. From the comparison, we also find that with an optimization of the apolar contribution, the PB model gives slightly better agreement with experiments than the SMD model, whereas the correlation between the optimized GB models and experiments remains poor. Further optimization of the apolar contribution is needed for GB models to be able to treat solvents other than water.

  7. 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.

  8. Solvation effects on like-charge attraction.

    PubMed

    Ghanbarian, Shahzad; Rottler, Jörg

    2013-02-28

    We present results of molecular dynamics simulations of the electrostatic interaction between two parallel charged rods in the presence of divalent counterions. Such polyelectrolytes have been considered as a simple model for understanding electrostatic interactions in highly charged biomolecules such as DNA. Since there are correlations between the free charge carriers, the phenomenon of like charge attraction appears for specific parameters. We explore the role of solvation effects and the resulting deviations from Coulomb's law on the nanoscale on this peculiar phenomenon. The behavior of the force between the charged rods in a simulation with atomistic representation of water molecules is completely different from a model in which water is modeled as a continuum dielectric. By calculating counterion-rodion pair correlation functions, we find that the presence of water molecules changes the structure of the counterion cloud and results in both qualitative and quantitative changes of the force between highly charged polyelectrolytes.

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

    PubMed

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

    2010-03-04

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

  10. 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.

  11. 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.

  12. Explicit consideration of spatial hydrogen bonding direction for activity coefficient prediction based on implicit solvation calculations.

    PubMed

    Chen, Wei-Lin; Lin, Shiang-Tai

    2017-08-09

    The activity coefficient of a chemical in a mixture is important in understanding the thermodynamic properties and non-ideality of the mixture. The COSMO-SAC model based on the result of quantum mechanical implicit solvation calculations has been shown to provide reliable predictions of activity coefficients for mixed fluids. However, it is found that the prediction accuracy is in general inferior for associating fluids. Existing methods for describing the hydrogen-bonding interaction consider the strength of the interaction based only on the polarity of the screening charges, neglecting the fact that the formation of hydrogen bonds requires a specific orientation between the donor and acceptor pairs. In this work, we propose a new approach that takes into account the spatial orientational constraints in hydrogen bonds. Based on the Valence Shell Electron Pair Repulsion (VSEPR) theory, the molecular surfaces associated with the formation of hydrogen bonds are limited to those in the projection of the lone pair electrons of hydrogen bond acceptors, in addition to the polarity of the surface screening charges. Our results show that this new directional hydrogen bond approach, denoted as the COSMO-SAC(DHB) model, requires fewer universal parameters and is significantly more accurate and reliable compared to previous models for a variety of properties, including vapor-liquid equilibria (VLE), infinite dilution activity coefficient (IDAC) and water-octanol partition coefficient (Kow).

  13. Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

    PubMed Central

    2008-01-01

    Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular structure, to influence on biomolecular dynamics, to key physiological influence on homeostasis and signaling. To properly model ionic interaction and stability in atomistic simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model or representation of the monovalent ions is critically necessary. A good model needs to simultaneously reproduce many properties of ions, including their structure, dynamics, solvation, and moreover both the interactions of these ions with each other in the crystal and in solution and the interactions of ions with other molecules. At present, the best force fields for biomolecules employ a simple additive, nonpolarizable, and pairwise potential for atomic interaction. In this work, we describe our efforts to build better models of the monovalent ions within the pairwise Coulombic and 6-12 Lennard-Jones framework, where the models are tuned to balance crystal and solution properties in Ewald simulations with specific choices of well-known water models. Although it has been clearly demonstrated that truly accurate treatments of ions will require inclusion of nonadditivity and polarizability (particularly with the anions) and ultimately even a quantum mechanical treatment, our goal was to simply push the limits of the additive treatments to see if a balanced model could be created. The applied methodology is general and can be extended to other ions and to polarizable force-field models. Our starting point centered on observations from long simulations of biomolecules in salt solution with the AMBER force fields where salt crystals formed well below their solubility limit. The likely cause of the artifact in the AMBER parameters relates to the naive mixing of the Smith and Dang chloride parameters with AMBER

  14. Solvation effects on the structure and reactivity of clusters

    SciTech Connect

    Castleman, A.W. Jr.

    1991-12-31

    Elucidating from a molecular point of view, the differences and similarities in the properties and reactivity of matter in the gaseous compared to the condensed state is a subject of considerable current interest. Although there are a number of promising approaches to this problem, one of the alternatives involves the use of clusters that enable detailed spectroscopy and reactivity investigations to be accomplished as a function of degree of solvation under well controlled conditions. New insight into a variety of phenomena of interest in liquids have been derived from recent studies. In particular, the findings have contributed to unraveling the reactions of ionized functional groups in organic molecules that are influenced by solvation effects, identifying the structure of protonated complexes among species of varying proton affinities, and quantifying the variations in spectroscopic properties of chromophores as influenced by solvation and aggregation. Various examples from the author`s laboratory are discussed, including solvation-driven reactions as well as alcohol and acetone dehydration reactions, the influence of clustering on the reaction of OH{sup {minus}} with CO{sub 2}, structures of protonated species comprised of water, ammonia, and trimethylamine; also presented are the results of studies of the influence of solvation on the absorption of photons in the chromophore of tyrosine, namely phenol.

  15. An improved coarse-grained model of solvation and the hydrophobic effect

    PubMed Central

    Varilly, Patrick; Patel, Amish J.; Chandler, David

    2011-01-01

    We present a coarse-grained lattice model of solvation thermodynamics and the hydrophobic effect that implements the ideas of Lum–Chandler–Weeks theory [J. Phys. Chem. B 134, 4570 (1999)] and improves upon previous lattice models based on it. Through comparison with molecular simulation, we show that our model captures the length-scale and curvature dependence of solvation free energies with near-quantitative accuracy and 2–3 orders of magnitude less computational effort, and further, correctly describes the large but rare solvent fluctuations that are involved in dewetting, vapor tube formation, and hydrophobic assembly. Our model is intermediate in detail and complexity between implicit-solvent models and explicit-water simulations. PMID:21341830

  16. 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

  17. 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

  18. 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

  19. Effect of processing on Celecoxib and its solvates.

    PubMed

    Chawla, Garima; Bansal, Arvind K

    2004-11-01

    Pharmaceuticals mostly exist in crystalline form and exhibit the phenomenon of differential crystal packing and configurational arrangements of molecules, called polymorphism. Pharmaceutical processing by introducing significant amount of stress alters the molecular interactions in the system engendering polymorphic transformations. The energy supplied by these processing steps tends to overcome the energy barriers between different solid-state forms, thus yielding undesirable changes in the physicochemical and material characteristics of drugs or their dosage forms. Therefore, the role of these unit processes in solid-state transformations must be cautiously studied and if required appropriate controls should be used to monitor such events. The present study was aimed at studying the effect of major energy imparting pharmaceutical unit processes, like size reduction, wet granulation, consolidation, and compression on solid-state transformation of Celecoxib, a selective cyclooxygenase-II inhibitor and its N,N-dimethyl acetamide and N,N-dimethyl formamide solvated forms. A qualitative estimation of crystal transformation in processed samples was performed using DSC, microscopy, FTIR spectroscopy, and XRPD. FTIR was also applied for the development of a quantification method to find the percentage of transformation in N,N-dimethyl acetamide solvated form during compression.

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

    PubMed

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

    2014-09-25

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

  1. Solvation of chromone using combined Discrete/SCRF models

    NASA Astrophysics Data System (ADS)

    Alemán, Carlos; Galembeck, Sergio E.

    1998-06-01

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

  2. 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

  3. Age effects on explicit and implicit memory

    PubMed Central

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

    2013-01-01

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

  4. Age effects on explicit and implicit memory.

    PubMed

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

    2013-01-01

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

  5. 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.

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

    ERIC Educational Resources Information Center

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

    2014-01-01

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

  7. 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.

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

    DOE PAGES

    See, Kimberly A.; Wu, Heng -Liang; Lau, Kah Chun; ...

    2016-11-16

    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 bemore » 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. Furthermore, 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.« less

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

    SciTech Connect

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

    2016-11-16

    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. Furthermore, 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.

  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. 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.

  12. 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.

  13. Environmental context effects in conceptual explicit and implicit memory.

    PubMed

    Parker, Andrew; Dagnall, Neil; Coyle, Anne-Marie

    2007-05-01

    Previous research has found environmental context effects for both conceptual explicit and conceptual implicit memory (Parker, Gellatly, & Waterman, 1999). The research presented here challenges these findings on methodological grounds. Experiment 1 assessed the effects of context change on category-exemplar generation (conceptual implicit memory test) and category-cued recall (conceptual explicit memory test). Experiment 2 assessed the effects of context change on word association (conceptual implicit memory test) and word associate cued recall (conceptual explicit memory test). In both experiments, study-test changes in environmental context were found to influence performance only on tests of explicit memory. It is concluded that when retrieval cues across explicit and implicit tests are matched, and the probability of explicit contamination is reduced, then only conceptual explicit test performance is reduced by study-test changes in environmental context.

  14. 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.

  15. The effect of solvation on vertical ionization energy of thymine: from microhydration to bulk

    PubMed Central

    Ghosh, Debashree; Isayev, Olexandr; Slipchenko, Lyudmila V.; Krylov, Anna I.

    2011-01-01

    The effect of hydration on the vertical ionization energy (VIE) of thymine was characterized using equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods. We considered several microsolvated clusters as well as thymine solvated in bulk water. The VIE in bulk water was computed by averaging over solvent-solute configurations obtained from equilibrium MD trajectories at 300 K. The effect of microsolvation was analyzed and contrasted against the combined effect of the first solvation shell in bulk water. Microsolvation reduces the ionization energy (IE) by about 0.1 eV per water molecule while the first solvation shell increases the IE by 0.1 eV. The subsequent solvation lowers the IE, and the bulk value of the solvent-induced shift of thymine’s VIE is approximately −0.9 eV. The combined effect of the first solvation shell was explained in terms of specific solute-solvent interactions, which were investigated using model geometries. The convergence of IE to the bulk value requires the hydration sphere of approximately 13.5 Å radius. The performance of the EOM-IP-CCSD/EFP scheme was benchmarked against full EOM-IP-CCSD using microhydrated structures. The errors were found to be less than 0.01–0.02 eV. The relative importance of the polarization and higher multipole moments in EFP model was also investigated. PMID:21500795

  16. 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.

  17. 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.

  18. 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

  19. 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…

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

    ERIC Educational Resources Information Center

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

    2016-01-01

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

  1. 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.

  2. 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

  3. 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.

  4. Effects of subtle and explicit health messages on food choice.

    PubMed

    Wagner, Heather Scherschel; Howland, Maryhope; Mann, Traci

    2015-01-01

    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. 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. 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. Subtle messages may be more useful than explicit health messages in encouraging individuals to make a healthy snack choice.

  5. 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.

  6. A quantum molecular dynamics study of aqueous solvation dynamics

    NASA Astrophysics Data System (ADS)

    Videla, Pablo E.; Rossky, Peter J.; Laria, D.

    2013-10-01

    Ring polymer molecular dynamics experiments have been carried out to examine effects derived from nuclear quantum fluctuations at ambient conditions on equilibrium and non-equilibrium dynamical characteristics of charge solvation by a popular simple, rigid, water model, SPC/E, and for a more recent, and flexible, q-TIP4P/F model, to examine the generality of conclusions. In particular, we have recorded the relaxation of the solvent energy gap following instantaneous, ±e charge jumps in an initially uncharged Lennard-Jones-like solute. In both charge cases, quantum effects are reflected in sharper decays at the initial stages of the relaxation, which produce up to a ˜20% reduction in the characteristic timescales describing the solvation processes. For anionic solvation, the magnitude of polarization fluctuations controlling the extent of the water proton localization in the first solvation shell is somewhat more marked than for cations, bringing the quantum solvation process closer to the classical case. Effects on the solvation response from the explicit incorporation of flexibility in the water Hamiltonian are also examined. Predictions from linear response theories for the overall relaxation profile and for the corresponding characteristic timescales are reasonably accurate for the solvation of cations, whereas we find that they are much less satisfactory for the anionic case.

  7. 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.

  8. 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

  9. 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.

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

    PubMed Central

    England, Jeremy L.; Haran, Gilad

    2011-01-01

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

  11. Investigation of Solvation Effects on Optical Rotatory Dispersion Using the Polarizable Continuum Model

    NASA Astrophysics Data System (ADS)

    Aharon, Tal; Lemler, Paul M.; Vaccaro, Patrick; Caricato, Marco

    2017-06-01

    The Optical Rotatory Dispersion (ORD) of a chiral solute is heavily affected by solvation, but this effect does not follow the usual correlation with the solvent polarity, i.e., larger solvent polarity does not imply a larger change in the solute's property. Therefore, a great deal of experimental and theoretical effort has been directed towards correlating the solvation effect on the ORD and the solvent properties. This discovery followed from the development of cavity ring down polarimetry (CRPD), which allows measurements of gas-phase ORD. In order to investigate this phenomenon, we chose a set of five rigid molecules to limit the effect of molecular vibrations and isolate the role of solvation. The latter was investigated with the Polarizable Continuum Model (PCM), and compared to experimental results. We used Bondi radii to build the PCM cavity, and performed extensive calculations at multiple frequencies using density functional theory (DFT) with two functionals: B3LYP and CAM-B3LYP, together with the aug-cc-pVDZ basis set. We also performed coupled cluster singles and doubles (CCSD/aug-cc-pVDZ) calculations at the wavelengths where gas-phase data are available, all of which are augmented with zero point vibrational corrections. These results are compared to experimental data and seem to indicate that PCM does not entirely account for the environmental effects on the ORD.

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

    PubMed Central

    Kalyuzhnyi, Yuriy V.; Vlachy, Vojko

    2016-01-01

    Effects of addition of salts on stability of aqueous protein solutions are studied theoretically and the results are compared with experimental data. In our approach, all the interacting species, proteins, ions, and water molecules, are accounted for explicitly. Water molecules are modeled as hard spheres with four off-center attractive square-well sites. These sites serve to bind either another water or to solvate the ions or protein charges. The ions are represented as charged hard spheres, and decorated by attractive sites to allow solvation. Spherical proteins simultaneously possess positive and negative groups, represented by charged hard spheres, attached to the surface of the protein. The attractive square-well sites, mimicking the protein–protein van der Waals interaction, are located on the surface of the protein. To obtain numerical results, we utilized the energy route of Wertheim’s associative mean spherical approximation. From measurable properties, we choose to calculate the second virial coefficient B2, which is closely related to the tendency of proteins to aggregate and eventually crystalize. Calculations are in agreement with experimental trends: (i) For low concentration of added salt, the alkali halide salts follow the inverse Hofmeister series. (ii) At higher concentration of added salt, the trend is reversed. (iii) When cations are varied, the salts follow the direct Hofmeister series. (iv) In contrast to the colloidal theories, our approach correctly predicts the non-monotonic behavior of B2 upon addition of salts. (v) With respect to anions, the theory predicts for the B2 values to follow different sequences below and above the iso-ionic point, as also confirmed experimentally. (vi) A semi-quantitative agreement between measured and calculated values for the second virial coefficient, as functions of pH of solution and added salt type and concentration, is obtained. PMID:27276970

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

    NASA Astrophysics Data System (ADS)

    Kalyuzhnyi, Yuriy V.; Vlachy, Vojko

    2016-06-01

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

  14. 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.

  15. Moderating Effects of Mathematics Anxiety on the Effectiveness of Explicit Timing

    ERIC Educational Resources Information Center

    Grays, Sharnita D.; Rhymer, Katrina N.; Swartzmiller, Melissa D.

    2017-01-01

    Explicit timing is an empirically validated intervention to increase problem completion rates by exposing individuals to a stopwatch and explicitly telling them of the time limit for the assignment. Though explicit timing has proven to be effective for groups of students, some students may not respond well to explicit timing based on factors such…

  16. The Effects of Explicit Visual Cues in Reading Biological Diagrams

    ERIC Educational Resources Information Center

    Ge, Yun-Ping; Unsworth, Len; Wang, Kuo-Hua

    2017-01-01

    Drawing on cognitive theories, this study intends to investigate the effects of explicit visual cues which have been proposed as a critical factor in facilitating understanding of biological images. Three diagrams from Taiwanese textbooks with implicit visual cues, involving the concepts of biological classification systems, fish taxonomy, and…

  17. 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.

  18. Effect of C60 adducts on the dynamic structure of aromatic solvation shells

    NASA Astrophysics Data System (ADS)

    Peerless, James S.; Bowers, G. Hunter; Kwansa, Albert L.; Yingling, Yaroslava G.

    2017-06-01

    We report herein on the use of all-atom molecular dynamics simulations to investigate the solvation environment of C60 and four C60-derived fullerenes immersed in a variety of aromatic solvents. Utilizing a recently developed solvation shell analysis technique that quantifies the spatial relationships between fullerenes and solvent on a molecular level, we show that the number of fullerene substituents and solvent chemistry are crucial determinants of the solvation shell structure and thus fullerene solvation behavior. Specifically, it is shown for the derivatives investigated that the number of fullerene substituents is more critical to solvation behavior than the substituent chemistry.

  19. 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

  20. 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.

  1. 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

  2. Effect of Polymethylene Spacer of Cationic Gemini Surfactants on Solvation Dynamics and Rotational Relaxation of Coumarin 153 in Aqueous Micelles.

    PubMed

    Sonu; Kumari, Sunita; Saha, Subit K

    2015-07-30

    The present work demonstrates the solvation dynamics and rotational relaxation of Coumarin 153 (C-153) in the micelles of a series of cationic gemini surfactants, 12-s-12, 2Br(-) containing a hydrophobic polymethylene spacer with s = 3, 4, 6, 8, 12. Steady-state and time-correlated single-photon counting (TCSPC) fluorescence spectroscopic techniques have been used to carry out this study. Steady-state and TCSPC fluorescence data suggest that C-153 molecules are located at the Stern layer of micelles. While probe molecules feel more or less the same micropolarity in the micellar phase, the microviscosity of micelles decreases with spacer chain length. Solvation dynamics at the Stern layer is bimodal in nature with fast solvation as a major component. Counter ions and water molecules bonded with the polar headgroups of surfactant molecules are responsible for the slow component. Average solvation time increases with spacer chain length because of the increased degree of counter ion dissociation. Some water molecules are involved in the solvation of counter ions themselves, resulting in the decrease in "free" water molecules to be available for the solvation of C-153. The hydrophobic spacer chain also has an effect on increasing the solvation time with increasing chain length. The average rotational relaxation time for C-153 decreases with spacer chain length with a rapid decrease at s > 4. The anisotropy decay of C-153 in micelles is biexponential in nature. The slow rotational relaxation is due to the lateral diffusion of C-153 in micelles. Lateral diffusion is much faster than the rotational motion of a micelle as a whole. The rotational motion of the micelle as a whole becomes faster with the decreasing size of micelles.

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  16. 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.

  17. 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.

  18. The Effect of Solvation on Electron Attachment to Pure and Hydrated Pyrimidine Clusters†

    PubMed Central

    Neustetter, Michael; Aysina, Julia

    2015-01-01

    Abstract The interaction of low‐energy electrons with biomolecules plays an important role in the radiation‐induced alteration of biological tissue at the molecular level. At electron energies below 15 eV, dissociative electron attachment is one of the most important processes in terms of the chemical transformation of molecules. So far, a common approach to study processes at the molecular level has been to carry out investigations with single biomolecular building blocks like pyrimidine as model molecules. Electron attachment to single pyrimidine, as well as to pure clusters and hydrated clusters, was investigated in this study. In striking contrast to the situation with isolated molecules and hydrated clusters, where no anionic monomer is detectable, we were able to observe the molecular anion for the pure clusters. Furthermore, there is evidence that solvation effectively prevents the ring fragmentation of pyrimidine after electron capture. PMID:26110285

  19. Effects of explicit atmospheric convection at high CO2.

    PubMed

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

    2014-07-29

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

  20. 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

  1. The recency effect: implicit learning with explicit retrieval?

    PubMed

    Baddeley, A D; Hitch, G

    1993-03-01

    The recency effect in free recall features prominently in 1960s' theorizing about short-term memory, but has since been largely ignored. We argue that this stems from a preoccupation with the role of recency in the concept of primary memory and the neglect of its role in a broader working-memory framework. It is suggested that the recency effect reflects the application of an explicit retrieval strategy to the residue of implicit learning within a range of cognitive systems. When retrieved implicitly, the same residue is assumed to form the basis of priming effects. The various criteria for implicit learning described by Tulving and Schacter (1990) are successfully applied to the recency effect, and a retrieval process is outlined that can account for both long- and short-term recency effects. It is suggested that a framework combining recency, priming, and implicit learning provides a basis for understanding one of the most important features of cognition and memory, namely, that of maintaining orientation in time and place.

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

    NASA Astrophysics Data System (ADS)

    Limmer, Krista; Williams, Kristen; Andzelm, Jan

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

  3. Effect of Higher Order Solvation and Temperature on SN2 and E2 Reactivity (Postprint)

    DTIC Science & Technology

    2014-07-05

    Theoretical work has suggested that increasing the solvation of the reactant ion for a reaction that has competing pathways will stabilize the SN2...activation energy of both pathways with increasing solvation, but preferentially stabilizing the SN2 transition state at a lower energy than that of the E2...low temperature. For instance association may occur at levels significantly above the trace detected. This stabilized complex F(CH3OH)2(RBr) can then

  4. [Implicit and explicit effects of frequency on judgments of recency].

    PubMed

    Yano, Madoka

    2010-02-01

    There is general agreement that repetition enhances various kinds of memory performance, but it remains unclear how repetition of identical items affects judgments of recency (JOR). The present study examined implicit repetition effects on JOR and the relationship between JOR and explicit judgments of frequency (JOF). Participants learned three lists consisting of 13 items, some of which were repeated from once to four times, and after learning each list, they judged how many times each list item was presented. Only after learning all three lists, participants could recognize the number of lists, and were asked to perform a temporal list discrimination task. The results showed that there was no significant effect of repetition on the accuracy of list discrimination but the response times for the most frequent items were significantly shorter. The results also showed a significant positive correlation between the accuracy of list discrimination and of JOF. These results suggest that higher frequency does not improve the accuracy of JOR, but intensifies the sense of easiness for the judgments, and that the ability to judge frequency contributes to JOR.

  5. 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

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

    PubMed Central

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

    2013-01-01

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

  7. Anion solvation in alcohols

    SciTech Connect

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

    1996-03-01

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

  8. 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.

  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. Solvation models: theory and validation.

    PubMed

    Purisima, Enrico O; Sulea, Traian

    2014-01-01

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

  12. A Monte Carlo simulation study of the solvent effect on the relative free energies of solvation and the partition coefficients of organic solutes

    NASA Astrophysics Data System (ADS)

    Kim, Hag-Sung

    2000-02-01

    A study of Monte Carlo simulations (MCS) with statistical perturbation theory has been carried out to investigate the solvent effects on the relative free energies of solvation and the difference in partition coefficients (log P) for two solutes mutated to each other. It is proved that three or five MCS using doublewide sampling are necessary for obtaining results with enough precision and fluid simulations are required in which pyrazine is mutated to pyridine in several solvents. The computed results are compared with the previous published relative free energies of solvation and Δ log P data. For the present solute pairs, the solvent permittivity and the differences of solvation dominate the differences in the relative free energies of solvation and partition coefficients.

  13. 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.

  14. Predicting Cumulative Watershed Effects using Spatially Explicit Models

    NASA Astrophysics Data System (ADS)

    MacDonald, L. H.; Litschert, S.

    2004-12-01

    Cumulative watershed effects /(CWEs/) result from the combined effects of land disturbances distributed over both space and time. They are of concern because changes in flow and sediment yields can adversely affect aquatic habitat, channel morphology, water yields, and water quality. The assessment procedures currently used by agencies such as the U.S. Forest Service generally rely on a lumped approach to quantify disturbance, despite the widespread recognition that site conditions and location do matter! The overall goal of our work is to develop spatially-explicit models to quantify changes in flow and sediment yields. Key objectives include: use of readily available GIS data; ease of use for resource managers with minimal GIS experience; modularity so that models can be added or updated; and allowing users to select the models and values for key parameters. The DeltaQ model calculates changes in peak, median, and low flows due to forest management activities and fires. Inputs include GIS data with disturbance polygons, an initial change in flow rate, and the time to recovery. Data from paired watershed studies are provided to help guide the user. The initial version of FORest Erosion Simulation Tools /(FOREST/) calculates sediment production from forest harvest, fires, and unpaved roads. Additional modules are being developed to deliver this sediment to the stream channel and route it to downstream locations. In accordance with our objectives, the user can predict sediment production rates using different empirical equations, assign an initial sediment production rate and a specified linear recovery period, or develop a look-up table based on local knowledge, published values, or data from other models such as WEPP. The required GIS layers vary according to the model/(s/) selected, but generally include past disturbances /(e.g., fires and timber harvest/), roads, and elevation. Outputs include GIS layers and text files that can be subjected to additional

  15. 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.

  16. 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.

  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. 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.

  19. 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

  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. 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.

  3. The Effects of Peer Influences and Implicit and Explicit Attitudes on Smoking Initiation in Adolescence

    ERIC Educational Resources Information Center

    Bountress, Kaitlin; Chassin, Laurie; Presson, Clark C.; Jackson, Corrie

    2016-01-01

    Using participants from an 1-and-1/2-year longitudinal study of smoking socialization (N = 709), we examined peer smoking, and implicit and explicit attitudes on smoking initiation among initial nonsmoking adolescents. We also tested whether implicit and explicit attitudes mediated the effect of peer smoking on smoking initiation, and whether…

  4. 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…

  5. 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…

  6. 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…

  7. Thiolated gold nanoparticle solvation in near-critical fluids: The role of density, temperature, and topology

    NASA Astrophysics Data System (ADS)

    Yadav, Hari O. S.; Chakravarty, Charusita

    2017-05-01

    We employ molecular dynamics simulations to study the structure and solvation thermodynamics of thiolated gold nanoparticles of size 1.2 and 1.6 nm with ligand of chain length 8-16 carbons in ethane and propane over a wide range of densities close to the critical isotherm. The Helmholtz free energy is estimated by explicitly calculating the change in entropy and internal energy of solvation, and the effect of density and temperature on fluctuation-driven inherent anisotropy in the ligand corona is characterized. Since the topological variation further accentuates this instantaneous asymmetry in the ligand cloud, the anisotropy with varying surface coverage and chain length is also studied including the solvent contributions to the entropic and energetic metrics. Our results are consistent with the experiment, suggesting a route of obtaining structural insights into solvation thermodynamics that could be useful for understanding the stability of nanoparticle dispersions.

  8. Thiolated gold nanoparticle solvation in near-critical fluids: The role of density, temperature, and topology.

    PubMed

    Yadav, Hari O S; Chakravarty, Charusita

    2017-05-07

    We employ molecular dynamics simulations to study the structure and solvation thermodynamics of thiolated gold nanoparticles of size 1.2 and 1.6 nm with ligand of chain length 8-16 carbons in ethane and propane over a wide range of densities close to the critical isotherm. The Helmholtz free energy is estimated by explicitly calculating the change in entropy and internal energy of solvation, and the effect of density and temperature on fluctuation-driven inherent anisotropy in the ligand corona is characterized. Since the topological variation further accentuates this instantaneous asymmetry in the ligand cloud, the anisotropy with varying surface coverage and chain length is also studied including the solvent contributions to the entropic and energetic metrics. Our results are consistent with the experiment, suggesting a route of obtaining structural insights into solvation thermodynamics that could be useful for understanding the stability of nanoparticle dispersions.

  9. Like-charge attraction of molecular cations in water: subtle balance between interionic interactions and ionic solvation effect.

    PubMed

    Inagaki, Taichi; Aono, Shinji; Nakano, Hiroshi; Yamamoto, Takeshi

    2014-05-22

    Despite strong electrostatic repulsion, like-charged ions in aqueous solution can effectively attract each other via ion-water interactions. In this paper we investigate such an effective interaction of like-charged ions in water by using the 3D-RISM-SCF method (i.e., electronic structure theory combined with three-dimensional integral equation theory for molecular solvents). Free energy profiles are calculated at the CCSD(T) level for a series of molecular ions including guanidinium (Gdm(+)), alkyl-substituted ammonium, and aromatic amine cations. Polarizable continuum model (PCM) and mean-field QM/MM free energy calculations are also performed for comparison. The results show that the stability of like-charged ion pairs in aqueous solution is determined by a very subtle balance between interionic interactions (including dispersion and π-stacking interactions) and ionic solvation/hydrophobic effects and that the Gdm(+) ion has a rather favorable character for like-charge association among all the cations studied. Furthermore, we investigate the like-charge pairing in Arg-Ala-Arg and Lys-Ala-Lys tripeptides in water and show that the Arg-Arg pair has a contact free-energy minimum of about -6 kcal/mol. This result indicates that arginine pairing observed on protein surfaces and interfaces is stabilized considerably by solvation effects.

  10. 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

  11. 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".

  12. 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…

  13. 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…

  14. 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

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

    PubMed

    Qiao, Yu; Tu, Bin; Lu, Benzhuo

    2014-05-07

    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

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

    PubMed

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

    2006-12-13

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

  17. Effects of context on implicit and explicit lexical knowledge: an event-related potential study.

    PubMed

    Choi, Sungmook; Kim, Jingu; Ryu, Kwangmin

    2014-10-01

    Although much is known about how contextualized and decontextualized learning affects explicit lexical knowledge, how these learning conditions contribute to implicit lexical knowledge remains unclear. To address this problem, Korean high school students were instructed to learn 30 English words by reading meaningful passages (i.e., in context) and another 30 English words using a wordlist (i.e., out of context). Five weeks later, implicit lexical knowledge was gauged by reaction time and the N400 event-related brain potential component, and explicit lexical knowledge was assessed with an explicit behavioral measure. Results showed that neither learning type was superior to the other in terms of implicit lexical knowledge acquisition, whereas learning words out of context was more effective than learning words in context for establishing explicit lexical knowledge. These results suggest that the presence or absence of context may lead to dissociation in the development of implicit and explicit lexical knowledge. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. 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.

  19. 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)

  20. 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)

  1. 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.

  2. 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.

  3. Biomolecular electrostatics and solvation: a computational perspective

    SciTech Connect

    Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G.; Schnieders, Michael; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A.

    2012-11-01

    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 summarize the common characteristics of biomolecular solvation (e.g., solvent structure, polarization, ion binding, and nonpolar behavior) in order to provide reasonable backgrounds to understand the solvation models.

  4. 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.

  5. 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

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

    PubMed

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

    2017-03-27

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

  7. 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

  8. Explicit inclusion of electronic correlation effects in molecular dynamics

    NASA Astrophysics Data System (ADS)

    Julien, Jean-Pierre; Kress, Joel D.; Zhu, Jian-Xin

    2017-07-01

    We design a quantum molecular dynamics method for strongly correlated electron metals. The strong electronic correlation effects are treated within a real-space version of the Gutzwiller variational approximation (GA), which is suitable for the inhomogeneity inherent in the process of quantum molecular dynamics (MD) simulations. We also propose an efficient algorithm based on the second-moment approximation to the electronic density of states for the search of the optimal variation parameters, from which the renormalized interatomic MD potentials are fully determined. By considering a minimal one-correlated-orbital Anderson model with parameterized spatial dependence of tight-binding hopping integrals, this fast GA-MD method is benchmarked with that using exact diagonalization to solve the GA variational parameters. The efficiency and accuracy are illustrated. We have demonstrated the effect of temperature coupled with electronic correlation on structural properties simulated with MD. This method will open up an unprecedented opportunity enabling large-scale quantum MD simulations of strongly correlated electronic materials.

  9. 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.

  10. 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.

  11. Effects of aging and dopamine genotypes on the emergence of explicit memory during sequence learning.

    PubMed

    Schuck, Nicolas W; Frensch, Peter A; Schjeide, Brit-Maren M; Schröder, Julia; Bertram, Lars; Li, Shu-Chen

    2013-11-01

    The striatum and medial temporal lobe play important roles in implicit and explicit memory, respectively. Furthermore, recent studies have linked striatal dopamine modulation to both implicit as well as explicit sequence learning and suggested a potential role of the striatum in the emergence of explicit memory during sequence learning. With respect to aging, previous findings indicated that implicit memory is less impaired than explicit memory in older adults and that genetic effects on cognition are magnified by aging. To understand the links between these findings, we investigated effects of aging and genotypes relevant for striatal dopamine on the implicit and explicit components of sequence learning. Reaction time (RT) and error data from 80 younger (20-30 years) and 70 older adults (60-71 years) during a serial reaction time task showed that age differences in learning-related reduction of RTs emerged gradually over the course of learning. Verbal recall and measures derived from the process-dissociation procedure revealed that younger adults acquired more explicit memory about the sequence than older adults, potentially causing age differences in RT gains in later stages of learning. Of specific interest, polymorphisms of the dopamine- and cAMP-regulated neuronal phosphoprotein (DARPP-32, rs907094) and dopamine transporter (DAT, VNTR) genes showed interactive effects on overall RTs and verbal recall of the sequence in older but not in younger adults. Together our findings show that variations in genotypes relevant for dopamine functions are associated more with aging-related impairments in the explicit than the implicit component of sequence learning, providing support for theories emphasizing the role of dopaminergic modulation in cognitive aging and the magnification of genetic effects in human aging. © 2013 Elsevier Ltd. All rights reserved.

  12. 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

  13. 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.

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

    PubMed

    Frolov, Andrey I; Kiselev, Michael G

    2014-10-09

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

  15. 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…

  16. 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…

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

    NASA Astrophysics Data System (ADS)

    Lemler, Paul M.; Vaccaro, Patrick

    2016-06-01

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

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

    PubMed

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

    2013-09-12

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

  19. 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…

  20. 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.,…

  1. Emotion effects on implicit and explicit musical memory in normal aging.

    PubMed

    Narme, Pauline; Peretz, Isabelle; Strub, Marie-Laure; Ergis, Anne-Marie

    2016-12-01

    Normal aging affects explicit memory while leaving implicit memory relatively spared. Normal aging also modifies how emotions are processed and experienced, with increasing evidence that older adults (OAs) focus more on positive information than younger adults (YAs). The aim of the present study was to investigate how age-related changes in emotion processing influence explicit and implicit memory. We used emotional melodies that differed in terms of valence (positive or negative) and arousal (high or low). Implicit memory was assessed with a preference task exploiting exposure effects, and explicit memory with a recognition task. Results indicated that effects of valence and arousal interacted to modulate both implicit and explicit memory in YAs. In OAs, recognition was poorer than in YAs; however, recognition of positive and high-arousal (happy) studied melodies was comparable. Insofar as socioemotional selectivity theory (SST) predicts a preservation of the recognition of positive information, our findings are not fully consistent with the extension of this theory to positive melodies since recognition of low-arousal (peaceful) studied melodies was poorer in OAs. In the preference task, YAs showed stronger exposure effects than OAs, suggesting an age-related decline of implicit memory. This impairment is smaller than the one observed for explicit memory (recognition), extending to the musical domain the dissociation between explicit memory decline and implicit memory relative preservation in aging. Finally, the disproportionate preference for positive material seen in OAs did not translate into stronger exposure effects for positive material suggesting no age-related emotional bias in implicit memory. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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

  8. 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.

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

    PubMed

    French, Robert M; Thomas, Elizabeth

    2015-04-01

    David Marr's (1982) three-level analysis of computational cognition argues for three distinct levels of cognitive information processing-namely, the computational, representational, and implementational levels. But Marr's levels are-and were meant to be-descriptive, rather than interactive and dynamic. For this reason, we suggest that, had Marr been writing today, he might well have gone even farther in his analysis, including the emergence of structure-in particular, explicit structure at the conceptual level-from lower levels, and the effect of explicit emergent structures on the level (or levels) that gave rise to them. The message is that today's cognitive scientists need not only to understand how emergent structures-in particular, explicit emergent structures at the cognitive level-develop but also to understand how they feed back on the sub-structures from which they emerged. Copyright © 2015 Cognitive Science Society, Inc.

  10. Nature of Science Instruction to Turkish Prospective Chemistry Teachers: The Effect of Explicit-Reflective Approach

    ERIC Educational Resources Information Center

    Aglarci, Oya; Sariçayir, Hakan; Sahin, Musa

    2016-01-01

    The purpose of this study is to investigate the effect of explicit-reflective nature of science (NOS) instruction on Turkish prospective chemistry teachers' (PCTs) views of NOS. In the research, case study as a qualitative design was used and PCTs' views were examined thoroughly. The participants of the study consisted of 22 senior PCTs. Data…

  11. 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…

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

    ERIC Educational Resources Information Center

    Low, Jason; Simpson, Samantha

    2012-01-01

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

  13. 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…

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

    ERIC Educational Resources Information Center

    Zohar, Anat; Peled, Bracha

    2008-01-01

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

  15. 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.)…

  16. 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…

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

    ERIC Educational Resources Information Center

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

    2013-01-01

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

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

    ERIC Educational Resources Information Center

    Low, Jason; Simpson, Samantha

    2012-01-01

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

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

    ERIC Educational Resources Information Center

    Xu, Hainu; Lyster, Roy

    2014-01-01

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

  20. 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…

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

    ERIC Educational Resources Information Center

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

    2013-01-01

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

  2. 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…

  3. Elementary Teachers' Perceptions about the Effective Features of Explicit-Reflective Nature of Science Instruction

    ERIC Educational Resources Information Center

    Adibelli-Sahin, Elif; Deniz, Hasan

    2017-01-01

    This qualitative study explored elementary teachers' perceptions about the effective features of explicit-reflective nature of science (NOS) instruction. Our participants were four elementary teachers from a public charter school located in the Southwestern U.S.A. The four elementary teachers participated in an academic year-long professional…

  4. 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…

  5. 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…

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

    ERIC Educational Resources Information Center

    Yilmaz, Yucel

    2012-01-01

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

  7. The 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…

  8. 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…

  9. 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…

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

    ERIC Educational Resources Information Center

    White, Justin P.; DeMil, Andrew J.

    2013-01-01

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

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

    PubMed

    Reif, Maria M; Hünenberger, Philippe H

    2016-08-25

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

  12. 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

  13. Solvation of a chiral carboxylic acid: effects of hydrogen bonding on the IR and VCD spectra of α-methoxyphenylacetic acid.

    PubMed

    Bünnemann, Karoline; Merten, Christian

    2017-07-26

    Strong hydrogen bonding to solvent molecules can significantly alter the IR and VCD spectra of a chiral solute. This can be particularly troublesome for the determination of absolute configurations, as all spatial configurations of solute-solvent clusters need to be considered explicitly in spectra calculations. With this contribution, we aim to derive general guidelines for the explicit solvation of carboxylic acids, and characterize the solute-solvent interactions of the model compound α-methoxyphenylacetic acid (MPAA) in organic solvents of different polarity. We show that, in the typical concentration range employed for VCD studies, MPAA prefers the formation of dimers in chloroform. In the other investigated solvents (acetonitrile, methanol, and dimethyl sulfoxide), hydrogen bonded solute-solvent clusters have to be considered explicitly for the spectral analysis. We discuss the origin of the solvent dependence of the VCD spectra of MPAA in detail, show which vibrational modes are most strongly affected, and that the spectral response correlates with the hydrogen bonding strength.

  14. 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.

  15. 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.

  16. For better or worse? Stress inoculation effects for implicit but not explicit anxiety.

    PubMed

    Edge, Michael D; Ramel, Wiveka; Drabant, Emily M; Kuo, Janice R; Parker, Karen J; Gross, James J

    2009-01-01

    Severe early life stress (ELS) is associated with negative outcomes. It is not clear, however, what impact moderate ELS has. A growing stress inoculation literature suggests that moderate (vs. low or high) ELS is associated with diminished behavioral and physiological anxiety responses. At the same time, studies of trait anxiety suggest that moderate (vs. low) ELS is associated with greater self-reported anxiety. This study tested the hypothesis that stress inoculation effects are evident for implicit (nonconscious) but not explicit (conscious) aspects of anxiety. Ninety-seven healthy women were assessed for ELS and explicit anxiety using questionnaires and assessed for implicit anxiety using a version of the Implicit Association Test. Results indicated a quadratic relation between ELS and implicit anxiety, such that moderate ELS was associated with lower implicit anxiety levels than low or high ELS. By contrast, the relation between ELS and explicit anxiety was linear. These findings support the stress inoculation hypothesis and suggest that stress inoculation applies for implicit but not explicit aspects of anxiety.

  17. Solvent effect on the self-assembly of salt solvates of an antihypertensive drug azilsartan and 2-methylimidazole

    NASA Astrophysics Data System (ADS)

    Zhang, Xian-Rui; Zhang, Lei

    2017-06-01

    Three salt solvates of azilsartan (AZ) with 2-methylimidazole (2MI) (namely AZ-2MI-H2O, AZ-2MI-ACE and AZ-2MI-THF) and one azilsartan solvate (AZ-DIO, ACE = acetone, THF = tetrahydrofuran, and DIO = 1,4-dioxane) were manufactured by solvent-controlled self-assembly in aqueous-organic solutions. The experimental result of AZ-DIO shows that AZ is high affinity to DIO molecule, which has a unique ability to prevent salt formation between AZ and 2MI. Thermal studies of three salt solvates exhibit poor thermodynamic stability in environmental conditions. Solubility experiments show that AZ-2MI-ACE and AZ-2MI-THF are unstable and convert to AZ-2MI-H2O in aqueous solution, and that AZ-2MI-H2O exhibits increased solubility and retention stability in an aqueous medium compared with the commercial AZ-A crystalline form.

  18. Slow wave and REM sleep deprivation effects on explicit and implicit memory during sleep.

    PubMed

    Casey, Sarah J; Solomons, Luke C; Steier, Joerg; Kabra, Neeraj; Burnside, Anna; Pengo, Martino F; Moxham, John; Goldstein, Laura H; Kopelman, Michael D

    2016-11-01

    It has been debated whether different stages in the human sleep cycle preferentially mediate the consolidation of explicit and implicit memories, or whether all of the stages in succession are necessary for optimal consolidation. Here we investigated whether the selective deprivation of slow wave sleep (SWS) or rapid eye movement (REM) sleep over an entire night would have a specific effect on consolidation in explicit and implicit memory tasks. Participants completed a set of explicit and implicit memory tasks at night, prior to sleep. They had 1 control night of undisturbed sleep and 2 experimental nights, during which either SWS or REM sleep was selectively deprived across the entire night (sleep conditions counterbalanced across participants). Polysomnography recordings quantified precisely the amount of SWS and REM sleep that occurred during each of the sleep conditions, and spindle counts were recorded. In the morning, participants completed the experimental tasks in the same sequence as the night before. SWS deprivation disrupted the consolidation of explicit memories for visuospatial information (ηp2 = .23), and both SWS (ηp2 = .53) and REM sleep (ηp2 = .52) deprivation adversely affected explicit verbal recall. Neither SWS nor REM sleep deprivation affected aspects of short-term or working memory, and did not affect measures of verbal implicit memory. Spindle counts did not correlate significantly with memory performance. These findings demonstrate the importance of measuring the sleep cycles throughout the entire night, and the contribution of both SWS and REM sleep to memory consolidation. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  19. 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.

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

    PubMed

    Low, Jason; Simpson, Samantha

    2012-01-01

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

  1. 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.

  2. Enhancing divergent thinking in visual arts education: Effects of explicit instruction of meta-cognition.

    PubMed

    van de Kamp, Marie-Thérèse; Admiraal, Wilfried; van Drie, Jannet; Rijlaarsdam, Gert

    2015-03-01

    The main purposes of visual arts education concern the enhancement of students' creative processes and the originality of their art products. Divergent thinking is crucial for finding original ideas in the initial phase of a creative process that aims to result in an original product. This study aims to examine the effects of explicit instruction of meta-cognition on students' divergent thinking. A quasi-experimental design was implemented with 147 secondary school students in visual arts education. In the experimental condition, students attended a series of regular lessons with assignments on art reception and production, and they attended one intervention lesson with explicit instruction of meta-cognition. In the control condition, students attended a series of regular lessons only. Pre-test and post-test instances tests measured fluency, flexibility, and originality as indicators of divergent thinking. Explicit instruction of meta-cognitive knowledge had a positive effect on fluency and flexibility, but not on originality. This study implies that in the domain of visual arts, instructional support in building up meta-cognitive knowledge about divergent thinking may improve students' creative processes. This study also discusses possible reasons for the demonstrated lack of effect for originality. © 2014 The British Psychological Society.

  3. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  5. 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.

  6. Effects of Design Features of Explicit Values Clarification Methods: A Systematic Review.

    PubMed

    Witteman, Holly O; Gavaruzzi, Teresa; Scherer, Laura D; Pieterse, Arwen H; Fuhrel-Forbis, Andrea; Chipenda Dansokho, Selma; Exe, Nicole; Kahn, Valerie C; Feldman-Stewart, Deb; Col, Nananda F; Turgeon, Alexis F; Fagerlin, Angela

    2016-08-01

    Diverse values clarification methods exist. It is important to understand which, if any, of their design features help people clarify values relevant to a health decision. To explore the effects of design features of explicit values clarification methods on outcomes including decisional conflict, values congruence, and decisional regret. MEDLINE, all EBM Reviews, CINAHL, EMBASE, Google Scholar, manual search of reference lists, and expert contacts. Articles were included if they described the evaluation of 1 or more explicit values clarification methods. We extracted details about the evaluation, whether it was conducted in the context of actual or hypothetical decisions, and the results of the evaluation. We combined these data with data from a previous review about each values clarification method's design features. We identified 20 evaluations of values clarification methods within 19 articles. Reported outcomes were heterogeneous. Few studies reported values congruence or postdecision outcomes. The most promising design feature identified was explicitly showing people the implications of their values, for example, by displaying the extent to which each of their decision options aligns with what matters to them. Because of the heterogeneity of outcomes, we were unable to perform a meta-analysis. Results should be interpreted with caution. Few values clarification methods have been evaluated experimentally. More research is needed to determine effects of different design features of values clarification methods and to establish best practices in values clarification. When feasible, evaluations should assess values congruence and postdecision measures of longer-term outcomes. © The Author(s) 2016.

  7. Effect of the time-of-day of training on explicit memory.

    PubMed

    Barbosa, F F; Albuquerque, F S

    2008-06-01

    Studies have shown a time-of-day of training effect on long-term explicit memory with a greater effect being shown in the afternoon than in the morning. However, these studies did not control the chronotype variable. Therefore, the purpose of this study was to assess if the time-of-day effect on explicit memory would continue if this variable were controlled, in addition to identifying the occurrence of a possible synchronic effect. A total of 68 undergraduates were classified as morning, intermediate, or afternoon types. The subjects listened to a list of 10 words during the training phase and immediately performed a recognition task, a procedure which they repeated twice. One week later, they underwent an unannounced recognition test. The target list and the distractor words were the same in all series. The subjects were allocated to two groups according to acquisition time: a morning group (N = 32), and an afternoon group (N = 36). One week later, some of the subjects in each of these groups were subjected to a test in the morning (N = 35) or in the afternoon (N = 33). The groups had similar chronotypes. Long-term explicit memory performance was not affected by test time-of-day or by chronotype. However, there was a training time-of-day effect [F (1,56) = 53.667; P = 0.009] with better performance for those who trained in the afternoon. Our data indicated that the advantage of training in the afternoon for long-term memory performance does not depend on chronotype and also that this performance is not affected by the synchronic effect.

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

    ERIC Educational Resources Information Center

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

    2009-01-01

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

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

    USDA-ARS?s Scientific Manuscript database

    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...

  10. 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

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

    PubMed

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

    2014-12-19

    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. Copyright © 2014 John Wiley & Sons, Inc.

  12. Features of Ar solvation shells in neutral and ionic clustering: the competitive role of two-body and many-body interactions.

    PubMed

    Albertí, Margarita; Pirani, Fernando

    2011-06-23

    The semiempirical methodology, introduced to describe noncovalent intermolecular interactions in atom/ion-molecule systems, is here extended to investigate a prototype cluster, formed by benzene (Bz) and closed-shell ions (Na(+) and/or Cl(-)), surrounded by neutral species (Ar), forming solvation shells. The involved multidimensional potential energy surface (PES) is assumed to depend on a critical balancing of some effective interaction components. In particular, for the Ar solvated Bz-Na(+)-Cl(-) system, the nonelectrostatic component of the total interaction has been formulated as a combination of two-, three-, and four-body contributions, each one represented by a proper function, with the four-body and part of the three-body terms arising from nonadditive induction effects. The proposed formulation, in which the induction is included both implicitly and explicitly, ensures the accurate description of all dissociation channels, leading to simpler clusters and/or pure solvent. Some properties of the solvent, represented by an ensemble of 500 Ar atoms, have been analyzed by performing molecular dynamics simulations at several temperatures. The obtained results have been found to be consistent with experimental observations. In order to investigate propensities, similarities, and differences in the competing clusters, the Ar solvation shells of Bz, Bz-Na(+), Bz-Cl(-) and Bz-Na(+)-Cl(-) have been characterized. The inspection of the solvation shell of Bz allows one to distinguish between groups of Ar atoms occupying positions on and out of the plane defined by the aromatic ring. Regarding the solvation shells of Bz-Na(+) and Bz-Cl(-), it has been observed that they are strongly affected by the most stable structures of the unsolvated systems. However, Bz-Na(+) shows more compact solvation shells than Bz-Cl(-). Finally, important asymmetries, basically promoted by the additional many-body induction effects on the solvent atoms, have been observed in the solvation

  13. Solvation effect on isomer stability and electronic structures of protonated serotonin

    NASA Astrophysics Data System (ADS)

    Omidyan, Reza; Amanollahi, Zohreh; Azimi, Gholamhassan

    2017-07-01

    Microsolvation effect on geometry and transition energies of protonated serotonin has been investigated by MP2 and CC2 quantum chemical methods. Also, conductor-like screening model, implemented recently in the MP2 and ADC(2) methods, was examined to address the bulk water environment's effect on the isomer stability and electronic transition energies of protonated serotonin. It has been predicted that the dipole moment of gas phase isomers plays the main role on the isomer stabilization in water solution and electronic transition shifts. Also, both red- and blue-shift effects have been predicted to take place on electronic transition energies, upon hydration.

  14. 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.

  15. 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.

  16. 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).

  17. 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).

  18. 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

  19. Biomolecular electrostatics and solvation: a computational perspective.

    PubMed

    Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G; Schnieders, Michael J; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A

    2012-11-01

    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 toward 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 non-polar behavior) in order to provide a background to understand the different types of solvation models.

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

    PubMed

    Oakenfull, Gillian

    2007-01-01

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

  1. 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

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

    SciTech Connect

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

    2004-01-01

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

  3. 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.

  4. Solvation of apolar compounds in protic ionic liquids: the non-synergistic effect of electrostatic interactions and hydrogen bonds.

    PubMed

    Sedov, I A; Magsumov, T I; Salikov, T M; Solomonov, B N

    2017-09-27

    The solvation properties of protic ionic liquids such as alkylammonium salts are still virtually uncharacterized. Both electrostatic interactions between charged particles and hydrogen bond networks in a solvent are known to hinder the solubility of apolar species. Protic ionic liquids can be a priori expected to dissolve hydrocarbons worse than aprotic ionic liquids which do not form hydrogen bonds between the ions. We measured the limiting activity coefficients of several alkanes and alkylbenzenes in propylammonium and butylammonium nitrates at 298 K. Surprisingly, we observed the tendency of higher solubility than for the same compounds in aprotic ionic liquids with a similar molar volume. The calculations of the excess Gibbs free energies using test particle insertions into the snapshots of molecular dynamics trajectories reproduced lower values in protic rather than in aprotic ionic liquids for both methane molecules and hard sphere solutes. This can be explained by the favorable solvation of apolar species in the apolar domain of nanostructured PILs. For the first time, we point out at the essential difference between the solvation properties of two types of ionic liquids and prove that it arises from the cavity formation term.

  5. 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.

  6. 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).

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. Excited state reactions of metals in clusters: pluridimensional harpoon and solvation effects.

    PubMed

    Briant, M; Gaveau, M A; Fournier, P R; Mestdagh, J M; Visticot, J P; Soep, B

    2001-01-01

    Excited state reactions of metals produce electronically excited products efficiently, as revealed by studies performed both in the gas phase and in free Van der Waals complexes. The reaction mechanism is assigned to an excited state charge transfer from the metal to the molecular reactant (i.e. a harpoon mechanism). The present work uses the well established cluster isolated chemical reaction (CICR) technique and addresses these processes when the metal ... molecule Van der Waals pair is deposited at the surface of a large argon cluster. Such work is aimed at investigating the effect of the cluster substrate on the preparation and dynamics of the reaction. We have revisited the pluridimensional character of the harpoon reaction in these systems. More specifically, we studied the reaction of excited calcium with HBr near the calcium resonance line at 422.7 nm, forming CaBr in the A and B states. As in previous Van der Waals experiments, we could explore the dynamics of the reaction by recording action spectra. These spectra exhibit noticeable differences from those observed for unsupported Ca...HBr complexes. In particular the bending movement of the Ca...HBr complex which gives access to the transition state of the reaction is partly hindered by the presence of the argon cluster.

  13. 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.

  14. 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.

  15. Aqueous Solvation at Biomimetic Interfaces

    NASA Astrophysics Data System (ADS)

    Benderskii, Alexander V.; Eisenthal, Kenneth B.

    2002-03-01

    The process of solvation has been investigated at model aqueous interfaces designed to mimic surfaces of biomembranes. Second Harmonic Generation spectroscopy of a solvatochromic dye coumarin 314 is employed as the surface-selective probe technique. Monolayers of lipid amphiphiles at the air/water interface are used as model systems with neutral or charged hydrophilic headgroups of the surfactants chosen to represent common functional groups present at biological aqueous interfaces such as cell membranes. The red shift of the probe transition was measured using the steady-state frequency-resolved SHG spectroscopy to characterize the equilibrium solvation energies, i.e. the polarity at the lipid interfaces. Femtosecond time-resolved SHG measurements revealed two diffusive components of the solvation dynamics, associated with rearrangement of the water hydrogen bond network. Dynamics at the air/water interface, t1=250 fs and t2=2.0 ps, are similar to the timescales reported for bulk water t1 200 fs and t2 1.2 ps. The dynamical properties of water near the surfactant interfaces are significantly modified by the electrostatic and H-bonding interactions with the hydrophilic lipid headgroups. Neutral carboxyl headgroups (200 Å2/molecule) result in slowing of t1 to 400 fs and suppression of the slower t2 component. Different anionic lipids, carboxylate and sulfate, produce similar effects, slowing the t1 and t2 components without significantly affecting their relative amplitudes. Studies as a function of the sulfate surfactant concentration revealed that at low to intermediate surface coverage (500 to 250 Å2/molecule), the t1 component is unaffected, t1=250 fs, while the t2 component is lengthened first to 4.4 ps and then to 5.2 ps. At the highest surface coverage studied, 100 Å2/molecule, t1 changes to 600 fs, while t2 shows "saturation" at 5.4 ps. Different behavior of the two dynamical timescales t1 and t2 as a function of the surface charge density and chemical

  16. 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.

  17. 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.

  18. 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.

  19. Severity of explicit memory impairment due to Alzheimer's disease improves effectiveness of implicit learning.

    PubMed

    Klimkowicz-Mrowiec, Aleksandra; Slowik, Agnieszka; Krzywoszanski, Lukasz; Herzog-Krzywoszanska, Radosława; Szczudlik, Andrzej

    2008-04-01

    Consistent evidence from human and experimental animals studies indicates that memory is organized into two relatively independent systems with different functions and brain mechanisms. The explicit memory system, dependent on the hippocampus and adjacent medial temporal lobe structures, refers to conscious knowledge acquisition and intentional recollection of previous experiences. The implicit memory system, dependent on the striatum, refers to learning of complex information without awareness or intention. The functioning of implicit memory can be observed in progressive, gradual improvement across many trials in performance on implicit learning tasks. The influence of explicit memory on implicit memory has not been precisely identified yet. According to data from some studies, explicit memory seems to exhibit no influence on implicit memory,whereas the other studies indicate that explicit memory may inhibit or facilitate implicit memory. The analysis of performance on implicit learning tasks in patients with different severity of explicit memory impairment due to Alzheimer's disease allows one to identify the potential influence of the explicit memory system on the implicit memory system. 51 patients with explicit memory impairment due to Alzheimer's disease (AD) and 36 healthy controls were tested. Explicit memory was examined by means of a battery of neuropsychological tests. Implicit habit learning was examined on probabilistic classification task (weather prediction task). Patients with moderate explicit memory impairment performed the implicit task significantly better than those with mild AD and controls. Results of our study support the hypothesis of competition between the implicit and explicit memory systems in humans.

  20. Electrolytes in a nanometer slab-confinement: Ion-specific structure and solvation forces

    NASA Astrophysics Data System (ADS)

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

    2010-10-01

    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.

  1. 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.

  2. Cation solvation with quantum chemical effects modeled by a size-consistent multi-partitioning quantum mechanics/molecular mechanics method.

    PubMed

    Watanabe, Hiroshi C; Kubillus, Maximilian; Kubař, Tomáš; Stach, Robert; Mizaikoff, Boris; Ishikita, Hiroshi

    2017-07-21

    In the condensed phase, quantum chemical properties such as many-body effects and intermolecular charge fluctuations are critical determinants of the solvation structure and dynamics. Thus, a quantum mechanical (QM) molecular description is required for both solute and solvent to incorporate these properties. However, it is challenging to conduct molecular dynamics (MD) simulations for condensed systems of sufficient scale when adapting QM potentials. To overcome this problem, we recently developed the size-consistent multi-partitioning (SCMP) quantum mechanics/molecular mechanics (QM/MM) method and realized stable and accurate MD simulations, using the QM potential to a benchmark system. In the present study, as the first application of the SCMP method, we have investigated the structures and dynamics of Na(+), K(+), and Ca(2+) solutions based on nanosecond-scale sampling, a sampling 100-times longer than that of conventional QM-based samplings. Furthermore, we have evaluated two dynamic properties, the diffusion coefficient and difference spectra, with high statistical certainty. Furthermore the calculation of these properties has not previously been possible within the conventional QM/MM framework. Based on our analysis, we have quantitatively evaluated the quantum chemical solvation effects, which show distinct differences between the cations.

  3. 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.

  4. 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

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

    SciTech Connect

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

    2016-07-01

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

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

    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.

  7. 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.

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

    SciTech Connect

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

    2016-03-28

    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.

  9. Perspective on Foundations of Solvation Modeling: The Electrostatic Contribution to the Free Energy of Solvation

    SciTech Connect

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

    2008-06-01

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Solvation effects are essential components of all liquid-state chemistry, and it is impossible to understand liquid-phase organic, biological, or inorganic chemistry without including them. The Nobel-Prize-winning gas-phase quantum mechanical electronic structure methods of Pople1 and Kohn et al.2 require the additional inclusion of solvent for reliably addressing problems in liquid-phase chemistry. Methods that include the solvent implicitly are especially powerful because they allow one to retain the minimal representation of the solute, thereby facilitating progress with quantum mechanical calculations at the same high levels as those used in the gas phase,3,4 and because they allow one to model the solvent with the correct bulk permittivity. Reliable calculations of solutes in solution must take account of electrostatics, cavitation, dispersion, and solvent structure, but solvation effects are frequently dominated by electrostatics. Therefore, achieving a solid understanding of electrostatic solvation effects is an excellent starting point for understanding solvation and improving solvation models.

  10. 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.

  11. 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

  12. 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…

  13. 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…

  14. 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…

  15. Distinctive Solvation Patterns Make Renal Osmolytes Diverse

    PubMed Central

    Jackson-Atogi, Ruby; Sinha, Prem Kumar; Rösgen, Jörg

    2013-01-01

    The kidney uses mixtures of five osmolytes to counter the stress induced by high urea and NaCl concentrations. The individual roles of most of the osmolytes are unclear, and three of the five have not yet been thermodynamically characterized. Here, we report partial molar volumes and activity coefficients of glycerophosphocholine (GPC), taurine, and myo-inositol. We derive their solvation behavior from the experimental data using Kirkwood-Buff theory. We also provide their solubility data, including solubility data for scyllo-inositol. It turns out that renal osmolytes fall into three distinct classes with respect to their solvation. Trimethyl-amines (GPC and glycine-betaine) are characterized by strong hard-sphere-like self-exclusion; urea, taurine, and myo-inositol have a tendency toward self-association; sorbitol and most other nonrenal osmolytes have a relatively constant, intermediate solvation that has components of both exclusion and association. The data presented here show that renal osmolytes are quite diverse with respect to their solvation patterns, and they can be further differentiated based on observations from experiments examining their effect on macromolecules. It is expected, based on the available surface groups, that each renal osmolyte has distinct effects on various classes of biomolecules. This likely allows the kidney to use specific combinations of osmolytes independently to fine-tune the chemical activities of several types of molecules. PMID:24209862

  16. Quantifying spatially and temporally explicit CO2 fertilization effects on global terrestrial ecosystem carbon dynamics

    DOE PAGES

    Liu, Shaoqing; Zhuang, Qianlai; Chen, Min; ...

    2016-07-25

    Current terrestrial ecosystem models are usually driven with global average annual atmospheric carbon dioxide (CO2) concentration data at the global scale. However, high-precision CO2 measurement from eddy flux towers showed that seasonal, spatial surface atmospheric CO2 concentration differences were as large as 35 ppmv and the site-level tests indicated that the CO2 variation exhibited different effects on plant photosynthesis. Here we used a process-based ecosystem model driven with two spatially and temporally explicit CO2 data sets to analyze the atmospheric CO2 fertilization effects on the global carbon dynamics of terrestrial ecosystems from 2003 to 2010. Our results demonstrated that CO2more » seasonal variation had a negative effect on plant carbon assimilation, while CO2 spatial variation exhibited a positive impact. When both CO2 seasonal and spatial effects were considered, global gross primary production and net ecosystem production were 1.7 Pg C•yr–1 and 0.08 Pg C•yr–1 higher than the simulation using uniformly distributed CO2 data set and the difference was significant in tropical and temperate evergreen broadleaf forest regions. Moreover, this study suggests that the CO2 observation network should be expanded so that the realistic CO2 variation can be incorporated into the land surface models to adequately account for CO2 fertilization effects on global terrestrial ecosystem carbon dynamics.« less

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

    PubMed

    Bugg, Julie M; Smallwood, Alicia

    2016-01-01

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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Hydrophobic Solvation: Aqueous Methane Solutions

    ERIC Educational Resources Information Center

    Konrod, Oliver; Lankau, Timm

    2007-01-01

    A basic introduction to concept of a solvation shell around an apolar solute as well as its detection is presented. The hydrophobic solvation of toluene is found to be a good teaching example which connects macroscopic, phenomenological thermodynamic results with an atomistic point of view.

  5. 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.

  6. Evaluation of DNA Force Fields in Implicit Solvation

    PubMed Central

    Gaillard, Thomas; Case, David A.

    2011-01-01

    DNA structural deformations and dynamics are crucial to its interactions in the cell. Theoretical simulations are essential tools to explore the structure, dynamics, and thermodynamics of biomolecules in a systematic way. Molecular mechanics force fields for DNA have benefited from constant improvements during the last decades. Several studies have evaluated and compared available force fields when the solvent is modeled by explicit molecules. On the other hand, few systematic studies have assessed the quality of duplex DNA models when implicit solvation is employed. The interest of an implicit modeling of the solvent consists in the important gain in the simulation performance and conformational sampling speed. In this study, respective influences of the force field and the implicit solvation model choice on DNA simulation quality are evaluated. To this end, extensive implicit solvent duplex DNA simulations are performed, attempting to reach both conformational and sequence diversity convergence. Structural parameters are extracted from simulations and statistically compared to available experimental and explicit solvation simulation data. Our results quantitatively expose the respective strengths and weaknesses of the different DNA force fields and implicit solvation models studied. This work can lead to the suggestion of improvements to current DNA theoretical models. PMID:22043178

  7. 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.

  8. 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…

  9. 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…

  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. Field-SEA: A Model for Computing the Solvation Free Energies of Nonpolar, Polar, and Charged Solutes in Water

    PubMed Central

    2013-01-01

    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. PMID:24299013

  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. 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

  14. 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".

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. 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

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

    PubMed Central

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

    2010-01-01

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

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

    SciTech Connect

    Sun, Jian; Pritchard, Michael S.

    2016-07-25

    Here, 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 landatmosphere 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.

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

    DOE PAGES

    Sun, Jian; Pritchard, Michael S.

    2016-07-25

    Here, 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 landatmosphere feedback loop. At daily timescales, SPCAMmore » 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.« less

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

    NASA Astrophysics Data System (ADS)

    Sun, J.; Pritchard, M. S.

    2015-12-01

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

  6. 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.

  7. 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.

  8. [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.

  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. 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…

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

    ERIC Educational Resources Information Center

    Saito, Kazuya

    2013-01-01

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

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

    ERIC Educational Resources Information Center

    Saito, Kazuya

    2013-01-01

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

  14. 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,…

  15. 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…

  16. 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…

  17. 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…

  18. 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…

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

    ERIC Educational Resources Information Center

    Reed, Deborah K.

    2013-01-01

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

  20. 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.

  1. 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.

  2. 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…

  3. 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…

  4. 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)…

  5. 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…

  6. Explicit formulas for effective piezoelectric coefficients of ferroelectric 0-3 composites based on effective medium theory

    NASA Astrophysics Data System (ADS)

    Wong, C. K.; Poon, Y. M.; Shin, F. G.

    2003-01-01

    Explicit formulas were derived for the effective piezoelectric stress coefficients of a 0-3 composite of ferroelectric spherical particles in a ferroelectric matrix which were then combined to give the more commonly used strain coefficients. Assuming that the elastic stiffness of the inclusion phase is sufficiently larger than that of the matrix phase, the previously derived explicit expressions for the case of a low volume concentration of inclusion particles [C. K. Wong, Y. M. Poon, and F. G. Shin, Ferroelectrics 264, 39 (2001); J. Appl. Phys. 90, 4690 (2001)] were "transformed" analytically by an effective medium theory (EMT) with appropriate approximations, to suit the case of a more concentrated suspension. Predictions of the EMT expressions were compared with the experimental values of composites of lead zirconate titanate ceramic particles dispersed in polyvinylidene fluoride and polyvinylidene fluoride-trifluoroethylene copolymer, reported by Furukawa [IEEE Trans. Electr. Insul. 24, 375 (1989)] and by Ng et al. [IEEE Trans. Ultrason. Ferroelectr. Freq. Control 47, 1308 (2000)] respectively. Fairly good agreement was obtained. Comparisons with other predictions, including the predictions given by numerically solving the EMT scheme, were also made. It was found that the analytic and numeric EMT schemes agreed with each other very well for an inclusion of volume fraction not exceeding 60%.

  7. Impurity solvation in a liquid

    NASA Astrophysics Data System (ADS)

    Tehver, Riina; Cole, Milton W.; Maritan, Amos; Koplik, Joel; Banavar, Jayanth R.

    1998-02-01

    A set of model calculations is presented concerning the problem of impurity solvation. The methods include lattice gas, evaluated exactly as well as in the mean-field approximation, and molecular-dynamics simulation. Our results are in quantitative accord with simple energy balance arguments, but a solvation parameter suggested by Ancilotto, Lerner and Cole [J. Low Temp. Phys. 101, 1123 (1995)] is found to be nonuniversal.

  8. 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

  9. 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

  10. Exposure to graphic warning labels on cigarette packages: Effects on implicit and explicit attitudes towards smoking among young adults.

    PubMed

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

    2016-01-01

    To test the effect of exposure to the US Food and Drug Administration's proposed graphic images with text warning statements for cigarette packages on implicit and explicit attitudes towards smoking. A two-session web-based study was conducted with 2192 young adults 18-25-years-old. During session one, demographics, smoking behaviour, 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 US 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. 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 US Surgeon General's text warnings (p = .014), but there was no difference compared to those who viewed text-only warnings. Graphic health warnings on cigarette packages can influence young adult smokers' implicit attitudes towards smoking.

  11. 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

  12. 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.

  13. 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…

  14. 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…

  15. 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

  16. 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.

  17. Posthypnotic amnesia for material learned before or during hypnosis: explicit and implicit memory effects.

    PubMed

    Barnier, A J; Bryant, R A; Briscoe, S

    2001-10-01

    This article focuses on dissociations between explicit and implicit expressions of memory during posthypnotic amnesia (PHA). Despite evidence of such dissociations, experimental design in this area has not always been consistent with contemporary memory research. Within a paradigm that aimed for conceptual and methodological clarity, we presented 40 high and 38 low hypnotizable individuals with a word list either before or during hypnosis, gave them a PHA suggestion for the word list, and tested them on explicit and implicit memory tasks. In the absence of conscious recollection, highs showed equivalent levels of priming (perceptual and semantic) to lows. However, when analysis focused only on those highs who remained amnesic after the implicit memory tasks, we confirmed perceptual, but not semantic, priming. These findings highlight the impact of methodological choices on theoretical interpretations of memory performance following a suggestion for PHA.

  18. Sleep-Effects on Implicit and Explicit Memory in Repeated Visual Search

    PubMed Central

    Assumpcao, Leonardo; Gais, Steffen

    2013-01-01

    In repeated visual search tasks, facilitation of reaction times (RTs) due to repetition of the spatial arrangement of items occurs independently of RT facilitation due to improvements in general task performance. Whereas the latter represents typical procedural learning, the former is a kind of implicit memory that depends on the medial temporal lobe (MTL) memory system and is impaired in patients with amnesia. A third type of memory that develops during visual search is the observers’ explicit knowledge of repeated displays. Here, we used a visual search task to investigate whether procedural memory, implicit contextual cueing, and explicit knowledge of repeated configurations, which all arise independently from the same set of stimuli, are influenced by sleep. Observers participated in two experimental sessions, separated by either a nap or a controlled rest period. In each of the two sessions, they performed a visual search task in combination with an explicit recognition task. We found that (1) across sessions, MTL-independent procedural learning was more pronounced for the nap than rest group. This confirms earlier findings, albeit from different motor and perceptual tasks, showing that procedural memory can benefit from sleep. (2) Likewise, the sleep group compared with the rest group showed enhanced context-dependent configural learning in the second session. This is a novel finding, indicating that the MTL-dependent, implicit memory underlying contextual cueing is also sleep-dependent. (3) By contrast, sleep and wake groups displayed equivalent improvements in explicit recognition memory in the second session. Overall, the current study shows that sleep affects MTL-dependent as well as MTL-independent memory, but it affects different, albeit simultaneously acquired, forms of MTL-dependent memory differentially. PMID:23936363

  19. Sleep-effects on implicit and explicit memory in repeated visual search.

    PubMed

    Geyer, Thomas; Mueller, Hermann J; Assumpcao, Leonardo; Gais, Steffen

    2013-01-01

    In repeated visual search tasks, facilitation of reaction times (RTs) due to repetition of the spatial arrangement of items occurs independently of RT facilitation due to improvements in general task performance. Whereas the latter represents typical procedural learning, the former is a kind of implicit memory that depends on the medial temporal lobe (MTL) memory system and is impaired in patients with amnesia. A third type of memory that develops during visual search is the observers' explicit knowledge of repeated displays. Here, we used a visual search task to investigate whether procedural memory, implicit contextual cueing, and explicit knowledge of repeated configurations, which all arise independently from the same set of stimuli, are influenced by sleep. Observers participated in two experimental sessions, separated by either a nap or a controlled rest period. In each of the two sessions, they performed a visual search task in combination with an explicit recognition task. We found that (1) across sessions, MTL-independent procedural learning was more pronounced for the nap than rest group. This confirms earlier findings, albeit from different motor and perceptual tasks, showing that procedural memory can benefit from sleep. (2) Likewise, the sleep group compared with the rest group showed enhanced context-dependent configural learning in the second session. This is a novel finding, indicating that the MTL-dependent, implicit memory underlying contextual cueing is also sleep-dependent. (3) By contrast, sleep and wake groups displayed equivalent improvements in explicit recognition memory in the second session. Overall, the current study shows that sleep affects MTL-dependent as well as MTL-independent memory, but it affects different, albeit simultaneously acquired, forms of MTL-dependent memory differentially.

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

    PubMed Central

    Carroll, Timothy J.

    2016-01-01

    Insights into the neural representation of motor learning can be obtained by investigating how learning transfers to novel task conditions. We recently demonstrated that visuomotor rotation learning transferred strongly between left and right limbs when the task was performed in a sagittal workspace, which afforded a consistent remapping for the two limbs in both extrinsic and joint-based coordinates. In contrast, transfer was absent when performed in horizontal workspace, where the extrinsically defined perturbation required conflicting joint-based remapping for the left and right limbs. Because visuomotor learning is thought to be supported by both implicit and explicit forms of learning, however, it is unclear to what extent these distinct forms of learning contribute to interlimb transfer. In this study, we assessed the degree to which interlimb transfer, following visuomotor rotation training, reflects explicit vs. implicit learning by obtaining verbal reports of participants' aiming direction before each movement. We also determined the extent to which these distinct components of learning are constrained by the compatibility of coordinate systems by comparing transfer between groups of participants who reached to targets arranged in the horizontal and sagittal planes. Both sagittal and horizontal conditions displayed complete transfer of explicit learning to the untrained limb. In contrast, transfer of implicit learning was incomplete, but the sagittal condition showed greater transfer than the horizontal condition. These findings suggest that explicit strategies developed with one limb can be fully implemented in the opposite limb, whereas implicit transfer depends on the degree to which new sensorimotor maps are spatially compatible for the two limbs. PMID:27334955

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

    PubMed

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

    2016-09-01

    Insights into the neural representation of motor learning can be obtained by investigating how learning transfers to novel task conditions. We recently demonstrated that visuomotor rotation learning transferred strongly between left and right limbs when the task was performed in a sagittal workspace, which afforded a consistent remapping for the two limbs in both extrinsic and joint-based coordinates. In contrast, transfer was absent when performed in horizontal workspace, where the extrinsically defined perturbation required conflicting joint-based remapping for the left and right limbs. Because visuomotor learning is thought to be supported by both implicit and explicit forms of learning, however, it is unclear to what extent these distinct forms of learning contribute to interlimb transfer. In this study, we assessed the degree to which interlimb transfer, following visuomotor rotation training, reflects explicit vs. implicit learning by obtaining verbal reports of participants' aiming direction before each movement. We also determined the extent to which these distinct components of learning are constrained by the compatibility of coordinate systems by comparing transfer between groups of participants who reached to targets arranged in the horizontal and sagittal planes. Both sagittal and horizontal conditions displayed complete transfer of explicit learning to the untrained limb. In contrast, transfer of implicit learning was incomplete, but the sagittal condition showed greater transfer than the horizontal condition. These findings suggest that explicit strategies developed with one limb can be fully implemented in the opposite limb, whereas implicit transfer depends on the degree to which new sensorimotor maps are spatially compatible for the two limbs. Copyright © 2016 the American Physiological Society.

  2. Solvation in supercritical water

    SciTech Connect

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

    1991-01-01

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

  3. 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.

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

    PubMed

    Yadav, Rajeev; Sengupta, Bhaswati; Sen, Pratik

    2016-04-01

    The present study is devoted to understand the effect of sucrose on the hydration dynamics and rotational relaxation dynamics within the domain-I of HSA during chemically as well as thermally induced unfolding. It has been observed that the average solvation time become slower in the presence of sucrose for the lower concentrations of GnHCl, however at higher concentrations of GnHCl the effect of sucrose is almost negligible. From the time resolved fluorescence anisotropy it has been observed that in the lower concentration region of GnHCl the sucrose induced stabilization is small as compared to the higher concentrations of GnHCl. We have concluded that the hydration dynamics plays an important role in the sucrose induced stabilization process at the low concentration region; whereas environmental restriction is responsible at the higher concentration of GnHCl. However, we have observed a negligible stabilizing effect of sucrose towards the temperature induced unfolding. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. 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

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

    SciTech Connect

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

    2011-07-07

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

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

    PubMed

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

    2015-03-28

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

  8. 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

  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. 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.

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

    PubMed

    Yigit, Cemil; Heyda, Jan; Dzubiella, Joachim

    2015-08-14

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

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

    NASA Astrophysics Data System (ADS)

    Yigit, Cemil; Heyda, Jan; Dzubiella, Joachim

    2015-08-01

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

  13. Emotional Picture Perception: Repetition Effects in Free-Viewing and during an Explicit Categorization Task

    PubMed Central

    Mastria, Serena; Ferrari, Vera; Codispoti, Maurizio

    2017-01-01

    Several studies have found that, despite a decrease in the overall amplitude of the late positive potential (LPP) with repeated presentation of the same picture, emotional stimuli continue to elicit a larger LPP than neutral ones. These findings seem to support the hypothesis that the affective modulation of the LPP reflects a mandatory process and does not rely on stimulus novelty. However, in these studies participants were asked to merely look at the pictures, without carrying out any additional task (free-viewing), making picture emotionality the most salient aspect of the stimulus, despite its repetition. The current study aimed to examine the impact of an explicit categorization task on the emotional processing of repeated pictures. To this purpose, ERPs to novel and repeated pictures were measured during free-viewing as well as during an explicit categorization task, where the emotional content of the pictures was task-irrelevant. The within-subject comparison between the free-viewing and task context revealed that the overall LPP habituated more rapidly in the free-viewing condition, but, more importantly, the LPP affective modulation was unaffected by task requirements during both novel and repeated presentations. These results suggest that the affective modulation of the LPP reflects an automatic engagement of cortico-limbic motivational systems, which continues to take place regardless of stimulus novelty and task context. PMID:28725202

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. Heat does not come in different colours: entropy-enthalpy compensation, free energy windows, quantum confinement, pressure perturbation calorimetry, solvation and the multiple causes of heat capacity effects in biomolecular interactions.

    PubMed

    Cooper, A; Johnson, C M; Lakey, J H; Nöllmann, M

    2001-11-28

    Modern techniques in microcalorimetry allow us to measure directly the heat changes and associated thermodynamics for biomolecular processes in aqueous solution at reasonable concentrations. All these processes involve changes in solvation/hydration, and it is natural to assume that the heats for these processes should reflect, in some way, such changes in solvation. However, the interpretation of data is still somewhat ambiguous, since different non-covalent interactions may have similar thermodynamic signatures, and analysis is frustrated by large entropy-enthalpy compensation effects. Changes in heat capacity (Delta C(p)) have been related to changes in hydrophobic hydration and non-polar accessible surface areas, but more recent empirical and theoretical work has shown how this need not always be the case. Entropy-enthalpy compensation is a natural consequence of finite Delta C(p) values and, more generally, can arise as a result of quantum confinement effects, multiple weak interactions, and limited free energy windows, giving rise to thermodynamic homeostasis that may be of evolutionary and functional advantage. The new technique of pressure perturbation calorimetry (PPC) has enormous potential here as a means of probing solvation-related volumetric changes in biomolecules at modest pressures, as illustrated with preliminary data for a simple protein-inhibitor complex.

  19. Preparation of cerium halide solvate complexes

    DOEpatents

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

    2013-08-06

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

  20. 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.

  1. 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.

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

    PubMed

    Tanaka, Kanji; Watanabe, Katsumi

    2013-08-01

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

  3. 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.

  4. The Effects of Explicit Teaching of Strategies, Second-Order Concepts, and Epistemological Underpinnings on Students' Ability to Reason Causally in History

    ERIC Educational Resources Information Center

    Stoel, Gerhard L.; van Drie, Jannet P.; van Boxtel, Carla A. M.

    2017-01-01

    This article reports an experimental study on the effects of explicit teaching on 11th grade students' ability to reason causally in history. Underpinned by the model of domain learning, explicit teaching is conceptualized as multidimensional, focusing on strategies and second-order concepts to generate and verbalize causal explanations and…

  5. 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…

  6. Cluster expansion of the solvation free energy difference: Systematic improvements in the solvation of single ions

    NASA Astrophysics Data System (ADS)

    Pliego, Josefredo R.

    2017-07-01

    The cluster expansion method has been used in the imperfect gas theory for several decades. This paper proposes a cluster expansion of the solvation free energy difference. This difference, which results from a change in the solute-solvent potential energy, can be written as the logarithm of a finite series. Similar to the Mayer function, the terms in the series are related to configurational integrals, which makes the integrand relevant only for configurations of the solvent molecules close to the solute. In addition, the terms involve interaction of solute with one, two, and so on solvent molecules. The approach could be used for hybrid quantum mechanical and molecular mechanics methods or mixed cluster-continuum approximation. A simple form of the theory was applied for prediction of pKa in methanol; the results indicated that three explicit methanol molecules and the dielectric continuum lead to a root of mean squared error (RMSE) of only 1.3 pKa units, whereas the pure continuum solvation model based on density method leads to a RMSE of 6.6 pKa units.

  7. 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.

  8. Dynamic Jahn–Teller Effect in the Metastable High-Spin State of Solvated [Fe(terpy) 2 ] 2+

    SciTech Connect

    Zhang, X.; Lawson Daku, M. L.; Zhang, J.; Suarez-Alcantara, K.; Jennings, G.; Kurtz, C. A.; Canton, S. E.

    2015-02-12

    Characterizing structural distortions in the metastable spin states of d4- 11 d7 transition metal ion complexes is crucial to understand the nature of their bistability 12 and eventually control their switching dynamics. In particular, the impact of the Jahn- 13 Teller effect needs to be assessed for any electronic configuration that could be 14 effectively degenerate, as in e.g. the high-spin (HS) manifold of highly symmetric 15 homoleptic FeII complexes. However, capturing its manifestations remains challenging 16 since crystallization generally alters the molecular conformations and their 17 interconversion. With the rapid progress of ultrafast X-ray absorption spectroscopy, it 18 is now possible to collect data with unprecedented signal-to-noise ratio, opening up for 19 detailed structural characterization of transient species in the homogeneous solution phase. By combining the analysis of 20 picosecond X-ray absorption spectra with DFT simulations, the structure of the photoinduced HS state is elucidated for solvated 21 [Fe(terpy)2]2+ (terpy = 2,2':6',2''-terpyridine). This species can be viewed as the average 5B structure in D2 symmetry that 22 originates from a dynamic Jahn-Teller effect in the HS manifold. These results evidence the active role played by this particular 23 instance of vibronic coupling in the formation of the HS state for this benchmark molecule. Ultimately, correlating the interplay 24 between intramolecular and intermolecular degrees of freedom to conformational strain and distortions in real time should 25 contribute to the development of advanced functionalities in transition metal ion complexes.

  9. 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

  10. 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

  11. 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.

  12. Effects of gender, rape-supportive attitudes, and explicit instruction on perceptions of women's momentary sexual interest.

    PubMed

    Treat, Teresa A; Church, Erin K; Viken, Richard J

    2017-06-01

    Contemporary models of male-initiated sexual aggression toward female acquaintances implicate misperception of women's sexual interest. This study investigated the effects of gender, rape-supportive attitudes and an instructional manipulation on college students' sexual-interest judgments. Two hundred seventy-six women and 220 men judged the cues of momentary sexual interest expressed by photographed women; half received instruction on the differential validity of nonverbal cues of sexual interest for estimation of women's momentary sexual interest. Participants also completed an assessment of rape-supportive attitudes. Overall, college students' perceptions of women's momentary sexual interest are compromised both nomothetically and idiographically. Both male and female college students relied not only on women's nonverbal affect but also on the provocativeness of women's clothing and attractiveness when judging women's sexual interest. Men and women showed similar average ratings, but women relied more than men on women's affect, whereas men relied more than women on women's attractiveness. Both male and female students who endorsed more rape-supportive attitudes, relative to their peers, relied less on women's affect and more on women's clothing style and attractiveness. Explicit instruction regarding the greater validity of women's affective than nonaffective cues enhanced focus on nonverbal affective cues and decreased focus on clothing style and attractiveness. Although higher rape-supportive attitudes predicted more deficits in processing cues of sexual interest, explicit instruction proved to be effective for both higher-risk and lower-risk participants. These findings highlight the generalizability of the well-established effects of explicit instruction on category learning to sexual perception and may point to procedures that eventually could be incorporated into augmented prevention programs for sexual aggression on college campuses.

  13. 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),…

  14. 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),…

  15. 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

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

    PubMed

    Chaban, Vitaly V; Prezhdo, Oleg V

    2016-03-10

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

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

    PubMed

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

    2014-04-01

    In order to develop potential ligands to HIV-1 antibody 2G12 toward HIV-1 vaccine, binding mechanisms of the antibody 2G12 with the glycan ligand of D-mannose and D-fructose were theoretically examined. D-Fructose, whose molecular structure is slightly different from D-mannose, has experimentally shown to have stronger binding affinity to the antibody than that of D-mannose. To clarify the nature of D-fructose's higher binding affinity over D-mannose, we studied interaction between the monosaccharides and the antibody using ab initio fragment molecular orbital (FMO) method considering solvation effect as implicit model (FMO-PCM) as well as explicit water model. The calculated binding free energies of the glycans were qualitatively well consistent with the experimentally reported order of their affinities with the antibody 2G12. In addition, the FMO-PCM calculation elucidated the advantages of D-fructose over D-mannose in the solvation energy as well as the entropic contribution term obtained by MD simulations. The effects of explicit water molecules observed in the X-ray crystal structure were also scrutinized by means of FMO methods. Significant pair interaction energies among D-fructose, amino acids, and water molecules were uncovered, which indicated contributions from the water molecules to the strong binding ability of D-fructose to the antibody 2G12. These FMO calculation results of explicit water model as well as implicit water model indicated that the strong binding of D-fructose over D-mannose was due to the solvation effects on the D-fructose interaction energy. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. The Economy of Explicit Instruction

    ERIC Educational Resources Information Center

    Kraemer, Don J.

    2007-01-01

    The risk posed by explicit instruction in composition is that the reduction of writing to stock moves and effective devices may diminish the writer's agency and guarantee reproduction of the teacher's. The advantage of explicit instruction is power: overt and recursive attention to selected strategies can help students imagine the public agency…

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Effects of Explicit Convection on Land-Atmosphere Coupling in GLACE-Type Experiments Using the SuperParameterized CAM

    NASA Astrophysics Data System (ADS)

    Qin, H.; Pritchard, M. S.; Parishani, H.

    2016-12-01

    Understanding and realistically simulating the coupling between land and atmosphere in global climate models (GCMs) is an ongoing research frontier. We explore the hypothesis that past attempts to investigate these physics using GCM mechanism denial experiments may have suffered systematic limitations stemming from an overly strong sensitivity of deep convection parameterizations to surface conditions. Taking the philosophy of the Global Land-Atmosphere Coupling Experiment (GLACE), we therefore compare the effects of breaking the soil-atmosphere feedback mechanism in the Super-Parameterized Community Atmosphere Model version 3.5 (SPCAM3.5) - which uses O(10k) embedded cloud resolving models to explicitly resolve moist convection - against the conventionally parameterized CAM3.5. This helps isolate the influence of explicit convection on land-atmosphere coupling. We find that soil moisture - precipitation coupling strength is reduced over northern Africa, northern South America and Arabian Peninsula due to superparameterization. Several geographically distinct coupling "hotspots" emerge in SPCAM3.5 located upstream of major topographic features in the Northern Hemisphere mid-latitudes.

  5. 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. (c) 2015 APA, all rights reserved).

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

    ERIC Educational Resources Information Center

    Ferreira, Danielle

    2009-01-01

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

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

    PubMed

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

    2015-11-01

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

  8. A frontier orbital study with ab initio molecular dynamics of the effects of solvation on chemical reactivity: solvent-induced orbital control in FeO-activated hydroxylation reactions.

    PubMed

    Bernasconi, Leonardo; Baerends, Evert Jan

    2013-06-19

    Solvation effects on chemical reactivity are often rationalized using electrostatic considerations: the reduced stabilization of the transition state results in higher reaction barriers and lower reactivity in solution. We demonstrate that the effect of solvation on the relative energies of the frontier orbitals is equally important and may even reverse the trend expected from purely electrostatic arguments. We consider the H abstraction reaction from methane by quintet [EDTAH(n)·FeO]((n-2)+), (n = 0-4) complexes in the gas phase and in aqueous solution, which we examine using ab initio thermodynamic integration. The variation of the charge of the complex with the protonation of the EDTA ligand reveals that the free energy barrier in gas phase increases with the negative charge, varying from 16 kJ mol(-1) for [EDTAH4·FeO](2+) to 57 kJ mol(-1) for [EDTAHn·FeO](2-). In aqueous solution, the barrier for the +2 complex (38 kJ mol(-1)) is higher than in gas phase, as predicted by purely electrostatic arguments. For the negative complexes, however, the barrier is lower than in gas phase (e.g., 45 kJ mol(-1) for the -2 complex). We explain this increase in reactivity in terms of a stabilization of the virtual 3σ* orbital of FeO(2+), which acts as the dominant electron acceptor in the H-atom transfer from CH4. This stabilization originates from the dielectric screening caused by the reorientation of the water dipoles in the first solvation shell of the charged solute, which stabilizes the acceptor orbital energy for the -2 complex sufficiently to outweigh the unfavorable electrostatic destabilization of the transition-state relative to the reactants in solution.

  9. 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.

  10. 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

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

    NASA Technical Reports Server (NTRS)

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

    1998-01-01

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

  12. 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.

  13. Recasts in the Adult English L2 Classroom: Characteristics, Explicitness, and Effectiveness

    ERIC Educational Resources Information Center

    Loewen, Shawn; Philp, Jenefer

    2006-01-01

    A number of descriptive studies of language classrooms have identified recasts as a frequent form of feedback used by teachers following learners' nontarget-like oral production. Some classroom-based researchers (e.g., Lyster, 1998) have suggested that recasts are less effective than other forms of feedback because of the ambiguity of their…

  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 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,…

  17. 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,…

  18. 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,…

  19. Effects of an Explicit Group Contract on SelfDisclosure and Group Cohesiveness

    ERIC Educational Resources Information Center

    Ribner, Neil G.

    1974-01-01

    Effects of a group eontract specifically calling for self-disclosure was investigated. Frequency and depth of self disclosure were increased but level of intimacy of topics discussed was not. Group cohesiveness was enhanced by the contract but it decreased members' mutual liking. (Author/EAK)

  20. 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…

  1. 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…

  2. 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…

  3. Effectiveness of Explicit Phonological-Awareness Instruction for At-Risk English Learners

    ERIC Educational Resources Information Center

    Leafstedt, Jill M.; Richards, Catherine R.; Gerber, Michael M.

    2004-01-01

    This article examines the effects of intensive phonological-awareness (PA) instruction for kindergarten English learners. One intact kindergarten class was provided 300 minutes of intensive instruction in PA. Results indicate that students who received intervention made significant growth in word reading when compared to a cohort of kindergarten…

  4. The effects of an 'explicit' values clarification exercise in a woman's decision aid regarding postmenopausal hormone therapy.

    PubMed

    O'Connor, Annette M.; Wells, George A.; Tugwell, Peter; Laupacis, Andreas; Elmslie, Tom; Drake, Elizabeth

    1999-03-01

    OBJECTIVE: To evaluate the incremental effect of a graphic weigh-scale values clarification exercise to explicitly consider the personal importance of the benefits versus the risks in a woman's decision aid regarding postmenopausal hormone therapy. DESIGN: Randomized controlled trial. Intervention Decision aid including information on options, benefits and risks, and their probabilities either followed by: (1) a graphic weigh-scale values clarification exercise to explicitly consider the personal importance of each benefit and risk; or (2) a summary of the main benefits and risks to implicitly consider benefits versus the risks. SAMPLE: Two-hundred and one women aged 50-69 years from Ottawa, Canada, who had never used hormone therapy. OUTCOME: Perceived clarity of values, a sub-scale of the decisional conflict scale; congruence between personal values of benefits and risks (measured on 0-10 importance rating scale) and choices (accept, decline, unsure regarding preventive hormone therapy [HRT]) using discriminant function analysis. RESULTS: There were no statistically significant differences between interventions in perceived clarity of values and overall congruence between values and choices. Amongst those choosing HRT, there was a trend in those exposed to the graphic weigh-scale exercise to have better congruence between values and choices compared to implicit values clarification (P = 0.06). CONCLUSION: The use of the graphic weigh-scale exercise in a decision aid conveys no overall short-term benefit. Further study is needed to specifically determine effects in those changing the status quo and on the quality of patient-practitioner communication and persistence with decisions.

  5. 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.

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

    PubMed Central

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

    2014-01-01

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

  7. Comparison of select polarizable and non-polarizable water models in predicting solvation dynamics of water confined between MgO slabs.

    PubMed

    Kamath, Ganesh; Deshmukh, Sanket A; Sankaranarayanan, Subramanian K R S

    2013-07-31

    We present a molecular dynamics simulation study in which we compare and contrast the performance of a polarizable shell water potential model and non-polarizable water force field-extended simple point charge (SPC/EF) model in predicting the solvation dynamics of confined water molecules sandwiched between MgO(100) slabs. Structural features based on radial distribution functions, atomic density profiles, adsorption patterns, orientational ordering and dynamical correlations such as diffusional characteristics, hydrogen bonding lifetimes and residence probabilities are used as metrics for comparison. The simulations yield significant ordering of water molecules in the two layers adjacent to the oxide interface and the extent of ordering decreases with increasing distance from the oxide-water interface. These results elucidate that the dependence of local ordering and solvation dynamics on the molecular geometry and charge distribution, observed for typical three- and four-site water models, is generally lost for confined water if polarization is explicitly included. While the interfacial water structure predicted by the polarizable and non-polarizable models are similar, the confinement and interface proximity effects on the solvation dynamics are seen to be more pronounced for polarizable water models in comparison to non-polarizable ones. The study also shows that the polarizable water model over predicts the orientational order and under predicts the transport properties of confined water. In addition, analysis of the orientational preferences and hydrogen bonding characteristics of water near oxide interfaces suggests a higher degree of tetrahedral disorder in the polarizable shell compared to the non-polarizable SPC/E flexible model. The origin of the differences in solvation behavior of confined water between oxide slabs is analyzed based on the energetic contributions of the dispersive and electrostatic terms in the two force fields. Our findings suggest

  8. 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

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

    PubMed

    Bastien, Renaud; Douady, Stéphane; Moulia, Bruno

    2014-01-01

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

  10. 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…

  11. 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…

  12. 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.}

  13. 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).

  14. 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.

  15. 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

  16. 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.

  17. Effects of Explicit Urban-Canopy Representation on Local Circulations Above a Tropical Mega-City

    NASA Astrophysics Data System (ADS)

    Flores Rojas, José L.; Pereira Filho, Augusto J.; Karam, Hugo A.; Vemado, Felipe; Masson, Valéry

    2017-08-01

    The Advanced Regional Prediction System (ARPS) is coupled with the tropical town energy budget (tTEB) scheme to analyze the effects of the urban canopy circulation over the metropolitan area of São Paulo and its interactions with the sea breeze and mountain-valley circulation in the eastern state of São Paulo, Brazil. Two experiments are carried out for the typical sea-breeze event occurring on 22 August 2014 under weak synoptic forcing and clear-sky conditions: (a) a control run with the default semi-desert surface parametrization and; (b) a tTEB run for the urban canopy of São Paulo. A realistic land-use database over the south-eastern domain of Brazil is used in the downscaling simulation to a horizontal grid resolution of 3 km. Our results indicate that ARPS effectively simulates features of the nighttime and early morning land-breeze circulation, which is affected by the surrounding hills and the nocturnal heat island of São Paulo. By early afternoon, the south-eastern sea-breeze circulation moves inland perpendicular to the upslope of the Serra do Mar scarp, which generates a line of moisture convergence and updrafts further inland. Later, the convergence line reaches São Paulo and interacts with the circulation arising from the urban heat island (UHI), which increases the moisture convergence and strength of updrafts. The surface energy balance indicates that the UHI is caused by large sensible heat storage within the urban canopy during the day, which is later released in the afternoon and at night. The simulations are verified with available radiosonde and surface weather station data, land-surface-temperature estimates from the moderate resolution imaging spectroradiometer, as well as the National Center for Atmospheric Research reanalysis databases. The three-dimensional geometry of the urban canyons within the tTEB scheme consistently improves the thermodynamically-induced circulation over São Paulo.

  18. A Spatially Explicit Modeling Approach to Capture the Hydrological Effects on Biogeochemical Processes in a Boreal Watershed

    NASA Astrophysics Data System (ADS)

    Govind, A.; Chen, J.

    2009-05-01

    Current estimates of terrestrial carbon (C) fluxes overlook hydrological controls. A modeling study was conducted to explore the hydrological, ecophysiological and biogeochemical interactions in a humid boreal ecosystem. Several hydro-ecological processes were simulated and validated using field measurements for two years. After gaining confidence in the model's ability and having understood that topographically driven sub-surface baseflow is the main process determining the soil moisture regime in humid boreal ecosystem, its influence on ecophysiological and biogeochemical processes were investigated. Three modeling scenarios were designed that represent strategies that are commonly used in ecological models to represent hydrological controls. These scenarios were: 1) Explicit, where realistic lateral water routing was considered; 2) Implicit, where calculations were based on a bucket-modeling approach; and 3) NoFlow, where the lateral sub-surface flow was turned off in the model. In general, the Implicit scenario overestimated GPP, ET and NEP, as opposed to the Explicit scenario. The NoFlow scenario underestimated GPP and ET but overestimated NEP. The key processes controlling the differences were due to the combined effects of variations in plant physiology, photosynthesis, heterotrophic respiration, autotrophic respiration and nitrogen mineralization; all of which occurred simultaneously in different directions, at different rates, affecting the spatio-temporal distribution of terrestrial C-sources or sinks (NEP). The scientific implication of this work is that regional or global scale terrestrial C estimates could have significant errors if proper hydrological constraints are not considered for modeling ecological and biogeochemical processes due to large topographic variations of the Earth's surface and also because of the non-linear interactions between these processes.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  1. 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)

  2. 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)

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

    USDA-ARS?s Scientific Manuscript database

    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...

  4. Propositional Versus Dual-Process Accounts of Evaluative Conditioning: I. The Effects of Co-Occurrence and Relational Information on Implicit and Explicit Evaluations.

    PubMed

    Hu, Xiaoqing; Gawronski, Bertram; Balas, Robert

    2017-01-01

    Evaluative conditioning (EC) is defined as the change in the evaluation of a conditioned stimulus (CS) due to its pairing with a valenced unconditioned stimulus (US). According to propositional accounts, EC effects should be qualified by the relation between the CS and the US. Dual-process accounts suggest that relational information should qualify EC effects on explicit evaluations, whereas implicit evaluations should reflect the frequency of CS-US co-occurrences. Experiments 1 and 2 showed that, when relational information was provided before the encoding of CS-US pairings, it moderated EC effects on explicit, but not implicit, evaluations. In Experiment 3, relational information moderated EC effects on both explicit and implicit evaluations when it was provided simultaneously with CS-US pairings. Frequency of CS-US pairings had no effect on implicit evaluations. Although the results can be reconciled with both propositional and dual-process accounts, they are more parsimoniously explained by propositional accounts.

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

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

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

    PubMed Central

    Avancini, Chiara; Galfano, Giovanni; Szűcs, Dénes

    2014-01-01

    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. PMID:25450162

  11. 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

  12. 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.

  13. The effectiveness of the motion picture association of America's rating system in screening explicit violence and sex in top-ranked movies from 1950 to 2006.

    PubMed

    Nalkur, Priya G; Jamieson, Patrick E; Romer, Daniel

    2010-11-01

    Youth exposure to explicit film violence and sex is linked to adverse health outcomes and is a serious public health concern. The Motion Picture Association of America's (MPAA's) rating system's effectiveness in reducing youth exposure to harmful content has been questioned. To determine the MPAA's rating system's effectiveness in screening explicit violence and sex since the system's initiation (1968) and the introduction of the PG-13 category (1984). Also, to examine evidence of less restrictive ratings over time ("ratings creep"). Top-grossing movies from 1950 to 2006 (N = 855) were coded for explicitness of violent and sexual content. Trends in rating assignments and in the content of different rating categories since 1968 were assessed. The explicitness of violent and sexual content significantly increased following the rating system's initiation. The system did not differentiate violent content as well as sexual content, and ratings creep was only evident for violent films. Explicit violence in R-rated films increased, while films that would previously have been rated R were increasingly assigned to PG-13. This pattern was not evident for sex; only R-rated films exhibited higher levels of explicit sex compared to preratings period. While relatively effective for screening explicit sex, the rating system has allowed increasingly violent content into PG-13 films, thereby increasing youth access to more harmful content. Assignment of films in the current rating system should be more sensitive to the link between violent media exposure and youth violence. Copyright © 2010 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

  14. 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

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

    PubMed

    Bakhshiev, N G; Kiselev, M B

    1991-09-01

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

  16. 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.

  17. Divided attention enhances explicit but not implicit conceptual memory: an item-specific account of the attentional boost effect.

    PubMed

    Spataro, Pietro; Mulligan, Neil W; Bechi Gabrielli, Giulia; Rossi-Arnaud, Clelia

    2017-02-01

    The Attentional Boost Effect (ABE) refers to the counterintuitive finding that words encoded with to-be-responded targets in a divided-attention condition are remembered better than words encoded with distractors. Previous studies suggested that the ABE-related enhancement of verbal memory depends upon the activation of abstract lexical representations. In the present study, we extend this hypothesis by embedding it in the context of a broader perspective, which proposes that divided attention in the ABE paradigm affects item-specific, but not relational, processing. To this purpose, we examined the ABE in the matched tasks of category-cued recall (CCRT: explicit memory) and category exemplar generation (CEGT: implicit memory). In addition, study time was varied (500, 1500 or 4000 ms), to further determine whether the attentional boost manipulation could influence late-phase elaborative processing. In agreement with the predictions of the item-specific account, the results showed that exemplars encoded with targets were recalled better than exemplars encoded with distractors in the CCRT, but not in the CEGT. Moreover, performance in the CCRT increased with study time, whereas the size of the ABE-related enhancement tended to decrease, further confirming that this effect hinges upon early phase encoding processes.

  18. 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.

  19. Computational Protein Design Is a Challenge for Implicit Solvation Models

    PubMed Central

    Jaramillo, Alfonso; Wodak, Shoshana J.

    2005-01-01

    Increasingly complex schemes for representing solvent effects in an implicit fashion are being used in computational analyses of biological macromolecules. These schemes speed up the calculations by orders of magnitude and are assumed to compromise little on essential features of the solvation phenomenon. In this work we examine this assumption. Five implicit solvation models, a surface area-based empirical model, two models that approximate the generalized Born treatment and a finite difference Poisson-Boltzmann method are challenged in situations differing from those where these models were calibrated. These situations are encountered in automatic protein design procedures, whose job is to select sequences, which stabilize a given protein 3D structure, from a large number of alternatives. To this end we evaluate the energetic cost of burying amino acids in thousands of environments with different solvent exposures belonging, respectively, to decoys built with random sequences and to native protein crystal structures. In addition we perform actual sequence design calculations. Except for the crudest surface area-based procedure, all the tested models tend to favor the burial of polar amino acids in the protein interior over nonpolar ones, a behavior that leads to poor performance in protein design calculations. We show, on the other hand, that three of the examined models are nonetheless capable of discriminating between the native fold and many nonnative alternatives, a test commonly used to validate force fields. It is concluded that protein design is a particularly challenging test for implicit solvation models because it requires accurate estimates of the solvation contribution of individual residues. This contrasts with native recognition, which depends less on solvation and more on other nonbonded contributions. PMID:15377512

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

    PubMed

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

    2015-02-10

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

  1. An effect of age on implicit memory that is not due to explicit contamination: implications for single and multiple-systems theories.

    PubMed

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

    2013-06-01

    Recognition memory is typically weaker in healthy older relative to young adults, while performance on implicit tests (e.g., repetition priming) is often comparable between groups. Such observations are commonly taken as evidence for independent explicit and implicit memory systems. On a picture version of the continuous identification with recognition (CID-R) task, we found a reliable age-related reduction in recognition memory, while the age effect on priming did not reach statistical significance (Experiment 1). This pattern was consistent with the predictions of a formal single-system model. Experiment 2 replicated these observations using separate priming (continuous identification; CID) and recognition phases, while a combined data analysis revealed a significant effect of age on priming. In Experiment 3, we provide evidence that priming in this task is unaffected by explicit processing, and we conclude that the age difference in priming is unlikely to have been driven by differences in explicit processing between groups of young and older adults ("explicit contamination"). The results support the view that explicit and implicit expressions of memory are driven by a single underlying memory system. PsycINFO Database Record (c) 2013 APA, all rights reserved.

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

    NASA Astrophysics Data System (ADS)

    Rana, Malay Kumar; Chandra, Amalendu

    2012-10-01

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

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

    PubMed

    Rana, Malay Kumar; Chandra, Amalendu

    2012-10-07

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

  4. Parameterization of a Geometric Flow Implicit Solvation Model

    PubMed Central

    Thomas, Dennis G.; Chun, Jaehun; Chen, Zhan; Wei, Guowei; Baker, Nathan A.

    2012-01-01

    Implicit solvent models are popular for their high computational efficiency and simplicity over explicit solvent models and are extensively used for computing molecular solvation properties. The accuracy of implicit solvent models depends on the geometric description of the solute-solvent interface and the solvent dielectric profile that is defined near the surface of the solute molecule. Typically, it is assumed that the dielectric profile is spatially homogeneous in the bulk solvent medium and varies sharply across the solute-solvent interface. However, the specific form of this profile is often described by ad hoc geometric models rather than physical solute-solvent interactions. Hence, it is of significant interest to improve the accuracy of these implicit solvent models by more realistically defining the solute-solvent boundary within a continuum setting. Recently, a differential geometry-based geometric flow solvation model was developed, in which the polar and nonpolar free energies are coupled through a characteristic function that describes a smooth dielectric interface profile across the solvent–solute boundary in a thermodynamically self-consistent fashion. The main parameters of the model are the solute/solvent dielectric coefficients, solvent pressure on the solute, microscopic surface tension, solvent density, and molecular force-field parameters. In this work, we investigate how changes in the pressure, surface tension, solute dielectric coefficient, and choice of different force-field charge and radii parameters affect the prediction accuracy for hydration free energies of 17 small organic molecules based on the geometric flow solvation model. The results of our study provide insights on the parameterization, accuracy, and predictive power of this new implicit solvent model. PMID:23212974

  5. Segue between Favorable and Unfavorable Solvation

    SciTech Connect

    Maibaum, Lutz; Chandler, David

    2007-03-21

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

  6. 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.

  7. 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

  8. 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

  9. Effect of hydroxyl group substituted spacer group of cationic gemini surfactants on solvation dynamics and rotational relaxation of Coumarin-480 in aqueous micelles.

    PubMed

    Tiwari, Amit K; Sonu; Saha, Subit K

    2014-04-03

    The solvation dynamics and rotational relaxation of Coumarin 480 (C-480) have been investigated in the micelles of a series of gemini surfactants, 12-4(OH)n-12 (n = 0, 1, and 2), with increasing hydroxyl group substitution within the spacer group. Steady-state and time-correlated single photon counting (TCSPC) fluorescence spectroscopic techniques have been used to carry out such study. Steady-state and TCSPC fluorescence data support the location of probe molecule at the Stern layer. The solvation dynamics is found to be slower on hydroxyl substitution of spacer group due to the formation of hydrogen bonds between water molecules and hydroxyl group(s) of spacer group. Such kind of hydrogen bonding protects the probe molecule from its contact with water molecules and also results in restricted mobility of water molecules. The average rotational relaxation time increases on increasing number of substituted hydroxyl group on a spacer group. It is because of formations of more and more close packed micelles and larger extent of intermolecular hydrogen bonding interactions between C-480 and hydroxyl group(s). For micelles of each of 12-4-12 and 12-4(OH)-12, the slow rotational relaxation is dominated by the lateral diffusion of the fluorophore along the spherical surface of the micelle. However, for 12-4(OH)2-12, the slow rotational relaxation is mainly due to the rotational motion of the micelle as a whole. Because of high microviscosity of micelles of 12-4(OH)2-12 and greater extent of hydrogen bonding interactions with C-480, the relaxation time corresponding to the lateral diffusion of the fluorophore is very high in this case.

  10. 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…

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

    ERIC Educational Resources Information Center

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

    2014-01-01

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

  12. The Effects of Systematic and Explicit Instruction with Shared Stories on Comprehension and Generalization of Responding during Book Club for Students with Severe Disibilities

    ERIC Educational Resources Information Center

    Kemp-Inman, Amy

    2016-01-01

    The present study used a multiple probe across participants design to examine the effects of systematic and explicit instruction to teach students with severe disabilities (SD) to comprehend and discuss grade-aligned literature. The text was adapted and formatted as a read-aloud on an iPad2®. Using a modified system of least prompts, participants…

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

    ERIC Educational Resources Information Center

    Nullman, Susan L.

    2009-01-01

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

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

    ERIC Educational Resources Information Center

    Takimoto, Masahiro

    2006-01-01

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

  15. 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…

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

    ERIC Educational Resources Information Center

    Nullman, Susan L.

    2009-01-01

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

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

    ERIC Educational Resources Information Center

    Van Keer, Hilde; Verhaeghe, Jean Pierre

    2005-01-01

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

  18. 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…

  19. Estimation of Solvation Quantities from Experimental Thermodynamic Data: Development of the Comprehensive CompSol Databank for Pure and Mixed Solutes

    NASA Astrophysics Data System (ADS)

    Moine, Edouard; Privat, Romain; Sirjean, Baptiste; Jaubert, Jean-Noël

    2017-09-01

    The Gibbs energy of solvation measures the affinity of a solute for its solvent and is thus a key property for the selection of an appropriate solvent for a chemical synthesis or a separation process. More fundamentally, Gibbs energies of solvation are choice data for developing and benchmarking molecular models predicting solvation effects. The Comprehensive Solvation—CompSol—database was developed with the ambition to propose very large sets of new experimental solvation chemical-potential, solvation entropy, and solvation enthalpy data of pure and mixed components, covering extended temperature ranges. For mixed compounds, the solvation quantities were generated in infinite-dilution conditions by combining experimental values of pure-component and binary-mixture thermodynamic properties. Three types of binary-mixture properties were considered: partition coefficients, activity coefficients at infinite dilution, and Henry's-law constants. A rigorous methodology was implemented with the aim to select data at appropriate conditions of temperature, pressure, and concentration for the estimation of solvation data. Finally, our comprehensive CompSol database contains 21 671 data associated with 1969 pure species and 70 062 data associated with 14 102 binary mixtures (including 760 solvation data related to the ionic-liquid class of solvents). On the basis of the very large amount of experimental data contained in the CompSol database, it is finally discussed how solvation energies are influenced by hydrogen-bonding association effects.

  20. 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.

  1. 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.

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

    PubMed Central

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

    2014-01-01

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

  3. A solvated ligand rotamer approach and its application in computational protein design.

    PubMed

    Huang, Xiaoqiang; Yang, Ji; Zhu, Yushan

    2013-03-01

    The structure-based design of protein-ligand interfaces with respect to different small molecules is of great significance in the discovery of functional proteins. By statistical analysis of a set of protein-ligand complex structures, it was determined that water-mediated hydrogen bonding at the protein-ligand interface plays a crucial role in governing the binding between the protein and the ligand. Based on the novel statistic results, a solvated ligand rotamer approach was developed to explicitly describe the key water molecules at the protein-ligand interface and a water-mediated hydrogen bonding model was applied in the computational protein design context to complement the continuum solvent model. The solvated ligand rotamer approach produces only one additional solvated rotamer for each rotamer in the ligand rotamer library and does not change the number of side-chain rotamers at each protein design site. This has greatly reduced the total combinatorial number in sequence selection for protein design, and the accuracy of the model was confirmed by two tests. For the water placement test, 61% of the crystal water molecules were predicted correctly in five protein-ligand complex structures. For the sequence recapitulation test, 44.7% of the amino acid identities were recovered using the solvated ligand rotamer approach and the water-mediated hydrogen bonding model, while only 30.4% were recovered when the explicitly bound waters were removed. These results indicated that the developed solvated ligand rotamer approach is promising for functional protein design targeting novel protein-ligand interactions.

  4. Effects of Chocolate Deprivation on Implicit and Explicit Evaluation of Chocolate in High and Low Trait Chocolate Cravers.

    PubMed

    Richard, Anna; Meule, Adrian; Friese, Malte; Blechert, Jens

    2017-01-01

    Diet failures are often attributed to an increase in cravings for attractive foods. However, accumulating evidence shows that food cravings actually decrease during energy-restricting weight-loss interventions. The current study aimed at elucidating possible mechanisms that may explain how and under which circumstances food cravings in- or decrease during dieting. Specifically, decreases in food cravings during weight-loss diets may be due to effects of energy restriction (homeostatic changes) and to effects of avoiding specific foods (hedonic changes). Thus, we used a selective, hedonic deprivation (i.e., restricting intake of a specific food in the absence of an energy deficit) that precludes homeostatic changes due to energy restriction. Furthermore, interindividual differences in food craving experiences might affect why some individuals are more prone to experience cravings during dieting than others. Thus, we investigated whether a selective deprivation of chocolate would in- or decrease craving and implicit preference for chocolate as a function of trait-level differences in chocolate craving. Participants with high and low trait chocolate craving (HC, LC) refrained from consuming chocolate for 2 weeks but otherwise maintained their usual food intake. Both groups underwent laboratory assessments before and after deprivation, each including explicit (i.e., state chocolate craving) and implicit measures (i.e., Single Category Implicit Association Test, SC-IAT; Affect Misattribution Procedure, AMP). Results showed that hedonic deprivation increased state chocolate craving in HCs only. HCs also showed more positive implicit attitudes toward chocolate than LCs on the SC-IAT and the AMP irrespective of deprivation. Results help to disambiguate previous studies on the effects of dieting on food cravings. Specifically, while previous studies showed that energy-restricting diets appear to decrease food cravings, the current study showed that a selective, hedonic

  5. Effects of Chocolate Deprivation on Implicit and Explicit Evaluation of Chocolate in High and Low Trait Chocolate Cravers

    PubMed Central

    Richard, Anna; Meule, Adrian; Friese, Malte; Blechert, Jens

    2017-01-01

    Diet failures are often attributed to an increase in cravings for attractive foods. However, accumulating evidence shows that food cravings actually decrease during energy-restricting weight-loss interventions. The current study aimed at elucidating possible mechanisms that may explain how and under which circumstances food cravings in- or decrease during dieting. Specifically, decreases in food cravings during weight-loss diets may be due to effects of energy restriction (homeostatic changes) and to effects of avoiding specific foods (hedonic changes). Thus, we used a selective, hedonic deprivation (i.e., restricting intake of a specific food in the absence of an energy deficit) that precludes homeostatic changes due to energy restriction. Furthermore, interindividual differences in food craving experiences might affect why some individuals are more prone to experience cravings during dieting than others. Thus, we investigated whether a selective deprivation of chocolate would in- or decrease craving and implicit preference for chocolate as a function of trait-level differences in chocolate craving. Participants with high and low trait chocolate craving (HC, LC) refrained from consuming chocolate for 2 weeks but otherwise maintained their usual food intake. Both groups underwent laboratory assessments before and after deprivation, each including explicit (i.e., state chocolate craving) and implicit measures (i.e., Single Category Implicit Association Test, SC-IAT; Affect Misattribution Procedure, AMP). Results showed that hedonic deprivation increased state chocolate craving in HCs only. HCs also showed more positive implicit attitudes toward chocolate than LCs on the SC-IAT and the AMP irrespective of deprivation. Results help to disambiguate previous studies on the effects of dieting on food cravings. Specifically, while previous studies showed that energy-restricting diets appear to decrease food cravings, the current study showed that a selective, hedonic

  6. 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…

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

    SciTech Connect

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

    1996-04-01

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

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

    ERIC Educational Resources Information Center

    Halenko, Nicola; Jones, Christian

    2011-01-01

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

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  12. 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…

  13. 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…

  14. Laboratory Studies of Solvated Gas-Phase Anions.

    DTIC Science & Technology

    1982-02-01

    The Journal of Chemical Physics . 2. John F. Paulson, Michael J. Henchman, and Peter M. Hierl, "Effect of Reactant Ion Solvation on Gas-Phase SN2 Reactions," manuscript in final stages of preparation for submission to The Journal of Chemical Physics . D. PROFESSIONAL PERSONNEL Calvin Cole, Ph.D. Candidate, Department of Chemistry, University of Kansas, Lawrence, KS 66045 E. INTERACTIONS i. Oral Presentations P.M. Hierl, M.J. Henchman, and J; I Paulson,

  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. 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

  17. 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.

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

    SciTech Connect

    Sedlmeier, Felix; Netz, Roland R.

    2013-03-21

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

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

    PubMed

    Sedlmeier, Felix; Netz, Roland R

    2013-03-21

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

  1. Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge

    NASA Astrophysics Data System (ADS)

    Purisima, Enrico O.; Corbeil, Christopher R.; Sulea, Traian

    2010-04-01

    The SAMPL2 hydration free energy blind prediction challenge consisted of a data set of 41 molecules divided into three subsets: explanatory, obscure and investigatory, where experimental hydration free energies were given for the explanatory, withheld for the obscure, and not known for the investigatory molecules. We employed two solvation models for this challenge, a linear interaction energy (LIE) model based on explicit-water molecular dynamics simulations, and the first-shell hydration (FiSH) continuum model previously calibrated to mimic LIE data. On the 23 compounds from the obscure (blind) dataset, the prospectively submitted LIE and FiSH models provided predictions highly correlated with experimental hydration free energy data, with mean-unsigned-errors of 1.69 and 1.71 kcal/mol, respectively. We investigated several parameters that may affect the performance of these models, namely, the solute flexibility for the LIE explicit-solvent model, the solute partial charging method, and the incorporation of the difference in intramolecular energy between gas and solution phases for both models. We extended this analysis to the various chemical classes that can be formed within the SAMPL2 dataset. Our results strengthen previous findings on the excellent accuracy and transferability of the LIE explicit-solvent approach to predict transfer free energies across a wide spectrum of functional classes. Further, the current results on the SAMPL2 test dataset provide additional support for the FiSH continuum model as a fast yet accurate alternative to the LIE explicit-solvent model. Overall, both the LIE explicit-solvent model and the FiSH continuum solvation model show considerable improvement on the SAMPL2 data set over our previous continuum electrostatics-dispersion solvation model used in the SAMPL1 blind challenge.

  2. 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

  3. 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.

  4. 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).

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

    PubMed

    Jeschke, Steffen; Wiemhöfer, Hans-Dieter

    2016-03-15

    Combined computational/FTIR spectroscopic analyses of 3-methyl-2-oxazolidinone (NMO) solutions with varying molar ratios of lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) are reported. Based on the second derivative spectral profile, overlapping peaks are distinguished as well as assigned to the vibrational modes of implicitly and explicitly interacting NMO molecules. Thereby, the geometry of a monomeric, a dimeric and a simplified solvation structure [Li(NMO)1](+) are optimized with a polarizable continuum model at a B3LYP theoretical level. With increasing contents of LiTFSI, the formation of Li(+) solvation structures is scrutinized by semi-quantitative analysis of deconvoluted integral peak areas for three different ring-related vibrations and C=O-stretch vibration. A discrepancy in the obtained data is observed implying the influence of the TFSI anion the ring-related vibrations are prone to. The solvation number of 4 is determined according to the C=O-signal in diluted solution, which is proven by the computed Gibbs free energy for solvation of [Li(NMO)4](+) in a NMO medium (-41.7 kcal mol(-1)). Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Solvation thermodynamics and the physical-chemical meaning of the constant in Abraham solvation equations.

    PubMed

    van Noort, Paul C M

    2012-04-01

    Abraham solvation equations find widespread use in environmental chemistry. Until now, the intercept in these equations was determined by fitting experimental data. To simplify the determination of the coefficients in Abraham solvation equations, this study derives theoretical expressions for the value of the intercept for various partition processes. To that end, a modification of the description of the Ben-Naim standard state into the van der Waals volume is proposed. Differences between predicted and fitted values of the Abraham solvation equation intercept for the enthalpy of solvation, the entropy of solvation, solvent-water partitioning, air-solvent partitioning, partitioning into micelles, partitioning into lipid membranes and lipids, and chromatographic retention indices are comparable to experimental uncertainties in these values. Copyright © 2011 Elsevier Ltd. All rights reserved.

  7. 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.

  8. All-atom molecular dynamics simulations of an artificial sodium channel in a lipid bilayer: the effect of water solvation/desolvation of the sodium ion.

    PubMed

    Skelton, A A; Khedkar, V M; Fried, J R

    2016-01-01

    All-atom molecular dynamics is used to investigate the transport of Na(+) across a 1,2-dioleoyl-sn-glycero-3-phosphocholine lipid bilayer facilitated by a diazacrown hydraphile. Specifically, the free energy of Na(+) passing through the bilayer is calculated using the adaptive biasing force method to study the free energy associated with the increase in Na(+) transport in the presence of the hydraphile molecule. The results show that water interaction greatly influences Na(+) transport through the lipid bilayer as water is pulled through the bilayer with Na(+) forming a water channel. The hydraphile causes a reduction in the free energy barrier for the transport of Na(+) through the head group part of the lipid bilayer since it complexes the Na(+) reducing the necessity for water to be complexed and, therefore, dragged through with Na(+), an energetically unfavorable process. The free energy associated with Na(+) being desolvated within the bilayer is significantly decreased in the presence of the hydraphile molecule; the hydraphile increases the number of solvation states of Na(+) that can be adopted, and this increase in the number of available configurations provides an entropic explanation for the success of the hydraphile.

  9. 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

  10. 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

  11. 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)].

  12. 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.

  13. 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

  14. 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.

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed

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

    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 function combined with the HNC closure. Comparisons to molecular dynamics results are made for water as well as for the protein solute bovine pancreatic trypsin inhibitor. The proposed equations have less severe approximations and often provide results which compare favorably to molecular dynamics simulation where other methods fail.

  17. 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.

  18. 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.

  19. 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…

  20. 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…

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. Terror management theory and self-esteem revisited: the roles of implicit and explicit self-esteem in mortality salience effects.

    PubMed

    Schmeichel, Brandon J; Gailliot, Matthew T; Filardo, Emily-Ana; McGregor, Ian; Gitter, Seth; Baumeister, Roy F

    2009-05-01

    Three studies tested the roles of implicit and/or explicit self-esteem in reactions to mortality salience. In Study 1, writing about death versus a control topic increased worldview defense among participants low in implicit self-esteem but not among those high in implicit self-esteem. In Study 2, a manipulation to boost implicit self-esteem reduced the effect of mortality salience on worldview defense. In Study 3, mortality salience increased the endorsement of positive personality descriptions but only among participants with the combination of low implicit and high explicit self-esteem. These findings indicate that high implicit self-esteem confers resilience against the psychological threat of death, and therefore the findings provide direct support for a fundamental tenet of terror management theory regarding the anxiety-buffering role of self-esteem. Copyright (c) 2009 APA, all rights reserved.

  6. 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.

  7. Thermodynamic-ensemble independence of solvation free energy.

    PubMed

    Chong, Song-Ho; Ham, Sihyun

    2015-02-10

    Solvation free energy is the fundamental thermodynamic quantity in solution chemistry. Recently, it has been suggested that the partial molar volume correction is necessary to convert the solvation free energy determined in different thermodynamic ensembles. Here, we demonstrate ensemble-independence of the solvation free energy on general thermodynamic grounds. Theoretical estimates of the solvation free energy based on the canonical or grand-canonical ensemble are pertinent to experiments carried out under constant pressure without any conversion.

  8. 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

  9. 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

  10. Exploration of the secondary structure specific differential solvation dynamics between the native and molten globule states of the protein HP-36.

    PubMed

    Bandyopadhyay, Sanjoy; Chakraborty, Sudip; Bagchi, Biman

    2006-10-19

    Recent experiments have shown that the time dependence of fluorescence Stokes shift of a chromophore is substantially different when the chromophore is located in a molten globule (MG) state and in the native state of the same protein. To understand the origin of this difference, particularly the role of water in the differential solvation of the protein in the native and the MG states, we have carried out fully atomistic molecular dynamics simulations with explicit water of a partially unfolded MG state of the protein HP-36 and compared the results with the solvation dynamics of the protein in the folded native state. It is observed that the polar solvation dynamics of the three helical segments of the protein is influenced in a nonuniform heterogeneous manner in the MG state. While the equilibrium solvation time correlation function for helix-3 has been found to relax faster in the MG state as compared to that in the native state, the decay of the corresponding function for the other two helices slows down in the MG state. A careful analysis shows that the origin of such heterogeneous relative solvation behavior lies in the differential location of the polar probe residues and their exposure to bulk solvent. We find a significant negative cross-correlation between the contribution (to the solvation energy of a tagged amino acid residue) of water and the other groups of the protein, indicating a competing role in solvation. The sensitivity of solvation dynamics to the secondary structure and the immediate environment can be used to discriminate the partially unfolded and folded states. These results therefore should be useful in explaining recent solvation dynamics experiments on native and MG states of proteins.

  11. 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.

  12. 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

  13. 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

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

    PubMed

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

    2015-06-30

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

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

    PubMed

    Sedov, I A; Magsumov, T I

    2015-07-16

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

  16. Redox Potentials from Ab Initio Molecular Dynamics and Explicit Entropy Calculations: Application to Transition Metals in Aqueous Solution.

    PubMed

    Caro, Miguel A; Lopez-Acevedo, Olga; Laurila, Tomi

    2017-08-08

    We present a complete methodology to consistently estimate redox potentials strictly from first-principles, without any experimental input. The methodology is based on (i) ab initio molecular dynamics (MD) simulations, (ii) all-atom explicit solvation, (iii) the two-phase thermodynamic (2PT) model, and (iv) the use of electrostatic potentials as references for the absolute electrochemical scale. We apply the approach presented to compute reduction potentials of the following redox couples: Cr(2+/3+), V(2+/3+), Ru(NH3)6(2+/3+), Sn(2+/4+), Cu(1+/2+), FcMeOH(0/1+), and Fe(2+/3+) (in aqueous solution) and Fc(0/1+) (in acetonitrile). We argue that fully quantum-mechanical simulations are required to correctly model the intricate dynamical effects of the charged complexes on the surrounding solvent molecules within the solvation shell. Using the proposed methodology allows for a computationally efficient and statistically stable approach to compute free energy differences, yielding excellent agreement between our computed redox potentials and the experimental references. The root-mean-square deviation with respect to experiment for the aqueous test set and the two exchange-correlation density functionals used, PBE and PBE with van der Waals corrections, are 0.659 and 0.457 V, respectively. At this level of theory, depending on the functional employed, its ability to correctly describe each particular molecular complex seems to be the factor limiting the accuracy of the calculations.

  17. 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.)

  18. 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.

  19. Dynamics of electron solvation in molecular clusters.

    PubMed

    Ehrler, Oli T; Neumark, Daniel M

    2009-06-16

    Solvated electrons, and hydrated electrons in particular, are important species in condensed phase chemistry, physics, and biology. Many studies have examined the formation mechanism, reactivity, spectroscopy, and dynamics of electrons in aqueous solution and other solvents, leading to a fundamental understanding of the electron-solvent interaction. However, key aspects of solvated electrons remain controversial, and the interaction between hydrated electrons and water is of central interest. For example, although researchers generally accept that hydrated electrons, eaq-, occupy solvent cavities, another picture suggests that the electron resides in a diffuse orbital localized on a H3O radical. In addition, researchers have proposed two physically distinct models for the relaxation mechanism when the electron is excited. These models, formulated to interpret condensed phase experiments, have markedly different timescales for the internal conversion from the excited p state to the ground s state.Studies of negatively charged clusters, such as (H2O)n- and I-(H2O)n, offer a complementary perspective for studying aqueous electron solvation. In this Account, we use time-resolved photoelectron spectroscopy (TRPES), a femtosecond pump-probe technique in which mass-selected anions are electronically excited and then photodetached at a series of delay times, to focus on time-resolved dynamics in these and similar species. In (H2O)n-,TRPES gives evidence for ultrafast internal conversion in clusters up to n=100. Extrapolation of these results yields a p-state lifetime of 50 fs in the bulk limit. This is in good agreement with the nonadiabatic solvation model, one of the models proposed for relaxation of eaq-. Similarly, experiments on (MeOH)n- up to n=450 give an extrapolated p-state lifetime of 150fs. TRPES investigations of I-(H2O)n and I-(CH3CN)n probe a different aspect of electron solvation dynamics. In these experiments,an ultraviolet pump pulse excites the cluster

  20. 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.