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Sample records for solvent molecules explicitly

  1. Implicit solvent simulations of DNA and DNA-protein complexes: Agreement with explicit solvent vs experiment

    Czech Academy of Sciences Publication Activity Database

    Chocholoušová, Jana; Feig, M.

    2006-01-01

    Roč. 110, č. 34 (2006), s. 17240-17251 ISSN 1520-6106 Keywords : implicit solvent * explicit solvent * protein DNA complex Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.115, year: 2006

  2. Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents.

    Directory of Open Access Journals (Sweden)

    Hailey R Bureau

    Full Text Available Steered Molecular Dynamics (SMD has been seen to provide the potential of mean force (PMF along a peptide unfolding pathway effectively but at significant computational cost, particularly in all-atom solvents. Adaptive steered molecular dynamics (ASMD has been seen to provide a significant computational advantage by limiting the spread of the trajectories in a staged approach. The contraction of the trajectories at the end of each stage can be performed by taking a structure whose nonequilibrium work is closest to the Jarzynski average (in naive ASMD or by relaxing the trajectories under a no-work condition (in full-relaxation ASMD--namely, FR-ASMD. Both approaches have been used to determine the energetics and hydrogen-bonding structure along the pathway for unfolding of a benchmark peptide initially constrained as an α-helix in a water environment. The energetics are quite different to those in vacuum, but are found to be similar between implicit and explicit solvents. Surprisingly, the hydrogen-bonding pathways are also similar in the implicit and explicit solvents despite the fact that the solvent contact plays an important role in opening the helix.

  3. Filming the Birth of Molecules and Accompanying Solvent Rearrangement

    DEFF Research Database (Denmark)

    Lee, Jae Hyuk; Wulff, Michael; Bratos, Savo

    2013-01-01

    Molecules are often born with high energy and large-amplitude vibrations. In solution, a newly formed molecule cools down by transferring energy to the surrounding solvent molecules. The progression of the molecular and solute−solvent cage structure during this fundamental process has been elusiv...

  4. Towards ligand docking including explicit interface water molecules.

    Directory of Open Access Journals (Sweden)

    Gordon Lemmon

    Full Text Available Small molecule docking predicts the interaction of a small molecule ligand with a protein at atomic-detail accuracy including position and conformation the ligand but also conformational changes of the protein upon ligand binding. While successful in the majority of cases, docking algorithms including RosettaLigand fail in some cases to predict the correct protein/ligand complex structure. In this study we show that simultaneous docking of explicit interface water molecules greatly improves Rosetta's ability to distinguish correct from incorrect ligand poses. This result holds true for both protein-centric water docking wherein waters are located relative to the protein binding site and ligand-centric water docking wherein waters move with the ligand during docking. Protein-centric docking is used to model 99 HIV-1 protease/protease inhibitor structures. We find protease inhibitor placement improving at a ratio of 9:1 when one critical interface water molecule is included in the docking simulation. Ligand-centric docking is applied to 341 structures from the CSAR benchmark of diverse protein/ligand complexes [1]. Across this diverse dataset we see up to 56% recovery of failed docking studies, when waters are included in the docking simulation.

  5. Explicit versus Implicit Solvent Modeling of Raman Optical Activity Spectra

    Czech Academy of Sciences Publication Activity Database

    Hopmann, K. H.; Ruud, K.; Pecul, M.; Kudelski, A.; Dračínský, Martin; Bouř, Petr

    2011-01-01

    Roč. 115, č. 14 (2011), s. 4128-4137 ISSN 1520-6106 R&D Projects: GA MŠk(CZ) LH11033; GA ČR GAP208/11/0105 Grant - others:AV ČR(CZ) M200550902 Institutional research plan: CEZ:AV0Z40550506 Keywords : raman optical activity * lactamide * solvent models Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.696, year: 2011

  6. Solvent friction effects propagate over the entire protein molecule through low-frequency collective modes.

    Science.gov (United States)

    Moritsugu, Kei; Kidera, Akinori; Smith, Jeremy C

    2014-07-24

    Protein solvation dynamics has been investigated using atom-dependent Langevin friction coefficients derived directly from molecular dynamics (MD) simulations. To determine the effect of solvation on the atomic friction coefficients, solution and vacuum MD simulations were performed for lysozyme and staphylococcal nuclease and analyzed by Langevin mode analysis. The coefficients thus derived are roughly correlated with the atomic solvent-accessible surface area (ASA), as expected from the fact that friction occurs as the result of collisions with solvent molecules. However, a considerable number of atoms with higher friction coefficients are found inside the core region. Hence, the influence of solvent friction propagates into the protein core. The internal coefficients have large contributions from the low-frequency modes, yielding a simple picture of the surface-to-core long-range damping via solvation governed by collective low-frequency modes. To make use of these findings in implicit-solvent modeling, we compare the all-atom friction results with those obtained using Langevin dynamics (LD) with two empirical representations: the constant-friction and the ASA-dependent (Pastor-Karplus) friction models. The constant-friction model overestimates the core and underestimates the surface damping whereas the ASA-dependent friction model, which damps protein atoms only on the solvent-accessible surface, reproduces well the friction coefficients for both the surface and core regions observed in the explicit-solvent MD simulations. Therefore, in LD simulation, the solvent friction coefficients should be imposed only on the protein surface.

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

    Science.gov (United States)

    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.

  8. Guessing unknown and disordered solvent molecules with squeeze in the structure validation platon

    International Nuclear Information System (INIS)

    Weng, S.

    2014-01-01

    This report describes the assignment of the nature and number of solvent molecules in the refinement of several solvated crystal structures without a prior knowledge of the solvent system used for crystallization for the cases when the solvent molecule cannot be properly modeled. The solvent molecules can be assigned even for twinned crystal structures. (author)

  9. On the theory of electric double layer with explicit account of a polarizable co-solvent

    Energy Technology Data Exchange (ETDEWEB)

    Budkov, Yu. A., E-mail: urabudkov@rambler.ru [Laboratory of NMR Spectroscopy and Numerical Investigations of Liquids, G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Ivanovo (Russian Federation); Department of Applied Mathematics, National Research University Higher School of Economics, Moscow (Russian Federation); Kolesnikov, A. L. [Institut für Nichtklassische Chemie e.V., Universität Leipzig, Leipzig (Germany); Kiselev, M. G. [Laboratory of NMR Spectroscopy and Numerical Investigations of Liquids, G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Ivanovo (Russian Federation)

    2016-05-14

    We present a continuation of our theoretical research into the influence of co-solvent polarizability on a differential capacitance of the electric double layer. We formulate a modified Poisson-Boltzmann theory, using the formalism of density functional approach on the level of local density approximation taking into account the electrostatic interactions of ions and co-solvent molecules as well as their excluded volume. We derive the modified Poisson-Boltzmann equation, considering the three-component symmetric lattice gas model as a reference system and minimizing the grand thermodynamic potential with respect to the electrostatic potential. We apply present modified Poisson-Boltzmann equation to the electric double layer theory, showing that accounting for the excluded volume of co-solvent molecules and ions slightly changes the main result of our previous simplified theory. Namely, in the case of small co-solvent polarizability with its increase under the enough small surface potentials of electrode, the differential capacitance undergoes the significant growth. Oppositely, when the surface potential exceeds some threshold value (which is slightly smaller than the saturation potential), the increase in the co-solvent polarizability results in a differential capacitance decrease. However, when the co-solvent polarizability exceeds some threshold value, its increase generates a considerable enhancement of the differential capacitance in a wide range of surface potentials. We demonstrate that two qualitatively different behaviors of the differential capacitance are related to the depletion and adsorption of co-solvent molecules at the charged electrode. We show that an additive of the strongly polarizable co-solvent to an electrolyte solution can shift significantly the saturation potential in two qualitatively different manners. Namely, a small additive of strongly polarizable co-solvent results in a shift of saturation potential to higher surface potentials. On

  10. On the theory of electric double layer with explicit account of a polarizable co-solvent

    International Nuclear Information System (INIS)

    Budkov, Yu. A.; Kolesnikov, A. L.; Kiselev, M. G.

    2016-01-01

    We present a continuation of our theoretical research into the influence of co-solvent polarizability on a differential capacitance of the electric double layer. We formulate a modified Poisson-Boltzmann theory, using the formalism of density functional approach on the level of local density approximation taking into account the electrostatic interactions of ions and co-solvent molecules as well as their excluded volume. We derive the modified Poisson-Boltzmann equation, considering the three-component symmetric lattice gas model as a reference system and minimizing the grand thermodynamic potential with respect to the electrostatic potential. We apply present modified Poisson-Boltzmann equation to the electric double layer theory, showing that accounting for the excluded volume of co-solvent molecules and ions slightly changes the main result of our previous simplified theory. Namely, in the case of small co-solvent polarizability with its increase under the enough small surface potentials of electrode, the differential capacitance undergoes the significant growth. Oppositely, when the surface potential exceeds some threshold value (which is slightly smaller than the saturation potential), the increase in the co-solvent polarizability results in a differential capacitance decrease. However, when the co-solvent polarizability exceeds some threshold value, its increase generates a considerable enhancement of the differential capacitance in a wide range of surface potentials. We demonstrate that two qualitatively different behaviors of the differential capacitance are related to the depletion and adsorption of co-solvent molecules at the charged electrode. We show that an additive of the strongly polarizable co-solvent to an electrolyte solution can shift significantly the saturation potential in two qualitatively different manners. Namely, a small additive of strongly polarizable co-solvent results in a shift of saturation potential to higher surface potentials. On

  11. Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.

    Science.gov (United States)

    Goh, Garrett B; Hulbert, Benjamin S; Zhou, Huiqing; Brooks, Charles L

    2014-07-01

    pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMD(MSλD)). In the CPHMD(MSλD) framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMD(MSλD) simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal protein L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMD(MSλD) framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules-proteins and nucleic acids is now possible. © 2013 Wiley Periodicals, Inc.

  12. Nonadiabatic dynamics of electron transfer in solution: Explicit and implicit solvent treatments that include multiple relaxation time scales

    International Nuclear Information System (INIS)

    Schwerdtfeger, Christine A.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon

    2014-01-01

    The development of efficient theoretical methods for describing electron transfer (ET) reactions in condensed phases is important for a variety of chemical and biological applications. Previously, dynamical dielectric continuum theory was used to derive Langevin equations for a single collective solvent coordinate describing ET in a polar solvent. In this theory, the parameters are directly related to the physical properties of the system and can be determined from experimental data or explicit molecular dynamics simulations. Herein, we combine these Langevin equations with surface hopping nonadiabatic dynamics methods to calculate the rate constants for thermal ET reactions in polar solvents for a wide range of electronic couplings and reaction free energies. Comparison of explicit and implicit solvent calculations illustrates that the mapping from explicit to implicit solvent models is valid even for solvents exhibiting complex relaxation behavior with multiple relaxation time scales and a short-time inertial response. The rate constants calculated for implicit solvent models with a single solvent relaxation time scale corresponding to water, acetonitrile, and methanol agree well with analytical theories in the Golden rule and solvent-controlled regimes, as well as in the intermediate regime. The implicit solvent models with two relaxation time scales are in qualitative agreement with the analytical theories but quantitatively overestimate the rate constants compared to these theories. Analysis of these simulations elucidates the importance of multiple relaxation time scales and the inertial component of the solvent response, as well as potential shortcomings of the analytical theories based on single time scale solvent relaxation models. This implicit solvent approach will enable the simulation of a wide range of ET reactions via the stochastic dynamics of a single collective solvent coordinate with parameters that are relevant to experimentally accessible

  13. Modeling the oxidation of ebselen and other organoselenium compounds using explicit solvent networks.

    Science.gov (United States)

    Bayse, Craig A; Antony, Sonia

    2009-05-14

    The oxidation of dimethylselenide, dimethyldiselenide, S-methylselenenyl-methylmercaptan, and truncated and full models of ebselen (N-phenyl-1,2-benzisoselenazol-3(2H)-one) by methyl hydrogen peroxide has been modeled using density functional theory (DFT) and solvent-assisted proton exchange (SAPE), a method of microsolvation that employs explicit solvent networks to facilitate proton transfer reactions. The calculated activation barriers for these systems were substantially lower in energy (DeltaG(double dagger) + DeltaG(solv) = 13 to 26 kcal/mol) than models that neglect the participation of solvent in proton exchange. The comparison of two- and three-water SAPE networks showed a reduction in the strain in the model system but without a substantial reduction in the activation barriers. Truncating the ebselen model to N-methylisoselenazol-3(2H)-one gave a larger activation barrier than ebselen or N-methyl-1,2-benzisoselenazol-3(2H)-one but provided an efficient means of determining an initial guess for larger transition-state models. The similar barriers obtained for ebselen and Me(2)Se(2) (DeltaG(double dagger) + DeltaG(solv) = 20.65 and 20.40 kcal/mol, respectively) were consistent with experimentally determined rate constants. The activation barrier for MeSeSMe (DeltaG(double dagger) + DeltaG(solv) = 21.25 kcal/mol) was similar to that of ebselen and Me(2)Se(2) despite its significantly lower experimental rate for oxidation of an ebselen selenenyl sulfide by hydrogen peroxide relative to ebselen and ebselen diselenide. The disparity is attributed to intramolecular Se-O interactions, which decrease the nucleophilicity of the selenium center of the selenenyl sulfide.

  14. Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Yuqi; Wang, Jinan; Shao, Qiang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn; Zhu, Weiliang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn [ACS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203 (China); Shi, Jiye, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn [UCB Pharma, 216 Bath Road, Slough SL1 4EN (United Kingdom)

    2015-03-28

    The application of temperature replica exchange molecular dynamics (REMD) simulation on protein motion is limited by its huge requirement of computational resource, particularly when explicit solvent model is implemented. In the previous study, we developed a velocity-scaling optimized hybrid explicit/implicit solvent REMD method with the hope to reduce the temperature (replica) number on the premise of maintaining high sampling efficiency. In this study, we utilized this method to characterize and energetically identify the conformational transition pathway of a protein model, the N-terminal domain of calmodulin. In comparison to the standard explicit solvent REMD simulation, the hybrid REMD is much less computationally expensive but, meanwhile, gives accurate evaluation of the structural and thermodynamic properties of the conformational transition which are in well agreement with the standard REMD simulation. Therefore, the hybrid REMD could highly increase the computational efficiency and thus expand the application of REMD simulation to larger-size protein systems.

  15. Optimization of partial multicanonical molecular dynamics simulations applied to an alanine dipeptide in explicit water solvent.

    Science.gov (United States)

    Okumura, Hisashi

    2011-01-07

    The partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations samples a wide range of an important part of the potential energy. Although it is a strong technique for structure prediction of biomolecules, the choice of the partial potential energy has not been optimized. In order to find the best choice, partial multicanonical molecular dynamics simulations of an alanine dipeptide in explicit water solvent were performed with 15 trial choices for the partial potential energy. The best choice was found to be the sum of the electrostatic, Lennard-Jones, and torsion-angle potential energies between solute atoms. In this case, the partial multicanonical simulation sampled all of the local-minimum free-energy states of the P(II), C(5), α(R), α(P), α(L), and C states and visited these states most frequently. Furthermore, backbone dihedral angles ϕ and ψ rotated very well. It is also found that the most important term among these three terms is the electrostatic potential energy and that the Lennard-Jones term also helps the simulation to overcome the steric restrictions. On the other hand, multicanonical simulation sampled all of the six states, but visited these states fewer times. Conventional canonical simulation sampled only four of the six states: The P(II), C(5), α(R), and α(P) states.

  16. Watching the Solvation of Atoms in Liquids One Solvent Molecule at a Time

    Science.gov (United States)

    Bragg, Arthur E.; Glover, William J.; Schwartz, Benjamin J.

    2010-06-01

    We use mixed quantum-classical molecular dynamics simulations and ultrafast transient hole-burning spectroscopy to build a molecular-level picture of the motions of solvent molecules around Na atoms in liquid tetrahydrofuran. We find that even at room temperature, the solvation of Na atoms occurs in discrete steps, with the number of solvent molecules nearest the atom changing one at a time. This explains why the rate of solvent relaxation differs for different initial nonequilibrium states, and reveals how the solvent helps determine the identity of atomic species in liquids.

  17. Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid.

    Science.gov (United States)

    Xiao, Li; Luo, Ray

    2017-12-07

    We explored a multi-scale algorithm for the Poisson-Boltzmann continuum solvent model for more robust simulations of biomolecules. In this method, the continuum solvent/solute interface is explicitly simulated with a numerical fluid dynamics procedure, which is tightly coupled to the solute molecular dynamics simulation. There are multiple benefits to adopt such a strategy as presented below. At this stage of the development, only nonelectrostatic interactions, i.e., van der Waals and hydrophobic interactions, are included in the algorithm to assess the quality of the solvent-solute interface generated by the new method. Nevertheless, numerical challenges exist in accurately interpolating the highly nonlinear van der Waals term when solving the finite-difference fluid dynamics equations. We were able to bypass the challenge rigorously by merging the van der Waals potential and pressure together when solving the fluid dynamics equations and by considering its contribution in the free-boundary condition analytically. The multi-scale simulation method was first validated by reproducing the solute-solvent interface of a single atom with analytical solution. Next, we performed the relaxation simulation of a restrained symmetrical monomer and observed a symmetrical solvent interface at equilibrium with detailed surface features resembling those found on the solvent excluded surface. Four typical small molecular complexes were then tested, both volume and force balancing analyses showing that these simple complexes can reach equilibrium within the simulation time window. Finally, we studied the quality of the multi-scale solute-solvent interfaces for the four tested dimer complexes and found that they agree well with the boundaries as sampled in the explicit water simulations.

  18. Computational scheme for pH-dependent binding free energy calculation with explicit solvent.

    Science.gov (United States)

    Lee, Juyong; Miller, Benjamin T; Brooks, Bernard R

    2016-01-01

    We present a computational scheme to compute the pH-dependence of binding free energy with explicit solvent. Despite the importance of pH, the effect of pH has been generally neglected in binding free energy calculations because of a lack of accurate methods to model it. To address this limitation, we use a constant-pH methodology to obtain a true ensemble of multiple protonation states of a titratable system at a given pH and analyze the ensemble using the Bennett acceptance ratio (BAR) method. The constant pH method is based on the combination of enveloping distribution sampling (EDS) with the Hamiltonian replica exchange method (HREM), which yields an accurate semi-grand canonical ensemble of a titratable system. By considering the free energy change of constraining multiple protonation states to a single state or releasing a single protonation state to multiple states, the pH dependent binding free energy profile can be obtained. We perform benchmark simulations of a host-guest system: cucurbit[7]uril (CB[7]) and benzimidazole (BZ). BZ experiences a large pKa shift upon complex formation. The pH-dependent binding free energy profiles of the benchmark system are obtained with three different long-range interaction calculation schemes: a cutoff, the particle mesh Ewald (PME), and the isotropic periodic sum (IPS) method. Our scheme captures the pH-dependent behavior of binding free energy successfully. Absolute binding free energy values obtained with the PME and IPS methods are consistent, while cutoff method results are off by 2 kcal mol(-1) . We also discuss the characteristics of three long-range interaction calculation methods for constant-pH simulations. © 2015 The Protein Society.

  19. Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes.

    Science.gov (United States)

    Gkionis, Konstantinos; Kruse, Holger; Šponer, Jiří

    2016-04-12

    Modern dispersion-corrected DFT methods have made it possible to perform reliable QM studies on complete nucleic acid (NA) building blocks having hundreds of atoms. Such calculations, although still limited to investigations of potential energy surfaces, enhance the portfolio of computational methods applicable to NAs and offer considerably more accurate intrinsic descriptions of NAs than standard MM. However, in practice such calculations are hampered by the use of implicit solvent environments and truncation of the systems. Conventional QM optimizations are spoiled by spurious intramolecular interactions and severe structural deformations. Here we compare two approaches designed to suppress such artifacts: partially restrained continuum solvent QM and explicit solvent QM/MM optimizations. We report geometry relaxations of a set of diverse double-quartet guanine quadruplex (GQ) DNA stems. Both methods provide neat structures without major artifacts. However, each one also has distinct weaknesses. In restrained optimizations, all errors in the target geometries (i.e., low-resolution X-ray and NMR structures) are transferred to the optimized geometries. In QM/MM, the initial solvent configuration causes some heterogeneity in the geometries. Nevertheless, both approaches represent a decisive step forward compared to conventional optimizations. We refine earlier computations that revealed sizable differences in the relative energies of GQ stems computed with AMBER MM and QM. We also explore the dependence of the QM/MM results on the applied computational protocol.

  20. Modeling Loop Reorganization Free Energies of Acetylcholinesterase: A Comparison of Explicit and Implicit Solvent Models

    National Research Council Canada - National Science Library

    Olson, Mark

    2004-01-01

    ... screening of charge-charge interactions. This paper compares different solvent models applied to the problem of estimating the free-energy difference between two loop conformations in acetylcholinesterase...

  1. Depolarization of fluorescence of polyatomic molecules in noble gas solvents

    Science.gov (United States)

    Blokhin, A. P.; Gelin, M. F.; Kalosha, I. I.; Matylitsky, V. V.; Erohin, N. P.; Barashkov, M. V.; Tolkachev, V. A.

    2001-10-01

    The collisional depolarization of fluorescence is studied for p-quarterphenyl (PQP) in He, Ar, Xe solvents, under pressures ranging from zero to nearly atmospheric. The results are interpreted within the Keilson-Storer model of the orientational relaxation and smooth rigid body collision dynamics. This allows us to estimate the rate of the angular momentum scrambling due to encounters of PQP with its partners. The collisions are shown to be neither strong nor weak, so that the averaged number of encounters giving rise to the PQP angular momentum randomization equals to 33 (PQP-He), 4.5 (PQP-Ar), and 2.1 (PQP-Xe).

  2. Quasiparticle Approach to Molecules Interacting with Quantum Solvents.

    Science.gov (United States)

    Lemeshko, Mikhail

    2017-03-03

    Understanding the behavior of molecules interacting with superfluid helium represents a formidable challenge and, in general, requires approaches relying on large-scale numerical simulations. Here, we demonstrate that experimental data collected over the last 20 years provide evidence that molecules immersed in superfluid helium form recently predicted angulon quasiparticles [Phys. Rev. Lett. 114, 203001 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.203001]. Most important, casting the many-body problem in terms of angulons amounts to a drastic simplification and yields effective molecular moments of inertia as straightforward analytic solutions of a simple microscopic Hamiltonian. The outcome of the angulon theory is in good agreement with experiment for a broad range of molecular impurities, from heavy to medium-mass to light species. These results pave the way to understanding molecular rotation in liquid and crystalline phases in terms of the angulon quasiparticle.

  3. Explicit Consideration of Water Molecules to Study Vibrational Circular DICHROÎSM of Monosaccharide's

    Science.gov (United States)

    Moussi, Sofiane; Ouamerali, Ourida

    2014-06-01

    Carbohydrates have multiples roles in biological systems. It has been found that the glycoside bond is fundamentally important in many aspects of chemistry and biology and forms the basis of carbohydrate chemistry. That means the stereochemical information, namely, glycosidic linkages α or β, gives an significant features of the carbohydrate glycosidation position of the glycosylic acceptor. For these reasons, much effort was made for the synthesis and analysis of the glycoside bond. Vibrational circular dichroism VCD has some advantages over conventional electronic circular dichroism (ECD) due to the applicability to all organic molecules and the reliability of ab initio quantum calculation. However, for a molecule with many chiral centers such as carbohydrates, determination of the absolute configuration tends to be difficult because the information from each stereochemical center is mixed and averaged over the spectrum. In the CH stretching region, only two VCD studies on carbohydrates have been reported and spectra--structure correlation, as determined for the glycoside band, remains to be investigated. T. Taniguchi and collaborators report that methyl glycosides exhibit a characteristic VCD peak, the sign of which solely reflects the C-1 absolute configuration. This work is a theoretical contribution to study the behaviour of VCD spectrum's of the monosaccharides when the water molecules are taken explicitly. This study is focused on six different monosaccharides in theirs absolute configuration R and S. We used the method of density functional theory DFT by means of the B3LYP hybrid functional and 6-31G * basis set.

  4. Single molecule studies of solvent-dependent diffusion and entrapment in poly(dimethylsiloxane) thin films.

    Science.gov (United States)

    Lange, Jeffrey J; Culbertson, Christopher T; Higgins, Daniel A

    2008-12-15

    Single molecule microscopic and spectroscopic methods are employed to probe the mobility and physical entrapment of dye molecules in dry and solvent-loaded poly(dimethylsiloxane) (PDMS) films. PDMS films of approximately 220 nm thickness are prepared by spin casting dilute solutions of Sylgard 184 onto glass coverslips, followed by low temperature curing. A perylene diimide dye (BPPDI) is used to probe diffusion and molecule-matrix interactions. Two classes of dye-loaded samples are investigated: (i) those incorporating dye dispersed throughout the films ("in film" samples) and (ii) those in which the dye is restricted primarily to the PDMS surface ("on film" samples). Experiments are performed under dry nitrogen and at various levels of isopropyl alcohol (IPA) loading from the vapor phase. A PDMS-coated quartz-crystal microbalance is employed to monitor solvent loading and drying of the PDMS and to ensure equilibrium conditions are achieved. Single molecules are shown to be predominantly immobile under dry conditions and mostly mobile under IPA-saturated conditions. Quantitative methods for counting the fluorescent spots produced by immobile single molecules in optical images of the samples demonstrate that the population of mobile molecules increases nonlinearly with IPA loading. Even under IPA saturated conditions, the population of fixed molecules is found to be greater than zero and is greatest for "in film" samples. Fluorescence correlation spectroscopy is used to measure the apparent diffusion coefficient for the mobile molecules, yielding a mean value of D = 1.4(+/-0.4) x 10(-8) cm(2)/s that is virtually independent of IPA loading and sample class. It is concluded that a nonzero population of dye molecules is physically entrapped within the PDMS matrix under all conditions. The increase in the population of mobile molecules under high IPA conditions is attributed to the filling of film micropores with solvent, rather than by incorporation of molecularly

  5. Sampling the equilibrium kinetic network of Trp-cage in explicit solvent

    NARCIS (Netherlands)

    Du, W.; Bolhuis, P.G.

    2014-01-01

    We employed the single replica multiple state transition interface sampling (MSTIS) approach to sample the kinetic (un) folding network of Trp-cage mini-protein in explicit water. Cluster analysis yielded 14 important metastable states in the network. The MSTIS simulation thus resulted in a full 14

  6. Characterisation of aggregation of tributylphosphate molecules in organic solvent

    International Nuclear Information System (INIS)

    Mandin, C.; Martinet, L.; Zemb, Th.; Berthon, L.; Madic, Ch.

    2000-01-01

    This report presents a structural study of the aggregates formed with the organic phases of the extractant tri-n-butyl phosphate, used in the industrial PUREX process (Plutonium and Uranium Extraction; liquid-liquid solvent extraction) for the treatment of high radioactive waste. Combined Small Angle X-ray Scattering and Small Angle Neutron Scattering show that organic TBP solutions (in equilibrium with acid solutions) are organised in oligomeric aggregates. The influence of various parameters such as HNO 3 or TBP concentrations, diluent or acid natures, does not seem to modify the aggregate shape and size, whereas the interactions are modified. Moreover the aggregates disappear under high temperatures, whereas the attractive interactions between them increase at low temperatures. The 'drop weight' method gives the critical micellar concentration values of TBP in case of H 2 O or HNO 3 extractions (H 2 O: 0.48 M; HNO 3 2M: 0.65 M; at 21 deg C). Furthermore, the measures at different acid concentrations show that the c.m.c. varies with the acidity. The more acid the aqueous phase is, the smaller is the entropy in the system because of the numerous negative charges, i.e. the harder the micellization occurs, so the higher the c.m.c. value is. The sticky sphere model proposed by Baxter, can be used to model successfully small reverse micelles of the organic TBP phases. The aggregation number would be 4±1 (water extraction) and 5±1(HNO 3 2M extraction). These values are also given by vapor pressure measurements. (authors)

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

    Science.gov (United States)

    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

  8. Explicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: Inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines.

    Science.gov (United States)

    Hylsová, Michaela; Carbain, Benoit; Fanfrlík, Jindřich; Musilová, Lenka; Haldar, Susanta; Köprülüoğlu, Cemal; Ajani, Haresh; Brahmkshatriya, Pathik S; Jorda, Radek; Kryštof, Vladimír; Hobza, Pavel; Echalier, Aude; Paruch, Kamil; Lepšík, Martin

    2017-01-27

    We present comprehensive testing of solvent representation in quantum mechanics (QM)-based scoring of protein-ligand affinities. To this aim, we prepared 21 new inhibitors of cyclin-dependent kinase 2 (CDK2) with the pyrazolo[1,5-a]pyrimidine core, whose activities spanned three orders of magnitude. The crystal structure of a potent inhibitor bound to the active CDK2/cyclin A complex revealed that the biphenyl substituent at position 5 of the pyrazolo[1,5-a]pyrimidine scaffold was located in a previously unexplored pocket and that six water molecules resided in the active site. Using molecular dynamics, protein-ligand interactions and active-site water H-bond networks as well as thermodynamics were probed. Thereafter, all the inhibitors were scored by the QM approach utilizing the COSMO implicit solvent model. Such a standard treatment failed to produce a correlation with the experiment (R 2  = 0.49). However, the addition of the active-site waters resulted in significant improvement (R 2  = 0.68). The activities of the compounds could thus be interpreted by taking into account their specific noncovalent interactions with CDK2 and the active-site waters. In summary, using a combination of several experimental and theoretical approaches we demonstrate that the inclusion of explicit solvent effects enhance QM/COSMO scoring to produce a reliable structure-activity relationship with physical insights. More generally, this approach is envisioned to contribute to increased accuracy of the computational design of novel inhibitors. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  9. Morphology versus Vertical Phase Segregation in Solvent Annealed Small Molecule Bulk Heterojunction Organic Solar Cells

    Directory of Open Access Journals (Sweden)

    Alexander Kovalenko

    2015-01-01

    Full Text Available The deep study of solvent annealed small molecules bulk heterojunction organic solar cells based on DPP(TBFu2 : PC60BM blend is carried out. To reveal the reason of the solvent annealing advantage over the thermal one, capacitance-voltage measurements were applied. It was found that controlling the vertical phase segregation in the solar cells a high fullerene population in the vicinity of the cathode could be achieved. This results in increase of the shunt resistance of the cell, thus improving the light harvesting efficiency.

  10. NMR studies of liquid crystals and molecules dissolved in liquid crystal solvents

    Energy Technology Data Exchange (ETDEWEB)

    Drobny, Gary Peter [Univ. of California, Berkeley, CA (United States)

    1982-11-01

    zero at the smectic A - smectic C transition and reaching a maximum at 9° at the smectic C - smectic BA transition. This finding contradicts the results of X-ray diffraction studies which indicate that the tilt angle is 18° and temperature independent. The smectic BA - smectic BC phase transition is observed for the first time, and is found to be first order, a result that contradicts the prediction of a mean theory by McMillian. Chapter 3 is a multiple quantum nmr study of n-hexane oriented in a nematic liquid crystal solvent. The basic three pulse multiple quantum experiment is discussed which enables the observation of transitions for which |Δm|>1, and then the technique of the separation of multiple quantum orders by phase incrementation in the multiple quantum evolution period is reviewed (TPPI). An explicit example of multiple quantum nmr is given by the calculation of the multiple quantum spectrum of an oriented methyl group.

  11. Non-equilibrium reaction and relaxation dynamics in a strongly interacting explicit solvent: F + CD{sub 3}CN treated with a parallel multi-state EVB model

    Energy Technology Data Exchange (ETDEWEB)

    Glowacki, David R., E-mail: drglowacki@gmail.com [School of Chemistry, University of Bristol, Bristol BS8 1TS (United Kingdom); Department of Computer Science, University of Bristol, Bristol BS8 1UB (United Kingdom); PULSE Institute and Department of Chemistry, Stanford University, Stanford, California 94305 (United States); SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States); Orr-Ewing, Andrew J. [School of Chemistry, University of Bristol, Bristol BS8 1TS (United Kingdom); Harvey, Jeremy N. [Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Heverlee (Belgium)

    2015-07-28

    We describe a parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to explicitly correlated coupled cluster theory, we built a 64-state MS-EVB model designed to study the F + CD{sub 3}CN → DF + CD{sub 2}CN reaction in CD{sub 3}CN solvent (recently reported in Dunning et al. [Science 347(6221), 530 (2015)]). This approach allows us to build a reactive potential energy surface whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We ran molecular dynamics simulations to examine a range of observables which follow in the wake of the reactive event: energy deposition in the nascent reaction products, vibrational relaxation rates of excited DF in CD{sub 3}CN solvent, equilibrium power spectra of DF in CD{sub 3}CN, and time dependent spectral shifts associated with relaxation of the nascent DF. Many of our results are in good agreement with time-resolved experimental observations, providing evidence for the accuracy of our MS-EVB framework in treating both the solute and solute/solvent interactions. The simulations provide additional insight into the dynamics at sub-picosecond time scales that are difficult to resolve experimentally. In particular, the simulations show that (immediately following deuterium abstraction) the nascent DF finds itself in a non-equilibrium regime in two different respects: (1) it is highly vibrationally excited, with ∼23 kcal mol{sup −1} localized in the stretch and (2) its post-reaction solvation environment, in which it is not yet hydrogen-bonded to CD{sub 3}CN solvent molecules, is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational

  12. Non-equilibrium reaction and relaxation dynamics in a strongly interacting explicit solvent: F + CD3CN treated with a parallel multi-state EVB model.

    Science.gov (United States)

    Glowacki, David R; Orr-Ewing, Andrew J; Harvey, Jeremy N

    2015-07-28

    We describe a parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to explicitly correlated coupled cluster theory, we built a 64-state MS-EVB model designed to study the F + CD3CN → DF + CD2CN reaction in CD3CN solvent (recently reported in Dunning et al. [Science 347(6221), 530 (2015)]). This approach allows us to build a reactive potential energy surface whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We ran molecular dynamics simulations to examine a range of observables which follow in the wake of the reactive event: energy deposition in the nascent reaction products, vibrational relaxation rates of excited DF in CD3CN solvent, equilibrium power spectra of DF in CD3CN, and time dependent spectral shifts associated with relaxation of the nascent DF. Many of our results are in good agreement with time-resolved experimental observations, providing evidence for the accuracy of our MS-EVB framework in treating both the solute and solute/solvent interactions. The simulations provide additional insight into the dynamics at sub-picosecond time scales that are difficult to resolve experimentally. In particular, the simulations show that (immediately following deuterium abstraction) the nascent DF finds itself in a non-equilibrium regime in two different respects: (1) it is highly vibrationally excited, with ∼23 kcal mol(-1) localized in the stretch and (2) its post-reaction solvation environment, in which it is not yet hydrogen-bonded to CD3CN solvent molecules, is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational relaxation of the nascent DF results in a spectral

  13. FT-IR study and solvent-implicit and explicit effect on stepwise tautomerism of Guanylurea: M06-2X as a case of study.

    Science.gov (United States)

    Karimzadeh, Morteza; Manouchehri, Neda; Saberi, Dariush; Niknam, Khodabakhsh

    2018-06-15

    All 66 conformers of guanylurea were optimized and frequency calculations were performed at M06-2X/6-311++G(d,p) level of theory. Theses conformers were categorized into five tautomers, and the most stable conformer of each tautomer were found. Geometrical parameters indicated that these tautomers have almost planar structure. Complete stepwise tautomerism were studied through both intramolecular proton transfer routs and internal rotations. Results indicated that the proton transfer routs involving four-membered heterocyclic structures were rate-determining steps. Also, intramolecular proton movement having six-membered transition state structures had very low energy barrier comparable to the transition states of internal rotation routs. Differentiation of studied tautomers could easily be done through their FT-IR spectra in the range of 3200 to 3900cm -1 by comparing absorption bands and intensity of peaks. Solvent-implicit effects on the stability of tautomers were also studied through re-optimization and frequency calculation in four solvents. Water, DMSO, acetone and toluene had stabilization effect on all considered tautomers, but the order of stabilization effect was as follows: water>DMSO>acetone>toluene. Finally, solvent-explicit, base-explicit and acid-explicit effect were also studied by taking place of studied tautomer nearside of acid, base or solvent and optimization of them. Frequency calculation for proton movement by contribution of explicit effect showed that formic acid had a very strong effect on proton transfer from tautomer A1 to tautomer D8 by lowering the energy barrier from 42.57 to 0.8kcal/mol. In addition, ammonia-explicit effect was found to lower the barrier from 42.57 to 22.46kcal/mol, but this effect is lower than that of water and methanol-explicit effect. Copyright © 2018 Elsevier B.V. All rights reserved.

  14. FT-IR study and solvent-implicit and explicit effect on stepwise tautomerism of Guanylurea: M06-2X as a case of study

    Science.gov (United States)

    Karimzadeh, Morteza; Manouchehri, Neda; Saberi, Dariush; Niknam, Khodabakhsh

    2018-06-01

    All 66 conformers of guanylurea were optimized and frequency calculations were performed at M06-2X/6-311++G(d,p) level of theory. Theses conformers were categorized into five tautomers, and the most stable conformer of each tautomer were found. Geometrical parameters indicated that these tautomers have almost planar structure. Complete stepwise tautomerism were studied through both intramolecular proton transfer routs and internal rotations. Results indicated that the proton transfer routs involving four-membered heterocyclic structures were rate-determining steps. Also, intramolecular proton movement having six-membered transition state structures had very low energy barrier comparable to the transition states of internal rotation routs. Differentiation of studied tautomers could easily be done through their FT-IR spectra in the range of 3200 to 3900 cm-1 by comparing absorption bands and intensity of peaks. Solvent-implicit effects on the stability of tautomers were also studied through re-optimization and frequency calculation in four solvents. Water, DMSO, acetone and toluene had stabilization effect on all considered tautomers, but the order of stabilization effect was as follows: water > DMSO > acetone > toluene. Finally, solvent-explicit, base-explicit and acid-explicit effect were also studied by taking place of studied tautomer nearside of acid, base or solvent and optimization of them. Frequency calculation for proton movement by contribution of explicit effect showed that formic acid had a very strong effect on proton transfer from tautomer A1 to tautomer D8 by lowering the energy barrier from 42.57 to 0.8 kcal/mol. In addition, ammonia-explicit effect was found to lower the barrier from 42.57 to 22.46 kcal/mol, but this effect is lower than that of water and methanol-explicit effect.

  15. Solvent additive effects on small molecule crystallization in bulk heterojunction solar cells probed during spin casting

    KAUST Repository

    Pérez, Louis A.

    2013-09-04

    Solvent additive processing can lead to drastic improvements in the power conversion efficiency (PCE) in solution processable small molecule (SPSM) bulk heterojunction solar cells. In situ grazing incidence wide-angle X-ray scattering is used to investigate the kinetics of crystallite formation during and shortly after spin casting. The additive is shown to have a complex effect on structural evolution invoking polymorphism and enhanced crystalline quality of the donor SPSM. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Solvent additive effects on small molecule crystallization in bulk heterojunction solar cells probed during spin casting

    KAUST Repository

    Pé rez, Louis A.; Chou, Kang Wei; Love, John A.; Van Der Poll, Thomas S.; Smilgies, Detlef Matthias; Nguyen, Thuc Quyen; Krä mer, Edward J.; Amassian, Aram; Bazan, Guillermo C.

    2013-01-01

    Solvent additive processing can lead to drastic improvements in the power conversion efficiency (PCE) in solution processable small molecule (SPSM) bulk heterojunction solar cells. In situ grazing incidence wide-angle X-ray scattering is used to investigate the kinetics of crystallite formation during and shortly after spin casting. The additive is shown to have a complex effect on structural evolution invoking polymorphism and enhanced crystalline quality of the donor SPSM. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Role of solvent environments in single molecule conductance used insulator-modified mechanically controlled break junctions

    Science.gov (United States)

    Muthusubramanian, Nandini; Maity, Chandan; Galan Garcia, Elena; Eelkema, Rienk; Grozema, Ferdinand; van der Zant, Herre; Kavli Institute of Nanoscience Collaboration; Department of Chemical Engineering Collaboration

    We present a method for studying the effects of polar solvents on charge transport through organic/biological single molecules by developing solvent-compatible mechanically controlled break junctions of gold coated with a thin layer of aluminium oxide using plasma enhanced atomic layer deposition (ALD). The optimal oxide thickness was experimentally determined to be 15 nm deposited at ALD operating temperature of 300°C which yielded atomically sharp electrodes and reproducible single-barrier tunnelling behaviour across a wide conductance range between 1 G0 and 10-7 G0. The insulator protected MCBJ devices were found to be effective in various solvents such as deionized water, phosphate buffered saline, methanol, acetonitrile and dichlorobenzene. The yield of molecular junctions using such insulated electrodes was tested by developing a chemical protocol for synthesizing an amphipathic form of oligo-phenylene ethynylene (OPE3-PEO) with thioacetate anchoring groups. This work has further applications in studying effects of solvation, dipole orientation and other thermodynamic interactions on charge transport. Eu Marie Curie Initial Training Network (ITN). MOLECULAR-SCALE ELECTRONICS: ``MOLESCO'' Project Number 606728.

  18. Discrete and continuum modeling of solvent effects in a twisted intramolecular charge transfer system: The 4-N,N-dimethylaminobenzonitrile (DMABN) molecule.

    Science.gov (United States)

    Modesto-Costa, Lucas; Borges, Itamar

    2018-08-05

    The 4-N,N-dimethylaminobenzonitrile (DMABN) molecule is a prototypical system displaying twisted intramolecular (TICT) charge transfer effects. The ground and the first four electronic excited states (S 1 -S 4 ) in gas phase and upon solvation were studied. Charge transfer values as function of the torsion angle between the donor group (dimethylamine) and the acceptor moiety (benzonitrile) were explicitly computed. Potential energy curves were also obtained. The algebraic diagrammatic construction method at the second-order [ADC(2)] ab initio wave function was employed. Three solvents of increased polarities (benzene, DMSO and water) were investigated using discrete (average solvent electrostatic configuration - ASEC) and continuum (conductor-like screening model - COSMO) models. The results for the S 3 and S 4 excited states and the S 1 -S 4 charge transfer curves were not previously available in the literature. Electronic gas phase and solvent vertical spectra are in good agreement with previous theoretical and experimental results. In the twisted (90°) geometry the optical oscillator strengths have negligible values even for the S 2 bright state. Potential energy curves show two distinct pairs of curves intersecting at decreasing angles or not crossing in the more polar solvents. Charge transfer and electric dipole values allowed the rationalization of these results. The former effects are mostly independent of the solvent model and polarity. Although COSMO and ASEC solvent models mostly lead to similar results, there is an important difference: some crossings of the excitation energy curves appear only in the ASEC solvation model, which has important implications to the photochemistry of DMABN. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. Dynamic Behaviors of Solvent Molecules Restricted in Poly (Acryl Amide Gels Analyzed by Dielectric and Diffusion NMR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Hironobu Saito

    2018-06-01

    Full Text Available Dynamics of solvent molecules restricted in poly (acryl amide gels immersed in solvent mixtures of acetone–, 1,4-dioxane–, and dimethyl sulfoxide–water were analyzed by the time domain reflectometry method of dielectric spectroscopy and the pulse field gradient method of nuclear magnetic resonance. Restrictions of dynamic behaviors of solvent molecules were evaluated from relaxation parameters such as the relaxation time, its distribution parameter, and the relaxation strength obtained by dielectric measurements, and similar behaviors with polymer concentration dependences for the solutions were obtained except for the high polymer concentration in collapsed gels. Scaling analyses for the relaxation time and diffusion coefficient respectively normalized by those for bulk solvent suggested that the scaling exponent determined from the scaling variable defined as a ratio of the size of solvent molecule to mesh size of polymer networks were three and unity, respectively, except for collapsed gels. The difference in these components reflects characteristic molecular interactions in the rotational and translational diffusions, and offered a physical picture of the restriction of solvent dynamics. A universal treatment of slow dynamics due to the restriction from polymer chains suggests a new methodology of characterization of water structures.

  20. Solvent vapor annealing in the molecular regime drastically improves carrier transport in small-molecule thin-film transistors

    KAUST Repository

    Khan, Hadayat Ullah

    2013-04-10

    We demonstrate a new way to investigate and control the solvent vapor annealing of solution-cast organic semiconductor thin films. Solvent vapor annealing of spin-cast films of 6,13-bis(triisopropylsilylethynyl) pentacene (TIPS-Pn) is investigated in situ using quartz crystal microbalance with dissipation (QCM-D) capability, allowing us to monitor both solvent mass uptake and changes in the mechanical rigidity of the film. Using time-resolved grazing incidence wide angle X-ray scattering (GIWAXS) and complementary static atomic force microscopy (AFM), we demonstrate that solvent vapor annealing in the molecular regime can cause significant performance improvements in organic thin film transistors (OTFTs), whereas allowing the solvent to percolate and form a liquid phase results in catastrophic reorganization and dewetting of the film, making the process counterproductive. Using these lessons we devise processing conditions which prevent percolation of the adsorbed solvent vapor molecules for extended periods, thus extending the benefits of solvent vapor annealing and improving carrier mobility by nearly two orders of magnitude. Ultimately, it is demonstrated that QCM-D is a very powerful sensor of the state of the adsorbed solvent as well as the thin film, thus making it suitable for process development as well as in-line process monitoring both in laboratory and in future manufacturing settings. © 2013 American Chemical Society.

  1. Solvent vapor annealing in the molecular regime drastically improves carrier transport in small-molecule thin-film transistors

    KAUST Repository

    Khan, Hadayat Ullah; Li, Ruipeng; Ren, Yi; Chen, Long; Payne, Marcia M.; Bhansali, Unnat Sampatraj; Smilgies, Detlef Matthias; Anthony, John Edward; Amassian, Aram

    2013-01-01

    We demonstrate a new way to investigate and control the solvent vapor annealing of solution-cast organic semiconductor thin films. Solvent vapor annealing of spin-cast films of 6,13-bis(triisopropylsilylethynyl) pentacene (TIPS-Pn) is investigated in situ using quartz crystal microbalance with dissipation (QCM-D) capability, allowing us to monitor both solvent mass uptake and changes in the mechanical rigidity of the film. Using time-resolved grazing incidence wide angle X-ray scattering (GIWAXS) and complementary static atomic force microscopy (AFM), we demonstrate that solvent vapor annealing in the molecular regime can cause significant performance improvements in organic thin film transistors (OTFTs), whereas allowing the solvent to percolate and form a liquid phase results in catastrophic reorganization and dewetting of the film, making the process counterproductive. Using these lessons we devise processing conditions which prevent percolation of the adsorbed solvent vapor molecules for extended periods, thus extending the benefits of solvent vapor annealing and improving carrier mobility by nearly two orders of magnitude. Ultimately, it is demonstrated that QCM-D is a very powerful sensor of the state of the adsorbed solvent as well as the thin film, thus making it suitable for process development as well as in-line process monitoring both in laboratory and in future manufacturing settings. © 2013 American Chemical Society.

  2. Capturing the Role of Explicit Solvent in the Dimerization of RuV (bda) Water Oxidation Catalysts.

    Science.gov (United States)

    Zhan, Shaoqi; Mårtensson, Daniel; Purg, Miha; Kamerlin, Shina C L; Ahlquist, Mårten S G

    2017-06-06

    A ground-breaking empirical valence bond study for a soluble transition-metal complex is presented. The full reaction of catalyst monomers approaching and reacting in the Ru V oxidation state were studied. Analysis of the solvation shell in the reactant and along the reaction coordinate revealed that the oxo itself is hydrophobic, which adds a significant driving force to form the dimer. The effect of the solvent on the reaction between the prereactive dimer and the product was small. The solvent seems to lower the barrier for the isoquinoline (isoq) complex while it is increased for pyridines. By comparing the reaction in the gas phase and solution, the proposed π-stacking interaction of the isoq ligands is found to be entirely driven by the water medium. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Thermophysical properties and solubility of different sugar-derived molecules in deep eutectic solvents

    NARCIS (Netherlands)

    Dietz, C.H.J.T.; Kroon, M.C.; van Sint Annaland, M.; Gallucci, F.

    2017-01-01

    Deep eutectic solvents (DESs) are designer solvents analogous to ionic liquids but with lower preparation cost. Most known DESs are water-miscible, but recently water-immiscible DESs have also been presented, which are a combination of hydrogen bond donors and acceptors with long hydrophobic alkyl

  4. Xe-129 NMR chemical shift in Xe@C-60 calculated at experimental conditions: Essential role of the relativity, dynamics, and explicit solvent

    Czech Academy of Sciences Publication Activity Database

    Standara, Stanislav; Kulhánek, P.; Marek, R.; Straka, Michal

    2013-01-01

    Roč. 34, č. 22 (2013), s. 1890-1898 ISSN 0192-8651 R&D Projects: GA ČR GA203/09/2037; GA ČR GA13-03978S Grant - others:7th European Community Framework Program(XE) FP7-286154; CEITEC-Central European Institute of Technology (European Regional Development)(XE) CZ.1.05/1.1.00/02.0068; Operational Program Research and Development for Innovations(XE) CZ.1.05/3.2.00/08.0144 Institutional support: RVO:61388963 Keywords : Xe-129 NMR * Xe@C-60 * dynamical averaging * explicit solvent * relativistic effects Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.601, year: 2013

  5. How many molecular layers of polar solvent molecules control chemistry? The concept of compensating dipoles.

    Science.gov (United States)

    Langhals, Heinz; Braun, Patricia; Dietl, Christian; Mayer, Peter

    2013-09-27

    The extension of the solvent influence of the shell into the volume of a polar medium was examined by means of anti-collinear dipoles on the basis of the E(T)(30) solvent polarity scale (i.e., the molar energy of excitation of a pyridinium-N-phenolatebetaine dye; generally: E(T) =28,591 nm kcal mol(-1)/λmax) where no compensation effects were found. As a consequence, solvent polarity effects are concentrated to a very thin layer of a few thousand picometres around the solute where extensions into the bulk solvent become unimportant. A parallelism to the thin surface layer of water to the gas phase is discussed. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium: DFT and Car–Parrinello molecular dynamics study

    International Nuclear Information System (INIS)

    Dutta, Bipan; De, Rina; Chowdhury, Joydeep

    2015-01-01

    Highlights: • The tautomerism of 4-MTTN molecule in solvent water medium has been investigated. • CPMD presage the possibility of PT reactions through the solvent water medium. • Concerted PT processes in 4-MTTN have been estimated from the DFT and NBO analyses. • Percentage evolution and breaking of the concerned bonds are estimated. - Abstract: The ground state prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium has been investigated with the aid of DFT and Car–Parrinello molecular dynamics (CPMD) simulation studies. The CPMD simulations envisage the possibility of proton transfer reactions of the molecule through the solvent water medium. Probable proton transfer pathways have been predicted from the DFT calculations which are substantiated by the natural bond orbital analyses. The evolution and breaking of the concerned bonds of the molecule for different proton transfer reaction pathways are also estimated.

  7. Laser Raman spectroscopy of the effect of solvent on the low-frequency oscillations of organic molecules

    Science.gov (United States)

    Brandt, N. N.; Chikishev, A. Yu.; Dolgovskii, V. I.; Lebedenko, S. I.

    2007-09-01

    The effect of solvent on low-frequency oscillations is studied using an example of the 1,1,2,2-tetrachloroethane (TCE) and 1,1,2,2-tetrabromoethane (TBE) molecules, which exhibit torsional oscillations in the terahertz range. Dimethylsulfoxide (DMSO) and carbon tetrachloride (CTC) are used as solvents. It is demonstrated that a decrease in the concentration of the substance under study in the TBE/CTC, TCE/DMSO, and TCE/CTC mixtures leads to a frequency shift of the low-frequency oscillation. The shift is not observed in the TBE/DMSO mixture but a decrease in the TBE concentration causes significant broadening of the low-frequency line.

  8. Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water.

    Science.gov (United States)

    Paschek, Dietmar; Nymeyer, Hugh; García, Angel E

    2007-03-01

    We simulate the folding/unfolding equilibrium of the 20-residue miniprotein Trp-cage. We use replica exchange molecular dynamics simulations of the AMBER94 atomic detail model of the protein explicitly solvated by water, starting from a completely unfolded configuration. We employ a total of 40 replicas, covering the temperature range between 280 and 538 K. Individual simulation lengths of 100 ns sum up to a total simulation time of about 4 micros. Without any bias, we observe the folding of the protein into the native state with an unfolding-transition temperature of about 440 K. The native state is characterized by a distribution of root mean square distances (RMSD) from the NMR data that peaks at 1.8A, and is as low as 0.4A. We show that equilibration times of about 40 ns are required to yield convergence. A folded configuration in the entire extended ensemble is found to have a lifetime of about 31 ns. In a clamp-like motion, the Trp-cage opens up during thermal denaturation. In line with fluorescence quenching experiments, the Trp-residue sidechain gets hydrated when the protein opens up, roughly doubling the number of water molecules in the first solvation shell. We find the helical propensity of the helical domain of Trp-cage rather well preserved even at very high temperatures. In the folded state, we can identify states with one and two buried internal water molecules interconnecting parts of the Trp-cage molecule by hydrogen bonds. The loss of hydrogen bonds of these buried water molecules in the folded state with increasing temperature is likely to destabilize the folded state at elevated temperatures.

  9. Conformational Ensembles of an Intrinsically Disordered Protein pKID with and without a KIX Domain in Explicit Solvent Investigated by All-Atom Multicanonical Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Haruki Nakamura

    2012-02-01

    Full Text Available The phosphorylated kinase-inducible activation domain (pKID adopts a helix–loop–helix structure upon binding to its partner KIX, although it is unstructured in the unbound state. The N-terminal and C-terminal regions of pKID, which adopt helices in the complex, are called, respectively, αA and αB. We performed all-atom multicanonical molecular dynamics simulations of pKID with and without KIX in explicit solvents to generate conformational ensembles. Although the unbound pKID was disordered overall, αA and αB exhibited a nascent helix propensity; the propensity of αA was stronger than that of αB, which agrees with experimental results. In the bound state, the free-energy landscape of αB involved two low free-energy fractions: native-like and non-native fractions. This result suggests that αB folds according to the induced-fit mechanism. The αB-helix direction was well aligned as in the NMR complex structure, although the αA helix exhibited high flexibility. These results also agree quantitatively with experimental observations. We have detected that the αB helix can bind to another site of KIX, to which another protein MLL also binds with the adopting helix. Consequently, MLL can facilitate pKID binding to the pKID-binding site by blocking the MLL-binding site. This also supports experimentally obtained results.

  10. Communication: Potentials of mean force study of ionic liquid ion pair aggregation in polar covalent molecule solvents

    Science.gov (United States)

    Bandlamudi, Santosh Rathan Paul; Benjamin, Kenneth M.

    2018-05-01

    Molecular dynamics (MD) simulations were conducted for 1-ethyl-3-methylimidazolium methylsulfate [EMIM][MeSO4] dissolved in six polar covalent molecules [acetic acid, acetone, chloroform, dimethyl sulfoxide (DMSO), isopropyl alcohol, and methanol] to understand the free energies of ionic liquid (IL) ion pairing/aggregation in the limit of infinite dilution. Free energy landscapes or potentials of mean force (PMF) were computed using umbrella sampling and the weighted histogram analysis method. The PMF studies showed the strongest IL ion pairing in chloroform, and the strength of IL ion pairing decreases in the order of chloroform, acetone, propanol, acetic acid, DMSO, and methanol. In the limit of infinite dilution, the free energy curves for IL ion aggregation in co-solvents were characterized by two distinct minima [global (˜3.6 Å) and local (˜5.7 Å)], while free energy values at these minima differed significantly for IL in each co-solvent. The PMF studies were extended for determining the free energy of IL ion aggregation as a function of concentration of methanol. Studies showed that as the concentration of methanol increased, the free energy of ion aggregation decreased, suggesting greater ion pair stability, in agreement with previously reported MD clustering and radial distribution function data.

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  12. Origin of Reduced Open-Circuit Voltage in Highly Efficient Small-Molecule-Based Solar Cells upon Solvent Vapor Annealing.

    Science.gov (United States)

    Deng, Wanyuan; Gao, Ke; Yan, Jun; Liang, Quanbin; Xie, Yuan; He, Zhicai; Wu, Hongbin; Peng, Xiaobin; Cao, Yong

    2018-03-07

    In this study, we demonstrate that remarkably reduced open-circuit voltage in highly efficient organic solar cells (OSCs) from a blend of phenyl-C 61 -butyric acid methyl ester and a recently developed conjugated small molecule (DPPEZnP-THD) upon solvent vapor annealing (SVA) is due to two independent sources: increased radiative recombination and increased nonradiative recombination. Through the measurements of electroluminescence due to the emission of the charge-transfer state and photovoltaic external quantum efficiency measurement, we can quantify that the open-circuit voltage losses in a device with SVA due to the radiative recombination and nonradiative recombination are 0.23 and 0.31 V, respectively, which are 0.04 and 0.07 V higher than those of the as-cast device. Despite of the reduced open-circuit voltage, the device with SVA exhibited enhanced dissociation of charge-transfer excitons, leading to an improved short-circuit current density and a remarkable power conversion efficiency (PCE) of 9.41%, one of the best for solution-processed OSCs based on small-molecule donor materials. Our study also clearly shows that removing the nonradiative recombination pathways and/or suppressing energetic disorder in the active layer would result in more long-lived charge carriers and enhanced open-circuit voltage, which are prerequisites for further improving the PCE.

  13. Single-Molecule Tracking Study of the Permeability and Transverse Width of Individual Cylindrical Microdomains in Solvent-Swollen Polystyrene-block-poly(ethylene oxide) Films.

    Science.gov (United States)

    Sapkota, Dol Raj; Tran-Ba, Khanh-Hoa; Elwell-Cuddy, Trevor; Higgins, Daniel A; Ito, Takashi

    2016-12-01

    Understanding the properties of solvent-swollen block copolymer (BCP) microdomains is important for better solvent-based control of microdomain morphology, orientation, and permeability. In this study, single-molecule tracking (SMT) was explored to assess the permeability and transverse width of individual cylindrical microdomains in solvent-swollen polystyrene-block-poly(ethylene oxide) (PS-b-PEO) films. PS-b-PEO films comprising shear-elongated cylindrical PEO microdomains were prepared by sandwiching its benzene or tetrahydrofuran (THF) solution between two glass substrates. SMT measurements were performed at different drying times to investigate the effects of solvent evaporation on the microdomain properties. SMT data showed one-dimensional (1D) motions of single fluorescent molecules (sulforhodamine B) based on their diffusion within the cylindrical microdomains. Microdomain permeability and transverse width were assessed from the single-molecule diffusion coefficients (D SMT ) and transverse variance of the 1D trajectories (σ δ 2 ), respectively. The D SMT and σ δ 2 values from individual 1D trajectories were widely distributed with no evidence of correlation on a single molecule basis, possibly because the individual microdomains in a film were swollen to different extents. On average, microdomain permeability (D) and effective radius (r) gradually decreased within the first 3 days of drying due to solvent evaporation, and changed negligibly thereafter. PS-b-PEO films prepared from THF solutions exhibited larger changes in D and r as compared with those from benzene solutions due to the better swelling of the PEO microdomains by THF. Importantly, changes in D were more prominent than those in r, suggesting that the permeability of the PEO microdomains is very susceptible to the presence of solvent. These results reveal the unique capability of SMT to assess the properties of individual cylindrical microdomains in a solvent-swollen BCP film.

  14. Rapid phenolic O-glycosylation of small molecules and complex unprotected peptides in aqueous solvent

    Science.gov (United States)

    Wadzinski, Tyler J.; Steinauer, Angela; Hie, Liana; Pelletier, Guillaume; Schepartz, Alanna; Miller, Scott J.

    2018-06-01

    Glycosylated natural products and synthetic glycopeptides represent a significant and growing source of biochemical probes and therapeutic agents. However, methods that enable the aqueous glycosylation of endogenous amino acid functionality in peptides without the use of protecting groups are scarce. Here, we report a transformation that facilitates the efficient aqueous O-glycosylation of phenolic functionality in a wide range of small molecules, unprotected tyrosine, and tyrosine residues embedded within a range of complex, fully unprotected peptides. The transformation, which uses glycosyl fluoride donors and is promoted by Ca(OH)2, proceeds rapidly at room temperature in water, with good yields and selective formation of unique anomeric products depending on the stereochemistry of the glycosyl donor. High functional group tolerance is observed, and the phenol glycosylation occurs selectively in the presence of virtually all side chains of the proteinogenic amino acids with the singular exception of Cys. This method offers a highly selective, efficient, and operationally simple approach for the protecting-group-free synthesis of O-aryl glycosides and Tyr-O-glycosylated peptides in water.

  15. Solvent-molecule-mediated manipulation of crystalline grains for efficient planar binary lead and tin triiodide perovskite solar cells

    Science.gov (United States)

    Zhu, Leize; Yuh, Brian; Schoen, Stefan; Li, Xinpei; Aldighaithir, Mohammed; Richardson, Beau J.; Alamer, Ahmed; Yu, Qiuming

    2016-03-01

    Binary lead and tin perovskites offer the benefits of narrower band gaps for broader adsorption of solar spectrum and better charge transport for higher photocurrent density. Here, we report the growth of large, smooth crystalline grains of bianry lead and tin triiodide perovskite films via a two-step solution process with thermal plus solvent vapor-assisted thermal annealing. The crystalline SnxPb1-xI2 films formed in the first step served as the templates for the formation of crystalline CH3NH3SnxPb1-xI3 films during the second step interdiffusion of methylammonium iodide (MAI). Followed by dimethylsulfoxide (DMSO) vapor-assisted thermal annealing, small, faceted perovskite grains grew into large, smooth grains via the possible mechanism involving bond breaking and reforming mediated by DMSO solvent molecules. The absorption onset was extended to 950 and 1010 nm for the CH3NH3SnxPb1-xI3 perovskites with x = 0.1 and 0.25, respectively. The highest PCE of 10.25% was achieved from the planar perovskite solar cell with the CH3NH3Sn0.1Pb0.9I3 layer prepared via the thermal plus DMSO vapor-assisted thermal annealing. This research provides a way to control and manipulate film morphology, grain size, and especially the distribution of metal cations in binary metal perovskite layers, which opens an avenue to grow perovskite materials with desired properties to enhance device performance.Binary lead and tin perovskites offer the benefits of narrower band gaps for broader adsorption of solar spectrum and better charge transport for higher photocurrent density. Here, we report the growth of large, smooth crystalline grains of bianry lead and tin triiodide perovskite films via a two-step solution process with thermal plus solvent vapor-assisted thermal annealing. The crystalline SnxPb1-xI2 films formed in the first step served as the templates for the formation of crystalline CH3NH3SnxPb1-xI3 films during the second step interdiffusion of methylammonium iodide (MAI

  16. The effect of micro-environment on luminescence of aequorin: the role of amino acids and explicit water molecules on spectroscopic properties of coelenteramide.

    Science.gov (United States)

    Li, Zuo-Sheng; Zou, Lu-Yi; Min, Chun-Gang; Ren, Ai-Min

    2013-10-05

    Despite the fact that the luminescence reaction mechanism of aequorin has been intensively investigated, details in luminescence such as the effect of important amino acids residues and explicit water molecules on spectroscopic properties of coelenteramide remain unclear. In this work, the effect of amino acids residues His16, Tyr82, Trp86, Phe113, Trp129, Tyr132, explicit water molecules Wat505 and Wat405 on the spectral properties of CLM(-) has been studied by CAM-B3LYP, TD M06L and TD CAM-B3LYP methods in hydrophobic environment and aqueous solution. In hydrophobic environment, the amino acids or water molecules have no significant effect on the absorption. Tyr82 and Trp86 move close to CLM(-) changes the hydrogen bond network, and thus, the spectral properties is significantly affected by the hydrogen bonds between His16H(+)+Tyr82+Trp86 and CLM(-). Tyr82, Trp86 hydrogen bonding to CLM(-) upshifts the excited energy and helps emission spectra shift to blue region. Therefore, it is concluded that His16H(+)+Tyr82+Trp86 modify the emission spectra. The molecular electrostatic potential indicated that the greater electron density is located at the oxygen atom of 6-p-hydroxyphenyl group of CLM(-), and it facilitates the formation of hydrogen bond with His16H(+)+Tyr82+Trp86. It is a critical condition for the modification of emission spectra. It is expected to help to understand the interactions between emitter and amino acids in the micro environment. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles.

    Science.gov (United States)

    Okumura, Hisashi; Itoh, Satoru G; Okamoto, Yuko

    2007-02-28

    The authors propose explicit symplectic integrators of molecular dynamics (MD) algorithms for rigid-body molecules in the canonical and isobaric-isothermal ensembles. They also present a symplectic algorithm in the constant normal pressure and lateral surface area ensemble and that combined with the Parrinello-Rahman algorithm. Employing the symplectic integrators for MD algorithms, there is a conserved quantity which is close to Hamiltonian. Therefore, they can perform a MD simulation more stably than by conventional nonsymplectic algorithms. They applied this algorithm to a TIP3P pure water system at 300 K and compared the time evolution of the Hamiltonian with those by the nonsymplectic algorithms. They found that the Hamiltonian was conserved well by the symplectic algorithm even for a time step of 4 fs. This time step is longer than typical values of 0.5-2 fs which are used by the conventional nonsymplectic algorithms.

  18. Small-Molecule Organic Photovoltaic Modules Fabricated via Halogen-Free Solvent System with Roll-to-Roll Compatible Scalable Printing Method.

    Science.gov (United States)

    Heo, Youn-Jung; Jung, Yen-Sook; Hwang, Kyeongil; Kim, Jueng-Eun; Yeo, Jun-Seok; Lee, Sehyun; Jeon, Ye-Jin; Lee, Donmin; Kim, Dong-Yu

    2017-11-15

    For the first time, the photovoltaic modules composed of small molecule were successfully fabricated by using roll-to-roll compatible printing techniques. In this study, blend films of small molecules, BTR and PC 71 BM were slot-die coated using a halogen-free solvent system. As a result, high efficiencies of 7.46% and 6.56% were achieved from time-consuming solvent vapor annealing (SVA) treatment and roll-to-roll compatible solvent additive approaches, respectively. After successful verification of our roll-to-roll compatible method on small-area devices, we further fabricated large-area photovoltaic modules with a total active area of 10 cm 2 , achieving a power conversion efficiency (PCE) of 4.83%. This demonstration of large-area photovoltaic modules through roll-to-roll compatible printing methods, even based on a halogen-free solvent, suggests the great potential for the industrial-scale production of organic solar cells (OSCs).

  19. The Indigo Molecule Revisited Again: Assessment of the Minnesota Family of Density Functionals for the Prediction of Its Maximum Absorption Wavelengths in Various Solvents

    Directory of Open Access Journals (Sweden)

    Francisco Cervantes-Navarro

    2013-01-01

    Full Text Available The Minnesota family of density functionals (M05, M05-2X, M06, M06L, M06-2X, and M06-HF were evaluated for the calculation of the UV-Vis spectra of the indigo molecule in solvents of different polarities using time-dependent density functional theory (TD-DFT and the polarized continuum model (PCM. The maximum absorption wavelengths predicted for each functional were compared with the known experimental results.

  20. Bis{μ-cis-1,3-bis[(di-tert-butylphosphanyloxy]cyclohexane-κ2P:P′}bis[carbonylnickel(0] including an unknown solvent molecule

    Directory of Open Access Journals (Sweden)

    Klara J. Jonasson

    2014-05-01

    Full Text Available The title compound, [Ni2(C22H46P2O22(CO2], is located about a centre of inversion with the Ni0 atom within a distorted trigonal–planar geometry. The cyclohexyl rings are in the usual chair conformation with the 1,3-cis substituents equatorially oriented. No specific intermolecular interactions are noted in the crystal packing. A region of disordered electron density, most probably a disordered deuterobenzene solvent molecule, was treated using the SQUEEZE routine in PLATON [Spek (2009. Acta Cryst. D65, 148–155]. Its formula mass and unit-cell characteristics were not taken into account during refinement.

  1. Computing pKa Values in Different Solvents by Electrostatic Transformation.

    Science.gov (United States)

    Rossini, Emanuele; Netz, Roland R; Knapp, Ernst-Walter

    2016-07-12

    We introduce a method that requires only moderate computational effort to compute pKa values of small molecules in different solvents with an average accuracy of better than 0.7 pH units. With a known pKa value in one solvent, the electrostatic transform method computes the pKa value in any other solvent if the proton solvation energy is known in both considered solvents. To apply the electrostatic transform method to a molecule, the electrostatic solvation energies of the protonated and deprotonated molecular species are computed in the two considered solvents using a dielectric continuum to describe the solvent. This is demonstrated for 30 molecules belonging to 10 different molecular families by considering 77 measured pKa values in 4 different solvents: water, acetonitrile, dimethyl sulfoxide, and methanol. The electrostatic transform method can be applied to any other solvent if the proton solvation energy is known. It is exclusively based on physicochemical principles, not using any empirical fetch factors or explicit solvent molecules, to obtain agreement with measured pKa values and is therefore ready to be generalized to other solute molecules and solvents. From the computed pKa values, we obtained relative proton solvation energies, which agree very well with the proton solvation energies computed recently by ab initio methods, and used these energies in the present study.

  2. Effects of solvent additive on “s-shaped” curves in solution-processed small molecule solar cells

    Directory of Open Access Journals (Sweden)

    John A. Love

    2016-11-01

    Full Text Available A novel molecular chromophore, p-SIDT(FBTThCA82, is introduced as an electron-donor material for bulk heterojunction (BHJ solar cells with broad absorption and near ideal energy levels for the use in combination with common acceptor materials. It is found that films cast from chlorobenzene yield devices with strongly s-shaped current–voltage curves, drastically limiting performance. We find that addition of the common solvent additive diiodooctane, in addition to facilitating crystallization, leads to improved vertical phase separation. This yields much better performing devices, with improved curve shape, demonstrating the importance of morphology control in BHJ devices and improving the understanding of the role of solvent additives.

  3. Dimer formation enhances structural differences between amyloid β-protein (1-40 and (1-42: an explicit-solvent molecular dynamics study.

    Directory of Open Access Journals (Sweden)

    Bogdan Barz

    Full Text Available Amyloid β-protein (Aβ is central to the pathology of Alzheimer's disease. A 5% difference in the primary structure of the two predominant alloforms, Aβ(1-40 and Aβ(1-42, results in distinct assembly pathways and toxicity properties. Discrete molecular dynamics (DMD studies of Aβ(1-40 and Aβ(1-42 assembly resulted in alloform-specific oligomer size distributions consistent with experimental findings. Here, a large ensemble of DMD-derived Aβ(1-40 and Aβ(1-42 monomers and dimers was subjected to fully atomistic molecular dynamics (MD simulations using the OPLS-AA force field combined with two water models, SPCE and TIP3P. The resulting all-atom conformations were slightly larger, less compact, had similar turn and lower β-strand propensities than those predicted by DMD. Fully atomistic Aβ(1-40 and Aβ(1-42 monomers populated qualitatively similar free energy landscapes. In contrast, the free energy landscape of Aβ(1-42 dimers indicated a larger conformational variability in comparison to that of Aβ(1-40 dimers. Aβ(1-42 dimers were characterized by an increased flexibility in the N-terminal region D1-R5 and a larger solvent exposure of charged amino acids relative to Aβ(1-40 dimers. Of the three positively charged amino acids, R5 was the most and K16 the least involved in salt bridge formation. This result was independent of the water model, alloform, and assembly state. Overall, salt bridge propensities increased upon dimer formation. An exception was the salt bridge propensity of K28, which decreased upon formation of Aβ(1-42 dimers and was significantly lower than in Aβ(1-40 dimers. The potential relevance of the three positively charged amino acids in mediating the Aβ oligomer toxicity is discussed in the light of available experimental data.

  4. Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points.

    Science.gov (United States)

    Harris, Robert C; Deng, Nanjie; Levy, Ronald M; Ishizuka, Ryosuke; Matubayasi, Nobuyuki

    2017-06-05

    Many biomolecules undergo conformational changes associated with allostery or ligand binding. Observing these changes in computer simulations is difficult if their timescales are long. These calculations can be accelerated by observing the transition on an auxiliary free energy surface with a simpler Hamiltonian and connecting this free energy surface to the target free energy surface with free energy calculations. Here, we show that the free energy legs of the cycle can be replaced with energy representation (ER) density functional approximations. We compute: (1) The conformational free energy changes for alanine dipeptide transitioning from the right-handed free energy basin to the left-handed basin and (2) the free energy difference between the open and closed conformations of β-cyclodextrin, a "host" molecule that serves as a model for molecular recognition in host-guest binding. β-cyclodextrin contains 147 atoms compared to 22 atoms for alanine dipeptide, making β-cyclodextrin a large molecule for which to compute solvation free energies by free energy perturbation or integration methods and the largest system for which the ER method has been compared to exact free energy methods. The ER method replaced the 28 simulations to compute each coupling free energy with two endpoint simulations, reducing the computational time for the alanine dipeptide calculation by about 70% and for the β-cyclodextrin by > 95%. The method works even when the distribution of conformations on the auxiliary free energy surface differs substantially from that on the target free energy surface, although some degree of overlap between the two surfaces is required. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  5. Size effects of solvent molecules on the phase behavior and effective interaction of colloidal systems with the bridging attraction

    International Nuclear Information System (INIS)

    Chen, Jie; Wang, Xuewu; Kline, Steven R; Liu, Yun

    2016-01-01

    There has been much recent research interest towards understanding the phase behavior of colloidal systems interacting with a bridging attraction, where the small solvent particles and large solute colloidal particles can be reversibly associated with each other. These systems show interesting phase behavior compared to the more widely studied depletion attraction systems. Here, we use Baxter’s two-component sticky hard sphere model with a Percus–Yevick closure to solve the Ornstein–Zernike equation and study the size effect on colloidal systems with bridging attractions. The spinodal decomposition regions, percolation transition boundaries and binodal regions are systematically investigated as a function of the relative size of the small solvent and large solute particles as well as the attraction strength between the small and large particles. In the phase space determined by the concentrations of small and large particles, the spinodal and binodal regions form isolated islands. The locations and shapes of the spinodal and binodal regions sensitively depend on the relative size of the small and large particles and the attraction strength between them. The percolation region shrinks by decreasing the size ratio, while the binodal region slightly expands with the decrease of the size ratio. Our results are very important in understanding the phase behavior for a bridging attraction colloidal system, a model system that provides insight into oppositely charged colloidal systems, protein phase behavior, and colloidal gelation mechanisms. (paper)

  6. Size effects of solvent molecules on the phase behavior and effective interaction of colloidal systems with the bridging attraction.

    Science.gov (United States)

    Chen, Jie; Wang, Xuewu; Kline, Steven R; Liu, Yun

    2016-11-16

    There has been much recent research interest towards understanding the phase behavior of colloidal systems interacting with a bridging attraction, where the small solvent particles and large solute colloidal particles can be reversibly associated with each other. These systems show interesting phase behavior compared to the more widely studied depletion attraction systems. Here, we use Baxter's two-component sticky hard sphere model with a Percus-Yevick closure to solve the Ornstein-Zernike equation and study the size effect on colloidal systems with bridging attractions. The spinodal decomposition regions, percolation transition boundaries and binodal regions are systematically investigated as a function of the relative size of the small solvent and large solute particles as well as the attraction strength between the small and large particles. In the phase space determined by the concentrations of small and large particles, the spinodal and binodal regions form isolated islands. The locations and shapes of the spinodal and binodal regions sensitively depend on the relative size of the small and large particles and the attraction strength between them. The percolation region shrinks by decreasing the size ratio, while the binodal region slightly expands with the decrease of the size ratio. Our results are very important in understanding the phase behavior for a bridging attraction colloidal system, a model system that provides insight into oppositely charged colloidal systems, protein phase behavior, and colloidal gelation mechanisms.

  7. Recovery of bioactive molecules from chestnut (Castanea sativa Mill.) by-products through extraction by different solvents.

    Science.gov (United States)

    Vella, Filomena Monica; Laratta, Bruna; La Cara, Francesco; Morana, Alessandra

    2018-05-01

    The underutilised forest and industrial biomass of Castanea sativa (Mill.) is generally discarded during post-harvest and food processing, with high impact on environmental quality. The searching on alternative sources of natural antioxidants from low-cost supplies, by methods involving environment-friendly techniques, has become a major goal of numerous researches in recent times. The aim of the present study was the set-up of a biomolecules extraction procedure from chestnut leaves, burs and shells and the assessing of their potential antioxidant activity. Boiling water was the best extraction solvent referring to polyphenols from chestnut shells and burs, whereas the most efficient for leaves resulted 60% ethanol at room temperature. Greatest polyphenol contents were 90.35, 60.01 and 17.68 mg gallic acid equivalents g -1 in leaves, burs and shells, respectively. Moreover, flavonoids, tannins and antioxidant activity were assessed on the best extract obtained from each chestnut by-product.

  8. A novel method for determining the solubility of small molecules in aqueous media and polymer solvent systems using solution calorimetry.

    Science.gov (United States)

    Fadda, Hala M; Chen, Xin; Aburub, Aktham; Mishra, Dinesh; Pinal, Rodolfo

    2014-07-01

    To explore the application of solution calorimetry for measuring drug solubility in experimentally challenging situations while providing additional information on the physical properties of the solute material. A semi-adiabatic solution calorimeter was used to measure the heat of dissolution of prednisolone and chlorpropamide in aqueous solvents and of griseofulvin and ritonavir in viscous solutions containing polyvinylpyrrolidone and N-ethylpyrrolidone. Dissolution end point was clearly ascertained when heat generation stopped. The heat of solution was a linear function of dissolved mass for all drugs (solution of 9.8 ± 0.8, 28.8 ± 0.6, 45.7 ± 1.6 and 159.8 ± 20.1 J/g were obtained for griseofulvin, ritonavir, prednisolone and chlorpropamide, respectively. Saturation was identifiable by a plateau in the heat signal and the crossing of the two linear segments corresponds to the solubility limit. The solubilities of prednisolone and chlopropamide in water by the calorimetric method were 0.23 and 0.158 mg/mL, respectively, in agreement with the shake-flask/HPLC-UV determined values of 0.212 ± 0.013 and 0.169 ± 0.015 mg/mL, respectively. For the higher solubility and high viscosity systems of griseofulvin and ritonavir in NEP/PVP mixtures, respectively, solubility values of 65 and 594 mg/g, respectively, were obtained. Solution calorimetry offers a reliable method for measuring drug solubility in organic and aqueous solvents. The approach is complementary to the traditional shake-flask method, providing information on the solid properties of the solute. For highly viscous solutions, the calorimetric approach is advantageous.

  9. Tar removal from biosyngas in the biomass gasification process. (Liquid + liquid) equilibrium {water + solvent (paraxylene and methyl hexadecanoate) + model molecules of tar (benzene, toluene, phenol)}

    International Nuclear Information System (INIS)

    Bassil, Georgio; Mokbel, Ilham; Abou Naccoul, Ramy; Stephan, Juliette; Jose, Jacques; Goutaudier, Christelle

    2012-01-01

    Highlights: ► (Liquid + liquid) equilibria at atmospheric pressure. ► Solubility of benzene (or toluene or phenol) in paraxylene at (303 to 343) K. ► Solubility of benzene (or toluene or phenol) in methyl palmitate or methyl hexadecanoate at (303 to 343) K. ► Correlation of LLE using NRTL model. - Abstract: Tar is generated in the process by the condensation of the gas resulting from biomass gasification. The objective of this work is a contribution to the database on thermodynamic quantity which will be useful at the operation of tar removal from aqueous medium. With this aim, (liquid + liquid) equilibrium of {water + solvent (paraxylene and methyl hexadecanoate) + model molecules of tar (benzene, toluene, phenol)} was studied at temperatures (303.2, 323.2, and 343.2) K. The data obtained were correlated with the non-random two-liquid (NRTL) model.

  10. Radii of gyration and screening lengths of polystyrene molecules dissolved in a good solvent as a function of concentration

    International Nuclear Information System (INIS)

    King, J.S.; Ullman, R.; Boyer, W.; Wignall, G.D.

    1985-01-01

    The swelling of macromolecules in a good solvent arises from excluded volume interactions between pairs of monomer units on a single polymer chain. As the polymer concentration increases, the excluded volume effect is screened and diminished, and in the limit of the bulk polymer, the conformation of a single chain can be described as an unperturbed random coil as originally predicted by Flory and verified by numerous SANS measurements. Since the early 1970s, developments in polymer solution theory involving the application of scaling methods have led to an upsurge of interest in this area, although only one systematic experimental study of chain dimensions as a function of concentration, c, has been hitherto attempted. That study showed that for polystyrene in CS 2 the radius of gyration R/sub g/ varied as c/sup -0.25/ in apparent agreement with the then current prediction of scaling laws. Since that time, there have been reports of many violations of scaling laws which should be valid in principle only in the asymptotic limit of infinite molecular weight

  11. Explicit Interaction

    DEFF Research Database (Denmark)

    Löwgren, Jonas; Eriksen, Mette Agger; Linde, Per

    2006-01-01

    We report an ongoing study of palpable computing to support surgical rehabilitation, in the general field of interaction design for ubiquitous computing. Through explorative design, fieldwork and participatory design techniques, we explore the design principle of explicit interaction as an interp...

  12. From the depletion attraction to the bridging attraction: the effect of solvent molecules on the effective colloidal interactions.

    Science.gov (United States)

    Chen, Jie; Kline, Steven R; Liu, Yun

    2015-02-28

    Depletion attraction induced by non-adsorbing polymers or small particles in colloidal solutions has been widely used as a model colloidal interaction to understand aggregation behavior and phase diagrams, such as glass transitions and gelation. However, much less attention has been paid to study the effective colloidal interaction when small particles/molecules can be reversibly attracted to large colloidal particles. At the strong attraction limit, small particles can introduce bridging attraction as it can simultaneously attach to neighbouring large colloidal particles. We use Baxter's multi-component method for sticky hard sphere systems with the Percus-Yevick approximation to study the bridging attraction and its consequence to phase diagrams, which are controlled by the concentration of small particles and their interaction with large particles. When the concentration of small particles is very low, the bridging attraction strength increases very fast with the increase of small particle concentration. The attraction strength eventually reaches a maximum bridging attraction (MBA). Adding more small particles after the MBA concentration keeps decreasing the attraction strength until reaching a concentration above which the net effect of small particles only introduces an effective repulsion between large colloidal particles. These behaviors are qualitatively different from the concentration dependence of the depletion attraction on small particles and make phase diagrams very rich for bridging attraction systems. We calculate the spinodal and binodal regions, the percolation lines, the MBA lines, and the equivalent hard sphere interaction line for bridging attraction systems and have proposed a simple analytic solution to calculate the effective attraction strength using the concentrations of large and small particles. Our theoretical results are found to be consistent with experimental results reported recently.

  13. Reformulation of Maxwell's equations to incorporate near-solute solvent structure.

    Science.gov (United States)

    Yang, Pei-Kun; Lim, Carmay

    2008-09-04

    Maxwell's equations, which treat electromagnetic interactions between macroscopic charged objects in materials, have explained many phenomena and contributed to many applications in our lives. Derived in 1861 when no methods were available to determine the atomic structure of macromolecules, Maxwell's equations assume the solvent to be a structureless continuum. However, near-solute solvent molecules are highly structured, unlike far-solute bulk solvent molecules. Current methods cannot treat both the near-solute solvent structure and time-dependent electromagnetic interactions in a macroscopic system. Here, we derive "microscopic" electrodynamics equations that can treat macroscopic time-dependent electromagnetic field problems like Maxwell's equations and reproduce the solvent molecular and dipole density distributions observed in molecular dynamics simulations. These equations greatly reduce computational expense by not having to include explicit solvent molecules, yet they treat the solvent electrostatic and van der Waals effects more accurately than continuum models. They provide a foundation to study electromagnetic interactions between molecules in a macroscopic system that are ubiquitous in biology, bioelectromagnetism, and nanotechnology. The general strategy presented herein to incorporate the near-solute solvent structure would enable studies on how complex cellular protein-ligand interactions are affected by electromagnetic radiation, which could help to prevent harmful electromagnetic spectra or find potential therapeutic applications.

  14. Variation and decomposition of the partial molar volume of small gas molecules in different organic solvents derived from molecular dynamics simulations.

    Science.gov (United States)

    Klähn, Marco; Martin, Alistair; Cheong, Daniel W; Garland, Marc V

    2013-12-28

    The partial molar volumes, V(i), of the gas solutes H2, CO, and CO2, solvated in acetone, methanol, heptane, and diethylether are determined computationally in the limit of infinite dilution and standard conditions. Solutions are described with molecular dynamics simulations in combination with the OPLS-aa force field for solvents and customized force field for solutes. V(i) is determined with the direct method, while the composition of V(i) is studied with Kirkwood-Buff integrals (KBIs). Subsequently, the amount of unoccupied space and size of pre-formed cavities in pure solvents is determined. Additionally, the shape of individual solvent cages is analyzed. Calculated V(i) deviate only 3.4 cm(3) mol(-1) (7.1%) from experimental literature values. Experimental V(i) variations across solutions are reproduced qualitatively and also quantitatively in most cases. The KBI analysis identifies differences in solute induced solvent reorganization in the immediate vicinity of H2 (<0.7 nm) and solvent reorganization up to the third solvation shell of CO and CO2 (<1.6 nm) as the origin of V(i) variations. In all solutions, larger V(i) are found in solvents that exhibit weak internal interactions, low cohesive energy density and large compressibility. Weak internal interactions facilitate solvent displacement by thermal solute movement, which enhances the size of solvent cages and thus V(i). Additionally, attractive electrostatic interactions of CO2 and the solvents, which do not depend on internal solvent interactions only, partially reversed the V(i) trends observed in H2 and CO solutions where electrostatic interactions with the solvents are absent. More empty space and larger pre-formed cavities are found in solvents with weak internal interactions, however, no evidence is found that solutes in any considered solvent are accommodated in pre-formed cavities. Individual solvent cages are found to be elongated in the negative direction of solute movement. This wake behind

  15. Variation and decomposition of the partial molar volume of small gas molecules in different organic solvents derived from molecular dynamics simulations

    Science.gov (United States)

    Klähn, Marco; Martin, Alistair; Cheong, Daniel W.; Garland, Marc V.

    2013-12-01

    The partial molar volumes, bar V_i, of the gas solutes H2, CO, and CO2, solvated in acetone, methanol, heptane, and diethylether are determined computationally in the limit of infinite dilution and standard conditions. Solutions are described with molecular dynamics simulations in combination with the OPLS-aa force field for solvents and customized force field for solutes. bar V_i is determined with the direct method, while the composition of bar V_i is studied with Kirkwood-Buff integrals (KBIs). Subsequently, the amount of unoccupied space and size of pre-formed cavities in pure solvents is determined. Additionally, the shape of individual solvent cages is analyzed. Calculated bar V_i deviate only 3.4 cm3 mol-1 (7.1%) from experimental literature values. Experimental bar V_i variations across solutions are reproduced qualitatively and also quantitatively in most cases. The KBI analysis identifies differences in solute induced solvent reorganization in the immediate vicinity of H2 (<0.7 nm) and solvent reorganization up to the third solvation shell of CO and CO2 (<1.6 nm) as the origin of bar V_i variations. In all solutions, larger bar V_i are found in solvents that exhibit weak internal interactions, low cohesive energy density and large compressibility. Weak internal interactions facilitate solvent displacement by thermal solute movement, which enhances the size of solvent cages and thus bar V_i. Additionally, attractive electrostatic interactions of CO2 and the solvents, which do not depend on internal solvent interactions only, partially reversed the bar V_i trends observed in H2 and CO solutions where electrostatic interactions with the solvents are absent. More empty space and larger pre-formed cavities are found in solvents with weak internal interactions, however, no evidence is found that solutes in any considered solvent are accommodated in pre-formed cavities. Individual solvent cages are found to be elongated in the negative direction of solute

  16. Towards Better Precision Medicine: PacBio Single-Molecule Long Reads Resolve the Interpretation of HIV Drug Resistant Mutation Profiles at Explicit Quasispecies (Haplotype) Level.

    Science.gov (United States)

    Huang, Da Wei; Raley, Castle; Jiang, Min Kang; Zheng, Xin; Liang, Dun; Rehman, M Tauseef; Highbarger, Helene C; Jiao, Xiaoli; Sherman, Brad; Ma, Liang; Chen, Xiaofeng; Skelly, Thomas; Troyer, Jennifer; Stephens, Robert; Imamichi, Tomozumi; Pau, Alice; Lempicki, Richard A; Tran, Bao; Nissley, Dwight; Lane, H Clifford; Dewar, Robin L

    2016-01-01

    Development of HIV-1 drug resistance mutations (HDRMs) is one of the major reasons for the clinical failure of antiretroviral therapy. Treatment success rates can be improved by applying personalized anti-HIV regimens based on a patient's HDRM profile. However, the sensitivity and specificity of the HDRM profile is limited by the methods used for detection. Sanger-based sequencing technology has traditionally been used for determining HDRM profiles at the single nucleotide variant (SNV) level, but with a sensitivity of only ≥ 20% in the HIV population of a patient. Next Generation Sequencing (NGS) technologies offer greater detection sensitivity (~ 1%) and larger scope (hundreds of samples per run). However, NGS technologies produce reads that are too short to enable the detection of the physical linkages of individual SNVs across the haplotype of each HIV strain present. In this article, we demonstrate that the single-molecule long reads generated using the Third Generation Sequencer (TGS), PacBio RS II, along with the appropriate bioinformatics analysis method, can resolve the HDRM profile at a more advanced quasispecies level. The case studies on patients' HIV samples showed that the quasispecies view produced using the PacBio method offered greater detection sensitivity and was more comprehensive for understanding HDRM situations, which is complement to both Sanger and NGS technologies. In conclusion, the PacBio method, providing a promising new quasispecies level of HDRM profiling, may effect an important change in the field of HIV drug resistance research.

  17. Density functional theory studies on the solvent effects in Al(H2O)63+ water-exchange reactions: the number and arrangement of outer-sphere water molecules.

    Science.gov (United States)

    Liu, Li; Zhang, Jing; Dong, Shaonan; Zhang, Fuping; Wang, Ye; Bi, Shuping

    2018-03-07

    Density functional theory (DFT) calculations combined with cluster models are performed at the B3LYP/6-311+G(d,p) level for investigating the solvent effects in Al(H 2 O) 6 3+ water-exchange reactions. A "One-by-one" method is proposed to obtain the most representative number and arrangement of explicit H 2 Os in the second hydration sphere. First, all the possible ways to locate one explicit H 2 O in second sphere (N m ' = 1) based on the gas phase structure (N m ' = 0) are examined, and the optimal pathway (with the lowest energy barrier) for N m ' = 1 is determined. Next, more explicit H 2 Os are added one by one until the inner-sphere is fully hydrogen bonded. Finally, the optimal pathways with N m ' = 0-7 are obtained. The structural and energetic parameters as well as the lifetimes of the transition states are compared with the results obtained with the "Independent-minimum" method and the "Independent-average" method, and all three methods show that the pathway with N m ' = 6 may be representative. Our results give a new idea for finding the representative pathway for water-exchange reactions in other hydrated metal ion systems.

  18. A multi target approach to control chemical reactions in their inhomogeneous solvent environment

    International Nuclear Information System (INIS)

    Keefer, Daniel; Thallmair, Sebastian; Zauleck, Julius P P; Vivie-Riedle, Regina de

    2015-01-01

    Shaped laser pulses offer a powerful tool to manipulate molecular quantum systems. Their application to chemical reactions in solution is a promising concept to redesign chemical synthesis. Along this road, theoretical developments to include the solvent surrounding are necessary. An appropriate theoretical treatment is helpful to understand the underlying mechanisms. In our approach we simulate the solvent by randomly selected snapshots from molecular dynamics trajectories. We use multi target optimal control theory to optimize pulses for the various arrangements of explicit solvent molecules simultaneously. This constitutes a major challenge for the control algorithm, as the solvent configurations introduce a large inhomogeneity to the potential surfaces. We investigate how the algorithm handles the new challenges and how well the controllability of the system is preserved with increasing complexity. Additionally, we introduce a way to statistically estimate the efficiency of the optimized laser pulses in the complete thermodynamical ensemble. (paper)

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. Unexpected solvent effects on the UV/Vis absorption spectra of o-cresol in toluene and benzene: in contrast with non-aromatic solvents.

    Science.gov (United States)

    Zheng, Dong; Yuan, Xiang-Ai; Ma, Haibo; Li, Xiaoxiong; Wang, Xizhang; Liu, Ziteng; Ma, Jing

    2018-03-01

    Cresol is a prototype molecule in understanding intermolecular interactions in material and biological systems, because it offers different binding sites with various solvents and protonation states under different pH values. It is found that the UV/Vis absorption spectra of o -cresol in aromatic solvents (benzene, toluene) are characterized by a sharp peak, unlike the broad double-peaks in 11 non-aromatic solvents. Both molecular dynamics simulations and electronic structure calculations revealed the formation of intermolecular π-complexation between o -cresol and aromatic solvents. The thermal movements of solvent and solute molecules render the conformations of o -cresol changing between trans and cis isomers. The π-interaction makes the cis configuration a dominant isomer, hence leading to the single keen-edged UV/Vis absorption peak at approximately 283 nm. The free conformation changes between trans and cis in aqueous solution rationalize the broader absorption peaks in the range of 260-280 nm. The pH dependence of the UV/Vis absorption spectra in aqueous solutions is also rationalized by different protonation states of o -cresol. The explicit solvent model with long-ranged interactions is vital to describe the effects of π-complexation and electrostatic interaction on the UV/Vis absorption spectra of o -cresol in toluene and alkaline aqueous (pH > 10.3) solutions, respectively.

  1. Synergistic Impact of Solvent and Polymer Additives on the Film Formation of Small Molecule Blend Films for Bulk Heterojunction Solar Cells

    KAUST Repository

    McDowell, Caitlin

    2015-07-14

    The addition of polystyrene (PS), a typical insulator, is empirically shown to increase the power conversion efficiencies (PCEs) of a solution-deposited bulk heterojunction (BHJ) molecular blend film used in solar cell fabrication: p-DTS(FBTTh2)2/PC71BM. The performance is further improved by small quantities of diiodooctane (DIO), an established solvent additive. In this study, how the addition of PS and DIO affects the film formation of this bulk heterojunction blend film are probed via in situ monitoring of absorbance, thickness, and crystallinity. PS and DIO additives are shown to promote donor crystallite formation on different time scales and through different mechanisms. PS-containing films retain chlorobenzene solvent, extending evaporation time and promoting phase separation earlier in the casting process. This extended time is insufficient to attain the morphology for optimal PCE results before the film sets. Here is where the presence of DIO comes into play: its low vapor pressure further extends the time scale of film evolution and allows for crystalline rearrangement of the donor phase long after casting, ultimately leading to the best BHJ organization. In situ measurement shows that polystyrene (PS) and diiodooctane (DIO) additives promote donor crystallite formation synergistically, on different time scales, and through different mechanisms. PS-rich films retain solvent, promoting phase separation early in the casting process. Meanwhile, the low vapor pressure of DIO extends the time scale of film evolution and allows for crystalline rearrangement of the donor phase after casting. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. The impact of solvent relative permittivity on the dimerisation of organic molecules well below their solubility limits: examples from brewed coffee and beyond.

    Science.gov (United States)

    Bradley, Ellen S; Hendon, Christopher H

    2017-03-22

    The formation of aqueous intermolecular dimers is governed by both the nature and strength of the intermolecular interactions and the entropy of dissolution. The former interaction energies are determined by the polarity of the solvent and the functionality of the solute. Using quantum chemical methods, we probe the energetics of dimer formation of representative compounds found in coffee well below their solubility limits. We find that with the exclusion of entropy, the dimer formation is thermodynamically unfavorable with negligible dependence on the dielectric medium.

  3. Solvent extraction

    Energy Technology Data Exchange (ETDEWEB)

    Coombs, D.M.; Latimer, E.G.

    1988-01-05

    It is an object of this invention to provide for the demetallization and general upgrading of heavy oil via a solvent extracton process, and to improve the efficiency of solvent extraction operations. The yield and demetallization of product oil form heavy high-metal content oil is maximized by solvent extractions which employ either or all of the following techniques: premixing of a minor amount of the solvent with feed and using countercurrent flow for the remaining solvent; use of certain solvent/free ratios; use of segmental baffle tray extraction column internals and the proper extraction column residence time. The solvent premix/countercurrent flow feature of the invention substantially improves extractions where temperatures and pressures above the critical point of the solvent are used. By using this technique, a greater yield of extract oil can be obtained at the same metals content or a lower metals-containing extract oil product can be obtained at the same yield. Furthermore, the premixing of part of the solvent with the feed before countercurrent extraction gives high extract oil yields and high quality demetallization. The solvent/feed ratio features of the invention substanially lower the captial and operating costs for such processes while not suffering a loss in selectivity for metals rejection. The column internals and rsidence time features of the invention further improve the extractor metals rejection at a constant yield or allow for an increase in extract oil yield at a constant extract oil metals content. 13 figs., 3 tabs.

  4. Phenothiazine-based small-molecule organic solar cells with power conversion efficiency over 7% and open circuit voltage of about 1.0 V using solvent vapor annealing.

    Science.gov (United States)

    Rout, Yogajivan; Misra, Rajneesh; Singhal, Rahul; Biswas, Subhayan; Sharma, Ganesh D

    2018-02-28

    We have used two unsymmetrical small molecules, named phenothiazine 1 and 2 with a D-A-D-π-D configuration, where phenothiazine is used as a central unit, triphenylamine is used as a terminal unit and TCBD and cyclohexa-2,5-diene-1,4-diylidene-expanded TCBD are used as an acceptor between the phenothiazine and triphenylamine units, as a small molecule donor along with PC 71 BM as an acceptor for solution processed bulk heterojunction solar cells. The variation of acceptors in the phenothiazine derivatives makes an exciting change in the photophysical and electrochemical properties, hole mobility and therefore photovoltaic performance. The optimized device based on phenothiazine 2 exhibited a high power conversion efficiency of 7.35% (J sc = 11.98 mA cm -2 , V oc = 0.99 V and FF = 0.62), while the device based on phenothiazine 1 showed a low PCE of 4.81% (J sc = 8.73 mA cm -2 , V oc = 0.95 V and FF = 0.58) after solvent vapour annealing (SVA) treatment. The higher value of power conversion efficiency of the 2 based devices irrespective of the processing conditions may be related to the broader absorption and lower band gap of 2 as compared to 1. The improvement in the SVA treated active layer may be related to the enhanced crystallinity, molecular ordering and aggregation and shorter π-π stacking distance of the small molecule donors.

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

    Science.gov (United States)

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

    2013-11-14

    calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol(-1)). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

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

    Energy Technology Data Exchange (ETDEWEB)

    Rocklin, Gabriel J. [Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550, USA and Biophysics Graduate Program, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550 (United States); Mobley, David L. [Departments of Pharmaceutical Sciences and Chemistry, University of California Irvine, 147 Bison Modular, Building 515, Irvine, California 92697-0001, USA and Department of Chemistry, University of New Orleans, 2000 Lakeshore Drive, New Orleans, Louisiana 70148 (United States); Dill, Ken A. [Laufer Center for Physical and Quantitative Biology, 5252 Stony Brook University, Stony Brook, New York 11794-0001 (United States); Hünenberger, Philippe H., E-mail: phil@igc.phys.chem.ethz.ch [Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich (Switzerland)

    2013-11-14

    -periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol{sup −1}). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pK{sub a} and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

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

    Science.gov (United States)

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

    2013-11-01

    calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol-1). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

  8. Solvent-resistant small molecule solar cells by roll-to-roll fabrication via introduction of azide cross-linkable group

    DEFF Research Database (Denmark)

    Chen, Mei-Rong; Fan, Cong-Cheng; Andersen, Thomas Rieks

    2014-01-01

    A novel cross-linkable azide-functionalized diketopyrrolopyrrole based compound DPP(BT-N-3)(2) was designed and synthesized via Stille coupling. Cross-linking of such molecule could help us fabricate insoluble film which could be used to fabricate heterostructures through solution processing......, without dissolving the pre-patterned layers. In order to investigate the photovoltaic performances of the newly synthesized compound, large area solar cells were produced by roll coating technique. Two set of devices were fabricated by employing DPP(BT-N-3)(2) as either an electron donor or acceptor....... A best power conversion efficiency of 0.067%, combined with an open circuit voltage of 0.53 V, and a fill factor of 37.6% were obtained for the device with DPP(BT-N-3)(2) as an electron acceptor. In addition, we could prove that the large area small molecule based organic solar cells could be fabricated...

  9. Solvent Clathrate Driven Dynamic Stereomutation of a Supramolecular Polymer with Molecular Pockets.

    Science.gov (United States)

    Kulkarni, Chidambar; Korevaar, Peter A; Bejagam, Karteek K; Palmans, Anja R A; Meijer, E W; George, Subi J

    2017-10-04

    Control over the helical organization of synthetic supramolecular systems is intensively pursued to manifest chirality in a wide range of applications ranging from electron spin filters to artificial enzymes. Typically, switching the helicity of supramolecular assemblies involves external stimuli or kinetic traps. However, efforts to achieve helix reversal under thermodynamic control and to understand the phenomena at a molecular level are scarce. Here we present a unique example of helix reversal (stereomutation) under thermodynamic control in the self-assembly of a coronene bisimide that has a 3,5-dialkoxy substitution on the imide phenyl groups (CBI-35CH), leading to "molecular pockets" in the assembly. The stereomutation was observed only if the CBI monomer possesses molecular pockets. Detailed chiroptical studies performed in alkane solvents with different molecular structures reveal that solvent molecules intercalate or form clathrates within the molecular pockets of CBI-35CH at low temperature (263 K), thereby triggering the stereomutation. The interplay among the helical assembly, molecular pockets, and solvent molecules is further unraveled by explicit solvent molecular dynamics simulations. Our results demonstrate how the molecular design of self-assembling building blocks can orchestrate the organization of surrounding solvent molecules, which in turn dictates the helical organization of the resulting supramolecular assembly.

  10. Solvent effect in implicit/explicit model on FT-IR, 1H, 13C and 19F NMR, UV-vis and fluorescence spectra, linear, second- and third-nonlinear optical parameters of 2-(trifluoromethyl)benzoic acid: Experimental and computational study

    Science.gov (United States)

    Avcı, Davut; Altürk, Sümeyye; Tamer, Ömer; Kuşbazoğlu, Mustafa; Atalay, Yusuf

    2017-09-01

    FT-IR, 1H, 13C and 19F NMR, UV-vis and fluorescence spectra for 2-(trifluoromethyl)benzoic acid (2-TFMBA) were recorded. DFT//B3LYP/6-31++G(d,p) calculations were used to determine the optimized molecular geometry, vibrational frequencies, 1H, 13C and 19F GIAO-NMR chemical shifts of 2-TFMBA. The detailed assignments of vibrational frequencies were carried out on the basis of potential energy distribution (PED) by using VEDA program. TD-DFT/B3LYP/6-31++G(d,p) calculations with the PCM (polarizable continuum model) in ethanol and DMSO solvents based on implicit/explicit model and gas phase in the excited state were employed to investigate UV-vis absorption and fluorescence emission wavelengths. The UV-vis and emission spectra were given in ethanol and DMSO solvents, and the major contributions to the electronic transitions were obtained. In addition, the NLO parameters (β, γ and χ(3)) and frontier molecular orbital energies of 2-TFMBA were calculated by using B3LYP/6-31++G(d,p) level. The NLO parameters of 2-TFMBA were compared with that of para-Nitroaniline (pNA) and urea which are the typical NLO materials. The refractive index (n) is calculated by using the Lorentz-Lorenz equation to observe polarization behavior of 2-TFMBA in DMSO and ethanol solvents. In order to investigate intramolecular and hydrogen bonding interactions, NBO calculations were also performed by the same level. To sum up, considering the well-known biological role, photochemical properties of 2-TFMBA were discussed.

  11. Deasphalting solvents

    International Nuclear Information System (INIS)

    Carrillo, J. A; Caceres, J; Vela, G; Bueno, H

    1996-01-01

    This paper describes how the deasphalted oil (DMO) or demetalized oil (DMO) quality (CCR, Ni, V end asphaltenes contents) changes with: DAO or DMO yield, solvent/feed ratio, type of vacuum reside (from paraffinic to blends with vis breaking bottoms), extraction temperature and extraction solvent (propane, propylene, n-butane and I butane)

  12. Solvent substitution

    International Nuclear Information System (INIS)

    1990-01-01

    The DOE Environmental Restoration and Waste Management Office of Technology Development and the Air Force Engineering and Services Center convened the First Annual International Workshop on Solvent Substitution on December 4--7, 1990. The primary objectives of this joint effort were to share information and ideas among attendees in order to enhance the development and implementation of required new technologies for the elimination of pollutants associated with industrial use of hazardous and toxic solvents; and to aid in accelerating collaborative efforts and technology transfer between government and industry for solvent substitution. There were workshop sessions focusing on Alternative Technologies, Alternative Solvents, Recovery/Recycling, Low VOC Materials and Treatment for Environmentally Safe Disposal. The 35 invited papers presented covered a wide range of solvent substitution activities including: hardware and weapons production and maintenance, paint stripping, coating applications, printed circuit boards, metal cleaning, metal finishing, manufacturing, compliance monitoring and process control monitoring. This publication includes the majority of these presentations. In addition, in order to further facilitate information exchange and technology transfer, the US Air Force and DOE solicited additional papers under a general ''Call for Papers.'' These papers, which underwent review and final selection by a peer review committee, are also included in this combined Proceedings/Compendium. For those involved in handling, using or managing hazardous and toxic solvents, this document should prove to be a valuable resource, providing the most up-to-date information on current technologies and practices in solvent substitution. Individual papers are abstracted separated

  13. Solvent substitution

    Energy Technology Data Exchange (ETDEWEB)

    1990-01-01

    The DOE Environmental Restoration and Waste Management Office of Technology Development and the Air Force Engineering and Services Center convened the First Annual International Workshop on Solvent Substitution on December 4--7, 1990. The primary objectives of this joint effort were to share information and ideas among attendees in order to enhance the development and implementation of required new technologies for the elimination of pollutants associated with industrial use of hazardous and toxic solvents; and to aid in accelerating collaborative efforts and technology transfer between government and industry for solvent substitution. There were workshop sessions focusing on Alternative Technologies, Alternative Solvents, Recovery/Recycling, Low VOC Materials and Treatment for Environmentally Safe Disposal. The 35 invited papers presented covered a wide range of solvent substitution activities including: hardware and weapons production and maintenance, paint stripping, coating applications, printed circuit boards, metal cleaning, metal finishing, manufacturing, compliance monitoring and process control monitoring. This publication includes the majority of these presentations. In addition, in order to further facilitate information exchange and technology transfer, the US Air Force and DOE solicited additional papers under a general Call for Papers.'' These papers, which underwent review and final selection by a peer review committee, are also included in this combined Proceedings/Compendium. For those involved in handling, using or managing hazardous and toxic solvents, this document should prove to be a valuable resource, providing the most up-to-date information on current technologies and practices in solvent substitution. Individual papers are abstracted separated.

  14. Characterisation of aggregation of tributylphosphate molecules in organic solvent; Caracterisation de l'auto-organisation du phosphate de tributyle en solvant organique

    Energy Technology Data Exchange (ETDEWEB)

    Mandin, C.; Martinet, L.; Zemb, Th.; Berthon, L.; Madic, Ch

    2000-07-01

    This report presents a structural study of the aggregates formed with the organic phases of the extractant tri-n-butyl phosphate, used in the industrial PUREX process (Plutonium and Uranium Extraction; liquid-liquid solvent extraction) for the treatment of high radioactive waste. Combined Small Angle X-ray Scattering and Small Angle Neutron Scattering show that organic TBP solutions (in equilibrium with acid solutions) are organised in oligomeric aggregates. The influence of various parameters such as HNO{sub 3} or TBP concentrations, diluent or acid natures, does not seem to modify the aggregate shape and size, whereas the interactions are modified. Moreover the aggregates disappear under high temperatures, whereas the attractive interactions between them increase at low temperatures. The 'drop weight' method gives the critical micellar concentration values of TBP in case of H{sub 2}O or HNO{sub 3} extractions (H{sub 2}O: 0.48 M; HNO{sub 3} 2M: 0.65 M; at 21 deg C). Furthermore, the measures at different acid concentrations show that the c.m.c. varies with the acidity. The more acid the aqueous phase is, the smaller is the entropy in the system because of the numerous negative charges, i.e. the harder the micellization occurs, so the higher the c.m.c. value is. The sticky sphere model proposed by Baxter, can be used to model successfully small reverse micelles of the organic TBP phases. The aggregation number would be 4{+-}1 (water extraction) and 5{+-}1(HNO{sub 3}2M extraction). These values are also given by vapor pressure measurements. (authors)

  15. Shift in the Equilibrium between On and Off States of the Allosteric Switch in Ras-GppNHp Affected by Small Molecules and Bulk Solvent Composition

    Energy Technology Data Exchange (ETDEWEB)

    Holzapfel, Genevieve; Buhrman, Greg; Mattos, Carla (NCSU)

    2012-08-31

    Ras GTPase cycles between its active GTP-bound form promoted by GEFs and its inactive GDP-bound form promoted by GAPs to affect the control of various cellular functions. It is becoming increasingly apparent that subtle regulation of the GTP-bound active state may occur through promotion of substates mediated by an allosteric switch mechanism that induces a disorder to order transition in switch II upon ligand binding at an allosteric site. We show with high-resolution structures that calcium acetate and either dithioerythritol (DTE) or dithiothreitol (DTT) soaked into H-Ras-GppNHp crystals in the presence of a moderate amount of poly(ethylene glycol) (PEG) can selectively shift the equilibrium to the 'on' state, where the active site appears to be poised for catalysis (calcium acetate), or to what we call the 'ordered off' state, which is associated with an anticatalytic conformation (DTE or DTT). We also show that the equilibrium is reversible in our crystals and dependent on the nature of the small molecule present. Calcium acetate binding in the allosteric site stabilizes the conformation observed in the H-Ras-GppNHp/NOR1A complex, and PEG, DTE, and DTT stabilize the anticatalytic conformation observed in the complex between the Ras homologue Ran and Importin-{beta}. The small molecules are therefore selecting biologically relevant conformations in the crystal that are sampled by the disordered switch II in the uncomplexed GTP-bound form of H-Ras. In the presence of a large amount of PEG, the ordered off conformation predominates, whereas in solution, in the absence of PEG, switch regions appear to remain disordered in what we call the off state, unable to bind DTE.

  16. Difficulties in applying pure Kohn-Sham density functional theory electronic structure methods to protein molecules

    Science.gov (United States)

    Rudberg, Elias

    2012-02-01

    Self-consistency-based Kohn-Sham density functional theory (KS-DFT) electronic structure calculations with Gaussian basis sets are reported for a set of 17 protein-like molecules with geometries obtained from the Protein Data Bank. It is found that in many cases such calculations do not converge due to vanishing HOMO-LUMO gaps. A sequence of polyproline I helix molecules is also studied and it is found that self-consistency calculations using pure functionals fail to converge for helices longer than six proline units. Since the computed gap is strongly correlated to the fraction of Hartree-Fock exchange, test calculations using both pure and hybrid density functionals are reported. The tested methods include the pure functionals BLYP, PBE and LDA, as well as Hartree-Fock and the hybrid functionals BHandHLYP, B3LYP and PBE0. The effect of including solvent molecules in the calculations is studied, and it is found that the inclusion of explicit solvent molecules around the protein fragment in many cases gives a larger gap, but that convergence problems due to vanishing gaps still occur in calculations with pure functionals. In order to achieve converged results, some modeling of the charge distribution of solvent water molecules outside the electronic structure calculation is needed. Representing solvent water molecules by a simple point charge distribution is found to give non-vanishing HOMO-LUMO gaps for the tested protein-like systems also for pure functionals.

  17. Difficulties in applying pure Kohn-Sham density functional theory electronic structure methods to protein molecules

    International Nuclear Information System (INIS)

    Rudberg, Elias

    2012-01-01

    Self-consistency-based Kohn-Sham density functional theory (KS-DFT) electronic structure calculations with Gaussian basis sets are reported for a set of 17 protein-like molecules with geometries obtained from the Protein Data Bank. It is found that in many cases such calculations do not converge due to vanishing HOMO-LUMO gaps. A sequence of polyproline I helix molecules is also studied and it is found that self-consistency calculations using pure functionals fail to converge for helices longer than six proline units. Since the computed gap is strongly correlated to the fraction of Hartree-Fock exchange, test calculations using both pure and hybrid density functionals are reported. The tested methods include the pure functionals BLYP, PBE and LDA, as well as Hartree-Fock and the hybrid functionals BHandHLYP, B3LYP and PBE0. The effect of including solvent molecules in the calculations is studied, and it is found that the inclusion of explicit solvent molecules around the protein fragment in many cases gives a larger gap, but that convergence problems due to vanishing gaps still occur in calculations with pure functionals. In order to achieve converged results, some modeling of the charge distribution of solvent water molecules outside the electronic structure calculation is needed. Representing solvent water molecules by a simple point charge distribution is found to give non-vanishing HOMO-LUMO gaps for the tested protein-like systems also for pure functionals. (fast track communication)

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

    Science.gov (United States)

    Li, Shen; Bradley, Philip

    2013-01-01

    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 non-specific 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 to its fully implicit counterpart, we find that explicit treatment of interfacial waters results in a modest but significant improvement in protein sidechain 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. PMID:23444044

  19. Selection and design of solvents

    DEFF Research Database (Denmark)

    Gani, Rafiqul

    and design of solvents will be presented together with application examples. The selection problem is defined as finding known chemicals that match the desired functions of a solvent for a specified set of applications. The design problem is defined as finding the molecular structure (or mixture of molecules....... With increasing interest on issues such as waste, sustainability, environmental impact and green chemistry, the selection and design of solvents have become important problems that need to be addressed during chemical product-process design and development. Systematic methods and tools suitable for selection......) that match the desired functions of a solvent for a specified set of applications. Use of organic chemicals and ionic liquids as solvents will be covered....

  20. Solvent substitutes

    International Nuclear Information System (INIS)

    Evanoff, S.P.

    1995-01-01

    The environmental and industrial hygiene regulations promulgated since 1980, most notably the Superfund Amendments and Reauthorization Act (SARA), the Hazardous and Solid Waste Amendments to the Resources Conservation and Recovery Act (RCRA), and the Clean Air Act Amendments of 1990, have brought about an increased emphasis on user exposure, hazardous waste generation, and air emissions. As a result, industry is performing a fundamental reassessment of cleaning solvents, processes, and procedures. The more progressive organizations have made their goal the elimination of solvents that may pose significant potential human health and environmental hazards. This chapter discusses solvent cleaning in metal-finishing, metal-manufacturing, and industrial maintenance applications; precision cleaning; and electronics manufacturing. Nonmetallic cleaning, adhesives, coatings, inks, and aerosols also will be addressed, but in a more cursory manner

  1. Zirconium silicate assisted removal of residual proteins after organic solvent deproteinization of human plasma, enhancing the stability of the LC–ESI-MS response for the bioanalysis of small molecules

    Energy Technology Data Exchange (ETDEWEB)

    Hussain, Shah; Pezzei, Cornelia [Institute of Analytical Chemistry and Radiochemistry, CCB-Center for Chemistry and Biomedicine, Leopold-Franzens University, Innrain 80/82, 6020 Innsbruck (Austria); Güzel, Yüksel [Institute of Analytical Chemistry and Radiochemistry, CCB-Center for Chemistry and Biomedicine, Leopold-Franzens University, Innrain 80/82, 6020 Innsbruck (Austria); ADSI-Austrian Drug Screening Institute, Innrain 66a, 6020 Innsbruck (Austria); Rainer, Matthias [Institute of Analytical Chemistry and Radiochemistry, CCB-Center for Chemistry and Biomedicine, Leopold-Franzens University, Innrain 80/82, 6020 Innsbruck (Austria); Huck, Christian W., E-mail: Christian.W.Huck@uibk.ac.at [Institute of Analytical Chemistry and Radiochemistry, CCB-Center for Chemistry and Biomedicine, Leopold-Franzens University, Innrain 80/82, 6020 Innsbruck (Austria); Bonn, Günther K. [Institute of Analytical Chemistry and Radiochemistry, CCB-Center for Chemistry and Biomedicine, Leopold-Franzens University, Innrain 80/82, 6020 Innsbruck (Austria); ADSI-Austrian Drug Screening Institute, Innrain 66a, 6020 Innsbruck (Austria)

    2014-12-10

    Highlights: • A novel sample preparation technique for isolation of small molecules from human plasma. • Effectiveness of zirconium silicate for the removal of residual proteins after protein precipitation. • Abolishing the consumption of salts for the depletion of residual proteins after protein precipitation. • More than 99.6% removal of plasma proteins. - Abstract: An efficient blood plasma clean-up method was developed, where methanol protein precipitation was applied, followed by zirconium silicate assisted exclusion of residual proteins. A strong binding of zirconium (IV) silicate to the proteins enabled the elimination of remaining proteins after solvent deproteinization through a rapid solid-phase extraction (SPE) procedure. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI/TOF MS) was used for monitoring the proteins during clean-up practice applied to human plasma samples. The proteins were quantified by colorimetric detection using the bicinchoninic acid (BCA) assay. The presented analytical strategy resulted in the depletion of >99.6% proteins from human plasma samples. Furthermore, high-performance liquid chromatography hyphenated to diode-array and electrospray ionization mass spectrometric detection (HPLC–DAD/ESI MS) was applied for qualitative and quantitative analysis of the caffeoylquinic acids (CQAs) and their metabolites in human plasma. The procedure demonstrated high recoveries for the standard compounds spiked at different concentrations. Cynarin and chlorogenic acid were recovered in the range of 81–86% and 78–83%, respectively. Caffeic acid was extracted in the excess of 89–92%, while ferulic acid and dihydroxyhydrocinnamic acid showed a recovery of 87–91% and 92–95%, respectively. The method was partially validated in accordance with FDA-Industry Guidelines for Bioanalytical Method Validation (2001). The presented scheme improves the clean-up efficacy of the methanol deproteinization

  2. Zirconium silicate assisted removal of residual proteins after organic solvent deproteinization of human plasma, enhancing the stability of the LC–ESI-MS response for the bioanalysis of small molecules

    International Nuclear Information System (INIS)

    Hussain, Shah; Pezzei, Cornelia; Güzel, Yüksel; Rainer, Matthias; Huck, Christian W.; Bonn, Günther K.

    2014-01-01

    Highlights: • A novel sample preparation technique for isolation of small molecules from human plasma. • Effectiveness of zirconium silicate for the removal of residual proteins after protein precipitation. • Abolishing the consumption of salts for the depletion of residual proteins after protein precipitation. • More than 99.6% removal of plasma proteins. - Abstract: An efficient blood plasma clean-up method was developed, where methanol protein precipitation was applied, followed by zirconium silicate assisted exclusion of residual proteins. A strong binding of zirconium (IV) silicate to the proteins enabled the elimination of remaining proteins after solvent deproteinization through a rapid solid-phase extraction (SPE) procedure. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI/TOF MS) was used for monitoring the proteins during clean-up practice applied to human plasma samples. The proteins were quantified by colorimetric detection using the bicinchoninic acid (BCA) assay. The presented analytical strategy resulted in the depletion of >99.6% proteins from human plasma samples. Furthermore, high-performance liquid chromatography hyphenated to diode-array and electrospray ionization mass spectrometric detection (HPLC–DAD/ESI MS) was applied for qualitative and quantitative analysis of the caffeoylquinic acids (CQAs) and their metabolites in human plasma. The procedure demonstrated high recoveries for the standard compounds spiked at different concentrations. Cynarin and chlorogenic acid were recovered in the range of 81–86% and 78–83%, respectively. Caffeic acid was extracted in the excess of 89–92%, while ferulic acid and dihydroxyhydrocinnamic acid showed a recovery of 87–91% and 92–95%, respectively. The method was partially validated in accordance with FDA-Industry Guidelines for Bioanalytical Method Validation (2001). The presented scheme improves the clean-up efficacy of the methanol deproteinization

  3. Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.

    Science.gov (United States)

    Katkova, E V; Onufriev, A V; Aguilar, B; Sulimov, V B

    2017-03-01

    In this study several commonly used implicit solvent models are compared with respect to their accuracy of estimating solvation energies of small molecules and proteins, as well as desolvation penalty in protein-ligand binding. The test set consists of 19 small proteins, 104 small molecules, and 15 protein-ligand complexes. We compared predicted hydration energies of small molecules with their experimental values; the results of the solvation and desolvation energy calculations for small molecules, proteins and protein-ligand complexes in water were also compared with Thermodynamic Integration calculations based on TIP3P water model and Amber12 force field. The following implicit solvent (water) models considered here are: PCM (Polarized Continuum Model implemented in DISOLV and MCBHSOLV programs), GB (Generalized Born method implemented in DISOLV program, S-GB, and GBNSR6 stand-alone version), COSMO (COnductor-like Screening Model implemented in the DISOLV program and the MOPAC package) and the Poisson-Boltzmann model (implemented in the APBS program). Different parameterizations of the molecules were examined: we compared MMFF94 force field, Amber12 force field and the quantum-chemical semi-empirical PM7 method implemented in the MOPAC package. For small molecules, all of the implicit solvent models tested here yield high correlation coefficients (0.87-0.93) between the calculated solvation energies and the experimental values of hydration energies. For small molecules high correlation (0.82-0.97) with the explicit solvent energies is seen as well. On the other hand, estimated protein solvation energies and protein-ligand binding desolvation energies show substantial discrepancy (up to 10kcal/mol) with the explicit solvent reference. The correlation of polar protein solvation energies and protein-ligand desolvation energies with the corresponding explicit solvent results is 0.65-0.99 and 0.76-0.96 respectively, though this difference in correlations is caused

  4. Solvent Annealing Effects in Dithieno[3,2-b:2',3'-d]pyrrole–5,6-Difluorobenzo[c][1,2,5]thiadiazole Small Molecule Donors for BHJ Solar Cells

    KAUST Repository

    Wang, Kai; Azouz, Mehdi; Babics, Maxime; Cruciani, Federico; Marszalek, Tomasz; Saleem, Qasim; Pisula, Wojciech; Beaujuge, Pierre

    2016-01-01

    Low-bandgap small molecule (SM) donors that can be solution-processed with fullerene acceptors (e.g. PC61/71BM) are proving particularly promising in bulk-heterojunction (BHJ) solar cells. Compared to their π-conjugated polymer counterparts, SM donors are well defined (monodispersed) and more synthetically modular –with relatively wide ranges of bandgaps achievable in stepwise couplings of various donor and acceptor motifs. However, the optimization of SM-fullerene morphologies and BHJ device efficiencies relies more specifically on the use of processing additives, post-processing thermal or solvent vapor annealing (SVA) approaches, and achieving adequate interpenetrating networks and structural order in BHJ thin films can be challenging. In this report, we examine the correlated effects of molecular structure and post-processing SVA on the BHJ solar cell performance of a set of π-extended SM donors composed of dithieno[3,2-b:2',3'-d]pyrrole (DTP) and 5,6-difluorobenzo[c][1,2,5]thiadiazole ([2F]BT) units. In these systems (SM1-3), the introduction of additional alkyl substituents and unsubstituted thiophene rings on the peripheral unit groups critically impacts the effects of SVA steps on BHJ solar cell efficiency. We show that the more π-extended and alkyl-substituted analogue SM3 stands out –with BHJ device efficiencies of ca. 6% obtained from SVA with CS2– while SVA-treated SM3-based active layers also show the most favorable ordering and carrier mobility patterns. However, unlike numbers of SM donors reported in recent years, DTP–[2F]BT SM analogues are in general not prone to dramatic performance variations in BHJ thin films cast with processing additives. Our results indicate that the role of SVA steps is not independent of the molecular structure of the SM donors used in the BHJ solar cells.

  5. Solvent Annealing Effects in Dithieno[3,2-b:2',3'-d]pyrrole–5,6-Difluorobenzo[c][1,2,5]thiadiazole Small Molecule Donors for BHJ Solar Cells

    KAUST Repository

    Wang, Kai

    2016-06-17

    Low-bandgap small molecule (SM) donors that can be solution-processed with fullerene acceptors (e.g. PC61/71BM) are proving particularly promising in bulk-heterojunction (BHJ) solar cells. Compared to their π-conjugated polymer counterparts, SM donors are well defined (monodispersed) and more synthetically modular –with relatively wide ranges of bandgaps achievable in stepwise couplings of various donor and acceptor motifs. However, the optimization of SM-fullerene morphologies and BHJ device efficiencies relies more specifically on the use of processing additives, post-processing thermal or solvent vapor annealing (SVA) approaches, and achieving adequate interpenetrating networks and structural order in BHJ thin films can be challenging. In this report, we examine the correlated effects of molecular structure and post-processing SVA on the BHJ solar cell performance of a set of π-extended SM donors composed of dithieno[3,2-b:2\\',3\\'-d]pyrrole (DTP) and 5,6-difluorobenzo[c][1,2,5]thiadiazole ([2F]BT) units. In these systems (SM1-3), the introduction of additional alkyl substituents and unsubstituted thiophene rings on the peripheral unit groups critically impacts the effects of SVA steps on BHJ solar cell efficiency. We show that the more π-extended and alkyl-substituted analogue SM3 stands out –with BHJ device efficiencies of ca. 6% obtained from SVA with CS2– while SVA-treated SM3-based active layers also show the most favorable ordering and carrier mobility patterns. However, unlike numbers of SM donors reported in recent years, DTP–[2F]BT SM analogues are in general not prone to dramatic performance variations in BHJ thin films cast with processing additives. Our results indicate that the role of SVA steps is not independent of the molecular structure of the SM donors used in the BHJ solar cells.

  6. Solvent dielectric effect and side chain mutation on the structural stability of Burkholderia cepacia lipase active site: a quantum mechanical/molecular mechanics study.

    Science.gov (United States)

    Tahan, A; Monajjemi, M

    2011-12-01

    Quantum mechanical and molecular dynamics methods were used to analyze the structure and stability of neutral and zwitterionic configurations of the extracted active site sequence from a Burkholderia cepacia lipase, histidyl-seryl-glutamin (His86-Ser87-Gln88) and its mutated form, histidyl-cysteyl-glutamin (His86-Cys87-Gln88) in vacuum and different solvents. The effects of solvent dielectric constant, explicit and implicit water molecules and side chain mutation on the structure and stability of this sequence in both neutral and zwitterionic forms are represented. The quantum mechanics computations represent that the relative stability of zwitterionic and neutral configurations depends on the solvent structure and its dielectric constant. Therefore, in vacuum and the considered non-polar solvents, the neutral form of the interested sequences is more stable than the zwitterionic form, while their zwitterionic form is more stable than the neutral form in the aqueous solution and the investigated polar solvents in most cases. However, on the potential energy surfaces calculated, there is a barrier to proton transfer from the positively charged ammonium group to the negatively charged carboxylat group or from the ammonium group to the adjacent carbonyl oxygen and or from side chain oxygen and sulfur to negatively charged carboxylat group. Molecular dynamics simulations (MD) were also performed by using periodic boundary conditions for the zwitterionic configuration of the hydrated molecules in a box of water molecules. The obtained results demonstrated that the presence of explicit water molecules provides the more compact structures of the studied molecules. These simulations also indicated that side chain mutation and replacement of sulfur with oxygen leads to reduction of molecular flexibility and packing.

  7. A solvent/non-solvent system for achieving solution-processed multilayer organic light-emitting devices

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Yue; Wu, Zhaoxin, E-mail: zhaoxinwu@mail.xjtu.edu.cn; He, Lin; Jiao, Bo; Hou, Xun

    2015-08-31

    We developed a solvent/non-solvent system to fabricate the multilayer organic light-emitting devices (OLEDs) based on poly(N-vinylcarbazole) (PVK) by solution-process. This solvent system consists of both the solvent and non-solvent of PVK, in which fluorescent small molecules could be fully dissolved and directly spin-coated on top of the PVK layer; it could effectively avoid the redissolution of PVK during the spin-coating process of small molecules emitting layer. In the further investigation of this system, we also demonstrated the three-component solvent system, and found out that the third component, a less volatile solvent of PVK, was crucial for preparing a smoother interface between PVK and emitting layer. Compared with OLEDs through the vacuum deposition, the devices fabricated by solution-process from the solvent/non-solvent system showed comparable efficiency, which indicate that the solvent/non-solvent system can be used as an alternative process to prepare the polymer and small molecule multilayer devices through all-solution-process. - Highlights: • We fabricate the multilayer OLEDs by solution-process using a novel system. • We develop a solvent/non-solvent system of polymer (PVK) to avoid redissolution. • Small molecules could be fully dissolved and directly spin-coated on PVK layer. • The devices fabricated by the system and vacuum deposition show comparable efficiency.

  8. studies dielectric behaviour of some long chain alcohols and their mixtures with a non-polar solvent at various concentration

    International Nuclear Information System (INIS)

    Yaqub, M.; Ahmed, S.S.; Hussain, A.

    2006-01-01

    Dielectric constant, refractive index and the Kirkwood linear correlation factor of 1-propanol, 1-butanol and 1-pentanol in mixtures with carbon tetrachloride at various concentration have been measured at fixed frequency (100 KHz) at 303.15 K. For the study of dielectric properties of polar molecules in a non-polar solvent at different concentrations, polarization per unit volume and excess free-energy of mixing were evaluated at this temperature. In order to study the association of polar molecules in such a non-polar solvent, the Kirkwood correlation factor (g) between molecular pairs, which exists due to the hydrogen bond association suggesting the presence of some dimension in the liquid phase with a number of dimmers, was determined. The refractive index and dielectric constant measurements are expected to shed some light on the configuration of molecules in various mixtures, and give some idea about the specific interactions between components, which decrese with the increase in the concentration of alcohol. All the three mixtures showed different behaviour for the value of correlation factor (g) as a function of concentration. The response of 1-pentanol was broadly identical to that of small chain alcohols. The different behaviour of the correlation factor (g) was interpreted in terms of the Kirkwood-Frohlich theory, as it takes into account, explicitly, such type of short and long range interactions of a mixture of polar molecules with non-polar solvents. (author)

  9. Explicit dissipative structures

    International Nuclear Information System (INIS)

    Roessler, O.E.

    1987-01-01

    Dissipative structures consisting of a few macrovariables arise out of a sea of reversible microvariables. Unexpected residual effects of the massive underlying reversibility, on the macrolevel, cannot therefore be excluded. In the age of molecular-dynamics simulations, explicit dissipative structures like excitable systems (explicit observers) can be generated in a computer from first reversible principles. A class of classical, 1-D Hamiltonian systems of chaotic type is considered which has the asset that the trajectorial behavior in phase space can be understood geometrically. If, as nuatural, the number of particle types is much smaller than that of particles, the Gibbs symmetry must be taken into account. The permutation invariance drastically changes the behavior in phase space (quasi-periodization). The explicity observer becomes effectively reversible on a short time scale. In consequence, his ability to measure microscopic motions is suspended in a characteristic fashion. Unlike quantum mechanics whose holistic nature cannot be transcended, the present holistic (internal-interface) effects - mimicking the former to some extent - can be understood fully in principle

  10. NMR spectroscopy using liquid crystal solvents

    CERN Document Server

    Emsley, JW

    2013-01-01

    NMR Spectroscopy using Liquid Crystal Solvents covers the importance of using a liquid crystal solvent in NMR to derive nuclear dipolar spin-spin coupling constants. This book is composed of ten chapters, and begins with a brief description of the features and benefits of liquid crystal in NMR spectroscopic analysis. The succeeding chapters deal with the mode of operation of nuclear spin Hamiltonian for partially oriented molecules and the analysis of NMR spectra of partially oriented molecules, as well as the determination of rigid molecule structure. These topics are followed by discussions

  11. Explicit ions/implicit water generalized Born model for nucleic acids

    Science.gov (United States)

    Tolokh, Igor S.; Thomas, Dennis G.; Onufriev, Alexey V.

    2018-05-01

    The ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure, and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model and utilizes a non-standard approach to define the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes—disconnected dielectric boundary around the solute-ion or ion-ion pairs. A fully analytical description of all energy components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force for Na+-Cl- ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. The monovalent (Na+) and trivalent (CoHex3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within kBT. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. These features include preferential CoHex binding inside the major groove of the RNA duplex, in contrast to CoHex biding at the "external" surface of the sugar-phosphate backbone of the DNA duplex; these differences in the counterion binding patters were earlier shown to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. MC simulations of CoHex ions interacting with the homopolymeric poly(dA.dT) DNA duplex with modified (de

  12. Brownian motion of a nano-colloidal particle: the role of the solvent.

    Science.gov (United States)

    Torres-Carbajal, Alexis; Herrera-Velarde, Salvador; Castañeda-Priego, Ramón

    2015-07-15

    Brownian motion is a feature of colloidal particles immersed in a liquid-like environment. Usually, it can be described by means of the generalised Langevin equation (GLE) within the framework of the Mori theory. In principle, all quantities that appear in the GLE can be calculated from the molecular information of the whole system, i.e., colloids and solvent molecules. In this work, by means of extensive Molecular Dynamics simulations, we study the effects of the microscopic details and the thermodynamic state of the solvent on the movement of a single nano-colloid. In particular, we consider a two-dimensional model system in which the mass and size of the colloid are two and one orders of magnitude, respectively, larger than the ones associated with the solvent molecules. The latter ones interact via a Lennard-Jones-type potential to tune the nature of the solvent, i.e., it can be either repulsive or attractive. We choose the linear momentum of the Brownian particle as the observable of interest in order to fully describe the Brownian motion within the Mori framework. We particularly focus on the colloid diffusion at different solvent densities and two temperature regimes: high and low (near the critical point) temperatures. To reach our goal, we have rewritten the GLE as a second kind Volterra integral in order to compute the memory kernel in real space. With this kernel, we evaluate the momentum-fluctuating force correlation function, which is of particular relevance since it allows us to establish when the stationarity condition has been reached. Our findings show that even at high temperatures, the details of the attractive interaction potential among solvent molecules induce important changes in the colloid dynamics. Additionally, near the critical point, the dynamical scenario becomes more complex; all the correlation functions decay slowly in an extended time window, however, the memory kernel seems to be only a function of the solvent density. Thus, the

  13. Making the Tacit Explicit

    DEFF Research Database (Denmark)

    Blasco, Maribel

    2015-01-01

    The article proposes an approach, broadly inspired by culturally inclusive pedagogy, to facilitate international student academic adaptation based on rendering tacit aspects of local learning cultures explicit to international full degree students, rather than adapting them. Preliminary findings...... are presented from a focus group-based exploratory study of international student experiences at different stages of their studies at a Danish business school, one of Denmark’s most international universities. The data show how a major source of confusion for these students has to do with the tacit logics...... and expectations that shape how the formal steps of the learning cycle are understood and enacted locally, notably how learning and assessment moments are defined and related to one another. Theoretically, the article draws on tacit knowledge and sense-making theories to analyse student narratives...

  14. Ions, solutes and solvents, oh my!

    Energy Technology Data Exchange (ETDEWEB)

    Kemp, Daniel David [Iowa State Univ., Ames, IA (United States)

    2009-08-01

    Modern methods in ab initio quantum mechanics have become efficient and accurate enough to study many gas-phase systems. However, chemists often work in the solution phase. The presence of solvent molecules has been shown to affect reaction mechanisms1, lower reaction energy barriers2, participate in energy transfer with the solute3 and change the physical properties of the solute4. These effects would be overlooked in simple gas phase calculations. Careful study of specific solvents and solutes must be done in order to fully understand the chemistry of the solution phase. Water is a key solvent in chemical and biological applications. The properties of an individual water molecule (a monomer) and the behavior of thousands of molecules (bulk solution) are well known for many solvents. Much is also understood about aqueous microsolvation (small clusters containing ten water molecules or fewer) and the solvation characteristics when bulk water is chosen to solvate a solute. However, much less is known about how these properties behave as the cluster size transitions from the microsolvated cluster size to the bulk. This thesis will focus on species solvated with water clusters that are large enough to exhibit the properties of the bulk but small enough to consist of fewer than one hundred solvent molecules. New methods to study such systems will also be presented.

  15. Distribution of multi-component solvents in solvent vapor extraction chamber

    Energy Technology Data Exchange (ETDEWEB)

    Das, S. [Society of Petroleum Engineers, Richardson, TX (United States)]|[Marathon Oil Corp., Houston, TX (United States)

    2008-10-15

    Vapex process performance is sensitive to operating pressures, temperatures and the types of solvent used. The hydrocarbon solvents used in Vapex processes typically have between 5 and 10 per cent hydrocarbon impurities, and the accumulation of dense phases inside the vapor chamber reduces gravity drainage potential. This study investigated the partitioning of solvent compounds inside the vapor chamber during in situ Vapex processes.The aim of the study was to examine how the different components of the mixed solvent partitioned inside the extracted chamber during the oil and vapor phase. A 2-D homogenous reservoir model was used to simulate the Vapex process with a solvent mixture comprised of propane and methane at various percentages. The effect of injecting a hot solvent vapor was also investigated. The study showed that injected methane accumulated at both the top and the extraction interface. Accumulations near the top had a positive impact on solvent confinement in thin reservoirs. Diffusion of the solvent component was controlled by gas phase molecular diffusion, and was much faster than the diffusion of solvent molecules in the liquid phase. The use of hot solvent mixtures slowed the extraction process due to lower solvent solubility in the oil phase. It was concluded that the negative impact on viscosity reduction by dilution was not compensated by rises in temperature. 6 refs., 11 figs.

  16. Analysis of solvent extracts from coal liquefaction in a flowing solvent reactor

    Energy Technology Data Exchange (ETDEWEB)

    Li, Wen-Ying; Feng, Jie; Xie, Ke-Chang [Key Laboratory of Coal Science and Technology, Taiyuan University of Technology, Ministry of Education and Shanxi Province, No. 79 Yingze West Street, Taiyuan 030024 (China); Kandiyoti, R. [Department of Chemical Engineering and Chemical Technology, Imperial College, University of London, London SW7 2BY (United Kingdom)

    2004-10-15

    Point of Ayr coal has been extracted using three solvents, tetralin, quinoline and 1-methyl-2-pyrrolidinone (NMP) at two temperatures 350 and 450 C, corresponding approximately to before and after the onset of massive covalent bond scission by pyrolysis. The three solvents differ in solvent power and the ability to donate hydrogen atoms to stabilise free radicals produced by pyrolysis of the coal. The extracts were prepared in a flowing solvent reactor to minimise secondary thermal degradation of the primary extracts. Analysis of the pentane-insoluble fractions of the extracts was achieved by size exclusion chromatography, UV-fluorescence spectroscopy in NMP solvent and probe mass. With increasing extraction temperature, the ratio of the amount having big molecular weight to that having small molecular weight in tetralin extracts was increased; the tetralin extract yield increased from 12.8% to 75.9%; in quinoline, increasing extraction temperature did not have an effect on the molecular weight of products but there was a big increase in extract yield. The extracts in NMP showed the enhanced solvent extraction power at both temperatures, with a shift in the ratio of larger molecules to smaller molecules with increasing extraction temperature and with the highest conversion of Point of Ayr coal among these three solvents at both temperatures. Solvent adducts were detected in the tetralin and quinoline extracts by probe mass spectrometry; solvent products were formed from NMP at both temperatures.

  17. Small molecule hydration energy and entropy from 3D-RISM

    Science.gov (United States)

    Johnson, J.; Case, D. A.; Yamazaki, T.; Gusarov, S.; Kovalenko, A.; Luchko, T.

    2016-09-01

    Implicit solvent models offer an attractive way to estimate the effects of a solvent environment on the properties of small or large solutes without the complications of explicit simulations. One common test of accuracy is to compute the free energy of transfer from gas to liquid for a variety of small molecules, since many of these values have been measured. Studies of the temperature dependence of these values (i.e. solvation enthalpies and entropies) can provide additional insights into the performance of implicit solvent models. Here, we show how to compute temperature derivatives of hydration free energies for the 3D-RISM integral equation approach. We have computed hydration free energies of 1123 small drug-like molecules (both neutral and charged). Temperature derivatives were also used to calculate hydration energies and entropies of 74 of these molecules (both neutral and charged) for which experimental data is available. While direct results have rather poor agreement with experiment, we have found that several previously proposed linear hydration free energy correction schemes give good agreement with experiment. These corrections also provide good agreement for hydration energies and entropies though simple extensions are required in some cases.

  18. Small molecule hydration energy and entropy from 3D-RISM

    International Nuclear Information System (INIS)

    Johnson, J; Case, D A; Yamazaki, T; Gusarov, S; Kovalenko, A; Luchko, T

    2016-01-01

    Implicit solvent models offer an attractive way to estimate the effects of a solvent environment on the properties of small or large solutes without the complications of explicit simulations. One common test of accuracy is to compute the free energy of transfer from gas to liquid for a variety of small molecules, since many of these values have been measured. Studies of the temperature dependence of these values (i.e. solvation enthalpies and entropies) can provide additional insights into the performance of implicit solvent models. Here, we show how to compute temperature derivatives of hydration free energies for the 3D-RISM integral equation approach. We have computed hydration free energies of 1123 small drug-like molecules (both neutral and charged). Temperature derivatives were also used to calculate hydration energies and entropies of 74 of these molecules (both neutral and charged) for which experimental data is available. While direct results have rather poor agreement with experiment, we have found that several previously proposed linear hydration free energy correction schemes give good agreement with experiment. These corrections also provide good agreement for hydration energies and entropies though simple extensions are required in some cases. (paper)

  19. Implicit, explicit and speculative knowledge

    NARCIS (Netherlands)

    van Ditmarsch, H.; French, T.; Velázquez-Quesada, F.R.; Wáng, Y.N.

    We compare different epistemic notions in the presence of awareness of propositional variables: the logic of implicit knowledge (in which explicit knowledge is definable), the logic of explicit knowledge, and the logic of speculative knowledge. Speculative knowledge is a novel epistemic notion that

  20. Solvents and solvent effects in organic chemistry

    National Research Council Canada - National Science Library

    Reichardt, C; Welton, T

    2011-01-01

    .../guest complexation equilibria and reactions in biphasic solvent systems and neoteric solvents, respectively. More than 900 new references have been added, giving preference to review articles, and many older ones have been deleted. New references either replace older ones or are added to the end of the respective reference list of each chapter. Th...

  1. Organic Solvent Tropical Report

    International Nuclear Information System (INIS)

    COWLEY, W.L.

    2000-01-01

    This report provides the basis for closing the organic solvent safety issue. Sufficient information is presented to conclude that risk posed by an unmitigated organic solvent fire is within risk evaluation guidelines

  2. Canyon solvent cleaning

    International Nuclear Information System (INIS)

    Reif, D.J.

    1986-01-01

    The HM Process at the Savannah River Plant (SRP) uses 7.5% tributylphosphate in n-paraffin as an extraction solvent. During use, the solvent is altered due to hydrolysis and radiolysis, forming materials that influence product losses, produce decontamination, and separation efficiencies. Laboratory studies to improve online solvent cleaning have shown the carbonate washing, although removing residual solvent activity does not remove binding ligands that hold fission products in the solvent. Treatment of solvent by an alumina adsorption process removes binding ligands and significantly improves recycle solvent performance. Both laboratory work defining a full-scale alumina adsorption process and the use of the process to clean HM Process first cycle solvent are presented

  3. Solvent wash solution

    International Nuclear Information System (INIS)

    Neace, J.C.

    1986-01-01

    This patent describes a process for removing diluent degradation products from a solvent extraction solution comprising an admixture of an organic extractant for uranium and plutonium and a non-polar organic liquid diluent, which has been used to recover uranium and plutonium from spent nuclear fuel. Comprising combining a wash solution consisting of: (a) water; and (b) a positive amount up to about, an including, 50 volume percent of at least one highly-polar water-miscible organic solvent, based on the total volume of the water and the highly-polar organic solvent, with the solvent extraction solution after uranium and plutonium values have been stripped from the solvent extraction solution, the diluent degradation products dissolving in the highly-polar organic solvent and the extractant and diluent of the extraction solution not dissolving in the highly-polar organic solvent, and separating the highly-polar organic solvent and the extraction solution to obtain a purified extraction solution

  4. Multiconformation, Density Functional Theory-Based pKa Prediction in Application to Large, Flexible Organic Molecules with Diverse Functional Groups.

    Science.gov (United States)

    Bochevarov, Art D; Watson, Mark A; Greenwood, Jeremy R; Philipp, Dean M

    2016-12-13

    We consider the conformational flexibility of molecules and its implications for micro- and macro-pK a . The corresponding formulas are derived and discussed against the background of a comprehensive scientific and algorithmic description of the latest version of our computer program Jaguar pK a , a density functional theory-based pK a predictor, which is now capable of acting on multiple conformations explicitly. Jaguar pK a is essentially a complex computational workflow incorporating research and technologies from the fields of cheminformatics, molecular mechanics, quantum mechanics, and implicit solvation models. The workflow also makes use of automatically applied empirical corrections which account for the systematic errors resulting from the neglect of explicit solvent interactions in the algorithm's implicit solvent model. Applications of our program to large, flexible organic molecules representing several classes of functional groups are shown, with a particular emphasis in illustrations laid on drug-like molecules. It is demonstrated that a combination of aggressive conformational search and an explicit consideration of multiple conformations nearly eliminates the dependence of results on the initially chosen conformation. In certain cases this leads to unprecedented accuracy, which is sufficient for distinguishing stereoisomers that have slightly different pK a values. An application of Jaguar pK a to proton sponges, the pK a of which are strongly influenced by steric effects, showcases the advantages that pK a predictors based on quantum mechanical calculations have over similar empirical programs.

  5. "Tacit Knowledge" versus "Explicit Knowledge"

    DEFF Research Database (Denmark)

    Sanchez, Ron

    creators and carriers. By contrast, the explicit knowledge approach emphasizes processes for articulating knowledge held by individuals, the design of organizational approaches for creating new knowledge, and the development of systems (including information systems) to disseminate articulated knowledge...

  6. Performance of thermally-chargeable supercapacitors in different solvents.

    Science.gov (United States)

    Lim, Hyuck; Zhao, Cang; Qiao, Yu

    2014-07-07

    The influence of solvent on the temperature sensitivity of the electrode potential of thermally-chargeable supercapacitors (TCSs) is investigated. For large electrodes, the output voltage is positively correlated with the dielectric constant of solvent. When nanoporous carbon electrodes are used, different characteristics of system performance are observed, suggesting that possible size effects must be taken into consideration when the solvent molecules and solvated ions are confined in a nanoenvironment.

  7. Explicit Versus Implicit Income Insurance

    OpenAIRE

    Thomas J. Kniesner; James P. Z‎iliak

    2001-01-01

    October 2001 (Revised from July 2001). Abstract: By supplementing income explicitly through payments or implicitly through taxes collected, income-based taxes and transfers make disposable income less variable. Because disposable income determines consumption, policies that smooth disposable income also create welfare improving consumption insurance. With data from the Panel Study of Income Dynamics we find that annual consumption variation is reduced by almost 20 percent due to explicit and ...

  8. Molecule nanoweaver

    Science.gov (United States)

    Gerald, II; Rex, E [Brookfield, IL; Klingler, Robert J [Glenview, IL; Rathke, Jerome W [Homer Glen, IL; Diaz, Rocio [Chicago, IL; Vukovic, Lela [Westchester, IL

    2009-03-10

    A method, apparatus, and system for constructing uniform macroscopic films with tailored geometric assemblies of molecules on the nanometer scale. The method, apparatus, and system include providing starting molecules of selected character, applying one or more force fields to the molecules to cause them to order and condense with NMR spectra and images being used to monitor progress in creating the desired geometrical assembly and functionality of molecules that comprise the films.

  9. Influence of Solvent-Solvent and Solute-Solvent Interaction Properties on Solvent-Mediated Potential

    International Nuclear Information System (INIS)

    Zhou Shiqi

    2005-01-01

    A recently proposed universal calculational recipe for solvent-mediated potential is applied to calculate excess potential of mean force between two large Lennard-Jones (LJ) or hard core attractive Yukawa particles immersed in small LJ solvent bath at supercritical state. Comparison between the present prediction with a hypernetted chain approximation adopted for solute-solute correlation at infinitely dilute limit and existing simulation data shows high accuracy for the region with large separation, and qualitative reliability for the solute particle contact region. The calculational simplicity of the present recipe allows for a detailed investigation on the effect of the solute-solvent and solvent-solvent interaction details on the excess potential of mean force. The resultant conclusion is that gathering of solvent particles near a solute particle leads to repulsive excess PMF, while depletion of solvent particles away from the solute particle leads to attractive excess PMF, and minor change of the solvent-solvent interaction range has large influence on the excess PMF.

  10. Hazardous solvent substitution

    International Nuclear Information System (INIS)

    Twitchell, K.E.

    1995-01-01

    This article is an overview of efforts at INEL to reduce the generation of hazardous wastes through the elimination of hazardous solvents. To aid in their efforts, a number of databases have been developed and will become a part of an Integrated Solvent Substitution Data System. This latter data system will be accessible through Internet

  11. Interacting with the biomolecular solvent accessible surface via a haptic feedback device

    Directory of Open Access Journals (Sweden)

    Hayward Steven

    2009-10-01

    Full Text Available Abstract Background From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation. Results A haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere interactions with the biomolecule, the process of exploration has the further benefit of being able to determine regions on the molecular surface that are accessible to the solvent. This gives insight into how awkward it is for a water molecule to gain access to or escape from channels and cavities, indicating possible entropic bottlenecks. In the case of liver alcohol dehydrogenase bound to the inhibitor SAD, it was found that there is a channel just wide enough for a single water molecule to pass through. Placing the probe coincident with crystallographic water molecules suggests that they are sometimes located within small pockets that provide a sterically stable environment irrespective of hydrogen bonding considerations. Conclusion By using the software, named HaptiMol ISAS (available from http://www.haptimol.co.uk, one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water

  12. Different Supramolecular Coordination Polymers of [N,N'-di(pyrazin-2-yl-pyridine-2,6-diamine]Ni(II with Anions and Solvent Molecules as a Result of Hydrogen Bonding

    Directory of Open Access Journals (Sweden)

    Hsin-Ta Wang

    2007-04-01

    Full Text Available Ni(II complexes of N,N'–di(pyrazin–2–ylpyridine–2,6–diamine (H2dpzpda with different anions were synthesized and their structures were determined by X-ray diffraction. Hydrogen bonds between the amino groups and anions assembled the mononuclear molecules into different architectures. The perchlorate complex had a 1-D chain structure, whereas switching the anion from perchlorate to nitrate resulted in a corresponding change of the supramolecular structure from 1-D to 3-D. When the nitrate complex packed with the co-crystallized water, a double chain structure was formed through hydrogen bonding. The magnetic studies revealed values of g = 2.14 and D = 3.11 cm-1 for [Ni(H2dpzpda2](ClO42 (1 and g = 2.18 and D = 2.19 cm-1 for [Ni(H2dpzpda2](NO32 (2, respectively.

  13. Molecular microenvironments: Solvent interactions with nucleic acid bases and ions

    Science.gov (United States)

    Macelroy, R. D.; Pohorille, A.

    1986-01-01

    The possibility of reconstructing plausible sequences of events in prebiotic molecular evolution is limited by the lack of fossil remains. However, with hindsight, one goal of molecular evolution was obvious: the development of molecular systems that became constituents of living systems. By understanding the interactions among molecules that are likely to have been present in the prebiotic environment, and that could have served as components in protobiotic molecular systems, plausible evolutionary sequences can be suggested. When stable aggregations of molecules form, a net decrease in free energy is observed in the system. Such changes occur when solvent molecules interact among themselves, as well as when they interact with organic species. A significant decrease in free energy, in systems of solvent and organic molecules, is due to entropy changes in the solvent. Entropy-driven interactioins played a major role in the organization of prebiotic systems, and understanding the energetics of them is essential to understanding molecular evolution.

  14. Analysis of recovered solvents from coal liquefaction in a flowing-solvent reactor by SEC and UV-fluorescence

    Energy Technology Data Exchange (ETDEWEB)

    Li, W.Y.; Feng, J.; Xie, K.C.; Kandiyoti, R. [Taiyuan University of Technology, Taiyuan (China)

    2005-08-01

    Point of Ayr coal has been extracted using three solvents: tetralin, quinoline and 1-methyl-2-pyrrolidinone (NMP); at two temperatures: 350 {sup o}C and 450{sup o}C, corresponding approximately to before and after the onset of massive covalent bond scission by pyrolysis. These solvents differ in solvent power and the ability to donate hydrogen atoms to stabilize free radicals produced by pyrolysis of the coal. Analysis of the fresh solvents and recovered solvents from coal liquefaction was achieved by size exclusion chromatography and UV-fluorescence spectroscopy. In the blank run, it was testified that the filling material sand and the steel powder did not react with solvent with increasing reaction temperature. The role of hydrogen donation in the tetralin extracts was to increase the proportion of large molecules with increasing extraction temperature. Quinoline and NMP both have the powerful extracting capability to get more materials out of coal with increasing extraction temperature.

  15. Analysis of recovered solvents from coal liquefaction in a flowing-solvent reactor by SEC and UV-fluorescence

    Energy Technology Data Exchange (ETDEWEB)

    Wen-Ying Li; Jie Feng; Ke-Chang Xie; R. Kandiyoti [Taiyuan University of Technology, Taiyuan (China). Key Laboratory of Coal Science and Technology for Ministry of Education and Shanxi Province

    2005-08-01

    Point of Ayr coal has been extracted using three solvents: tetralin, quinoline and 1-methyl-2-pyrrolidinone (NMP); at two temperatures: 350{sup o}C and 450{sup o}C, corresponding approximately to before and after the onset of massive covalent bond scission by pyrolysis. These solvents differ in solvent power and the ability to donate hydrogen atoms to stabilize free radicals produced by pyrolysis of the coal. Analysis of the fresh solvents and recovered solvents from coal liquefaction was achieved by size exclusion chromatography and UV-fluorescence spectroscopy. In the blank run, it was testified that the filling material sand and the steel powder did not react with solvent with increasing reaction temperature. The role of hydrogen donation in the tetralin extracts was to increase the proportion of large molecules with increasing extraction temperature. Quinoline and NMP both have the powerful extracting capability to get more materials out of coal with increasing extraction temperature.

  16. Understanding and making practice explicit

    Directory of Open Access Journals (Sweden)

    Gráinne Conole

    2006-12-01

    Full Text Available This issue contains four, on the face of it, quite different papers, but on looking a little closer there are a number of interesting themes running through them that illustrate some of the key methodological and theoretical issues that e-learning researchers are currently struggling with; central to these is the issue of how do we understand and make practice explicit?

  17. Building an explicit de Sitter

    International Nuclear Information System (INIS)

    Louis, Jan; Hamburg Univ.; Rummel, Markus; Valandro, Roberto; Westphal, Alexander

    2012-11-01

    We construct an explicit example of a de Sitter vacuum in type IIB string theory that realizes the proposal of Kaehler uplifting. As the large volume limit in this method depends on the rank of the largest condensing gauge group we carry out a scan of gauge group ranks over the Kreuzer-Skarke set of toric Calabi-Yau threefolds. We find large numbers of models with the largest gauge group factor easily exceeding a rank of one hundred. We construct a global model with Kaehler uplifting on a two-parameter model on CP 4 11169 , by an explicit analysis from both the type IIB and F-theory point of view. The explicitness of the construction lies in the realization of a D7 brane configuration, gauge flux and RR and NS flux choices, such that all known consistency conditions are met and the geometric moduli are stabilized in a metastable de Sitter vacuum with spontaneous GUT scale supersymmetry breaking driven by an F-term of the Kaehler moduli.

  18. Building an explicit de Sitter

    Energy Technology Data Exchange (ETDEWEB)

    Louis, Jan [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik; Hamburg Univ. (Germany). Zentrum fuer Mathematische Physik; Rummel, Markus; Valandro, Roberto [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik; Westphal, Alexander [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Gruppe Theorie

    2012-11-15

    We construct an explicit example of a de Sitter vacuum in type IIB string theory that realizes the proposal of Kaehler uplifting. As the large volume limit in this method depends on the rank of the largest condensing gauge group we carry out a scan of gauge group ranks over the Kreuzer-Skarke set of toric Calabi-Yau threefolds. We find large numbers of models with the largest gauge group factor easily exceeding a rank of one hundred. We construct a global model with Kaehler uplifting on a two-parameter model on CP{sup 4}{sub 11169}, by an explicit analysis from both the type IIB and F-theory point of view. The explicitness of the construction lies in the realization of a D7 brane configuration, gauge flux and RR and NS flux choices, such that all known consistency conditions are met and the geometric moduli are stabilized in a metastable de Sitter vacuum with spontaneous GUT scale supersymmetry breaking driven by an F-term of the Kaehler moduli.

  19. Opportunities for Bio-Based Solvents Created as Petrochemical and Fuel Products Transition towards Renewable Resources.

    Science.gov (United States)

    Clark, James H; Farmer, Thomas J; Hunt, Andrew J; Sherwood, James

    2015-07-28

    The global bio-based chemical market is growing in size and importance. Bio-based solvents such as glycerol and 2-methyltetrahydrofuran are often discussed as important introductions to the conventional repertoire of solvents. However adoption of new innovations by industry is typically slow. Therefore it might be anticipated that neoteric solvent systems (e.g., ionic liquids) will remain niche, while renewable routes to historically established solvents will continue to grow in importance. This review discusses bio-based solvents from the perspective of their production, identifying suitable feedstocks, platform molecules, and relevant product streams for the sustainable manufacturing of conventional solvents.

  20. Opportunities for Bio-Based Solvents Created as Petrochemical and Fuel Products Transition towards Renewable Resources

    Science.gov (United States)

    Clark, James H.; Farmer, Thomas J.; Hunt, Andrew J.; Sherwood, James

    2015-01-01

    The global bio-based chemical market is growing in size and importance. Bio-based solvents such as glycerol and 2-methyltetrahydrofuran are often discussed as important introductions to the conventional repertoire of solvents. However adoption of new innovations by industry is typically slow. Therefore it might be anticipated that neoteric solvent systems (e.g., ionic liquids) will remain niche, while renewable routes to historically established solvents will continue to grow in importance. This review discusses bio-based solvents from the perspective of their production, identifying suitable feedstocks, platform molecules, and relevant product streams for the sustainable manufacturing of conventional solvents. PMID:26225963

  1. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 4. Molecule Matters – van der Waals Molecules - History and Some Perspectives on Intermolecular Forces. E Arunan. Feature Article Volume 14 Issue 4 April 2009 pp 346-356 ...

  2. Rate constant and reaction coordinate of Trp-cage folding in explicit water

    NARCIS (Netherlands)

    Juraszek, J.; Bolhuis, P.G.

    2008-01-01

    We report rate constant calculations and a reaction coordinate analysis of the rate-limiting folding and unfolding process of the Trp-cage mini-protein in explicit solvent using transition interface sampling. Previous transition path sampling simulations revealed that in this (un)folding process the

  3. Solvent - solute interaction

    International Nuclear Information System (INIS)

    Urbanczyk, A.; Kalinowski, M.K.

    1983-01-01

    The electronic absorption spectrum of vanadyl acetylacetonate has been studied in 15 organic solvents. It has been found that wavenumbers and molar absorptivities of the long-wavelength bands (d-d transitions) can be well described by a complementary Lewis acid-base model including Gutmann's donor number [Gutmann V., Wychera E., Inorg. Nucl. Chem. Letters 2, 257 (1966)] and acceptor number [Mayer U., Gutmann V., Gerger W., Monatsh. Chem. 106, 1235 (1975)] of a solvent. This model describes also the solvent effect of the hyperfine splitting constant, Asub(iso)( 51 V), from e.s.r. spectra of VOacac 2 . These observations are discussed in terms of the donor-acceptor concept for solvent-solute interactions. (Author)

  4. Spectral simulations of polar diatomic molecules immersed in He clusters: application to the ICl (X) molecule

    International Nuclear Information System (INIS)

    Villarreal, P; Lara-Castells, M P de; Prosmiti, R; Delgado-Barrio, G; Lopez-Duran, D; Gianturco, F A; Jellinek, J

    2007-01-01

    A recently developed quantum-chemistry-like methodology to study molecules solvated in atomic clusters is applied to the ICl (iodine chloride) polar diatomic molecule immersed in clusters of He atoms. The atoms of the solvent clusters are treated as the 'electrons' and the solvated molecule as a structured 'nucleus' of the combined solvent-solute system. The helium-helium and helium-dopant interactions are represented by parametrized two-body and ab initio three-body potentials, respectively. The ground-state wavefunctions are used to compute the infrared (IR) spectra of the solvated molecule. In agreement with the experimental observations, the computed spectra exhibit considerable differences depending on whether the solvent cluster is comprised of bosonic ( 4 He) or fermionic ( 3 He) atoms. The source of these differences is attributed to the different spin-statistics of the solvent clusters. The bosonic versus fermionic nature of the solvent is reflected in the IR absorption selection rules. Only P and R branches with single state transitions appear in the spectrum when the molecule is solvated in a bosonic cluster. On the other hand, when the solvent represents a fermionic environment, quasi-degenerate multiplets of spin states contribute to each branch and, in addition, the Q-branch becomes also allowed. Combined, these two factors explain the more congested nature of the spectrum in the fermionic case

  5. A computer-aided molecular design framework for crystallization solvent design

    DEFF Research Database (Denmark)

    Karunanithi, Arunprakash T.; Achenie, Luke E.K.; Gani, Rafiqul

    2006-01-01

    One of the key decisions in designing solution crystallization processes is the selection of solvents. In this paper, we present a computer-aided molecular design (CAMD) framework for the design and selection of solvents and/or anti-solvents for solution crystallization. The CAMD problem is formu......One of the key decisions in designing solution crystallization processes is the selection of solvents. In this paper, we present a computer-aided molecular design (CAMD) framework for the design and selection of solvents and/or anti-solvents for solution crystallization. The CAMD problem...... solvent molecules. Solvent design and selection for two types of solution crystallization processes namely cooling crystallization and drowning out crystallization are presented. In the first case study, the design of single compound solvent for crystallization of ibuprofen, which is an important...

  6. Atkins' molecules

    CERN Document Server

    Atkins, Peters

    2003-01-01

    Originally published in 2003, this is the second edition of a title that was called 'the most beautiful chemistry book ever written'. In it, we see the molecules responsible for the experiences of our everyday life - including fabrics, drugs, plastics, explosives, detergents, fragrances, tastes, and sex. With engaging prose Peter Atkins gives a non-technical account of an incredible range of aspects of the world around us, showing unexpected connections, and giving an insight into how this amazing world can be understood in terms of the atoms and molecules from which it is built. The second edition includes dozens of extra molecules, graphical presentation, and an even more accessible and enthralling account of the molecules themselves.

  7. Interstellar Molecules

    Science.gov (United States)

    Solomon, Philip M.

    1973-01-01

    Radioastronomy reveals that clouds between the stars, once believed to consist of simple atoms, contain molecules as complex as seven atoms and may be the most massive objects in our Galaxy. (Author/DF)

  8. A Correlation between the Activity of Candida antarctica Lipase B and Differences in Binding Free Energies of Organic Solvent and Substrate

    DEFF Research Database (Denmark)

    Banik, Sindrila Dutta; Nordblad, Mathias; Woodley, John

    2016-01-01

    in an inhibitory effect which is also confirmed by the binding free energies for the solvent and substrate molecules estimated from the simulations. Consequently, the catalytic activity of CALB decreases in polar solvents. This effect is significant, and CALB is over 10 orders of magnitude more active in nonpolar...... of the enzyme may be ascribed to binding of solvent molecules to the enzyme active site region and the solvation energy of substrate molecules in the different solvents. Polar solvent molecules interact strongly with CALB and compete with the substrate to bind to the active site region, resulting...

  9. Purex process solvent: literature review

    Energy Technology Data Exchange (ETDEWEB)

    Geier, R.G.

    1979-10-01

    This document summarizes the data on Purex process solvent presently published in a variety of sources. Extracts from these various sources are presented herein and contain the work done, the salient results obtained, and the original, unaltered conclusions of the author of each paper. Three major areas are addressed: solvent stability, solvent quality testing, and solvent treatment processes. 34 references, 44 tables.

  10. Purex process solvent: literature review

    International Nuclear Information System (INIS)

    Geier, R.G.

    1979-10-01

    This document summarizes the data on Purex process solvent presently published in a variety of sources. Extracts from these various sources are presented herein and contain the work done, the salient results obtained, and the original, unaltered conclusions of the author of each paper. Three major areas are addressed: solvent stability, solvent quality testing, and solvent treatment processes. 34 references, 44 tables

  11. Bio-remediation of aquifers polluted by chlorinated solvents

    International Nuclear Information System (INIS)

    Fayolle, F.

    1996-01-01

    Numerous cases of contamination of aquifers by chlorinated aliphatic solvents, largely utilized during the last decades, constitute a public health problem, because of the toxic effect of such compounds. Different types of aerobic or anaerobic bacteria are able to degrade these molecules. Processes of bio remediation are now experimented in order to restore polluted aquifers. We present here the microorganisms and the enzymatic reactions involved in the biodegradation of chlorinated solvents, and different examples of in situ bio remediation operations are described. (author)

  12. Electron Accumulative Molecules.

    Science.gov (United States)

    Buades, Ana B; Sanchez Arderiu, Víctor; Olid-Britos, David; Viñas, Clara; Sillanpää, Reijo; Haukka, Matti; Fontrodona, Xavier; Paradinas, Markos; Ocal, Carmen; Teixidor, Francesc

    2018-02-28

    With the goal to produce molecules with high electron accepting capacity and low reorganization energy upon gaining one or more electrons, a synthesis procedure leading to the formation of a B-N(aromatic) bond in a cluster has been developed. The research was focused on the development of a molecular structure able to accept and release a specific number of electrons without decomposing or change in its structural arrangement. The synthetic procedure consists of a parallel decomposition reaction to generate a reactive electrophile and a synthesis reaction to generate the B-N(aromatic) bond. This procedure has paved the way to produce the metallacarboranylviologen [M(C 2 B 9 H 11 )(C 2 B 9 H 10 )-NC 5 H 4 -C 5 H 4 N-M'(C 2 B 9 H 11 )(C 2 B 9 H 10 )] (M = M' = Co, Fe and M = Co and M' = Fe) and semi(metallacarboranyl)viologen [3,3'-M(8-(NC 5 H 4 -C 5 H 4 N-1,2-C 2 B 9 H 10 )(1',2'-C 2 B 9 H 11 )] (M = Co, Fe) electron cumulative molecules. These molecules are able to accept up to five electrons and to donate one in single electron steps at accessible potentials and in a reversible way. By targeted synthesis and corresponding electrochemical tests each electron transfer (ET) step has been assigned to specific fragments of the molecules. The molecules have been carefully characterized, and the electronic communication between both metal centers (when this situation applies) has been definitely observed through the coplanarity of both pyridine fragments. The structural characteristics of these molecules imply a low reorganization energy that is a necessary requirement for low energy ET processes. This makes them electronically comparable to fullerenes, but on their side, they have a wide range of possible solvents. The ET from one molecule to another has been clearly demonstrated as well as their self-organizing capacity. We consider that these molecules, thanks to their easy synthesis, ET, self-organizing capacity, wide range of solubility, and easy processability, can

  13. Tacit to explicit knowledge conversion.

    Science.gov (United States)

    Cairó Battistutti, Osvaldo; Bork, Dominik

    2017-11-01

    The ability to create, use and transfer knowledge may allow the creation or improvement of new products or services. But knowledge is often tacit: It lives in the minds of individuals, and therefore, it is difficult to transfer it to another person by means of the written word or verbal expression. This paper addresses this important problem by introducing a methodology, consisting of a four-step process that facilitates tacit to explicit knowledge conversion. The methodology utilizes conceptual modeling, thus enabling understanding and reasoning through visual knowledge representation. This implies the possibility of understanding concepts and ideas, visualized through conceptual models, without using linguistic or algebraic means. The proposed methodology is conducted in a metamodel-based tool environment whose aim is efficient application and ease of use.

  14. Separation by solvent extraction

    International Nuclear Information System (INIS)

    Holt, C.H. Jr.

    1976-01-01

    In a process for separating fission product values from U and Pu values contained in an aqueous solution, an oxidizing agent is added to the solution to secure U and Pu in their hexavalent state. The aqueous solution is contacted with a substantially water-immiscible organic solvent with agitation while the temperature is maintained at from -1 to -2 0 C until the major part of the water present is frozen. The solid ice phase is continuously separated as it is formed and a remaining aqueous liquid phase containing fission product values and a solvent phase containing Pu and U values are separated from each other. The last obtained part of the ice phase is melted and added to the separated liquid phase. The resulting liquid is treated with a new supply of solvent whereby it is practically depleted of U and Pu

  15. Adhesion molecules

    CERN Document Server

    Preedy, Victor R

    2016-01-01

    This book covers the structure and classification of adhesion molecules in relation to signaling pathways and gene expression. It discusses immunohistochemical localization, neutrophil migration, and junctional, functional, and inflammatory adhesion molecules in pathologies such as leukocyte decompression sickness and ischemia reperfusion injury. Highlighting the medical applications of current research, chapters cover diabetes, obesity, and metabolic syndrome; hypoxia; kidney disease; smoking, atrial fibrillation, and heart disease, the brain and dementia; and tumor proliferation. Finally, it looks at molecular imaging and bioinformatics, high-throughput technologies, and chemotherapy.

  16. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 16; Issue 12. Molecule Matters - Dinitrogen. A G Samuelson J Jabadurai. Volume 16 Issue 12 ... Author Affiliations. A G Samuelson1 J Jabadurai1. Department of Inroganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India.

  17. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 9. Molecule Matters - A Chromium Compound with a Quintuple Bond. K C Kumara Swamy. Feature Article Volume 11 Issue 9 September 2006 pp 72-75. Fulltext. Click here to view fulltext PDF. Permanent link:

  18. Organic solvent topical report

    Energy Technology Data Exchange (ETDEWEB)

    COWLEY, W.L.

    1999-05-13

    This report provides the basis for closing the organic solvent safety issue. Sufficient information is presented to conclude that risk posed by an organic solvent fire is within risk evaluation guidelines. This report updates information contained in Analysis of Consequences of Postulated Solvent Fires in Hanford Site Waste Tanks. WHC-SD-WM-CN-032. Rev. 0A (Cowley et al. 1996). However, this document will not replace Cowley et al (1996) as the primary reference for the Basis for Interim Operation (BIO) until the recently submitted BIO amendment (Hanson 1999) is approved by the US Department of Energy. This conclusion depends on the use of controls for preventing vehicle fuel fires and for limiting the use of flame cutting in areas where hot metal can fall on the waste surface.The required controls are given in the Tank Waste Remediation System Technical Safety Requirements (Noorani 1997b). This is a significant change from the conclusions presented in Revision 0 of this report. Revision 0 of this calcnote concluded that some organic solvent fire scenarios exceeded risk evaluation guidelines, even with controls imposed.

  19. Organic solvent topical report

    Energy Technology Data Exchange (ETDEWEB)

    Cowley, W.L.

    1998-04-30

    This report is the technical basis for the accident and consequence analyses used in the Hanford Tank Farms Basis for Interim Operation. The report also contains the scientific and engineering information and reference material needed to understand the organic solvent safety issue. This report includes comments received from the Chemical Reactions Subcommittee of the Tank Advisory Panel.

  20. Organic solvent topical report

    International Nuclear Information System (INIS)

    COWLEY, W.L.

    1999-01-01

    This report provides the basis for closing the organic solvent safety issue. Sufficient information is presented to conclude that risk posed by an organic solvent fire is within risk evaluation guidelines. This report updates information contained in Analysis of Consequences of Postulated Solvent Fires in Hanford Site Waste Tanks. WHC-SD-WM-CN-032. Rev. 0A (Cowley et al. 1996). However, this document will not replace Cowley et al (1996) as the primary reference for the Basis for Interim Operation (BIO) until the recently submitted BIO amendment (Hanson 1999) is approved by the US Department of Energy. This conclusion depends on the use of controls for preventing vehicle fuel fires and for limiting the use of flame cutting in areas where hot metal can fall on the waste surface.The required controls are given in the Tank Waste Remediation System Technical Safety Requirements (Noorani 1997b). This is a significant change from the conclusions presented in Revision 0 of this report. Revision 0 of this calcnote concluded that some organic solvent fire scenarios exceeded risk evaluation guidelines, even with controls imposed

  1. Organic solvent topical report

    International Nuclear Information System (INIS)

    Cowley, W.L.

    1998-01-01

    This report is the technical basis for the accident and consequence analyses used in the Hanford Tank Farms Basis for Interim Operation. The report also contains the scientific and engineering information and reference material needed to understand the organic solvent safety issue. This report includes comments received from the Chemical Reactions Subcommittee of the Tank Advisory Panel

  2. DESIGNING GREENER SOLVENTS

    Science.gov (United States)

    Computer-aided design of chemicals and chemical mixtures provides a powerful tool to help engineers identify cleaner process designs and more-benign alternatives to toxic industrial solvents. Three software programs are discussed: (1) PARIS II (Program for Assisting the Replaceme...

  3. Effect of Organic Solvents on Microalgae Growth, Metabolism and Industrial Bioproduct Extraction: A Review.

    Science.gov (United States)

    Miazek, Krystian; Kratky, Lukas; Sulc, Radek; Jirout, Tomas; Aguedo, Mario; Richel, Aurore; Goffin, Dorothee

    2017-07-04

    In this review, the effect of organic solvents on microalgae cultures from molecular to industrial scale is presented. Traditional organic solvents and solvents of new generation-ionic liquids (ILs), are considered. Alterations in microalgal cell metabolism and synthesis of target products (pigments, proteins, lipids), as a result of exposure to organic solvents, are summarized. Applications of organic solvents as a carbon source for microalgal growth and production of target molecules are discussed. Possible implementation of various industrial effluents containing organic solvents into microalgal cultivation media, is evaluated. The effect of organic solvents on extraction of target compounds from microalgae is also considered. Techniques for lipid and carotenoid extraction from viable microalgal biomass (milking methods) and dead microalgal biomass (classical methods) are depicted. Moreover, the economic survey of lipid and carotenoid extraction from microalgae biomass, by means of different techniques and solvents, is conducted.

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

    Science.gov (United States)

    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.

  5. Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water

    International Nuclear Information System (INIS)

    Oshima, Hiraku; Kinoshita, Masahiro

    2015-01-01

    In earlier works, we showed that the entropic effect originating from the translational displacement of water molecules plays the pivotal role in protein folding and denaturation. The two different solvent models, hard-sphere solvent and model water, were employed in theoretical methods wherein the entropic effect was treated as an essential factor. However, there were similarities and differences in the results obtained from the two solvent models. In the present work, to unveil the physical origins of the similarities and differences, we simultaneously consider structural transition, cold denaturation, and pressure denaturation for the same protein by employing the two solvent models and considering three different thermodynamic states for each solvent model. The solvent-entropy change upon protein folding/unfolding is decomposed into the protein-solvent pair (PA) and many-body (MB) correlation components using the integral equation theories. Each component is further decomposed into the excluded-volume (EV) and solvent-accessible surface (SAS) terms by applying the morphometric approach. The four physically insightful constituents, (PA, EV), (PA, SAS), (MB, EV), and (MB, SAS), are thus obtained. Moreover, (MB, SAS) is discussed by dividing it into two factors. This all-inclusive investigation leads to the following results: (1) the protein-water many-body correlation always plays critical roles in a variety of folding/unfolding processes; (2) the hard-sphere solvent model fails when it does not correctly reproduce the protein-water many-body correlation; (3) the hard-sphere solvent model becomes problematic when the dependence of the many-body correlation on the solvent number density and temperature is essential: it is not quite suited to studies on cold and pressure denaturating of a protein; (4) when the temperature and solvent number density are limited to the ambient values, the hard-sphere solvent model is usually successful; and (5) even at the ambient

  6. Spectroscopic and DFT study of solvent effects on the electronic absorption spectra of sulfamethoxazole in neat and binary solvent mixtures

    Science.gov (United States)

    Almandoz, M. C.; Sancho, M. I.; Blanco, S. E.

    2014-01-01

    The solvatochromic behavior of sulfamethoxazole (SMX) was investigated using UV-vis spectroscopy and DFT methods in neat and binary solvent mixtures. The spectral shifts of this solute were correlated with the Kamlet and Taft parameters (α, β and π*). Multiple lineal regression analysis indicates that both specific hydrogen-bond interaction and non specific dipolar interaction play an important role in the position of the absorption maxima in neat solvents. The simulated absorption spectra using TD-DFT methods were in good agreement with the experimental ones. Binary mixtures consist of cyclohexane (Cy)-ethanol (EtOH), acetonitrile (ACN)-dimethylsulfoxide (DMSO), ACN-dimethylformamide (DMF), and aqueous mixtures containing as co-solvents DMSO, ACN, EtOH and MeOH. Index of preferential solvation was calculated as a function of solvent composition and non-ideal characteristics are observed in all binary mixtures. In ACN-DMSO and ACN-DMF mixtures, the results show that the solvents with higher polarity and hydrogen bond donor ability interact preferentially with the solute. In binary mixtures containing water, the SMX molecules are solvated by the organic co-solvent (DMSO or EtOH) over the whole composition range. Synergistic effect is observed in the case of ACN-H2O and MeOH-H2O, indicating that at certain concentrations solvents interact to form association complexes, which should be more polar than the individual solvents of the mixture.

  7. STABILITY OF A CYLINDRICAL SOLUTE-SOLVENT INTERFACE: EFFECT OF GEOMETRY, ELECTROSTATICS, AND HYDRODYNAMICS.

    Science.gov (United States)

    Li, B O; Sun, Hui; Zhou, Shenggao

    The solute-solvent interface that separates biological molecules from their surrounding aqueous solvent characterizes the conformation and dynamics of such molecules. In this work, we construct a solvent fluid dielectric boundary model for the solvation of charged molecules and apply it to study the stability of a model cylindrical solute-solvent interface. The motion of the solute-solvent interface is defined to be the same as that of solvent fluid at the interface. The solvent fluid is assumed to be incompressible and is described by the Stokes equation. The solute is modeled simply by the ideal-gas law. All the viscous force, hydrostatic pressure, solute-solvent van der Waals interaction, surface tension, and electrostatic force are balanced at the solute-solvent interface. We model the electrostatics by Poisson's equation in which the solute-solvent interface is treated as a dielectric boundary that separates the low-dielectric solute from the high-dielectric solvent. For a cylindrical geometry, we find multiple cylindrically shaped equilibrium interfaces that describe polymodal (e.g., dry and wet) states of hydration of an underlying molecular system. These steady-state solutions exhibit bifurcation behavior with respect to the charge density. For their linearized systems, we use the projection method to solve the fluid equation and find the dispersion relation. Our asymptotic analysis shows that, for large wavenumbers, the decay rate is proportional to wavenumber with the proportionality half of the ratio of surface tension to solvent viscosity, indicating that the solvent viscosity does affect the stability of a solute-solvent interface. Consequences of our analysis in the context of biomolecular interactions are discussed.

  8. Solvent selection methodology for pharmaceutical processes: Solvent swap

    DEFF Research Database (Denmark)

    Papadakis, Emmanouil; Kumar Tula, Anjan; Gani, Rafiqul

    2016-01-01

    A method for the selection of appropriate solvents for the solvent swap task in pharmaceutical processes has been developed. This solvent swap method is based on the solvent selection method of Gani et al. (2006) and considers additional selection criteria such as boiling point difference...... in pharmaceutical processes as well as new solvent swap alternatives. The method takes into account process considerations such as batch distillation and crystallization to achieve the swap task. Rigorous model based simulations of the swap operation are performed to evaluate and compare the performance...

  9. Improvements in solvent extraction columns

    International Nuclear Information System (INIS)

    Aughwane, K.R.

    1987-01-01

    Solvent extraction columns are used in the reprocessing of irradiated nuclear fuel. For an effective reprocessing operation a solvent extraction column is required which is capable of distributing the feed over most of the column. The patent describes improvements in solvent extractions columns which allows the feed to be distributed over an increased length of column than was previously possible. (U.K.)

  10. Solvent extraction columns

    International Nuclear Information System (INIS)

    Middleton, P.; Smith, J.R.

    1979-01-01

    In pulsed columns for use in solvent extraction processes, e.g. the reprocessing of nuclear fuel, the horizontal perforated plates inside the column are separated by interplate spacers manufactured from metallic neutron absorbing material. The spacer may be in the form of a spiral or concentric circles separated by radial limbs, or may be of egg-box construction. Suitable neutron absorbing materials include stainless steel containing boron or gadolinium, hafnium metal or alloys of hafnium. (UK)

  11. Solvent jet desorption capillary photoionization-mass spectrometry.

    Science.gov (United States)

    Haapala, Markus; Teppo, Jaakko; Ollikainen, Elisa; Kiiski, Iiro; Vaikkinen, Anu; Kauppila, Tiina J; Kostiainen, Risto

    2015-03-17

    A new ambient mass spectrometry method, solvent jet desorption capillary photoionization (DCPI), is described. The method uses a solvent jet generated by a coaxial nebulizer operated at ambient conditions with nitrogen as nebulizer gas. The solvent jet is directed onto a sample surface, from which analytes are extracted into the solvent and ejected from the surface in secondary droplets formed in collisions between the jet and the sample surface. The secondary droplets are directed into the heated capillary photoionization (CPI) device, where the droplets are vaporized and the gaseous analytes are ionized by 10 eV photons generated by a vacuum ultraviolet (VUV) krypton discharge lamp. As the CPI device is directly connected to the extended capillary inlet of the MS, high ion transfer efficiency to the vacuum of MS is achieved. The solvent jet DCPI provides several advantages: high sensitivity for nonpolar and polar compounds with limit of detection down to low fmol levels, capability of analyzing small and large molecules, and good spatial resolution (250 μm). Two ionization mechanisms are involved in DCPI: atmospheric pressure photoionization, capable of ionizing polar and nonpolar compounds, and solvent assisted inlet ionization capable of ionizing larger molecules like peptides. The feasibility of DCPI was successfully tested in the analysis of polar and nonpolar compounds in sage leaves and chili pepper.

  12. Supramolecular Chirality: Solvent Chirality Transfer in Molecular Chemistry and Polymer Chemistry

    Directory of Open Access Journals (Sweden)

    Michiya Fujiki

    2014-08-01

    Full Text Available Controlled mirror symmetry breaking arising from chemical and physical origin is currently one of the hottest issues in the field of supramolecular chirality. The dynamic twisting abilities of solvent molecules are often ignored and unknown, although the targeted molecules and polymers in a fluid solution are surrounded by solvent molecules. We should pay more attention to the facts that mostly all of the chemical and physical properties of these molecules and polymers in the ground and photoexcited states are significantly influenced by the surrounding solvent molecules with much conformational freedom through non-covalent supramolecular interactions between these substances and solvent molecules. This review highlights a series of studies that include: (i historical background, covering chiral NaClO3 crystallization in the presence of d-sugars in the late 19th century; (ii early solvent chirality effects for optically inactive chromophores/fluorophores in the 1960s–1980s; and (iii the recent development of mirror symmetry breaking from the corresponding achiral or optically inactive molecules and polymers with the help of molecular chirality as the solvent use quantity.

  13. Hazardous solvent substitution

    International Nuclear Information System (INIS)

    Twitchell, K.E.

    1995-01-01

    Eliminating hazardous solvents is good for the environment, worker safety, and the bottom line. However, even though we are motivated to find replacements, the big question is 'What can we use as replacements for hazardous solvents?'You, too, can find replacements for your hazardous solvents. All you have to do is search for them. Search through the vendor literature of hundreds of companies with thousands of products. Ponder the associated material safety data sheets, assuming of course that you can obtain them and, having obtained them, that you can read them. You will want to search the trade magazines and other sources for product reviews. You will want to talk to users about how well the product actually works. You may also want to check US Environmental Protection Agency (EPA) and other government reports for toxicity and other safety information. And, of course, you will want to compare the product's constituent chemicals with the many hazardous constituency lists to ensure the safe and legal use of the product in your workplace

  14. A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water

    Science.gov (United States)

    Wu, Xiongwu; Brooks, Bernard R.

    2015-01-01

    Chemical and thermodynamic equilibrium of multiple states is a fundamental phenomenon in biology systems and has been the focus of many experimental and computational studies. This work presents a simulation method to directly study the equilibrium of multiple states. This method constructs a virtual mixture of multiple states (VMMS) to sample the conformational space of all chemical states simultaneously. The VMMS system consists of multiple subsystems, one for each state. The subsystem contains a solute and a solvent environment. The solute molecules in all subsystems share the same conformation but have their own solvent environments. Transition between states is implicated by the change of their molar fractions. Simulation of a VMMS system allows efficient calculation of relative free energies of all states, which in turn determine their equilibrium molar fractions. For systems with a large number of state transition sites, an implicit site approximation is introduced to minimize the cost of simulation. A direct application of the VMMS method is for constant pH simulation to study protonation equilibrium. Applying the VMMS method to a heptapeptide of 3 ionizable residues, we calculated the pKas of those residues both with all explicit states and with implicit sites and obtained consistent results. For mouse epidermal growth factor of 9 ionizable groups, our VMMS simulations with implicit sites produced pKas of all 9 ionizable groups and the results agree qualitatively with NMR measurement. This example demonstrates the VMMS method can be applied to systems of a large number of ionizable groups and the computational cost scales linearly with the number of ionizable groups. For one of the most challenging systems in constant pH calculation, SNase Δ+PHS/V66K, our VMMS simulation shows that it is the state-dependent water penetration that causes the large deviation in lysine66’s pKa. PMID:26506245

  15. A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water.

    Directory of Open Access Journals (Sweden)

    Xiongwu Wu

    2015-10-01

    Full Text Available Chemical and thermodynamic equilibrium of multiple states is a fundamental phenomenon in biology systems and has been the focus of many experimental and computational studies. This work presents a simulation method to directly study the equilibrium of multiple states. This method constructs a virtual mixture of multiple states (VMMS to sample the conformational space of all chemical states simultaneously. The VMMS system consists of multiple subsystems, one for each state. The subsystem contains a solute and a solvent environment. The solute molecules in all subsystems share the same conformation but have their own solvent environments. Transition between states is implicated by the change of their molar fractions. Simulation of a VMMS system allows efficient calculation of relative free energies of all states, which in turn determine their equilibrium molar fractions. For systems with a large number of state transition sites, an implicit site approximation is introduced to minimize the cost of simulation. A direct application of the VMMS method is for constant pH simulation to study protonation equilibrium. Applying the VMMS method to a heptapeptide of 3 ionizable residues, we calculated the pKas of those residues both with all explicit states and with implicit sites and obtained consistent results. For mouse epidermal growth factor of 9 ionizable groups, our VMMS simulations with implicit sites produced pKas of all 9 ionizable groups and the results agree qualitatively with NMR measurement. This example demonstrates the VMMS method can be applied to systems of a large number of ionizable groups and the computational cost scales linearly with the number of ionizable groups. For one of the most challenging systems in constant pH calculation, SNase Δ+PHS/V66K, our VMMS simulation shows that it is the state-dependent water penetration that causes the large deviation in lysine66's pKa.

  16. A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water.

    Science.gov (United States)

    Wu, Xiongwu; Brooks, Bernard R

    2015-10-01

    Chemical and thermodynamic equilibrium of multiple states is a fundamental phenomenon in biology systems and has been the focus of many experimental and computational studies. This work presents a simulation method to directly study the equilibrium of multiple states. This method constructs a virtual mixture of multiple states (VMMS) to sample the conformational space of all chemical states simultaneously. The VMMS system consists of multiple subsystems, one for each state. The subsystem contains a solute and a solvent environment. The solute molecules in all subsystems share the same conformation but have their own solvent environments. Transition between states is implicated by the change of their molar fractions. Simulation of a VMMS system allows efficient calculation of relative free energies of all states, which in turn determine their equilibrium molar fractions. For systems with a large number of state transition sites, an implicit site approximation is introduced to minimize the cost of simulation. A direct application of the VMMS method is for constant pH simulation to study protonation equilibrium. Applying the VMMS method to a heptapeptide of 3 ionizable residues, we calculated the pKas of those residues both with all explicit states and with implicit sites and obtained consistent results. For mouse epidermal growth factor of 9 ionizable groups, our VMMS simulations with implicit sites produced pKas of all 9 ionizable groups and the results agree qualitatively with NMR measurement. This example demonstrates the VMMS method can be applied to systems of a large number of ionizable groups and the computational cost scales linearly with the number of ionizable groups. For one of the most challenging systems in constant pH calculation, SNase Δ+PHS/V66K, our VMMS simulation shows that it is the state-dependent water penetration that causes the large deviation in lysine66's pKa.

  17. SOLVENT FIRE BY-PRODUCTS

    Energy Technology Data Exchange (ETDEWEB)

    Walker, D; Samuel Fink, S

    2006-05-22

    Southwest Research Institute (SwRI) conducted a burn test of the Caustic-Side Solvent Extraction (CSSX) solvent to determine the combustion products. The testing showed hydrogen fluoride gas is not a combustion product from a solvent fire when up to 70% of the solvent is consumed. The absence of HF in the combustion gases may reflect concentration of the modifier containing the fluoride groups in the unburned portion. SwRI reported results for other gases (CO, HCN, NOx, formaldehyde, and hydrocarbons). The results, with other supporting information, can be used for evaluating the consequences of a facility fire involving the CSSX solvent inventory.

  18. Nanospiral Formation by Droplet Drying: One Molecule at a Time

    Directory of Open Access Journals (Sweden)

    Wan Lei

    2011-01-01

    Full Text Available Abstract We have created nanospirals by self-assembly during droplet evaporation. The nanospirals, 60–70 nm in diameter, formed when solvent mixtures of methanol and m-cresol were used. In contrast, spin coating using only methanol as the solvent produced epitaxial films of stripe nanopatterns and using only m-cresol disordered structure. Due to the disparity in vapor pressure between the two solvents, droplets of m-cresol solution remaining on the substrate serve as templates for the self-assembly of carboxylic acid molecules, which in turn allows the visualization of solution droplet evaporation one molecule at a time.

  19. The role of the ion-molecule and molecule-molecule interactions in the formation of the two-ion average force interaction potential

    CERN Document Server

    Ajrian, E A; Sidorenko, S N

    2002-01-01

    The effect of the ion-molecule and intermolecular interactions on the formation of inter-ion average force potentials is investigated within the framework of a classical ion-dipole model of electrolyte solutions. These potentials are shown to possess the Coulomb asymptotics at large distances while in the region of mean distances they reveal creation and disintegration of solvent-shared ion pairs. The calculation results provide a qualitatively authentic physical picture which is experimentally observed in strong electrolytes solutions. In particular, an increased interaction between an ion and a molecule enhances formation of ion pairs in which the ions are separated by one solvent molecule

  20. Selective metal-vapor deposition on solvent evaporated polymer surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Yamaguchi, Koji; Tsujioka, Tsuyoshi, E-mail: tsujioka@cc.osaka-kyoiku.ac.jp

    2015-12-31

    We report a selective metal-vapor deposition phenomenon based on solvent printing and evaporation on polymer surfaces and propose a method to prepare fine metal patterns using maskless vacuum deposition. Evaporation of the solvent molecules from the surface caused large free volumes between surface polymer chains and resulted in high mobility of the chains, enhancing metal-vapor atom desorption from the surface. This phenomenon was applied to prepare metal patterns on the polymer surface using solvent printing and maskless metal vacuum deposition. Metal patterns with high resolution of micron scale were obtained for various metal species and semiconductor polymer substrates including poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] and poly(3-hexylthiophene-2,5-diyl). - Highlights: • Selective metal-vapor deposition using solvent evaporation on polymer was attained. • Metal patterns with high resolution were obtained for various metal species. • This method can be applied to achieve fine metal-electrodes for polymer electronics.

  1. Solvent vapor annealing of an insoluble molecular semiconductor

    KAUST Repository

    Amassian, Aram

    2010-01-01

    Solvent vapor annealing has been proposed as a low-cost, highly versatile, and room-temperature alternative to thermal annealing of organic semiconductors and devices. In this article, we investigate the solvent vapor annealing process of a model insoluble molecular semiconductor thin film - pentacene on SiO 2 exposed to acetone vapor - using a combination of optical reflectance and two-dimensional grazing incidence X-ray diffraction measurements performed in situ, during processing. These measurements provide valuable and new insight into the solvent vapor annealing process; they demonstrate that solvent molecules interact mainly with the surface of the film to induce a solid-solid transition without noticeable swelling, dissolving or melting of the molecular material. © 2010 The Royal Society of Chemistry.

  2. Evaluation of the detachment energy of hydrated phosphate anion over a wide range of cluster size and revisiting solvent-berg model: a theoretical study

    Science.gov (United States)

    Pathak, Arup Kumar

    2014-12-01

    An explicit analytical expression has been obtained for vertical detachment energy (VDE) that can be used to calculate the same over a wide range (both stable and unstable regions) of cluster sizes including the bulk from the knowledge of VDE for a finite number of stable clusters (n = 16-23). The calculated VDE for the bulk is found to be very good in agreement (within 1%) with the available experimental result and the domain of instability lies between n = 0 and n = 15 for the hydrated clusters, PO3 -4 . nH2O. The minimum number (n0) of water molecules needed to stabilise the phosphate anion is 16. We are able to explain the origin of solvent-berg model and anomalous conductivity from the knowledge of first stable cluster. We have also provided a scheme to calculate the radius of the solvent-berg for phosphate anion. The calculated conductivity using Stokes-Einstein relation and the radius of solvent-berg is found to be very good in agreement (within 4%) with the available experimental results.

  3. Implicit and Explicit Instruction of Spelling Rules

    Science.gov (United States)

    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…

  4. Explicit learning in Act-R

    NARCIS (Netherlands)

    Taatgen, N.A.; Schmid, U; Krems, J; Wysotzky, F

    1999-01-01

    A popular distinction in the learning literature is the distinction between implicit and explicit learning. Although many studies elaborate on the nature of implicit learning, little attention is left for explicit learning. The unintentional aspect of implicit learning corresponds well to the

  5. Quantification of residual solvents in antibody drug conjugates using gas chromatography

    Energy Technology Data Exchange (ETDEWEB)

    Medley, Colin D., E-mail: medley.colin@gene.com [Genentech Inc., Small Molecule Pharmaceutical Sciences, 1 DNA Way, South San Francisco, CA 94080 (United States); Kay, Jacob [Research Pharmaceutical Services, 520 Virginia Dr. Fort, Washington, PA (United States); Li, Yi; Gruenhagen, Jason; Yehl, Peter; Chetwyn, Nik P. [Genentech Inc., Small Molecule Pharmaceutical Sciences, 1 DNA Way, South San Francisco, CA 94080 (United States)

    2014-11-19

    Highlights: • Sensitive residual solvents detection in ADCs. • 125 ppm QL for common conjugation solvents. • Generic and validatable method. - Abstract: The detection and quantification of residual solvents present in clinical and commercial pharmaceutical products is necessary from both patient safety and regulatory perspectives. Head-space gas chromatography is routinely used for quantitation of residual solvents for small molecule APIs produced through synthetic processes; however residual solvent analysis is generally not needed for protein based pharmaceuticals produced through cultured cell lines where solvents are not introduced. In contrast, antibody drug conjugates and other protein conjugates where a drug or other molecule is covalently bound to a protein typically use solvents such as N,N-dimethylacetamide (DMA), N,N‑dimethylformamide (DMF), dimethyl sulfoxide (DMSO), or propylene glycol (PG) to dissolve the hydrophobic small molecule drug for conjugation to the protein. The levels of the solvent remaining following the conjugation step are therefore important to patient safety as these parental drug products are introduced directly into the patients bloodstream. We have developed a rapid sample preparation followed by a gas chromatography separation for the detection and quantification of several solvents typically used in these conjugation reactions. This generic method has been validated and can be easily implemented for use in quality control testing for clinical or commercial bioconjugated products.

  6. Simulated x-ray scattering of protein solutions using explicit-solvent models

    International Nuclear Information System (INIS)

    Park, Sanghyun; Bardhan, Jaydeep P.; Makowski, Lee; Roux, Benoit

    2009-01-01

    X-ray solution scattering shows new promise for the study of protein structures, complementing crystallography and nuclear magnetic resonance. In order to realize the full potential of solution scattering, it is necessary to not only improve experimental techniques but also develop accurate and efficient computational schemes to relate atomistic models to measurements. Previous computational methods, based on continuum models of water, have been unable to calculate scattering patterns accurately, especially in the wide-angle regime which contains most of the information on the secondary, tertiary, and quaternary structures. Here we present a novel formulation based on the atomistic description of water, in which scattering patterns are calculated from atomic coordinates of protein and water. Without any empirical adjustments, this method produces scattering patterns of unprecedented accuracy in the length scale between 5 and 100 A, as we demonstrate by comparing simulated and observed scattering patterns for myoglobin and lysozyme.

  7. Oligoquinolines under Solvent-free Microwave Irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Park, Kwi-Jeon; Kwon, Tae-Woo [Kyungsung University, Busan (Korea, Republic of)

    2015-01-15

    Quinolines are thermally stable and can be used as an excellent n-type semiconducting materials. Since quinolines are also known to be electron acceptor molecules, combination of various electron donor building blocks can be utilized in photonic and electronic organic light-emitting diode (OLED) applications. For example, donor.acceptor systems with phenothiazine (or carbazole) molecules as electron donors and the phenylquinoline group as an electron acceptor provide an efficient approach for the design of new materials exhibiting highly efficient charge-transfer photophysics and electroluminescence in OLEDs. We have described the Friedlander quinoline synthesis between aminobenzophenones and symmetrical diacetyl compounds having phenothiazine, carbazole, biphenyl, and phenyl moieties under solvent-free microwave irradiation in 12.98% isolated yields.

  8. Linear response coupled cluster theory with the polarizable continuum model within the singles approximation for the solvent response

    Science.gov (United States)

    Caricato, Marco

    2018-04-01

    We report the theory and the implementation of the linear response function of the coupled cluster (CC) with the single and double excitations method combined with the polarizable continuum model of solvation, where the correlation solvent response is approximated with the perturbation theory with energy and singles density (PTES) scheme. The singles name is derived from retaining only the contribution of the CC single excitation amplitudes to the correlation density. We compare the PTES working equations with those of the full-density (PTED) method. We then test the PTES scheme on the evaluation of excitation energies and transition dipoles of solvated molecules, as well as of the isotropic polarizability and specific rotation. Our results show a negligible difference between the PTED and PTES schemes, while the latter affords a significantly reduced computational cost. This scheme is general and can be applied to any solvation model that includes mutual solute-solvent polarization, including explicit models. Therefore, the PTES scheme is a competitive approach to compute response properties of solvated systems using CC methods.

  9. Solvent effects in chemistry

    CERN Document Server

    Buncel, Erwin

    2015-01-01

    This book introduces the concepts, theory and experimental knowledge concerning solvent effects on the rate and equilibrium of chemical reactions of all kinds.  It begins with basic thermodynamics and kinetics, building on this foundation to demonstrate how a more detailed understanding of these effects may be used to aid in determination of reaction mechanisms, and to aid in planning syntheses. Consideration is given to theoretical calculations (quantum chemistry, molecular dynamics, etc.), to statistical methods (chemometrics), and to modern day concerns such as ""green"" chemistry, where ut

  10. Microfluidic Extraction of Biomarkers using Water as Solvent

    Science.gov (United States)

    Amashukeli, Xenia; Manohara, Harish; Chattopadhyay, Goutam; Mehdi, Imran

    2009-01-01

    A proposed device, denoted a miniature microfluidic biomarker extractor (mu-EX), would extract trace amounts of chemicals of interest from samples, such as soils and rocks. Traditionally, such extractions are performed on a large scale with hazardous organic solvents; each solvent capable of dissolving only those molecules lying within narrow ranges of specific chemical and physical characteristics that notably include volatility, electric charge, and polarity. In contrast, in the mu-EX, extractions could be performed by use of small amounts (typically between 0.1 and 100 L) of water as a universal solvent. As a rule of thumb, in order to enable solvation and extraction of molecules, it is necessary to use solvents that have polarity sufficiently close to the polarity of the target molecules. The mu-EX would make selection of specific organic solvents unnecessary, because mu-EX would exploit a unique property of liquid water: the possibility of tuning its polarity to match the polarity of organic solvents appropriate for extraction of molecules of interest. The change of the permittivity of water would be achieved by exploiting interactions between the translational states of water molecules and an imposed electromagnetic field in the frequency range of 300 to 600 GHz. On a molecular level, these interactions would result in disruption of the three-dimensional hydrogen-bonding network among liquid-water molecules and subsequent solvation and hydrolysis of target molecules. The mu-EX is expected to be an efficient means of hydrolyzing chemical bonds in complex macromolecules as well and, thus, enabling analysis of the building blocks of these complex chemical systems. The mu-EX device would include a microfluidic channel, part of which would lie within a waveguide coupled to an electronically tuned source of broad-band electromagnetic radiation in the frequency range from 300 to 600 GHz (see figure). The part of the microfluidic channel lying in the waveguide would

  11. Molecule Matters van der Waals Molecules

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 12. Molecule Matters van der Waals Molecules - Noble Gas Clusters are London Molecules! E Arunan. Feature Article Volume 14 Issue 12 December 2009 pp 1210-1222 ...

  12. The spectral properties of (--epigallocatechin 3-O-gallate (EGCG fluorescence in different solvents: dependence on solvent polarity.

    Directory of Open Access Journals (Sweden)

    Vladislav Snitsarev

    Full Text Available (--Epigallocatechin 3-O-gallate (EGCG a molecule found in green tea and known for a plethora of bioactive properties is an inhibitor of heat shock protein 90 (HSP90, a protein of interest as a target for cancer and neuroprotection. Determination of the spectral properties of EGCG fluorescence in environments similar to those of binding sites found in proteins provides an important tool to directly study protein-EGCG interactions. The goal of this study is to examine the spectral properties of EGCG fluorescence in an aqueous buffer (AB at pH=7.0, acetonitrile (AN (a polar aprotic solvent, dimethylsulfoxide (DMSO (a polar aprotic solvent, and ethanol (EtOH (a polar protic solvent. We demonstrate that EGCG is a highly fluorescent molecule when excited at approximately 275 nm with emission maxima between 350 and 400 nm depending on solvent. Another smaller excitation peak was found when EGCG is excited at approximately 235 nm with maximum emission between 340 and 400 nm. We found that the fluorescence intensity (FI of EGCG in AB at pH=7.0 is significantly quenched, and that it is about 85 times higher in an aprotic solvent DMSO. The Stokes shifts of EGCG fluorescence were determined by solvent polarity. In addition, while the emission maxima of EGCG fluorescence in AB, DMSO, and EtOH follow the Lippert-Mataga equation, its fluorescence in AN points to non-specific solvent effects on EGCG fluorescence. We conclude that significant solvent-dependent changes in both fluorescence intensity and fluorescence emission shifts can be effectively used to distinguish EGCG in aqueous solutions from EGCG in environments of different polarity, and, thus, can be used to study specific EGCG binding to protein binding sites where the environment is often different from aqueous in terms of polarity.

  13. Solvent effects in the synergistic solvent extraction of Co2+

    International Nuclear Information System (INIS)

    Kandil, A.T.; Ramadan, A.

    1979-01-01

    The extraction of Co 2+ from a 0.1M ionic strength aqueous phase (Na + , CH 3 COOH) of pH = 5.1 was studied using thenoyltrifluoroacetone, HTTA, in eight different solvents and HTTA + trioctylphosphine oxide, TOPO, in the same solvents. A comparison of the effect of solvent dielectric constant on the equilibrium constant shows a synergism as a result of the increased hydrophobic character imparted to the metal complex due to the formation of the TOPO adduct. (author)

  14. Molecular accessibility in solvent swelled coals

    Energy Technology Data Exchange (ETDEWEB)

    Kispert, L.D.

    1993-02-01

    An EPR technique developed in this lab is being used to determine the pore size and number distribution changes after swelling the coal samples with various solvents. Stable nitroxide radical spin probes of different sizes, shapes and reactivity are dissolved in an appropriate solvent, the coal sample is added to the resulting solution, stirred over night at elevated temperature, filtered, washed with a non swelling solvent to eliminate any spin probes that are not trapped in the pores and the spin concentration is measured. Comparing these spin probe measurements to DRIFT data have shown that the relative number distribution of acidic functionalities can be accurately predicted by the spin probe method. The spin probe method had also been used to predict the increase in elongated voids in Pittsburgh No. 8 (APCS No. 4) upon swelling with pyridine in agreement with independent SANS data. NMR relaxation data show that it is possible to deduce the pore (accessibility) distribution as a function of size (up to 6 mn). It has also been possible by variable temperature and ENDOR measurements to determine the presence of hydrogen bonding as a function of pore shape and size. The advantage of the EPR method is that it permits molecules of selected shape and size to be used as probes of accessible regions of coal, thus providing information on the importance of molecular shape.

  15. Insights into the effects of solvent properties in graphene based electric double-layer capacitors with organic electrolytes

    Science.gov (United States)

    Zhang, Shuo; Bo, Zheng; Yang, Huachao; Yang, Jinyuan; Duan, Liangping; Yan, Jianhua; Cen, Kefa

    2016-12-01

    Organic electrolytes are widely used in electric double-layer capacitors (EDLCs). In this work, the microstructure of planar graphene-based EDLCs with different organic solvents are investigated with molecular dynamics simulations. Results show that an increase of solvent polarity could weaken the accumulation of counter-ions nearby the electrode surface, due to the screen of electrode charges and relatively lower ionic desolvation. It thus suggests that solvents with low polarity could be preferable to yield high EDL capacitance. Meanwhile, the significant effects of the size and structure of solvent molecules are reflected by non-electrostatic molecule-electrode interactions, further influencing the adsorption of solvent molecules on electrode surface. Compared with dimethyl carbonate, γ-butyrolactone, and propylene carbonate, acetonitrile with relatively small-size and linear structure owns weak non-electrostatic interactions, which favors the easy re-orientation of solvent molecules. Moreover, the shift of solvent orientation in surface layer, from parallel orientation to perpendicular orientation relative to the electrode surface, deciphers the solvent twin-peak behavior near negative electrode. The as-obtained insights into the roles of solvent properties on the interplays among particles and electrodes elucidate the solvent influences on the microstructure and capacitive behavior of EDLCs using organic electrolytes.

  16. Solvent extraction of zirconium

    International Nuclear Information System (INIS)

    Kim, S.S.; Yoon, J.H.

    1981-01-01

    The extraction of zirconium(VI) from an aqueous solution of constant ionic strength with versatic acid-10 dissolved in benzen was studied as a function of pH and the concentration of zirconium(VI) and organic acid. The effects of sulphate and chlorine ions on the extraction of the zirconium(VI) were briefly examined. It was revealed that (ZrOR 2 .2RH) is the predominant species of extracted zirconium(VI) in the versatic acid-10. The chemical equation and the apparent equilibrium constants thereof have been determined as follows. (ZrOsup(2+))aq+ 2(R 2 H 2 )sub(org) = (ZrOR 2 .2RH)sub(org)+2(H + )aq Ksub(Zr) = (ZrOR 2 .2RH)sub(org)(H + ) 2 /(ZrOsup(2+))sub(aq)(R 2 H 2 )sup(2)sub(org) = 3.3 x 10 -7 . The synergistic effects of TBP and D2EHPA were also studied. In the mixed solvent with 0.1M TBP, the synergistic effect was observed, while the mixed solvent with D2EHPA showed the antisynergistic effect. (Author)

  17. Dissolution of covalent adaptable network polymers in organic solvent

    Science.gov (United States)

    Yu, Kai; Yang, Hua; Dao, Binh H.; Shi, Qian; Yakacki, Christopher M.

    2017-12-01

    It was recently reported that thermosetting polymers can be fully dissolved in a proper organic solvent utilizing a bond-exchange reaction (BER), where small molecules diffuse into the polymer, break the long polymer chains into short segments, and eventually dissolve the network when sufficient solvent is provided. The solvent-assisted dissolution approach was applied to fully recycle thermosets and their fiber composites. This paper presents the first multi-scale modeling framework to predict the dissolution kinetics and mechanics of thermosets in organic solvent. The model connects the micro-scale network dynamics with macro-scale material properties: in the micro-scale, a model is developed based on the kinetics of BERs to describe the cleavage rate of polymer chains and evolution of chain segment length during the dissolution. The micro-scale model is then fed into a continuum-level model with considerations of the transportation of solvent molecules and chain segments in the system. The model shows good prediction on conversion rate of functional groups, degradation of network mechanical properties, and dissolution rate of thermosets during the dissolution. It identifies the underlying kinetic factors governing the dissolution process, and reveals the influence of different material and processing variables on the dissolution process, such as time, temperature, catalyst concentration, and chain length between cross-links.

  18. Explicit formulas for Clebsch-Gordan coefficients

    International Nuclear Information System (INIS)

    Rudnicki-Bujnowski, G.

    1975-01-01

    The problem is to obtain explicit algebraic formulas of Clebsch-Gordan coefficients for high values of angular momentum. The method of solution is an algebraic method based on the Racah formula using the FORMAC programming language. (Auth.)

  19. Solvent Flux Method (SFM): A Case Study of Water Access to Candida antarctica Lipase B.

    Science.gov (United States)

    Benson, Sven P; Pleiss, Jürgen

    2014-11-11

    The solvent flux method (SFM) was developed to comprehensively characterize the influx of solvent molecules from the solvent environment into the active site of a protein in the framework of molecular dynamics simulations. This was achieved by introducing a solvent concentration gradient as well as partially reorienting and rescaling the velocity vector of all solvent molecules contained within a spherical volume enclosing the protein, thus inducing an accelerated solvent influx toward the active site. In addition to the detection of solvent access pathway within the protein structure, it is hereby possible to identify potential amino acid positions relevant to solvent-related enzyme engineering with high statistical significance. The method is particularly aimed at improving the reverse hydrolysis reaction rates in nonaqueous media. Candida antarctica lipase B (CALB) binds to a triglyceride-water interface with its substrate entrance channel oriented toward the hydrophobic substrate interface. The lipase-triglyceride-water system served as a model system for SFM to evaluate the influx of water molecules to the active site. As a proof of principle for SFM, a previously known water access pathway in CALB was identified as the primary water channel. In addition, a secondary water channel and two pathways for water access which contribute to water leakage between the protein and the triglyceride-water interface were identified.

  20. Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Shenggao, E-mail: sgzhou@suda.edu.cn, E-mail: bli@math.ucsd.edu [Department of Mathematics and Mathematical Center for Interdiscipline Research, Soochow University, 1 Shizi Street, Jiangsu, Suzhou 215006 (China); Sun, Hui; Cheng, Li-Tien [Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112 (United States); Dzubiella, Joachim [Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, 14109 Berlin, Germany and Institut für Physik, Humboldt-Universität zu Berlin, 12489 Berlin (Germany); Li, Bo, E-mail: sgzhou@suda.edu.cn, E-mail: bli@math.ucsd.edu [Department of Mathematics and Quantitative Biology Graduate Program, University of California, San Diego, La Jolla, California 92093-0112 (United States); McCammon, J. Andrew [Department of Chemistry and Biochemistry, Department of Pharmacology, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0365 (United States)

    2016-08-07

    Recent years have seen the initial success of a variational implicit-solvent model (VISM), implemented with a robust level-set method, in capturing efficiently different hydration states and providing quantitatively good estimation of solvation free energies of biomolecules. The level-set minimization of the VISM solvation free-energy functional of all possible solute-solvent interfaces or dielectric boundaries predicts an equilibrium biomolecular conformation that is often close to an initial guess. In this work, we develop a theory in the form of Langevin geometrical flow to incorporate solute-solvent interfacial fluctuations into the VISM. Such fluctuations are crucial to biomolecular conformational changes and binding process. We also develop a stochastic level-set method to numerically implement such a theory. We describe the interfacial fluctuation through the “normal velocity” that is the solute-solvent interfacial force, derive the corresponding stochastic level-set equation in the sense of Stratonovich so that the surface representation is independent of the choice of implicit function, and develop numerical techniques for solving such an equation and processing the numerical data. We apply our computational method to study the dewetting transition in the system of two hydrophobic plates and a hydrophobic cavity of a synthetic host molecule cucurbit[7]uril. Numerical simulations demonstrate that our approach can describe an underlying system jumping out of a local minimum of the free-energy functional and can capture dewetting transitions of hydrophobic systems. In the case of two hydrophobic plates, we find that the wavelength of interfacial fluctuations has a strong influence to the dewetting transition. In addition, we find that the estimated energy barrier of the dewetting transition scales quadratically with the inter-plate distance, agreeing well with existing studies of molecular dynamics simulations. Our work is a first step toward the

  1. Selective solvent extraction of oils

    Energy Technology Data Exchange (ETDEWEB)

    1938-04-09

    In the selective solvent extraction of naphthenic base oils, the solvent used consists of the extract obtained by treating a paraffinic base oil with a selective solvent. The extract, or partially spent solvent is less selective than the solvent itself. Selective solvents specified for the extraction of the paraffinic base oil are phenol, sulphur dioxide, cresylic acid, nitrobenzene, B:B/sup 1/-dichlorethyl ether, furfural, nitroaniline and benzaldehyde. Oils treated are Coastal lubricating oils, or naphthenic oils from the cracking, or destructive hydrogenation of coal, tar, lignite, peat, shale, bitumen, or petroleum. The extraction may be effected by a batch or counter-current method, and in the presence of (1) liquefied propane, or butane, or naphtha, or (2) agents which modify the solvent power such as, water, ammonia, acetonitrile, glycerine, glycol, caustic soda or potash. Treatment (2) may form a post-treatment effected on the extract phase. In counter-current treatment in a tower some pure selective solvent may be introduced near the raffinate outlet to wash out any extract therefrom.

  2. Solvent extraction of Zn and metals in Zn ores by nonphosphorous solvents

    International Nuclear Information System (INIS)

    Auchapt, J.M.; Tostain, Jacqueline.

    1975-07-01

    This bibliography follows a first work on Zn solvent extraction by organo-phosphorous compounds. The other solvents used in Zn extraction, are studied: oxygenated nonphosphorous solvents (ketones, alcohols, carboxylic acids, sulfonates), nitrogenous solvents and hydrocarbons [fr

  3. Cesium Concentration in MCU Solvent

    International Nuclear Information System (INIS)

    Walker, D

    2006-01-01

    During Modular Caustic-Side Solvent Extraction (CSSX) Unit (MCU) operations, Cs-137 concentrations in product streams will vary depending on the location in the process and on the recent process conditions. Calculations of cesium concentrations under a variety of operating conditions reveal the following: (1) Under nominal operations with salt solution feed containing 1.1 Ci Cs-137 per gallon, the maximum Cs-137 concentration in the process will occur in the strip effluent (SE) and equal 15-16.5 Ci/gal. (2) Under these conditions, the majority of the solvent will contain 0.005 to 0.01 Ci/gal, with a limited portion of the solvent in the contactor stages containing ∼4 Ci/gal. (3) When operating conditions yield product near 0.1 Ci Cs-137/gal in the decontaminated salt solution (DSS), the SE cesium concentration will be the same or lower than in nominal operations, but majority of the stripped solvent will increase to ∼2-3 Ci/gal. (4) Deviations in strip and waste stream flow rates cause the largest variations in cesium content: (a) If strip flow rates deviate by -30% of nominal, the SE will contain ∼23 Ci/gal, although the cesium content of the solvent will increase to only 0.03 Ci/gal; (b) If strip flow rate deviates by -77% (i.e., 23% of nominal), the SE will contain 54 Ci/gal and solvent will contain 1.65 Ci/gal. At this point, the product DSS will just reach the limit of 0.1 Ci/gal, causing the DSS gamma monitors to alarm; and (c) Moderate (+10 to +30%) deviations in waste flow rate cause approximately proportional increases in the SE and solvent cesium concentrations. Recovery from a process failure due to poor cesium stripping can achieve any low cesium concentration required. Passing the solvent back through the contactors while recycling DSS product will produce a ∼70% reduction during one pass through the contactors (assuming the stripping D value is no worse than 0.36). If the solvent is returned to the solvent hold tank (containing additional

  4. Definition of a JA2 equivalent propellant to be produced by continuous solvent-less extrusion

    NARCIS (Netherlands)

    Manning, T.G.; Leone, J.; Zebregs, M.; Ramlal, D.R.; Driel, C.A. van

    2013-01-01

    The aim of this work is to demonstrate the manufacturing of a propellant by solvent-less continuous twin screw extrusion processing while maintaining gun performance characteristics of conventional JA-2 propellant. This is elucidated by explicitly researching the relationship between interior

  5. 3DRISM-HI-D2MSA: an improved analytic theory to compute solvent structure around hydrophobic solutes with proper treatment of solute–solvent electrostatic interactions

    Science.gov (United States)

    Cao, Siqin; Zhu, Lizhe; Huang, Xuhui

    2018-04-01

    The 3D reference interaction site model (3DRISM) is a powerful tool to study the thermodynamic and structural properties of liquids. However, for hydrophobic solutes, the inhomogeneity of the solvent density around them poses a great challenge to the 3DRISM theory. To address this issue, we have previously introduced the hydrophobic-induced density inhomogeneity theory (HI) for purely hydrophobic solutes. To further consider the complex hydrophobic solutes containing partial charges, here we propose the D2MSA closure to incorporate the short-range and long-range interactions with the D2 closure and the mean spherical approximation, respectively. We demonstrate that our new theory can compute the solvent distributions around real hydrophobic solutes in water and complex organic solvents that agree well with the explicit solvent molecular dynamics simulations.

  6. 3DRISM-HI-D2MSA: an improved analytic theory to compute solvent structure around hydrophobic solutes with proper treatment of solute–solvent electrostatic interactions

    KAUST Repository

    Cao, Siqin

    2017-12-22

    The 3D reference interaction site model (3DRISM) is a powerful tool to study the thermodynamic and structural properties of liquids. However, for hydrophobic solutes, the inhomogeneity of the solvent density around them poses a great challenge to the 3DRISM theory. To address this issue, we have previously introduced the hydrophobic-induced density inhomogeneity theory (HI) for purely hydrophobic solutes. To further consider the complex hydrophobic solutes containing partial charges, here we propose the D2MSA closure to incorporate the short-range and long-range interactions with the D2 closure and the mean spherical approximation, respectively. We demonstrate that our new theory can compute the solvent distributions around real hydrophobic solutes in water and complex organic solvents that agree well with the explicit solvent molecular dynamics simulations.

  7. 3DRISM-HI-D2MSA: an improved analytic theory to compute solvent structure around hydrophobic solutes with proper treatment of solute–solvent electrostatic interactions

    KAUST Repository

    Cao, Siqin; Zhu, Lizhe; Huang, Xuhui

    2017-01-01

    The 3D reference interaction site model (3DRISM) is a powerful tool to study the thermodynamic and structural properties of liquids. However, for hydrophobic solutes, the inhomogeneity of the solvent density around them poses a great challenge to the 3DRISM theory. To address this issue, we have previously introduced the hydrophobic-induced density inhomogeneity theory (HI) for purely hydrophobic solutes. To further consider the complex hydrophobic solutes containing partial charges, here we propose the D2MSA closure to incorporate the short-range and long-range interactions with the D2 closure and the mean spherical approximation, respectively. We demonstrate that our new theory can compute the solvent distributions around real hydrophobic solutes in water and complex organic solvents that agree well with the explicit solvent molecular dynamics simulations.

  8. Quantitative relationship between adsorbed amount of solute and solvent composition

    International Nuclear Information System (INIS)

    Wang Yan; Geng Xindu; Zebolsky, Don M.

    2003-01-01

    A new adsorption isotherm that relates the amount of solute adsorbed to the solvent concentration is proposed. The new equation is derived from Geng and Shi's stoichiometric displacement model for adsorption (SDM-A). The obtained equation may be simplified to an expression containing two parameters. The equation with two parameters, valid for low concentrations of solute, is a logarithmically linear relationship. The intercept contains a thermodynamic equilibrium constant of the solute displacing solvent from the adsorbent. The slope is the negative value of the stoichiometric displacement parameter (Z), the average total number of solvent molecules displaced from an active site on the adsorbent and from the solute. Tests with a homologous series of aromatic alcohols by frontal analysis in reversed phase liquid chromatography demonstrate that experimental results fit the equation well

  9. The effect of solvent upon molecularly thin rotaxane film formation

    Energy Technology Data Exchange (ETDEWEB)

    Farrell, Alan A. [Nanoscale Function Group, Centre for Research on Adaptive Nanostructures and Nanodevices, University of Dublin, Trinity College, Dublin 2 (Ireland)]. E-mail: farrelaa@tcd.ie; Kay, Euan R. [School of Chemistry, University of Edinburgh, The King' s Buildings, West Mains Road, Edinburgh EH9 3 JJ (United Kingdom); Bottari, Giovanni [School of Chemistry, University of Edinburgh, The King' s Buildings, West Mains Road, Edinburgh EH9 3 JJ (United Kingdom); Leigh, David A. [School of Chemistry, University of Edinburgh, The King' s Buildings, West Mains Road, Edinburgh EH9 3 JJ (United Kingdom); Jarvis, Suzanne P. [Nanoscale Function Group, Centre for Research on Adaptive Nanostructures and Nanodevices, University of Dublin, Trinity College, Dublin 2 (Ireland)

    2007-05-15

    We have investigated variations in molecularly thin rotaxane films deposited by solvent evaporation, using atomic force microscopy (AFM). Small changes in rotaxane structure result in significant differences in film morphology. The addition of exo-pyridyl moietes to the rotaxane macrocycle results in uniform domains having orientations corresponding to the underlying substrate lattice, while a larger, less symmetric molecule results in a greater lattice mismatch and smaller domain sizes. We have measured differences in film heights both as a function of the solvent of deposition and as a function of surface coverage of rotaxanes. Based on these observations we describe how the use of solvents with higher hydrogen-bond basicity results in films which are more likely to favour sub-molecular motion.

  10. Processing of polymers using reactive solvents

    NARCIS (Netherlands)

    Lemstra, P.J.; Kurja, J.; Meijer, H.E.H.; Meijer, H.E.H.

    1997-01-01

    A review with many refs. on processing of polymers using reactive solvents including classification of synthetic polymers, guidelines for the selection of reactive solvents, basic aspects of processing, examples of intractable and tractable polymer/reactive solvent system

  11. Implicit and explicit processes in social cognition

    DEFF Research Database (Denmark)

    Frith, Christopher; Frith, Uta

    2008-01-01

    In this review we consider research on social cognition in which implicit processes can be compared and contrasted with explicit, conscious processes. In each case, their function is distinct, sometimes complementary and sometimes oppositional. We argue that implicit processes in social interaction...... are automatic and are often opposed to conscious strategies. While we are aware of explicit processes in social interaction, we cannot always use them to override implicit processes. Many studies show that implicit processes facilitate the sharing of knowledge, feelings, and actions, and hence, perhaps...

  12. Explicitly computing geodetic coordinates from Cartesian coordinates

    Science.gov (United States)

    Zeng, Huaien

    2013-04-01

    This paper presents a new form of quartic equation based on Lagrange's extremum law and a Groebner basis under the constraint that the geodetic height is the shortest distance between a given point and the reference ellipsoid. A very explicit and concise formulae of the quartic equation by Ferrari's line is found, which avoids the need of a good starting guess for iterative methods. A new explicit algorithm is then proposed to compute geodetic coordinates from Cartesian coordinates. The convergence region of the algorithm is investigated and the corresponding correct solution is given. Lastly, the algorithm is validated with numerical experiments.

  13. Formation and decomposition of astatine molecules

    International Nuclear Information System (INIS)

    Takahashi, Naruto; Ishikuro, Mituhiro; Baba Hiroshi

    1989-01-01

    A method determining the boiling points of elementary astatine and astatine iodide has been developed (K. Otozai and N. Takahashi, Radio. Chim. Acta 31, (1982) 201). Further, it was concluded from the simple rule among the boiling point of elementary halogens and interhalogen compounds that elementary astatine might exist in diatomic molecules as the other halogens. In the present work the reaction mechanisms of elementary astatine with radioactive iodine and organic solvents were studied by means of radiogaschromatography in order to obtain further experimental evidences for diatomic astaine molecules. The following conclusions were obtained by the analysis of reaction kinetics. Two astatine atoms are lost from the elementary astatine fraction per each radioactive decay of astatine. The astatine radical or hot atom liberated by the decay of the complementary astatine atom immediately reacts with iodine or organic solvents. Thus formed astatine compounds decompose in turn due to the decay of astatine

  14. Handbook of organic solvent properties

    CERN Document Server

    Smallwood, Ian

    2012-01-01

    The properties of 72 of the most commonly used solvents are given, tabulated in the most convenient way, making this book a joy for industrial chemists to use as a desk reference. The properties covered are those which answer the basic questions of: Will it do the job? Will it harm the user? Will it pollute the air? Is it easy to handle? Will it pollute the water? Can it be recovered or incinerated? These are all factors that need to be considered at the early stages of choosing a solvent for a new product or process.A collection of the physical properties of most commonly used solvents, their

  15. Acetone-based cellulose solvent.

    Science.gov (United States)

    Kostag, Marc; Liebert, Tim; Heinze, Thomas

    2014-08-01

    Acetone containing tetraalkylammonium chloride is found to be an efficient solvent for cellulose. The addition of an amount of 10 mol% (based on acetone) of well-soluble salt triethyloctylammonium chloride (Et3 OctN Cl) adjusts the solvent's properties (increases the polarity) to promote cellulose dissolution. Cellulose solutions in acetone/Et3 OctN Cl have the lowest viscosity reported for comparable aprotic solutions making it a promising system for shaping processes and homogeneous chemical modification of the biopolymer. Recovery of the polymer and recycling of the solvent components can be easily achieved. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Organic solvents improve hydrocarbon desorption and biodegradation in highly contaminated weathered soils

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Rivero, M. [Tecnologico de Estudios Superiores de Ecatepec, Mexico City (Mexico); Saucedo-Casteneda, G.; Gutierrez-Rojas, M. [Autonoma Metropolitan Univ., Mexico City (Mexico). Dept. of Biotechnology

    2007-07-15

    A toluene-based microbial slurry phase system was used to remediate hydrocarbons (HC) in highly contaminated soil samples collected from a site next to a working refinery in Mexico. Initial HC concentrations of the samples were 237.2 {+-} 16,6 g kg{sup -1} in dry soil. The microbial consortium consisted of 10 different strains in a mineral solution. Non-polar solvents used in the phase system included hexane, benzene, and toluene. Polar solvents included n-butanol, acetone, and methanol. The bioavailability of the HCs was increased using both polar and nonpolar solvents in order to promote desorption from the soil and to enhance overall HC biodegradation. HC desorption was analyzed in an abiotic system. Respiration and residual HCs were examined after a period of 30 days in order to compare the effects of the 2 solvents. The biodegradation extracts were then fractionated in a silica gel column to determine if the solvents actually enhanced the biodegradation of specific HC fractions. The study showed that induced dipole interactions forces resulted when nonpolar molecules were dissolved into a nonpolar solvent. Results for desorption and solubility varied among the 6 solvents. Higher dielectric constants resulted in higher solubility and desorption of HCs for nonpolar solvents, while the opposite effect was observed for polar solvents. It was concluded that toluene produced better biodegradation results than any of the milder solvents. 34 refs., 4 tabs., 1 fig.

  17. Estimation of diffusion coefficients in bitumen solvent mixtures as derived from low field NMR spectra

    International Nuclear Information System (INIS)

    Wen, Y.; Bryan, J.; Kantzas, A.

    2005-01-01

    Use of solvents for the extraction of heavy oil and bitumen appears to be an increasingly feasible technology. Both vapour extraction and direct solvent injection are considered for conventional exploration and production schemes, while solvent dilution of bitumen is a standard technique in oil sands mining. Mass transfer between solvent and bitumen is a poorly understood process. In some cases, it is totally ignored compared to viscous force effects. In other cases, phenomenological estimations of diffusion and dispersion coefficients are used. Low field NMR has been used successfully in determining both solvent content and viscosity reduction in heavy oil and bitumen mixtures with various solvents. As a solvent comes into contact with a heavy oil or bitumen sample, the mobility of hydrogen bearing molecules of both solvent and oil changes. These changes are detectable through changes in the NMR relaxation characteristics of both solvent and oil. Relaxation changes can then be correlated to mass flux and concentration changes. Based on Fick's Second Law, a diffusion coefficient, which is independent of concentration, was calculated against three oils and six solvents. (author)

  18. Molecule Matters van der Waals Molecules

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 7. Molecule Matters van der Waals Molecules - Rg•••HF Complexes are Debye Molecules! E Arunan. Feature Article Volume 15 Issue 7 July 2010 pp 667-674. Fulltext. Click here to view fulltext PDF. Permanent link:

  19. TALSPEAK Solvent Degradation

    Energy Technology Data Exchange (ETDEWEB)

    Leigh R. Martin; Bruce J. Mincher

    2009-09-01

    Understanding the radiolytic degradation behavior of organic molecules involved in new or existing schemes for the recycle of used nuclear fuels is of significant interest for sustaining a closed nuclear fuel cycle. Here we have conducted several lines of investigation to begin understanding the effects of radiolysis on the aqueous phase of the TALSPEAK process for the separation of the trivalent lanthanides from the trivalent actinides. Using the 60-Co irradiator at the INL, we have begun to quantify the effects of radiation on the aqueous phase complexants used in this separation technique, and how this will affect the actinide lanthanide separation factor. In addition we have started to develop methodologies for stable product identification, a key element in determining the degradation pathways. We have also introduced a methodology to investigate the effects of alpha radiolysis that has previously received limited attention.

  20. Effect of electrostatic interaction on thermochemical behavior of 12-crown-4 ether in various polar solvents

    International Nuclear Information System (INIS)

    Barannikov, Vladimir P.; Guseynov, Sabir S.; Vyugin, Anatoliy I.

    2010-01-01

    The enthalpies of solution of 12-crown-4 ether have been measured in chloroform, ethyl acetate, acetone, pyridine, acetonitrile and methanol at 298.15 K. The values of enthalpy of solvation and solute-solvent interaction were determined from the obtained results and similar literature data for 12-crown-4 in solvents of various polarities. It was shown that the certain correlation is observed between the enthalpy of solute-solvent interaction and the squared dipole moment of the solvent molecules for solutions in tetrachlormethane, ethyl acetate, pyridine, acetonitrile, DMF, DMSO and propylene carbonate. This means that the electrostatic interaction of 12-crown-4 with polar solvent molecules contributes significantly to the exothermic effect of solvation. The understated negative value was found for the enthalpy of interaction of 12-crown-4 with acetone that can be connected with domination of low polar conformer of the crown ether in acetone medium. The most negative values of enthalpy of solvation are observed for solutions in chloroform and water because of hydrogen bonding between O-atoms of crown ether and molecules of the indicated solvents. This effect is not observed for methanol. The negative coefficient of pairwise solute-solute interaction in methanol indicates that the effects of solvophobic solute-solute interaction and H-bonding of the ether molecule with chain associates of methanol are not evinced in the thermochemical behavior of 12-crown-4.

  1. Organogels thermodynamics, structure, solvent role, and properties

    CERN Document Server

    Guenet, Jean-Michel

    2016-01-01

    This book provides a physics-oriented introduction to organogels with a comparison to polymer thermoreversible gels whenever relevant. The past decade has seen the development of a wide variety of newly-synthesized molecules that can spontaneously self-assemble or crystallize from their organic or aqueous solutions to produce fibrillar networks, namely organogels, with potential applications in organic electronics, light harvesting, bio-imaging, non-linear optics, and the like. This compact volume presents a detailed outlook of these novel molecular systems with special emphasis upon their thermodynamics, morphology, molecular structure, and rheology. The definition of these complex systems is also tackled, as well as the role of the solvent. The text features numerous temperature-phase diagrams for a variety of organogels as well as illustrations of their structures at the microscopic, mesoscopic and macroscopic level. A review of some potential applications is provided including hybrid functional materials ...

  2. Antichrist, Explicit Sex, Anxiety, and Care

    DEFF Research Database (Denmark)

    Grodal, Torben Kragh

    2015-01-01

    The article analyzes how von Trier's Antichrist uses explicit sex to discuss the relation between fear of human embodiment and a longing for care and spiritual intimacy. It discusses how lyrical episodes contrasts descriptions of embodied degradation and experiences of being imprisoned in the body....

  3. EXPLICIT PLANNING FOR PARAGRAPH WRITING CLASS

    Directory of Open Access Journals (Sweden)

    Lestari Setyowati

    2017-11-01

    Full Text Available The purpose of the study is to improve the students writing ability for paragraph writing class. The subjects of the study were 37 students of English Education Study Program who joined the paragraph writing class. The design of the study was Classroom Action Research with two cycles. Cycle 1 consisted of three meetings, and cycle 2 consisted of two meetings. The types of explicit planning used in the action research were word listing and word mapping with phrases and sentence for detail.  The instruments used were direct writing test, observation, and  documentation of students’ reflective essay. To score the students’ writing, two raters  were asked to rate the composition by using Jacobs ESL Composition profile scoring rubric. The finding shows that the use of explicit planning was able to improve the students’ paragraph writing performance, indicated with the achievement of the criteria of success. The students’ mean improved from cycle 1 (74.62  to cycle2 (76.78. Although explicit planning instruction was able to help the students to write better, data from their self-reflection essay showed that many of the students preferred to use free writing instead of explicit planning instruction.

  4. Orchestrating Semiotic Resources in Explicit Strategy Instruction

    Science.gov (United States)

    Shanahan, Lynn E.; Flury-Kashmanian, Caroline

    2014-01-01

    Research and pedagogical information provided to teachers on implementing explicit strategy instruction has primarily focused on teachers' speech, with limited attention to other modes of communication, such as gesture and artefacts. This interpretive case study investigates two teachers' use of different semiotic resources when introducing…

  5. Explicit Instruction Elements in Core Reading Programs

    Science.gov (United States)

    Child, Angela R.

    2012-01-01

    Classroom teachers are provided instructional recommendations for teaching reading from their adopted core reading programs (CRPs). Explicit instruction elements or what is also called instructional moves, including direct explanation, modeling, guided practice, independent practice, discussion, feedback, and monitoring, were examined within CRP…

  6. Sleep Enhances Explicit Recollection in Recognition Memory

    Science.gov (United States)

    Drosopoulos, Spyridon; Wagner, Ullrich; Born, Jan

    2005-01-01

    Recognition memory is considered to be supported by two different memory processes, i.e., the explicit recollection of information about a previous event and an implicit process of recognition based on a contextual sense of familiarity. Both types of memory supposedly rely on distinct memory systems. Sleep is known to enhance the consolidation of…

  7. Implicit and explicit prejudice and interracial interaction

    NARCIS (Netherlands)

    Dovidio, J.F.; Kawakami, K.L.; Gaertner, S.L.

    2002-01-01

    The present research examined how implicit racial associations and explicit racial attitudes of Whites relate to behaviors and impressions in interracial interactions, Specifically, the authors examined how response latency and self-report measures predicted bias and perceptions of bias in verbal

  8. Explicit Covariance Matrix for Particle Measurement Precision

    CERN Document Server

    Karimäki, Veikko

    1997-01-01

    We derive explicit and precise formulae for 3 by 3 error matrix of the particle transverse momentum, direction and impact parameter. The error matrix elements are expressed as functions of up to fourth order statistical moments of the measured coordinates. The formulae are valid for any curvature and track length in case of negligible multiple scattering.

  9. Uranium refining by solvent extraction

    International Nuclear Information System (INIS)

    Kraikaew, J.

    1996-01-01

    The yellow cake refining was studied in both laboratory and semi-pilot scales. The process units mainly consist of dissolution and filtration, solvent extraction, and precipitation and filtration. Effect of flow ratio (organic flow rate/ aqueous flow rate) on working efficiencies of solvent extraction process was studied. Detailed studies were carried out on extraction, scrubbing and stripping processes. Purity of yellow cake product obtained is high as 90.32% U 3 O 8

  10. Studies on the partial specific volume of a poly(ethylene glycol) derivative in different solvent systems

    NARCIS (Netherlands)

    Tziatzios, C.; Precup, A.A.; Weidl, C.H.; Schubert, U.S.; Schuck, P.; Durchschlag, H.; Mächtle, W.; Broek, van den J.A.; Schubert, D.

    2002-01-01

    The specific volume of charged supramolecular compounds dissolved in organic solvents varies considerably with the solvent system applied; in addition, it is influenced by the presence of salt. In this study we determined the specific volume of an uncharged molecule from the same molar mass range in

  11. Theoretical study of solvent effects on the coil-globule transition

    Science.gov (United States)

    Polson, James M.; Opps, Sheldon B.; Abou Risk, Nicholas

    2009-06-01

    The coil-globule transition of a polymer in a solvent has been studied using Monte Carlo simulations of a single chain subject to intramolecular interactions as well as a solvent-mediated effective potential. This solvation potential was calculated using several different theoretical approaches for two simple polymer/solvent models, each employing hard-sphere chains and hard-sphere solvent particles as well as attractive square-well potentials between some interaction sites. For each model, collapse is driven by variation in a parameter which changes the energy mismatch between monomers and solvent particles. The solvation potentials were calculated using two fundamentally different methodologies, each designed to predict the conformational behavior of polymers in solution: (1) the polymer reference interaction site model (PRISM) theory and (2) a many-body solvation potential (MBSP) based on scaled particle theory introduced by Grayce [J. Chem. Phys. 106, 5171 (1997)]. For the PRISM calculations, two well-studied solvation monomer-monomer pair potentials were employed, each distinguished by the closure relation used in its derivation: (i) a hypernetted-chain (HNC)-type potential and (ii) a Percus-Yevick (PY)-type potential. The theoretical predictions were each compared to results obtained from explicit-solvent discontinuous molecular dynamics simulations on the same polymer/solvent model systems [J. Chem. Phys. 125, 194904 (2006)]. In each case, the variation in the coil-globule transition properties with solvent density is mostly qualitatively correct, though the quantitative agreement between the theory and prediction is typically poor. The HNC-type potential yields results that are more qualitatively consistent with simulation. The conformational behavior of the polymer upon collapse predicted by the MBSP approach is quantitatively correct for low and moderate solvent densities but is increasingly less accurate for higher densities. At high solvent densities

  12. Solvent/Non-Solvent Sintering To Make Microsphere Scaffolds

    Science.gov (United States)

    Laurencin, Cato T.; Brown, Justin L.; Nair, Lakshmi

    2011-01-01

    A solvent/non-solvent sintering technique has been devised for joining polymeric microspheres to make porous matrices for use as drug-delivery devices or scaffolds that could be seeded with cells for growing tissues. Unlike traditional sintering at elevated temperature and pressure, this technique is practiced at room temperature and pressure and, therefore, does not cause thermal degradation of any drug, protein, or other biochemical with which the microspheres might be loaded to impart properties desired in a specific application. Also, properties of scaffolds made by this technique are more reproducible than are properties of comparable scaffolds made by traditional sintering. The technique involves the use of two miscible organic liquids: one that is and one that is not a solvent for the affected polymer. The polymeric microspheres are placed in a mold having the size and shape of the desired scaffold, then the solvent/non-solvent mixture is poured into the mold to fill the void volume between the microspheres, then the liquid mixture is allowed to evaporate. Some of the properties of the resulting scaffold can be tailored through choice of the proportions of the liquids and the diameter of the microspheres.

  13. Ultrasonication-Assisted Solvent Extraction of Quercetin Glycosides from ‘Idared’ Apple Peels

    Directory of Open Access Journals (Sweden)

    Gwendolyn M. Huber

    2011-11-01

    Full Text Available Quercetin and quercetin glycosides are physiologically active flavonol molecules that have been attributed numerous health benefits. Recovery of such molecules from plant matrices depends on a variety of factors including polarity of the extraction solvent. Among the solvents of a wide range of dielectric constants, methanol recovered the most quercetin and its glycosides from dehydrated ‘Idared’ apple peels. When ultra-sonication was employed to facilitate the extraction, exposure of 15 min of ultrasound wavelengths of dehydrated apple peel powder in 80% to 100% (v/v methanol in 1:50 (w:v solid to solvent ratio provided the optimum extraction conditions for quercetin and its glycosides. Acidification of extraction solvent with 0.1% (v/v or higher concentrations of HCl led to hydrolysis of naturally occurring quercetin glycosides into the aglycone as an extraction artifact.

  14. Efficacy of an explicit handwriting program.

    Science.gov (United States)

    Kaiser, Marie-Laure; Albaret, Jean-Michel; Doudin, Pierre-André

    2011-04-01

    The aim of this study was to investigate the effects of an explicit handwriting program introduced during the first grade of elementary school. Grade 1 children (N=23) with an age range of 6.1 to 7.4 yr. (15 girls, 8 boys) were administered an additional handwriting program of two weekly sessions of 45 min. over six weeks. Another group of 19 Grade 1 children (11 girls, 8 boys) received only the regular handwriting program of one weekly session. The Concise Assessment Scale for Children's Handwriting was administered to measure the changes in quality and speed of handwriting. The children given the explicit program showed better quality and speed of handwriting than did the control group. Their handwriting was more regular, with fewer ambiguous letters and fewer incorrect relative heights.

  15. Extrapolated stabilized explicit Runge-Kutta methods

    Science.gov (United States)

    Martín-Vaquero, J.; Kleefeld, B.

    2016-12-01

    Extrapolated Stabilized Explicit Runge-Kutta methods (ESERK) are proposed to solve multi-dimensional nonlinear partial differential equations (PDEs). In such methods it is necessary to evaluate the function nt times per step, but the stability region is O (nt2). Hence, the computational cost is O (nt) times lower than for a traditional explicit algorithm. In that way stiff problems can be integrated by the use of simple explicit evaluations in which case implicit methods usually had to be used. Therefore, they are especially well-suited for the method of lines (MOL) discretizations of parabolic nonlinear multi-dimensional PDEs. In this work, first s-stages first-order methods with extended stability along the negative real axis are obtained. They have slightly shorter stability regions than other traditional first-order stabilized explicit Runge-Kutta algorithms (also called Runge-Kutta-Chebyshev codes). Later, they are used to derive nt-stages second- and fourth-order schemes using Richardson extrapolation. The stability regions of these fourth-order codes include the interval [ - 0.01nt2, 0 ] (nt being the number of total functions evaluations), which are shorter than stability regions of ROCK4 methods, for example. However, the new algorithms neither suffer from propagation of errors (as other Runge-Kutta-Chebyshev codes as ROCK4 or DUMKA) nor internal instabilities. Additionally, many other types of higher-order (and also lower-order) methods can be obtained easily in a similar way. These methods also allow adaptation of the length step with no extra cost. Hence, the stability domain is adapted precisely to the spectrum of the problem at the current time of integration in an optimal way, i.e., with minimal number of additional stages. We compare the new techniques with other well-known algorithms with good results in very stiff diffusion or reaction-diffusion multi-dimensional nonlinear equations.

  16. Implicit and explicit attitudes among students

    OpenAIRE

    Félix Neto

    2009-01-01

    Mental processing and mental experience is not the same thing. The former is the operation of the mind; the latter is the subjective life that emerges from these operations. In social evaluation, implicit and explicit attitudes express this distinction. https://implicit.harvard.edu/ was created to provide experience with the Implicit Association Test (IAT) a procedure designed to measure social knowledge that may operate outside of awareness. In this paper we examined the relationships betwee...

  17. Towards single-molecule detection of intramolecular exciplexes: Photophysics of a benzanthrone derivative

    Energy Technology Data Exchange (ETDEWEB)

    Hattori, Akifumi [Graduate School of Bio-Applications and Systems Engineering (BASE), Tokyo University of Agriculture and Technology, 2-24-16 Naka-machi, Koganei, Tokyo, 184-8588 (Japan); Department of Organic and Polymeric Materials, Tokyo Institute of Technology, Ookayama 2-12-1-S8, Meguro-ku, Tokyo, 152-8552 (Japan); Sato, Hisaya [Graduate School of Bio-Applications and Systems Engineering (BASE), Tokyo University of Agriculture and Technology, 2-24-16 Naka-machi, Koganei, Tokyo, 184-8588 (Japan); Vacha, Martin [Department of Organic and Polymeric Materials, Tokyo Institute of Technology, Ookayama 2-12-1-S8, Meguro-ku, Tokyo, 152-8552 (Japan)]. E-mail: vacha@op.titech.ac.jp

    2007-01-15

    We report luminescence study of intramolecular exciplexes based on an aminobenzanthrone derivative, dimethyl-amino-N-acetyl-3-aminobenzanthrone (BDA). The BDA compound shows strong dependence of the exciplex emission band intensity on the solvent dielectric function and moderate dependence on its viscosity. The exciplex emission mechanism is discussed in view of the unusual solvent polarity dependence and solvent-dependent excited state lifetimes. Preliminary results on single-molecule detection in polymer films are also presented.

  18. Towards single-molecule detection of intramolecular exciplexes: Photophysics of a benzanthrone derivative

    International Nuclear Information System (INIS)

    Hattori, Akifumi; Sato, Hisaya; Vacha, Martin

    2007-01-01

    We report luminescence study of intramolecular exciplexes based on an aminobenzanthrone derivative, dimethyl-amino-N-acetyl-3-aminobenzanthrone (BDA). The BDA compound shows strong dependence of the exciplex emission band intensity on the solvent dielectric function and moderate dependence on its viscosity. The exciplex emission mechanism is discussed in view of the unusual solvent polarity dependence and solvent-dependent excited state lifetimes. Preliminary results on single-molecule detection in polymer films are also presented

  19. The influence of ultrasonic waves on molecular structure of high impact polystyrene solutions in different solvents

    International Nuclear Information System (INIS)

    Al-Asaly, S.I.

    1991-01-01

    The aim of the this research is to study some physical properties of polymer solutions of high-impact polystyrene (HIPS) solutions in two different solvents (carbon tetrachloride, xylene) by using ultrasonic technique. Absorption coefficient and velocity of ultrasonic waves through different concentrations of these solutions were measured using ultrasonic pulsed generator at constant frequency (800) KHz. The result implies that there is no chemical interaction between (HIPS) molecules and the solvents. 5 tabs.; 18 figs.; 59 refs

  20. Age effects on explicit and implicit memory

    Directory of Open Access Journals (Sweden)

    Emma eWard

    2013-09-01

    Full Text Available 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 favours the single-system view. Implications for the memory systems debate are discussed.

  1. Age effects on explicit and implicit memory.

    Science.gov (United States)

    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.

  2. Solvents interactions with thermochromic print

    Directory of Open Access Journals (Sweden)

    Mirela Rožić

    2017-12-01

    Full Text Available In this study, the interactions between different solvents (benzene, acetone, cyclohexanone, various alcohols and water and thermochromic printing ink were investigated. Thermochromic printing ink was printed on metal surface. Components of thermochromic printing inks are polymeric microcapsules and classic yellow offset printing ink. Below its activation temperature, dye and developer within the microcapsules form a blue coloured complex. Therefore, thermochromic print is green. By heating above the activation temperature, blue colour of the complex turns into the leuco dye colourless state and the green colour of the prints turns into the yellow colour of the classic offset pigment. The results of the interaction with various solvents show that the thermochromic print is stable in all tested solvents except in ethanol, acetone and cyclohexanone. In ethanol, the green colour of the print becomes yellow. SEM analysis shows that microcapsules are dissolved. In acetone and cyclohexanone, the green colour of the print turns into blue, and the microcapsules become significantly more visible. Thus, the yellow pigment interacts with examined ketones. Based on the obtained interactions it can be concluded that the microcapsules have more polar nature than the classical pigment particles. Solvent-thermocromic print interactions were analysed using Hansen solubility parameters that rank the solvents based on their estimated interaction capabilities.

  3. Sterically hindered solvent extractants

    International Nuclear Information System (INIS)

    Solka, J.L.; Reis, A.H. Jr.; Mason, G.W.; Lewey, S.M.; Peppard, D.F.

    1978-01-01

    Di-t-pentylphosphinic acid, [C(CH 3 ) 2 (CH 2 CH 3 )] 2 PO(OH), H[Dt-PeP], has been shown by single-crystal X-ray diffraction data to be dimeric in the solid state. H[Dt-PeP] crystallizes in the centro-symmetric orthorhombic space group, Cmca, with unit cell parameters, a = 17.694(7), b = 11.021(4), and c = 13.073(5) A, and Z = 8, indicating that the molecule must conform to a crystallographic mirror plane or 2-fold axis. A measured density of 1.088 g/cm 3 is in good agreement with a calculated value of 1.074 g/cm 3 for a unit cell volume of 2549.3(A) 3 and a formula weight of 206.25 g. A total of 646 three-dimensional X-ray data were collected on an automated XRD-490 G.E. diffractometer. The structure was solved using a combination of direct methods, Patterson, Fourier, and least-squares refinement techniques. Refinement of the data indicates that H[Dt-PeP] is dimeric, and contains a mirror plane in which the hydrogen-bonded, eight-membered ring lies. A structural disorder involving principally the ethylene carbon but affecting the methyl carbons as well precluded a precise determination of the carbon positions and severely reduced the precision of the final refinement. In the liquid-liquid extraction system consisting of a solution of H[Dt-PeP] in benzene vs an acidic aqueous chloride phase, the extraction of UO 2 2+ follows the stoichiometry: UO 2 sub(A) 2+ + 2(HY) 2 subO = UO 2 (HY 2 ) 2 sub(O) + 2Hsub(A) + where (HY) 2 represents the dimer of H[Dt-PeP] and A and O represent the mutually equilibrated aqueous and organic phases. The expression for the distribution ratio, k, for UO 2 2+ is given. (author)

  4. Simultaneously 'pushing' and 'pulling' graphene oxide into low-polar solvents through a designed interface.

    Science.gov (United States)

    Liu, Zhen; Liu, Jingquan; Wang, Yichao; Razal, Joselito M; Francis, Paul S; Biggs, Mark J; Barrow, Colin J; Yang, Wenrong

    2018-08-03

    Dispersing graphene oxide (GO) in low-polar solvents can realize a perfect self-assembly with functional molecules and application in removal of organic impurities that only dissolve in low-polar solvents. The surface chemistry of GO plays an important role in its dispersity in these solvents. The direct transfer of hydrophilic GO into low-polar solvents, however, has remained an experimental challenge. In this study, we design an interface to transfer GO by simultaneously 'pushing and pulling' the nanosheets into low-polar solvents. Our approach is outstanding due to the ability to obtain monolayers of chemically reduced GO (CRGO) with designed surface properties in the organic phase. Using the transferred GO or CRGO dispersions, we have fabricated GO/fullerene nanocomposites and assessed the ability of CRGOs for dye adsorption. We hope our work can provide a universal approach for the phase transfer of other nanomaterials.

  5. Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

    NARCIS (Netherlands)

    Zavadlav, J.; Podgornik, R.; Melo, M.n.; Marrink, S.j.; Praprotnik, M.

    2016-01-01

    We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MAR- TINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell

  6. Solvent effects on the crystal growth structure and morphology of the pharmaceutical dirithromycin

    Science.gov (United States)

    Wang, Yuan; Liang, Zuozhong

    2017-12-01

    Solvent effects on the crystal structure and morphology of pharmaceutical dirithromycin molecules were systematically investigated using both experimental crystallization and theoretical simulation. Dirithromycin is one of the new generation of macrolide antibiotics with two polymorphic forms (Form I and Form II) and many solvate forms. Herein, six solvates of the dirithromycin, including acetonitrile, acetonitrile/water, acetone, 1-propanol, N,N-dimethylformamide (DMF) and cyclohexane, were studied. Experimentally, we crystallized the dirithromycin molecules in different solvents by the solvent evaporating method and measured the crystal structures with the X-ray diffraction (XRD). We compared these crystal structures of dirithromycin solvates and analyzed the solvent property-determined structure evolution. The solvents have a strong interaction with the dirithromycin molecule due to the formation of inter-molecular interactions (such as the hydrogen bonding and close contacts (sum of vdW radii)). Theoretically, we calculated the ideal crystal habit based on the solvated structures with the attachment growth (AE) model. The predicted morphologies and aspect ratios of dirithromycin solvates agree well with the experimental results. This work could be helpful to better understand the structure and morphology evolution of solvates controlled by solvents and guide the crystallization of active pharmaceutical ingredients in the pharmaceutical industry.

  7. Preferential solvation of fluorenone and 4-hydroxyfluorenone in binary solvent mixtures

    International Nuclear Information System (INIS)

    Jozefowicz, Marek; Heldt, Janina R.

    2003-01-01

    Preferential solvation of fluorenone and 4-hydroxyfluorenone in binary solvent mixtures has been studied using steady-state spectroscopic measurements. This study concerns the solvent-induced shift of the absorption and fluorescence spectra of both molecules in two solvent mixtures, i.e., cyclohexane-tetrahydrofuran and cyclohexane-ethanol. The first system contains polar solute molecules, fluorenone and 4-hydroxyfluorenone, in a mixture of polar aprotic (tetrahydrofuran) and non-polar (cyclohexane) solvents. In the second solvents mixture, hydrogen bonding with solute molecules (ethanol) may occur. The results of spectroscopic measurements are analysed using theoretical models of Bakshiev, Mazurenko and Suppan which describe preferential solvation phenomena. In the case of cyclohexane-tetrahydrofuran mixtures, the deviation from linearity in the absorption and fluorescence solvatochromic shifts vs. the solution polarity is due to non-specific dipolar solvent-solute interactions. For cyclohexane-ethanol binary mixtures, both non-specific and specific (hydrogen bond and proton-relay tautomerization) interactions contribute to the observed solvatochromism

  8. Generalizations of the Toda molecule

    Science.gov (United States)

    Van Velthoven, W. P. G.; Bais, F. A.

    1986-12-01

    Finite-energy monopole solutions are constructed for the self-dual equations with spherical symmetry in an arbitrary integer graded Lie algebra. The constraint of spherical symmetry in a complex noncoordinate basis leads to a dimensional reduction. The resulting two-dimensional ( r, t) equations are of second order and furnish new generalizations of the Toda molecule equations. These are then solved by a technique which is due to Leznov and Saveliev. For time-independent solutions a further reduction is made, leading to an ansatz for all SU(2) embeddings of the Lie algebra. The regularity condition at the origin for the solutions, needed to ensure finite energy, is also solved for a special class of nonmaximal embeddings. Explicit solutions are given for the groups SU(2), SO(4), Sp(4) and SU(4).

  9. Multiple sclerosis and organic solvents

    DEFF Research Database (Denmark)

    Mortensen, J T; Brønnum-Hansen, Henrik; Rasmussen, K

    1998-01-01

    We investigated a possible causal relation between exposure to organic solvents in Danish workers (housepainters, typographers/printers, carpenters/cabinetmakers) and onset of multiple sclerosis. Data on men included in the Danish Multiple Sclerosis Register (3,241 men) were linked with data from......, and butchers. Over a follow-up period of 20 years, we observed no increase in the incidence of multiple sclerosis among men presumed to be exposed to organic solvents. It was not possible to obtain data on potential confounders, and the study design has some potential for selection bias. Nevertheless......, the study does not support existing hypotheses regarding an association between occupational exposure to organic solvents and multiple sclerosis....

  10. Indium recovery by solvent extraction

    International Nuclear Information System (INIS)

    Fortes, Marilia Camargos Botelho

    1999-04-01

    Indium has been recovered as a byproduct from residues generated from the sulfuric acid leaching circuits in mineral plants for zinc recovery. Once its recovery comes from the slags of other metals recovery, it is necessary to separate it from the other elements which usually are present in high concentrations. Many works have been approaching this separation and indicate the solvent extraction process as the main technique used. In Brazilian case, indium recovery depends on the knowledge of this technique and its development. This paper describes the solvent extraction knowledge for the indium recovery from aqueous solutions generated in mineral plants. The results for determination of the best experimental conditions to obtain a high indium concentration solution and minimum iron poisoning by solvent extraction with di (2-ethylhexyl)-phosphoric acid (D2EHPA) solubilized in isoparafin and exxsol has been presented. (author)

  11. Crystal Nucleation of Tolbutamide in Solution: Relationship to Solvent, Solute Conformation, and Solution Structure.

    Science.gov (United States)

    Zeglinski, Jacek; Kuhs, Manuel; Khamar, Dikshitkumar; Hegarty, Avril C; Devi, Renuka K; Rasmuson, Åke C

    2018-04-03

    The influence of the solvent in nucleation of tolbutamide, a medium-sized, flexible and polymorphic organic molecule, has been explored by measuring nucleation induction times, estimating solvent-solute interaction enthalpies using molecular modelling and calorimetric data, probing interactions and clustering with spectroscopy, and modelling solvent-dependence of molecular conformation in solution. The nucleation driving force required to reach the same induction time is strongly solvent-dependent, increasing in the order: acetonitrilenucleation difficulty is a function of the strength of solvent-solute interaction, with emphasis on the interaction with specific H-bonding polar sites of importance in the crystal structure. A clear exception from this rule is the most difficult nucleation in toluene despite the weakest solvent-solute interactions. However molecular dynamics modelling predicts that tolbutamide assumes an intramolecularly H-bonded conformation in toluene, substantially different from and more stable than the conformation in the crystal structure, and thus presenting an additional barrier to nucleation. This explains why nucleation in toluene is the most difficult and why the relatively higher propensity for aggregation of tolbutamide molecules in toluene solution, as observed with FTIR spectroscopy, does not translate into easier nucleation. Thus, our combined experimental and molecular modelling study suggests that the solvent can influence on the nucleation not only via differences in the desolvation but also through the influence on molecular conformation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Molecular studies on di-sodium tartrate molecule

    Science.gov (United States)

    Divya, P.; Jayakumar, S.; George, Preethamary; Shubashree, N. S.; Ahmed. M, Anees

    2015-06-01

    Structural characterization is important for the development of new material. The acoustical parameters such as Free Length, Internal Pressure have been measured from ultrasonic velocity, density for di sodium tartrate an optically active molecule at different temperatures using ultrasonic interferometer of frequency (2MHZ). The ultrasonic velocity increases with increase in concentration there is an increase in solute-solvent interaction. The stability constant had been calculated. SEM with EDAX studies has been done for Di-sodium tartrate an optically active molecule.

  13. Solvent sorting in (mixed solvent electrolyte) systems: Time-resolved ...

    Indian Academy of Sciences (India)

    lar solvents as an effective single component dipo- lar liquid that is characterized ... and time (t) dependent solvation energy of mobile dipo- lar solute with density ..... Even though this way for modification of C is purely ad- hoc, the observation ...

  14. Anti-solvent co-crystallization of carbamazepine and saccharin.

    Science.gov (United States)

    Wang, In-Chun; Lee, Min-Jeong; Sim, Sang-Jun; Kim, Woo-Sik; Chun, Nan-Hee; Choi, Guang J

    2013-06-25

    The co-crystal approach has been investigated extensively over the past decade as one of the most promising methods to enhance the dissolution properties of insoluble drug substances. Co-crystal powders are typically produced by mechanical grinding (neat or wet) or a solution method (evaporation or cooling). In this study, high-purity carbamazepine-saccharin (CBZ-SAC) co-crystals were manufactured by a novel method, anti-solvent addition. Among various solvents, methanol was found to perform well with water as the anti-solvent for the co-crystallization of CBZ and SAC. When water was added to the methanol solution of CBZ and SAC at room temperature under agitation, nucleation of CBZ-SAC co-crystals occurred within 2-3 min. Co-crystallization was complete after 30 min, giving a solid yield as high as 84.5% on a CBZ basis. The effects of initial concentrations, focusing on the SAC/CBZ ratio, were examined to establish optimal conditions. The whole anti-solvent co-crystallization process was monitored at-line via ATR-FTIR analysis of regularly sampled solutions. The nucleation and crystal growth of CBZ-SAC co-crystals were detected by a significant increase in absorption in the range of 2400-2260 cm(-1), associated with the formation of hydrogen bonds between the carbonyl group in CBZ and the N-H of SAC. When CBZ hydrates were formed as impurities during anti-solvent co-crystallization, the hydrogen bonding between methanol and water was reduced greatly, primarily due to the incorporation of water molecules into the CBZ crystal lattice. In conclusion, an anti-solvent approach can be used to produce highly pure CBZ-SAC co-crystal powders with a high solid yield. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. Extending the Solvation-Layer Interface Condition Continum Electrostatic Model to a Linearized Poisson-Boltzmann Solvent.

    Science.gov (United States)

    Molavi Tabrizi, Amirhossein; Goossens, Spencer; Mehdizadeh Rahimi, Ali; Cooper, Christopher D; Knepley, Matthew G; Bardhan, Jaydeep P

    2017-06-13

    We extend the linearized Poisson-Boltzmann (LPB) continuum electrostatic model for molecular solvation to address charge-hydration asymmetry. Our new solvation-layer interface condition (SLIC)/LPB corrects for first-shell response by perturbing the traditional continuum-theory interface conditions at the protein-solvent and the Stern-layer interfaces. We also present a GPU-accelerated treecode implementation capable of simulating large proteins, and our results demonstrate that the new model exhibits significant accuracy improvements over traditional LPB models, while reducing the number of fitting parameters from dozens (atomic radii) to just five parameters, which have physical meanings related to first-shell water behavior at an uncharged interface. In particular, atom radii in the SLIC model are not optimized but uniformly scaled from their Lennard-Jones radii. Compared to explicit-solvent free-energy calculations of individual atoms in small molecules, SLIC/LPB is significantly more accurate than standard parametrizations (RMS error 0.55 kcal/mol for SLIC, compared to RMS error of 3.05 kcal/mol for standard LPB). On parametrizing the electrostatic model with a simple nonpolar component for total molecular solvation free energies, our model predicts octanol/water transfer free energies with an RMS error 1.07 kcal/mol. A more detailed assessment illustrates that standard continuum electrostatic models reproduce total charging free energies via a compensation of significant errors in atomic self-energies; this finding offers a window into improving the accuracy of Generalized-Born theories and other coarse-grained models. Most remarkably, the SLIC model also reproduces positive charging free energies for atoms in hydrophobic groups, whereas standard PB models are unable to generate positive charging free energies regardless of the parametrized radii. The GPU-accelerated solver is freely available online, as is a MATLAB implementation.

  16. Theoretical investigation of the weak interaction between graphene and alcohol solvents

    Science.gov (United States)

    Wang, Haining; Chen, Sian; Lu, Shanfu; Xiang, Yan

    2017-05-01

    The dispersion of graphene in five different alcohol solvents was investigated by evaluating the binding energy between graphene and alcohol molecules using DFT-D method. The calculation showed the most stable binding energy appeared at the distance of ∼3.5 Å between graphene and alcohol molecules and increased linearly as changing the alcohol from methanol to 1-pentanol. The weak interaction was further graphically illustrated using the reduced density gradient method. The theoretical study revealed alcohols with more carbon atoms could be a good starting point for screening suitable solvents for graphene dispersion.

  17. Implicit and explicit timing in oculomotor control.

    Directory of Open Access Journals (Sweden)

    Ilhame Ameqrane

    Full Text Available The passage of time can be estimated either explicitly, e.g. before leaving home in the morning, or implicitly, e.g. when catching a flying ball. In the present study, the latency of saccadic eye movements was used to evaluate differences between implicit and explicit timing. Humans were required to make a saccade between a central and a peripheral position on a computer screen. The delay between the extinction of a central target and the appearance of an eccentric target was the independent variable that could take one out of four different values (400, 900, 1400 or 1900 ms. In target trials, the delay period lasted for one of the four durations randomly. At the end of the delay, a saccade was initiated by the appearance of an eccentric target. Cue&target trials were similar to target trials but the duration of the delay was visually cued. In probe trials, the duration of the upcoming delay was cued, but there was no eccentric target and subjects had to internally generate a saccade at the estimated end of the delay. In target and cue&target trials, the mean and variance of latency distributions decreased as delay duration increased. In cue&target trials latencies were shorter. In probe trials, the variance increased with increasing delay duration and scalar variability was observed. The major differences in saccadic latency distributions were observed between visually-guided (target and cue&target trials and internally-generated saccades (probe trials. In target and cue&target trials the timing of the response was implicit. In probe trials, the timing of the response was internally-generated and explicitly based on the duration of the visual cue. Scalar timing was observed only during probe trials. This study supports the hypothesis that there is no ubiquitous timing system in the brain but independent timing processes active depending on task demands.

  18. Explicit field realizations of W algebras

    International Nuclear Information System (INIS)

    Wei Shaowen; Liu Yuxiao; Ren Jirong; Zhang Lijie

    2009-01-01

    The fact that certain nonlinear W 2,s algebras can be linearized by the inclusion of a spin-1 current can provide a simple way to realize W 2,s algebras from linear W 1,2,s algebras. In this paper, we first construct the explicit field realizations of linear W 1,2,s algebras with double scalar and double spinor, respectively. Then, after a change of basis, the realizations of W 2,s algebras are presented. The results show that all these realizations are Romans-type realizations.

  19. Sexually explicit media use and relationship satisfaction

    DEFF Research Database (Denmark)

    Veit, Maria; Stulhofer, Aleksandar; Hald, Gert Martin

    2017-01-01

    Using a cross-sectional questionnaire design and a sample of 2284 coupled Croatian adults, this study investigated the association between Sexually Explicit Media (SEM) use and relationship satisfaction. Further, possible moderation of emotional intimacy on the relationship between SEM use...... and relationship satisfaction was investigated. Controlling for sociodemographic, psychosexual and relationship variables, no significant association between SEM use and relationship satisfaction was found. However, among men, a moderating effect of emotional intimacy was found. Thus, higher SEM use was found...... to be significantly associated with lower relationship satisfaction only among men who reported lower levels of emotional intimacy with their partner....

  20. Explicit field realizations of W algebras

    OpenAIRE

    Wei, Shao-Wen; Liu, Yu-Xiao; Zhang, Li-Jie; Ren, Ji-Rong

    2009-01-01

    The fact that certain non-linear $W_{2,s}$ algebras can be linearized by the inclusion of a spin-1 current can provide a simple way to realize $W_{2,s}$ algebras from linear $W_{1,2,s}$ algebras. In this paper, we first construct the explicit field realizations of linear $W_{1,2,s}$ algebras with double-scalar and double-spinor, respectively. Then, after a change of basis, the realizations of $W_{2,s}$ algebras are presented. The results show that all these realizations are Romans-type realiz...

  1. Explicit MDS Codes with Complementary Duals

    DEFF Research Database (Denmark)

    Beelen, Duals Peter; Jin, Lingfei

    2018-01-01

    In 1964, Massey introduced a class of codes with complementary duals which are called Linear Complimentary Dual (LCD for short) codes. He showed that LCD codes have applications in communication system, side-channel attack (SCA) and so on. LCD codes have been extensively studied in literature....... On the other hand, MDS codes form an optimal family of classical codes which have wide applications in both theory and practice. The main purpose of this paper is to give an explicit construction of several classes of LCD MDS codes, using tools from algebraic function fields. We exemplify this construction...

  2. Improved Purex solvent scrubbing methods

    International Nuclear Information System (INIS)

    Mailen, J.C.; Tallent, O.K.

    1984-01-01

    Studies of hydrazine and hydroxylamine salts as solvent scrubbing agents that can be decomposed into gases are summarized. Results from testing of countercurrent scrubbers and solid sorber columns that produce lesser amounts of permanent salts are reported. The status of studies of the acid-degradation of paraffin diluent and the options for removal of long-chain organic acids is given

  3. Risk assessment for halogenated solvents

    International Nuclear Information System (INIS)

    Travis, C.C.

    1988-01-01

    A recent development in the cancer risk area is the advent of biologically based pharmacokinetic and pharmacodynamic models. These models allow for the incorporation of biological and mechanistic data into the risk assessment process. These advances will not only improve the risk assessment process for halogenated solvents but will stimulate and guide basic research in the biological area

  4. Crystallization of Organic Semiconductor Molecules in Nanosized Cavities

    DEFF Research Database (Denmark)

    Milita, Silvia; Dionigi, Chiara; Borgatti, Francesco

    2008-01-01

    The crystallization of an organic semiconductor, viz., tetrahexil-sexithiophene (H4T6) molecules, confined into nanosized cavities of a self-organized polystyrene beads template, has been investigated by means of in situ grazing incidence X-ray diffraction measurements, during the solvent evapora...

  5. Detection of quorum sensing molecules from Vibrio harveyi and use ...

    African Journals Online (AJOL)

    This paper explores the extraction and detection processes of quorum sensing molecules such as N-aceyl homoserine lactone compounds (AHL) from marine Vibrio harveyi. The spent culture of V. harveyi was solvent partitioned for AHL, rotary evaporated and re-suspended in 50% acetonitrile then detected with reporter ...

  6. Spatially explicit modelling of cholera epidemics

    Science.gov (United States)

    Finger, F.; Bertuzzo, E.; Mari, L.; Knox, A. C.; Gatto, M.; Rinaldo, A.

    2013-12-01

    Epidemiological models can provide crucial understanding about the dynamics of infectious diseases. Possible applications range from real-time forecasting and allocation of health care resources to testing alternative intervention mechanisms such as vaccines, antibiotics or the improvement of sanitary conditions. We apply a spatially explicit model to the cholera epidemic that struck Haiti in October 2010 and is still ongoing. The dynamics of susceptibles as well as symptomatic and asymptomatic infectives are modelled at the scale of local human communities. Dissemination of Vibrio cholerae through hydrological transport and human mobility along the road network is explicitly taken into account, as well as the effect of rainfall as a driver of increasing disease incidence. The model is calibrated using a dataset of reported cholera cases. We further model the long term impact of several types of interventions on the disease dynamics by varying parameters appropriately. Key epidemiological mechanisms and parameters which affect the efficiency of treatments such as antibiotics are identified. Our results lead to conclusions about the influence of different intervention strategies on the overall epidemiological dynamics.

  7. Explicitly represented polygon wall boundary model for the explicit MPS method

    Science.gov (United States)

    Mitsume, Naoto; Yoshimura, Shinobu; Murotani, Kohei; Yamada, Tomonori

    2015-05-01

    This study presents an accurate and robust boundary model, the explicitly represented polygon (ERP) wall boundary model, to treat arbitrarily shaped wall boundaries in the explicit moving particle simulation (E-MPS) method, which is a mesh-free particle method for strong form partial differential equations. The ERP model expresses wall boundaries as polygons, which are explicitly represented without using the distance function. These are derived so that for viscous fluids, and with less computational cost, they satisfy the Neumann boundary condition for the pressure and the slip/no-slip condition on the wall surface. The proposed model is verified and validated by comparing computed results with the theoretical solution, results obtained by other models, and experimental results. Two simulations with complex boundary movements are conducted to demonstrate the applicability of the E-MPS method to the ERP model.

  8. Trp-cage: Folding free energy landscape in explicit water

    Science.gov (United States)

    Zhou, Ruhong

    2003-11-01

    Trp-cage is a 20-residue miniprotein, which is believed to be the fastest folder known so far. In this study, the folding free energy landscape of Trp-cage has been explored in explicit solvent by using an OPLSAA force field with periodic boundary condition. A highly parallel replica exchange molecular dynamics method is used for the conformation space sampling, with the help of a recently developed efficient molecular dynamics algorithm P3ME/RESPA (particle-particle particle-mesh Ewald/reference system propagator algorithm). A two-step folding mechanism is proposed that involves an intermediate state where two correctly formed partial hydrophobic cores are separated by an essential salt-bridge between residues Asp-9 and Arg-16 near the center of the peptide. This metastable intermediate state provides an explanation for the superfast folding process. The free energy landscape is found to be rugged at low temperatures, and then becomes smooth and funnel-like above 340 K. The lowest free energy structure at 300 K is only 1.50 Å C-RMSD (C-rms deviation) from the NMR structures. The simulated nuclear Overhauser effect pair distances are in excellent agreement with the raw NMR data. The temperature dependence of the Trp-cage population, however, is found to be significantly different from experiment, with a much higher melting transition temperature above 400 K (experimental 315 K), indicating that the current force fields, parameterized at room temperature, need to be improved to correctly predict the temperature dependence.

  9. Solvent density inhomogeneities and solvation free energies in supercritical diatomic fluids: a density functional approach.

    Science.gov (United States)

    Husowitz, B; Talanquer, V

    2007-02-07

    Density functional theory is used to explore the solvation properties of a spherical solute immersed in a supercritical diatomic fluid. The solute is modeled as a hard core Yukawa particle surrounded by a diatomic Lennard-Jones fluid represented by two fused tangent spheres using an interaction site approximation. The authors' approach is particularly suitable for thoroughly exploring the effect of different interaction parameters, such as solute-solvent interaction strength and range, solvent-solvent long-range interactions, and particle size, on the local solvent structure and the solvation free energy under supercritical conditions. Their results indicate that the behavior of the local coordination number in homonuclear diatomic fluids follows trends similar to those reported in previous studies for monatomic fluids. The local density augmentation is particularly sensitive to changes in solute size and is affected to a lesser degree by variations in the solute-solvent interaction strength and range. The associated solvation free energies exhibit a nonmonotonous behavior as a function of density for systems with weak solute-solvent interactions. The authors' results suggest that solute-solvent interaction anisotropies have a major influence on the nature and extent of local solvent density inhomogeneities and on the value of the solvation free energies in supercritical solutions of heteronuclear molecules.

  10. Implicit and explicit interethnic attitudes and ethnic discrimination in hiring

    NARCIS (Netherlands)

    Blommaert, E.C.C.A.; Tubergen, F.A. van; Coenders, M.T.A.

    2012-01-01

    We study effects of explicit and implicit interethnic attitudes on ethnic discrimination in hiring. Unlike explicit attitudes, implicit attitudes are characterised by reduced controllability, awareness or intention. Effects of implicit interethnic attitudes on ethnic discrimination in the labour

  11. Explicit estimating equations for semiparametric generalized linear latent variable models

    KAUST Repository

    Ma, Yanyuan; Genton, Marc G.

    2010-01-01

    which is similar to that of a sufficient complete statistic, which enables us to simplify the estimating procedure and explicitly to formulate the semiparametric estimating equations. We further show that the explicit estimators have the usual root n

  12. 1H NMR study of the solvent THF concerning their structural and dynamical properties in chemically Li-intercalated SWNT

    KAUST Repository

    Schmid, Marc R.

    2011-09-01

    Structural and dynamical properties of the THF solvent in single-walled carbon nanotubes intercalated with lithium are investigated by NMR. 1H NMR experiments reveal the existence of two types of inequivalent THF solvent molecules with different chemical environments and dynamical behavior. At low temperatures THF molecules perpendicularly arranged in between adjacent SWNT presumably exhibit a restricted rotation around their dipolar axis. At higher temperatures THF molecules are isotropically rotating and diffusing along the interstitial channels of the SWNT bundles. © 2011 Elsevier B.V. All rights reserved.

  13. 1H NMR study of the solvent THF concerning their structural and dynamical properties in chemically Li-intercalated SWNT

    KAUST Repository

    Schmid, Marc R.; Goze-Bac, Christophe; Bouhrara, Mohamed; Saih, Youssef; Mehring, Michael; Abou-Hamad, Edy

    2011-01-01

    Structural and dynamical properties of the THF solvent in single-walled carbon nanotubes intercalated with lithium are investigated by NMR. 1H NMR experiments reveal the existence of two types of inequivalent THF solvent molecules with different chemical environments and dynamical behavior. At low temperatures THF molecules perpendicularly arranged in between adjacent SWNT presumably exhibit a restricted rotation around their dipolar axis. At higher temperatures THF molecules are isotropically rotating and diffusing along the interstitial channels of the SWNT bundles. © 2011 Elsevier B.V. All rights reserved.

  14. Reactivity of solvent alcohol on degradation of CFC113

    International Nuclear Information System (INIS)

    Nakagawa, Seiko

    2003-01-01

    1,1,2-Trichloro-trifluoroethane (CFC113) was dissolved in alkaline 1-butanol, 2-butanol, iso-butyl alcohol, and phenyl ethyl alcohol and irradiated with 60 Co gamma rays after purged with pure nitrogen gas. In all these solvents, the concentration of CFC113 and hydroxide ion decreased and that of chloride ion increased with a dose observed in 2-propanol solution. The reaction efficiency increases in order of 1-butanol< iso-butyl alcohol< phenyl ethyl alcohol<2-butanol<2-propanol. The solvent effect will depend on the binding energy of the αC-H of the alcohol molecule and electron affinity and dipole moment of the ketones or aldehydes produced from the alcohols

  15. Solvent accessible surface area (ASA) of simulated phospholipid membranes

    DEFF Research Database (Denmark)

    Tuchsen, E.; Jensen, Morten Østergaard; Westh, P.

    2003-01-01

    The membrane-solvent interface has been investigated through calculations of the solvent accessible surface area (ASA) for simulated membranes of DPPC and POPE. For DPPC at 52 degreesC we found an ASA of 126 +/- 8 Angstrom(2) per lipid molecule, equivalent to twice the projected lateral area......, even the most exposed parts of the PC head-group show average ASAs of less than half of its maximal or 'fully hydrated' value. The average ASA of a simulated POPE membrane was 96 +/- 7 Angstrom(2) per lipid. The smaller value than for DPPC reflects much lower ASA of the ammonium ion, which is partially...... compensated by increased exposure of the ethylene and phosphate moieties. The ASA of the polar moieties Of (PO4, NH3 and COO) constitutes 65% of the total accessible area for POPE, making this interface more polar than that of DPPC. It is suggested that ASA information can be valuable in attempts...

  16. Iodine removing method in organic solvent

    International Nuclear Information System (INIS)

    Suzuki, Takeo; Sakurai, Manabu

    1988-01-01

    Purpose: To effectively remove iodine in an organic solvent to thereby remove iodine in the solvent that can be re-used or put to purning treatment. Method: Organic solvent formed from wastes of nuclear facilities is mixed with basic lead acetate, or silica gel or activated carbon incorporated with such a compound to adsorb iodine in the organic solvent to the basic lead acetate. Then, iodine in the organic solvent is removed by separating to eliminate the basic lead acetate adsorbing iodine from the organic solvent or by passing the organic solvent through a tower or column charged or pre-coated with silica gel or activated carbon incorporated with lead acetate. By using basic lead acetate as the adsorbents, iodine can effective by adsorbed and eliminated. Thus, the possibility of circumstantial release of iodine can be reduced upon reusing or burning treatment of the organic solvent. (Kamimura, M.)

  17. Computer Aided Solvent Selection and Design Framework

    DEFF Research Database (Denmark)

    Mitrofanov, Igor; Conte, Elisa; Abildskov, Jens

    and computer-aided tools and methods for property prediction and computer-aided molecular design (CAMD) principles. This framework is applicable for solvent selection and design in product design as well as process design. The first module of the framework is dedicated to the solvent selection and design...... in terms of: physical and chemical properties (solvent-pure properties); Environment, Health and Safety (EHS) characteristic (solvent-EHS properties); operational properties (solvent–solute properties). 3. Performing the search. The search step consists of two stages. The first is a generation and property...... identification of solvent candidates using special software ProCAMD and ProPred, which are the implementations of computer-aided molecular techniques. The second consists of assigning the RS-indices following the reaction–solvent and then consulting the known solvent database and identifying the set of solvents...

  18. Canyon solvent cleaning with solid adsorbents

    International Nuclear Information System (INIS)

    Reif, D.J.

    1987-01-01

    The HM Process at the Savannah River Plant (SRP) uses 7.5% tributyl phosphate in n-paraffin as an extraction solvent. During use, the solvent is altered due to hydrolysis and radiolysis, forming materials that influence product losses, product decontamination, and separation efficiencies. Laboratory studies to improve online solvent cleaning have shown that carbonate washing, although removing residual solvent activity, does not remove binding ligands that hold fission products in the solvent. Treatment of solvent with a solid adsorbent removes binding ligands and significantly improves recycle solvent performance. Both laboratory work defining a full-scale adsorption process and the use of the process to clean HM Process first cycle solvent are presented

  19. Developmental Differences in Implicit and Explicit Memory Performance.

    Science.gov (United States)

    Perez, Lori A.; Peynircioglu, Zehra F.; Blaxton, Teresa A.

    1998-01-01

    Compared perceptual and conceptual implicit and explicit memory performance of preschool, elementary, and college students. Found that conceptual explicit memory improved with age. Perceptual explicit memory and implicit memory showed no developmental change. Perceptual processing during study led to better performance than conceptual processing…

  20. Multiphoton photodegradation of indocyanine green: Solvent protolysis effect

    Energy Technology Data Exchange (ETDEWEB)

    Fuyuki, Masanori, E-mail: mn.fuyuki@kio.ac.jp

    2016-02-15

    The multiphoton photodegradation mechanism of indocyanine green (ICG) was investigated by using femtosecond near-infrared (NIR) pump and probe pulses. In the pump fluence region from 2 mJ/cm{sup 2} to 4 mJ/cm{sup 2}, the photodegradation rate was higher in acetic acid than in ethanol, and the rate was proportional to pump fluence to the 2.3th power in acetic acid and the 3.9th in ethanol. Considering that the degree of auto-protolysis of acetic acid is much higher than that of ethanol, the experimental results indicate that self-ionized solvent molecules played an essential role in the degradation of ICG molecules excited by NIR multiphoton process. - Highlights: • Photodegradation of ICG by femtosecond near-infrared pulses. • Photodegradation rate of ICG was higher in acetic acid than in ethanol. • Photodegradation rate was proportional to pump fluence to 2.3th power in acetic acid. • Photodegradation rate was proportional to pump fluence to 3.9th power in ethanol. • Self-ionized solvent molecules promoted ICG photodegradation in acetic acid.

  1. Recent solvent extraction experience at Savannah River

    International Nuclear Information System (INIS)

    Gray, L.W.; Burney, G.A.; Gray, J.H.; Hodges, M.E.; Holt, D.L.; Macafee, I.M.; Reif, D.J.; Shook, H.E.

    1986-01-01

    Tributyl phosphate-based solvent extraction processes have been used at Savannah River for more than 30 years to separate and purify thorium, uranium, neptunium, plutonium, americium, and curium isotopes. This report summarizes the advancement of solvent extraction technology at Savannah River during the 1980's. Topics that are discussed include equipment improvements, solvent treatment, waste reduction, and an improved understanding of the various chemistries in the process streams entering, within, and leaving the solvent extraction processes

  2. Solvent extraction studies of RERTR silicide fuels

    International Nuclear Information System (INIS)

    Gouge, Anthony P.

    1983-01-01

    Uranium silicide fuels, which are candidate RERTR fuel compositions, may require special considerations in solvent extraction reprocessing. Since Savannah River Plant may be reprocessing RERTR fuels as early as 1985, studies have been conducted at Savannah River Laboratory to demonstrate the solvent extraction behavior of this fuel. Results of solvent extraction studies with both unirradiated and irradiated fuel are presented along with the preliminary RERTR solvent extraction reprocessing flow sheet for Savannah River Plant. (author)

  3. Reporting transparency: making the ethical mandate explicit.

    Science.gov (United States)

    Nicholls, Stuart G; Langan, Sinéad M; Benchimol, Eric I; Moher, David

    2016-03-16

    Improving the transparency and quality of reporting in biomedical research is considered ethically important; yet, this is often based on practical reasons such as the facilitation of peer review. Surprisingly, there has been little explicit discussion regarding the ethical obligations that underpin reporting guidelines. In this commentary, we suggest a number of ethical drivers for the improved reporting of research. These ethical drivers relate to researcher integrity as well as to the benefits derived from improved reporting such as the fair use of resources, minimizing risk of harms, and maximizing benefits. Despite their undoubted benefit to reporting completeness, questions remain regarding the extent to which reporting guidelines can influence processes beyond publication, including researcher integrity or the uptake of scientific research findings into policy or practice. Thus, we consider investigation on the effects of reporting guidelines an important step in providing evidence of their benefits.

  4. Topology Optimization using an Explicit Interface Representation

    DEFF Research Database (Denmark)

    Christiansen, Asger Nyman; Nobel-Jørgensen, Morten; Bærentzen, J. Andreas

    to handle topology changes. It does so by discretizing the entire design domain into an irregular adaptive triangle mesh and thereby explicitly representing both the structure and the embedding space. In other words, the entire design domain is divided into triangles, where the interface is represented....... To increase performance, degrees of freedom associated with void triangles are eliminated from the FE equation. Using the triangle mesh for computations is possible since the DSC method ensures a mesh with no degenerate elements. If the mesh contained degenerate or close to degenerate elements the FEM...... seconds on an ordinary laptop utilizing a single thread. In addition, a coarse solution to the same problem has been obtained in approximately 10 seconds....

  5. Generating transverse response explicitly from harmonic oscillators

    Science.gov (United States)

    Yao, Yuan; Tang, Ying; Ao, Ping

    2017-10-01

    We obtain stochastic dynamics from a system-plus-bath mechanism as an extension of the Caldeira-Leggett (CL) model in the classical regime. An effective magnetic field and response functions with both longitudinal and transverse parts are exactly generated from the bath of harmonic oscillators. The effective magnetic field and transverse response are antisymmetric matrices: the former is explicitly time-independent corresponding to the geometric magnetism, while the latter can have memory. The present model can be reduced to previous representative examples of stochastic dynamics describing nonequilibrium processes. Our results demonstrate that a system coupled with a bath of harmonic oscillators is a general approach to studying stochastic dynamics, and provides a method to experimentally implement an effective magnetic field from coupling to the environment.

  6. Fast isogeometric solvers for explicit dynamics

    KAUST Repository

    Gao, Longfei

    2014-06-01

    In finite element analysis, solving time-dependent partial differential equations with explicit time marching schemes requires repeatedly applying the inverse of the mass matrix. For mass matrices that can be expressed as tensor products of lower dimensional matrices, we present a direct method that has linear computational complexity, i.e., O(N), where N is the total number of degrees of freedom in the system. We refer to these matrices as separable matrices. For non-separable mass matrices, we present a preconditioned conjugate gradient method with carefully designed preconditioners as an alternative. We demonstrate that these preconditioners, which are easy to construct and cheap to apply (O(N)), can deliver significant convergence acceleration. The performances of these preconditioners are independent of the polynomial order (p independence) and mesh resolution (h independence) for maximum continuity B-splines, as verified by various numerical tests. © 2014 Elsevier B.V.

  7. Biodegradation of Chlorinated Solvents: Reactions near DNAPL and Enzyme Function

    Energy Technology Data Exchange (ETDEWEB)

    McCarty, P. L.; Spormann, Alfred M.; Criddle, Craig, S.

    2003-12-11

    three to five times, leading to a more rapid clean-up of the DNAPL zone. The most favored electron donor to add is one which partitions well with the chlorinated solvent or can be concentrated near it. Unfortunately, an ideal electron donor, such as vegetable oil, is difficult to introduce and mix with DNAPL in the ground, doing this properly remains an engineering challenge. Numerical model studies have indicated that several factors may significantly influence the rate and extent of enhancement, including the inhibitory effects of PCE and cDCE, the level of ED concentration, DNAPL configuration, and competition for ED. Such factors need to be considered when contemplating engineered DNAPL bioremediation. Pseudomonas stuzeri KC is an organism that transforms CT to carbon dioxide and chloride without the formation of the hazardous intermediate, chloroform. This is accomplished by production and secretion of a molecule called PDTC. This study was direct ed towards determining how PDTC works. Cu (II) at a ratio of 1:1 Cu to PDTC was found to result in the most rapid CT transformation, confirming that the PDTC-Cu complex is both a reactant and a catalyst in CT transformation. CT degradation requires that the PDTC be in a reduced form, which is generated by contact with cell components. Fe(II) inhibits CT transformation by PDTC. Studies indicated that this inhibition is enhanced by some compound or factor in the supernatant with molecular weight greater than 10,000 Da. We have made progress in determining what this factor might be, but have not yet been able to identify it. In related studies, we found that CT transformation by another organism, Shewanella oneidensis MR1, also involves an excreted factor, but this factor is different from PDTC and results in chloroform transformation as an intermediate. Our studies have indicated that this factor is similar to vitamin K2, and we have also confirmed that vitamin K2 does transform C T into chloroform.

  8. Biodegradation of Chlorinated Solvents: Reactions near DNAPL and Enzyme Function

    International Nuclear Information System (INIS)

    McCarty, P. L.; Spormann, Alfred M.; Criddle, Craig S.

    2003-01-01

    three to five times, leading to a more rapid clean-up of the DNAPL zone. The most favored electron donor to add is one which partitions well with the chlorinated solvent or can be concentrated near it. Unfortunately, an ideal electron donor, such as vegetable oil, is difficult to introduce and mix with DNAPL in the ground, doing this properly remains an engineering challenge. Numerical model studies have indicated that several factors may significantly influence the rate and extent of enhancement, including the inhibitory effects of PCE and cDCE, the level of ED concentration, DNAPL configuration, and competition for ED. Such factors need to be considered when contemplating engineered DNAPL bioremediation. Pseudomonas stuzeri KC is an organism that transforms CT to carbon dioxide and chloride without the formation of the hazardous intermediate, chloroform. This is accomplished by production and secretion of a molecule called PDTC. This study was direct ed towards determining how PDTC works. Cu (II) at a ratio of 1:1 Cu to PDTC was found to result in the most rapid CT transformation, confirming that the PDTC-Cu complex is both a reactant and a catalyst in CT transformation. CT degradation requires that the PDTC be in a reduced form, which is generated by contact with cell components. Fe(II) inhibits CT transformation by PDTC. Studies indicated that this inhibition is enhanced by some compound or factor in the supernatant with molecular weight greater than 10,000 Da. We have made progress in determining what this factor might be, but have not yet been able to identify it. In related studies, we found that CT transformation by another organism, Shewanella oneidensis MR1, also involves an excreted factor, but this factor is different from PDTC and results in chloroform transformation as an intermediate. Our studies have indicated that this factor is similar to vitamin K2, and we have also confirmed that vitamin K2 does transform C T into chloroform

  9. Academic Publishing: Making the Implicit Explicit

    Directory of Open Access Journals (Sweden)

    Cecile Badenhorst

    2016-07-01

    Full Text Available For doctoral students, publishing in peer-reviewed journals is a task many face with anxiety and trepidation. The world of publishing, from choosing a journal, negotiating with editors and navigating reviewers’ responses is a bewildering place. Looking in from the outside, it seems that successful and productive academic writers have knowledge that is inaccessible to novice scholars. While there is a growing literature on writing for scholarly publication, many of these publications promote writing and publishing as a straightforward activity that anyone can achieve if they follow the rules. We argue that the specific and situated contexts in which academic writers negotiate publishing practices is more complicated and messy. In this paper, we attempt to make explicit our publishing processes to highlight the complex nature of publishing. We use autoethnographic narratives to provide discussion points and insights into the challenges of publishing peer reviewed articles. One narrative is by a doctoral student at the beginning of her publishing career, who expresses her desires, concerns and anxieties about writing for publication. The other narrative focuses on the publishing practices of a more experienced academic writer. Both are international scholars working in the Canadian context. The purpose of this paper is to explore academic publishing through the juxtaposition of these two narratives to make explicit some of the more implicit processes. Four themes emerge from these narratives. To publish successfully, academic writers need: (1 to be discourse analysts; (2 to have a critical competence; (3 to have writing fluency; and (4 to be emotionally intelligent.

  10. Restoring solvent for nuclear separation processes

    International Nuclear Information System (INIS)

    Reif, D.J.

    1987-01-01

    Solvent extraction separation processes are used to recover usable nuclear materials from spent fuels. These processes involve the use of an extractant/diluent (solvent) for separation of the reusable actinides from unwanted fission products. The most widely used processes employ tributyl phosphate as an extractant diluted with a normal-paraffin hydrocarbon. During use, the solvent is altered due to hydrolysis and radiolysis, forming materials that influence product losses, product decontamination, and separation efficiencies. In most processes, the solvent is recycled after cleaning. Solvent cleaning generally involves scrubbing with a sodium carbonate solution. Studies at the Savannah River Laboratory have shown that carbonate washing, although removing residual solvent activity, does not remove more solvent-soluble binding ligands (formed by solvent degradation), which hold fission products in the solvent. Treatment of the solvent with a solid adsorbent after carbonate washing removes binding ligands and significantly improves recycled solvent performance. Laboratory work to establish the advantage of adsorbent cleaning and the development of a full-scale adsorption process is described. The application of this process for cleaning the first cycle solvent of a Savannah River Plant production process is discussed

  11. Solvent Extraction of Furfural From Biomass

    Science.gov (United States)

    Humphrey, M. F.

    1984-01-01

    Solvent-extraction method reduces energy required to remove furfural produced during acid hydrolysis of biomass. Acid hydrolysis performed in vessel containing both solvents and reacting ingredients. With intimate contact between solvents and aqueous hydrolyis liqour, furfural removed form liquor almost as fast as it forms.

  12. Adaptive Resolution Simulation of MARTINI Solvents

    NARCIS (Netherlands)

    Zavadlav, Julija; Melo, Manuel N.; Cunha, Ana V.; de Vries, Alex H.; Marrink, Siewert J.; Praprotnik, Matej

    We present adaptive resolution dynamics simulations of aqueous and apolar solvents coarse-grained molecular models that are compatible with the MARTINI force field. As representatives of both classes solvents we have chosen liquid water and butane, respectively, at ambient temperature. The solvent

  13. The Solvent Selection framework: solvents for organic synthesis, separation processes and ionic-organic synthesis

    DEFF Research Database (Denmark)

    Mitrofanov, Igor; Sansonetti, Sascha; Abildskov, Jens

    2012-01-01

    This paper presents a systematic integrated framework for solvent selection and solvent design. The framework is divided into several modules, which can tackle specific problems in various solvent-based applications. In particular, three modules corresponding to the following solvent selection pr...

  14. Solvent cleaning system and method for removing contaminants from solvent used in resin recycling

    Science.gov (United States)

    Bohnert, George W [Harrisonville, MO; Hand, Thomas E [Lee's Summit, MO; DeLaurentiis, Gary M [Jamestown, CA

    2009-01-06

    A two step solvent and carbon dioxide based system that produces essentially contaminant-free synthetic resin material and which further includes a solvent cleaning system for periodically removing the contaminants from the solvent so that the solvent can be reused and the contaminants can be collected and safely discarded in an environmentally safe manner.

  15. Excipients used in lyophilization of small molecules

    Directory of Open Access Journals (Sweden)

    Ankit Baheti

    2010-03-01

    Full Text Available This review deals with the excipients used in various lyophilized formulations of small molecules. The role of excipients such as bulking agents, buffering agents, tonicity modifiers, antimicrobial agents, surfactants and co-solvents has been discussed. Additionally, a decision making process for their incorporation into the formulation matrix has been proposed. A list of ingredients used in lyophilized formulations marketed in USA has been created based on a survey of the Physician Desk Reference (PDR and the Handbook on Injectable Drugs. Information on the recommended quantities of various excipients has also been provided, based on the details given in the Inactive Ingredient Guide (IIG.

  16. Solvent effects on polymer sorting of carbon nanotubes with applications in printed electronics.

    Science.gov (United States)

    Wang, Huiliang; Hsieh, Bing; Jiménez-Osés, Gonzalo; Liu, Peng; Tassone, Christopher J; Diao, Ying; Lei, Ting; Houk, Kendall N; Bao, Zhenan

    2015-01-07

    Regioregular poly(3-alkylthiophene) (P3AT) polymers have been previously reported for the selective, high-yield dispersion of semiconducting single-walled carbon nanotubes (SWCNTs) in toluene. Here, five alternative solvents are investigated, namely, tetrahydrofuran, decalin, tetralin, m-xylene, and o-xylene, for the dispersion of SWCNTs by poly(3-dodecylthiophene) P3DDT. The dispersion yield could be increased to over 40% using decalin or o-xylene as the solvents while maintaining high selectivity towards semiconducting SWCNTs. Molecular dynamics (MD) simulations in explicit solvents are used to explain the improved sorting yield. In addition, a general mechanism is proposed to explain the selective dispersion of semiconducting SWCNTs by conjugated polymers. The possibility to perform selective sorting of semiconducting SWCNTs using various solvents provides a greater diversity of semiconducting SWCNT ink properties, such as boiling point, viscosity, and surface tension as well as toxicity. The efficacy of these new semiconducting SWCNT inks is demonstrated by using the high boiling point and high viscosity solvent tetralin for inkjet-printed transistors, where solvent properties are more compatible with the inkjet printing head and improved droplet formation. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Analytical energy gradients for explicitly correlated wave functions. I. Explicitly correlated second-order Møller-Plesset perturbation theory

    Science.gov (United States)

    Győrffy, Werner; Knizia, Gerald; Werner, Hans-Joachim

    2017-12-01

    We present the theory and algorithms for computing analytical energy gradients for explicitly correlated second-order Møller-Plesset perturbation theory (MP2-F12). The main difficulty in F12 gradient theory arises from the large number of two-electron integrals for which effective two-body density matrices and integral derivatives need to be calculated. For efficiency, the density fitting approximation is used for evaluating all two-electron integrals and their derivatives. The accuracies of various previously proposed MP2-F12 approximations [3C, 3C(HY1), 3*C(HY1), and 3*A] are demonstrated by computing equilibrium geometries for a set of molecules containing first- and second-row elements, using double-ζ to quintuple-ζ basis sets. Generally, the convergence of the bond lengths and angles with respect to the basis set size is strongly improved by the F12 treatment, and augmented triple-ζ basis sets are sufficient to closely approach the basis set limit. The results obtained with the different approximations differ only very slightly. This paper is the first step towards analytical gradients for coupled-cluster singles and doubles with perturbative treatment of triple excitations, which will be presented in the second part of this series.

  18. The behaviour of organic solvents containing C5-BTBP and CyMe4-BTBP at low irradiation doses

    International Nuclear Information System (INIS)

    Retegan, T.; Fermvik, A.; Skarnemark, G.; Foreman, M.R.S.

    2007-01-01

    Low doses of gamma radiation were given to four different solvents containing C5-BTBP and CyMe 4 -BTBP, each molecule dissolved both in cyclohexanone and hexanol. Four corresponding solvents were kept unirradiated and used as references for the extraction experiments. Multiple samples were taken from both the irradiated solutions and the reference solutions at certain time intervals. The samples were used in extraction experiments with the radionuclides 241 Am and 152 Eu. The protection against radiolysis of the extracting molecules by the diluent used for dissolution without adding a scavenger molecule was checked. The interplay between the diluent and the side group of the extracting molecule for protection against radiolysis was also studied by keeping the same type of core molecule for binding to the metal ions and varying the diluent and side group. The results were unexpected. The presence of a cyclic molecule as both a side group or diluent seems to keep the extraction of europium almost unaffected by radiolysis, while americium behaves differently from solvent to solvent. The diluent alone does not protect the extracting molecule. In some of the studied systems there is a distinct change in the extraction behaviour of Am between the irradiated and reference solutions, an effect that is however only present at the beginning of the experimental series. At later times the difference in distribution ratios between the irradiated and reference solution is constant. This phenomenon is found only when the side group and diluent are structurally dissimilar. (orig.)

  19. Lid opening and conformational stability of T1 Lipase is mediated by increasing chain length polar solvents

    Directory of Open Access Journals (Sweden)

    Jonathan Maiangwa

    2017-05-01

    Full Text Available The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD of a thermostable Geobacillus zalihae T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol and water mixture systems to a concentration of 50%. On the basis of the MD results, the structural deviations of the backbone atoms elucidated the dynamic effects of water/organic solvent mixtures on the equilibrium state of the protein simulations in decreasing solvent polarity. The results show that the solvent mixture gives rise to deviations in enzyme structure from the native one simulated in water. The drop in the flexibility in H2O, MtOH, EtOH and PrOH simulation mixtures shows that greater motions of residues were influenced in BtOH and PtOH simulation mixtures. Comparing the root mean square fluctuations value with the accessible solvent area (SASA for every residue showed an almost correspondingly high SASA value of residues to high flexibility and low SASA value to low flexibility. The study further revealed that the organic solvents influenced the formation of more hydrogen bonds in MtOH, EtOH and PrOH and thus, it is assumed that increased intraprotein hydrogen bonding is ultimately correlated to the stability of the protein. However, the solvent accessibility analysis showed that in all solvent systems, hydrophobic residues were exposed and polar residues tended to be buried away from the solvent. Distance variation of the tetrahedral intermediate packing of the active pocket was not conserved in organic solvent

  20. Studies of muonium-substituted molecules in 2-propanone and in aqueous solutions of 2-propanone

    International Nuclear Information System (INIS)

    Cox, S.F.J.; Renzi, R. De; Scott, C.A.; Hill, A.; Symons, M.C.R.; Bucci, C.; Vecli, A.

    1984-04-01

    The paper deals with muonium substituted molecules, which are formed when positive muons are implanted in pure 2-propanone and in binary aqueous systems; and are studied by the muon spin rotation technique. Studies of muonium substituted molecules are discussed under five topic headings: hyperfine interaction, influence of the solvent, radical formation, diamagnetic fraction and linewidths. (U.K.)

  1. Formation of Ultracold Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Cote, Robin [Univ. of Connecticut, Storrs, CT (United States)

    2016-01-28

    Advances in our ability to slow down and cool atoms and molecules to ultracold temperatures have paved the way to a revolution in basic research on molecules. Ultracold molecules are sensitive of very weak interactions, even when separated by large distances, which allow studies of the effect of those interactions on the behavior of molecules. In this program, we have explored ways to form ultracold molecules starting from pairs of atoms that have already reached the ultracold regime. We devised methods that enhance the efficiency of ultracold molecule production, for example by tuning external magnetic fields and using appropriate laser excitations. We also investigates the properties of those ultracold molecules, especially their de-excitation into stable molecules. We studied the possibility of creating new classes of ultra-long range molecules, named macrodimers, thousand times more extended than regular molecules. Again, such objects are possible because ultra low temperatures prevent their breakup by collision. Finally, we carried out calculations on how chemical reactions are affected and modified at ultracold temperatures. Normally, reactions become less effective as the temperature decreases, but at ultracold temperatures, they can become very effective. We studied this counter-intuitive behavior for benchmark chemical reactions involving molecular hydrogen.

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

    Science.gov (United States)

    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.

  3. Implicit and explicit ethnocentrism: revisiting the ideologies of prejudice.

    Science.gov (United States)

    Cunningham, William A; Nezlek, John B; Banaji, Mahzarin R

    2004-10-01

    Two studies investigated relationships among individual differences in implicit and explicit prejudice, right-wing ideology, and rigidity in thinking. The first study examined these relationships focusing on White Americans' prejudice toward Black Americans. The second study provided the first test of implicit ethnocentrism and its relationship to explicit ethnocentrism by studying the relationship between attitudes toward five social groups. Factor analyses found support for both implicit and explicit ethnocentrism. In both studies, mean explicit attitudes toward out groups were positive, whereas implicit attitudes were negative, suggesting that implicit and explicit prejudices are distinct; however, in both studies, implicit and explicit attitudes were related (r = .37, .47). Latent variable modeling indicates a simple structure within this ethnocentric system, with variables organized in order of specificity. These results lead to the conclusion that (a) implicit ethnocentrism exists and (b) it is related to and distinct from explicit ethnocentrism.

  4. Nonlocal Poisson-Fermi model for ionic solvent.

    Science.gov (United States)

    Xie, Dexuan; Liu, Jinn-Liang; Eisenberg, Bob

    2016-07-01

    We propose a nonlocal Poisson-Fermi model for ionic solvent that includes ion size effects and polarization correlations among water molecules in the calculation of electrostatic potential. It includes the previous Poisson-Fermi models as special cases, and its solution is the convolution of a solution of the corresponding nonlocal Poisson dielectric model with a Yukawa-like kernel function. The Fermi distribution is shown to be a set of optimal ionic concentration functions in the sense of minimizing an electrostatic potential free energy. Numerical results are reported to show the difference between a Poisson-Fermi solution and a corresponding Poisson solution.

  5. Is Water a Universal Solvent for Life?

    Science.gov (United States)

    Pohorill, Andrew

    2012-01-01

    There are strong reasons to believe that the laws, principles and constraints of physics and chemistry are universal. It is much less clear how this universality translates into our understanding of the origins of life. Conventionally, discussions of this topic focus on chemistry that must be sufficiently rich to seed life. Although this is clearly a prerequisite for the emergence of living systems, I propose to focus instead on self-organization of matter into functional structures capable of reproduction, evolution and responding to environmental changes. In biology, most essential functions are largely mediated by noncovalent interactions (interactions that do not involve making or breaking chemical bonds). Forming chemical bonds is only a small part of what living systems do. There are specific implications of this point of view for universality. I will concentrate on one of these implications. Strength of non-covalent interactions must be properly tuned. If they were too weak, the system would exhibit undesired, uncontrolled response to natural fluctuations of physical and chemical parameters. If they were too strong kinetics of biological processes would be slow and energetics costly. This balance, however, is not a natural property of complex chemical systems. Instead, it has to be achieved with the aid of an appropriate solvent for life. In particular, potential solvents for life must be characterized by a high dielectric constant to ensure solubility of polar species and sufficient flexibility of biological structures stabilized by electrostatic interactions. Among these solvents, water exhibits a remarkable trait that it also promotes solvophobic (hydrophobic) interactions between non-polar species, typically manifested by a tendency of these species to aggregate and minimize their contacts with the aqueous solvent. Hydrophobic interactions are responsible, at least in part, for many self-organization phenomena in biological systems, such as the formation

  6. Electron capture in ion-molecule collisions at intermediate energy

    International Nuclear Information System (INIS)

    Kumura, M.

    1986-01-01

    Recent progress of theoretical charge transfer study in ion-molecule collisions at the intermediate energy is reviewed. Concept of close and distant collisions obtained from extensive ion-atom collision studies is identified so that it can be utilized to model two distinct collision processes. For a close collision, explicit representation of the whole collision complex is necessary to describe collision dynamics correctly, while a model potential approach for molecule is appropriate for a distant collision. It is shown that these two distinct models are indeed capable of reproducing experimental charge transfer cross sections. Some remarks for further theoretical study of ion-molecule collisions are also given. 21 refs., 8 figs

  7. Insecticide solvents: interference with insecticidal action.

    Science.gov (United States)

    Brattsten, L B; Wilkinson, C F

    1977-06-10

    Several commercial solvent mixtures commonly used as insecticide carriers in spray formulations increase by more than threefold the microsomal N-demethylation of p-chloro N-methylaniline in midgut preparations of southern army-worm (Spodoptera eridania) larvae exposed orally to the test solvents. Under laboratory conditions, the same solvent mixtures exhibit a protective action against the in vivo toxicity of the insecticide carbaryl to the larvae. The data are discussed with respect to possible solvent-insecticide interactions occurring under field conditions and, more broadly, to potential toxicological hazards of these solvents to humans.

  8. Organic solvents in electromembrane extraction: recent insights

    DEFF Research Database (Denmark)

    Huang, Chuixiu; Gjelstad, Astrid; Pedersen-Bjergaard, Stig

    2016-01-01

    the introduction. Under the influence of an electrical field, EME is based on electrokinetic migration of the analytes through a supported liquid membrane (SLM), which is an organic solvent immobilized in the pores of the polymeric membrane, and into the acceptor solution. Up to date, close to 150 research...... articles with focus on EME have been published. The current review summarizes the performance of EME with different organic solvents and discusses several criteria for efficient solvents in EME. In addition, the authors highlight their personal perspective about the most promising organic solvents for EME...... and have indicated that more fundamental work is required to investigate and discover new organic solvents for EME....

  9. Aggregation behavior of cholic acid derivatives in organic solvents and in water

    NARCIS (Netherlands)

    Willemen, H.M.

    2002-01-01

    In this thesis various cholic acid derivatives are reported that display aggregation in water or in organic solvents. Spontaneous aggregation of single molecules into larger, ordered structures occurs at the borderline of solubility. Amphiphilic compounds, or surfactants, which possess a

  10. solvent effect on 14n nmr shielding of glycine, serine, leucine

    African Journals Online (AJOL)

    a

    ... provide detailed salvation structure enabling one to elucidate specific roles ... from measurements in the liquid phase differ as molecular interactions ... with molecular dynamics or Monte Carlo free-energy simulations would be .... reaction of proteins with other molecules in certain type of solvent, hydrolysis of protein, etc.

  11. Magnetic effects on the solvent properties investigated by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Moosavi, Fatemeh, E-mail: moosavibaigi@um.ac.ir; Gholizadeh, Mostafa

    2014-03-15

    This paper investigates how an external constant magnetic field in the Z-direction affects the performance of a solvent. The molecular dynamics simulation comprised common inorganic and organic solvents including water, acetone, acetonitrile, toluene, and n-hexane at the ambient temperature and pressure. A static magnetic field applied in the simulation process is able to reduce the solvent mobility in the solution in order to enhance the solvent–solute reaction. Simulation results show that the diffusivity decreases because of increasing the effective interactions. Besides, magnetic field reduces the volume of the solvent and increases the strength of the hydrogen bonds by maximizing attractive electrostatic and vdW interactions caused by changes in the radial distribution function of the solvents. Hydrogen-bonding characteristics of solvents investigated by molecular dynamics simulations were evidence for the hydrogen bonding strength of O···H that is a more efficient intermolecular hydrogen-bonding in comparison with N···H. - Highlights: • Molecular dynamics simulation technique investigates the effect of magnetic field on transport dynamics inside the solvent bulk. • External constant magnetic field influences on intermolecular interactions, thermophysics, and transport properties of the solvents. • Applying magnetic field strengthened hydrogen bond maximizes attractive electrostatic interactions, charge distribution becomes stronger, and the molecule mobility is demoted. • The low diffusivity of the solvents in the solutions increases the performance of the interactions and promotes the interactions. • On introducing a magnetic field of flux density parallel to the Z-direction, solvent acts as an obstacle to diffusion of solutes.

  12. Characterization of microenvironment polarity and solvent accessibility of polysilsesquioxane xerogels by the fluorescent probe technique

    Energy Technology Data Exchange (ETDEWEB)

    Shea, K.J.; Zhu, H.D. [Univ., of California, Irvine, CA (United States). Dept. of Chemistry; Loy, D.A. [Sandia National Labs., Albuquerque, NM (United States)

    1995-05-01

    Poly (1, 4 bis(triethoxysilyl)benzene) (PTESB), a representative of a new type of organic-inorganic hybrid polysilsesquioxane material, was characterized by fluorescence spectroscopy for both microenvironmental polarity and solvent accessibility. A dansyl fluorescent molecule was incorporated into the bulk as well as onto the surface of both PTESB and silica materials. Information about the microenvironment polarity and accessibility of PTESB to various organic solvents was determined and compared to that of silica gel. This study found that both the bulk and surface of PTESB are less polar than that of the silica material. The silica material is accessible to polar solvents and water, while YMB is accessible to polar solvents but not to water. The hydrophobicity of PTESB differentiates these new materials from silica gel.

  13. Effects of solvation on partition and dimerization of benzoic acid in mixed solvent systems.

    Science.gov (United States)

    Yamada, H; Yajima, K; Wada, H; Nakagawa, G

    1995-06-01

    The partition of benzoic acid between 0.1M perchloric acid solution and two kinds of mixed solvents has been carried out at 25 degrees C. The partition and dimerization constants of benzoic acid have been determined in the 1-octanol-benzene and 2-octanone-benzene systems. In both the mixed solvent systems, with increasing content of 1-octanol and 2-octanone in each mixed solvent, the partition constant of benzoic acid has been found to increase, and the dimerization constant of benzoic acid in each organic phase to decrease. These phenomena are attributable to solvation of monomeric benzoic acid by 1-octanol and 2-octanone molecules in each mixed solvent.

  14. The status of molecules

    International Nuclear Information System (INIS)

    Barnes, T.; Oak Ridge National Lab., TN; Tennessee Univ., Knoxville, TN

    1994-06-01

    This report summarizes the experimental and theoretical status of hadronic molecules, which are weakly-bound states of two or more hadrons. We begin with a brief history of the subject and discuss a few good candidates, and then abstract some signatures for molecules which may be of interest in the classification of possible molecule states. Next we argue that a more general understanding of 2 → 2 hadron-hadron scattering amplitudes will be crucial for molecule searches, and discuss some of our recent work in this area. We conclude with a discussion of a few more recent molecule candidates (notably the f o (1710)) which are not well established as molecules but satisfy some of the expected signatures. (Author)

  15. Solvent effect on the synthesis of clarithromycin: A molecular dynamics study

    Science.gov (United States)

    Duran, Dilek; Aviyente, Viktorya; Baysal, Canan

    2004-02-01

    Clarithromycin (6- O-methylerythromycin A) is a 14-membered macrolide antibiotic which is active in vitro against clinically important gram-positive and gram-negative bacteria. The selectivity of the methylation of the C-6 OH group is studied on erythromycin A derivatives. To understand the effect of the solvent on the methylation process, detailed molecular dynamics (MD) simulations are performed in pure DMSO, pure THF and DMSO:THF (1:1) mixture by using the anions at the C-6, C-11 and C-12 positions of 2',4''-[ O-bis(TMS)]erythromycin A 9-[ O-(dimethylthexylsilyl)oxime] under the assumption that the anions are stable on the sub-nanosecond time scale. The conformations of the anions are not affected by the presence of the solvent mixture. The radial distribution functions are computed for the distribution of different solvent molecules around the `O-' of the anions. At distances shorter than 5 Å, DMSO molecules are found to cluster around the C-11 anion, whereas the anion at the C-12 position is surrounded by the THF molecules. The anion at the C-6 position is not blocked by the solvent molecules. The results are consistent with the experimental finding that the methylation yield at the latter position is increased in the presence of a DMSO:THF (1:1) solvent mixture. Thus, the effect of the solvent in enhancing the yield during the synthesis is not by changing the conformational properties of the anions, but rather by creating a suitable environment for methylation at the C-6 position.

  16. Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes

    Czech Academy of Sciences Publication Activity Database

    Gkionis, Konstantinos; Kruse, Holger; Šponer, Jiří

    2016-01-01

    Roč. 12, č. 4 (2016), s. 2000-2016 ISSN 1549-9618 R&D Projects: GA ČR(CZ) GAP208/11/1822 Institutional support: RVO:68081707 Keywords : molecular-dynamics simulations * quantum-chemical computations * continuum solvation models Subject RIV: BO - Biophysics Impact factor: 5.245, year: 2016

  17. Effect of the Solvent Temperatures on Dynamics of Serine Protease Proteinase K

    Directory of Open Access Journals (Sweden)

    Peng Sang

    2016-02-01

    Full Text Available To obtain detailed information about the effect of the solvent temperatures on protein dynamics, multiple long molecular dynamics (MD simulations of serine protease proteinase K with the solute and solvent coupled to different temperatures (either 300 or 180 K have been performed. Comparative analyses demonstrate that the internal flexibility and mobility of proteinase K are strongly dependent on the solvent temperatures but weakly on the protein temperatures. The constructed free energy landscapes (FELs at the high solvent temperatures exhibit a more rugged surface, broader spanning range, and higher minimum free energy level than do those at the low solvent temperatures. Comparison between the dynamic hydrogen bond (HB numbers reveals that the high solvent temperatures intensify the competitive HB interactions between water molecules and protein surface atoms, and this in turn exacerbates the competitive HB interactions between protein internal atoms, thus enhancing the conformational flexibility and facilitating the collective motions of the protein. A refined FEL model was proposed to explain the role of the solvent mobility in facilitating the cascade amplification of microscopic motions of atoms and atomic groups into the global collective motions of the protein.

  18. Cold Rydberg molecules

    Science.gov (United States)

    Raithel, Georg; Zhao, Jianming

    2017-04-01

    Cold atomic systems have opened new frontiers at the interface of atomic and molecular physics. These include research on novel types of Rydberg molecules. Three types of molecules will be reviewed. Long-range, homonuclear Rydberg molecules, first predicted in [1] and observed in [2], are formed via low-energy electron scattering of the Rydberg electron from a ground-state atom within the Rydberg atom's volume. The binding mostly arises from S- and P-wave triplet scattering. We use a Fermi model that includes S-wave and P-wave singlet and triplet scattering, the fine structure coupling of the Rydberg atom and the hyperfine structure coupling of the 5S1/2 atom (in rubidium [3]). The hyperfine structure gives rise to mixed singlet-triplet potentials for both low-L and high-L Rydberg molecules [3]. A classification into Hund's cases [3, 4, 5] will be discussed. The talk further includes results on adiabatic potentials and adiabatic states of Rydberg-Rydberg molecules in Rb and Cs. These molecules, which have even larger bonding length than Rydberg-ground molecules, are formed via electrostatic multipole interactions. The leading interaction term of neutral Rydberg-Rydberg molecules is between two dipoles, while for ionic Rydberg molecules it is between a dipole and a monopole. NSF (PHY-1506093), NNSF of China (61475123).

  19. Implicit and explicit categorization of natural scenes.

    Science.gov (United States)

    Codispoti, Maurizio; Ferrari, Vera; De Cesarei, Andrea; Cardinale, Rossella

    2006-01-01

    Event-related potential (ERP) studies have consistently found that emotionally arousing (pleasant and unpleasant) pictures elicit a larger late positive potential (LPP) than neutral pictures in a window from 400 to 800 ms after picture onset. In addition, an early ERP component has been reported to vary with emotional arousal in a window from about 150 to 300 ms with affective, compared to neutral stimuli, prompting significantly less positivity over occipito-temporal sites. Similar early and late ERP components have been found in explicit categorization tasks, suggesting that selective attention to target features results in similar cortical changes. Several studies have shown that the affective modulation of the LPP persisted even when the same pictures are repeated several times, when they are presented as distractors, or when participants are engaged in a competing task. These results indicate that categorization of affective stimuli is an obligatory process. On the other hand, perceptual factors (e.g., stimulus size) seem to affect the early ERP component but not the affective modulation of the LPP. Although early and late ERP components vary with stimulus relevance, given that they are differentially affected by stimulus and task manipulations, they appear to index different facets of picture processing.

  20. Explicit constructions of automorphic L-functions

    CERN Document Server

    Gelbart, Stephen; Rallis, Stephen

    1987-01-01

    The goal of this research monograph is to derive the analytic continuation and functional equation of the L-functions attached by R.P. Langlands to automorphic representations of reductive algebraic groups. The first part of the book (by Piatetski-Shapiro and Rallis) deals with L-functions for the simple classical groups; the second part (by Gelbart and Piatetski-Shapiro) deals with non-simple groups of the form G GL(n), with G a quasi-split reductive group of split rank n. The method of proof is to construct certain explicit zeta-integrals of Rankin-Selberg type which interpolate the relevant Langlands L-functions and can be analyzed via the theory of Eisenstein series and intertwining operators. This is the first time such an approach has been applied to such general classes of groups. The flavor of the local theory is decidedly representation theoretic, and the work should be of interest to researchers in group representation theory as well as number theory.

  1. Explicit logic circuits discriminate neural states.

    Directory of Open Access Journals (Sweden)

    Lane Yoder

    Full Text Available The magnitude and apparent complexity of the brain's connectivity have left explicit networks largely unexplored. As a result, the relationship between the organization of synaptic connections and how the brain processes information is poorly understood. A recently proposed retinal network that produces neural correlates of color vision is refined and extended here to a family of general logic circuits. For any combination of high and low activity in any set of neurons, one of the logic circuits can receive input from the neurons and activate a single output neuron whenever the input neurons have the given activity state. The strength of the output neuron's response is a measure of the difference between the smallest of the high inputs and the largest of the low inputs. The networks generate correlates of known psychophysical phenomena. These results follow directly from the most cost-effective architectures for specific logic circuits and the minimal cellular capabilities of excitation and inhibition. The networks function dynamically, making their operation consistent with the speed of most brain functions. The networks show that well-known psychophysical phenomena do not require extraordinarily complex brain structures, and that a single network architecture can produce apparently disparate phenomena in different sensory systems.

  2. Explicit information reduces discounting behavior in monkeys

    Directory of Open Access Journals (Sweden)

    John ePearson

    2010-12-01

    Full Text Available Animals are notoriously impulsive in common laboratory experiments, preferring smaller, sooner rewards to larger, delayed rewards even when this reduces average reward rates. By contrast, the same animals often engage in natural behaviors that require extreme patience, such as food caching, stalking prey, and traveling long distances to high quality food sites. One possible explanation for this discrepancy is that standard laboratory delay discounting tasks artificially inflate impulsivity by subverting animals’ common learning strategies. To test this idea, we examined choices made by rhesus macaques in two variants of a standard delay discounting task. In the conventional variant, post-reward delays were uncued and adjusted to render total trial length constant; in the second, all delays were cued explicitly. We found that measured discounting was significantly reduced in the cued task, with discount rates well below those reported in studies using the standard uncued design. When monkeys had complete information, their decisions were more consistent with a strategy of reward rate maximization. These results indicate that monkeys, and perhaps other animals, are more patient than is normally assumed, and that laboratory measures of delay discounting may overstate impulsivity.

  3. Advanced integrated solvent extraction systems

    Energy Technology Data Exchange (ETDEWEB)

    Horwitz, E.P.; Dietz, M.L.; Leonard, R.A. [Argonne National Lab., IL (United States)

    1997-10-01

    Advanced integrated solvent extraction systems are a series of novel solvent extraction (SX) processes that will remove and recover all of the major radioisotopes from acidic-dissolved sludge or other acidic high-level wastes. The major focus of this effort during the last 2 years has been the development of a combined cesium-strontium extraction/recovery process, the Combined CSEX-SREX Process. The Combined CSEX-SREX Process relies on a mixture of a strontium-selective macrocyclic polyether and a novel cesium-selective extractant based on dibenzo 18-crown-6. The process offers several potential advantages over possible alternatives in a chemical processing scheme for high-level waste treatment. First, if the process is applied as the first step in chemical pretreatment, the radiation level for all subsequent processing steps (e.g., transuranic extraction/recovery, or TRUEX) will be significantly reduced. Thus, less costly shielding would be required. The second advantage of the Combined CSEX-SREX Process is that the recovered Cs-Sr fraction is non-transuranic, and therefore will decay to low-level waste after only a few hundred years. Finally, combining individual processes into a single process will reduce the amount of equipment required to pretreat the waste and therefore reduce the size and cost of the waste processing facility. In an ongoing collaboration with Lockheed Martin Idaho Technology Company (LMITCO), the authors have successfully tested various segments of the Advanced Integrated Solvent Extraction Systems. Eichrom Industries, Inc. (Darien, IL) synthesizes and markets the Sr extractant and can supply the Cs extractant on a limited basis. Plans are under way to perform a test of the Combined CSEX-SREX Process with real waste at LMITCO in the near future.

  4. Molecule of the Month

    Indian Academy of Sciences (India)

    Atoms in a molecule generally prefer, particularly among the neighbouring ones, certain optimmn geometrical relationships. These are manifested in specific ranges of bond lengths, bond angles, torsion angles etc. As it always happens, chemists are interested in making molecules where these 'standard relationships' are ...

  5. Molecule of the Month

    Indian Academy of Sciences (India)

    Cyclo bu tadiene (1) has been one of the most popular molecules for experimentalists and theoreticians. This molecule is unstable as . it is antiaromatic ( 4,n electrons in a cyclic array). Even though some highly substituted cyclobutadienes, for example, compound 2 and the Fe(CO)3 complex of cyclobutadiene (3) are ...

  6. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 2. Single-Molecule Spectroscopy: Every Molecule is Different! Kankan Bhattacharyya. General Article Volume 20 Issue 2 February 2015 pp 151-164. Fulltext. Click here to view fulltext PDF. Permanent link:

  7. Single molecule conductance

    NARCIS (Netherlands)

    Willems, R.

    2008-01-01

    This thesis represents an excursion into the world of molecular electronics, i.e. the field of research trying to use individual (organic) molecules as electronic components; in this work various experimental methods have been explored to connect individual molecules to metallic contacts and

  8. Molecular accessibility in solvent swelled coals. Quarterly report

    Energy Technology Data Exchange (ETDEWEB)

    Kispert, L.D.

    1993-02-01

    An EPR technique developed in this lab is being used to determine the pore size and number distribution changes after swelling the coal samples with various solvents. Stable nitroxide radical spin probes of different sizes, shapes and reactivity are dissolved in an appropriate solvent, the coal sample is added to the resulting solution, stirred over night at elevated temperature, filtered, washed with a non swelling solvent to eliminate any spin probes that are not trapped in the pores and the spin concentration is measured. Comparing these spin probe measurements to DRIFT data have shown that the relative number distribution of acidic functionalities can be accurately predicted by the spin probe method. The spin probe method had also been used to predict the increase in elongated voids in Pittsburgh No. 8 (APCS No. 4) upon swelling with pyridine in agreement with independent SANS data. NMR relaxation data show that it is possible to deduce the pore (accessibility) distribution as a function of size (up to 6 mn). It has also been possible by variable temperature and ENDOR measurements to determine the presence of hydrogen bonding as a function of pore shape and size. The advantage of the EPR method is that it permits molecules of selected shape and size to be used as probes of accessible regions of coal, thus providing information on the importance of molecular shape.

  9. Thin porphyrin composite membranes with enhanced organic solvent transport

    KAUST Repository

    Phuoc, Duong

    2018-05-01

    Extending the stability of polymeric membranes in organic solvents is important for applications in chemical and pharmaceutical industry. Thin-film composite membranes with enhanced solvent permeance are proposed, using porphyrin as a building block. Hybrid polyamide films are formed by interfacial polymerization of 5,10,15,20-(tetra-4-aminophenyl)porphyrin/m-phenylene diamine (MPD) mixtures with trimesoyl chloride. Porphyrin is a non-planar molecule, containing a heterocyclic tetrapyrrole unit. Its incorporation into a polyamide film leads to higher free volume than that of a standard polyamide film. Polyamide films derived from porphyrin and MPD amines with a fixed total amine concentration of 1wt% and various porphyrin/MPD ratios were fabricated and characterized. The porphyrin/MPD polyamide film was complexed with Cu(II), due to the binding capacity of porphyrin to metal ions. By coupling scanning transmission electron microscopy (STEM) with electron energy-loss spectroscopy (EELS), Cu mapping was obtained, revealing the distribution of porphyrin in the interfacial polymerized layer. By using porphyrin as amine-functionalized monomer a membrane with thin selective skin and enhanced solvent transport is obtained, with good dye selectivity in the nanofiltration range. For instance, an ultra-fast hexane permeance, 40-fold increased, was confirmed when using 0.5/0.5 porphyrin/MPD mixtures, instead of only MPD as amine monomer. A rejection of 94.2% Brilliant Blue R (826g/mol) in methanol was measured.

  10. Spatially explicit modeling in ecology: A review

    Science.gov (United States)

    DeAngelis, Donald L.; Yurek, Simeon

    2017-01-01

    The use of spatially explicit models (SEMs) in ecology has grown enormously in the past two decades. One major advancement has been that fine-scale details of landscapes, and of spatially dependent biological processes, such as dispersal and invasion, can now be simulated with great precision, due to improvements in computer technology. Many areas of modeling have shifted toward a focus on capturing these fine-scale details, to improve mechanistic understanding of ecosystems. However, spatially implicit models (SIMs) have played a dominant role in ecology, and arguments have been made that SIMs, which account for the effects of space without specifying spatial positions, have an advantage of being simpler and more broadly applicable, perhaps contributing more to understanding. We address this debate by comparing SEMs and SIMs in examples from the past few decades of modeling research. We argue that, although SIMs have been the dominant approach in the incorporation of space in theoretical ecology, SEMs have unique advantages for addressing pragmatic questions concerning species populations or communities in specific places, because local conditions, such as spatial heterogeneities, organism behaviors, and other contingencies, produce dynamics and patterns that usually cannot be incorporated into simpler SIMs. SEMs are also able to describe mechanisms at the local scale that can create amplifying positive feedbacks at that scale, creating emergent patterns at larger scales, and therefore are important to basic ecological theory. We review the use of SEMs at the level of populations, interacting populations, food webs, and ecosystems and argue that SEMs are not only essential in pragmatic issues, but must play a role in the understanding of causal relationships on landscapes.

  11. Molecules in stars

    International Nuclear Information System (INIS)

    Tsuji, T.

    1986-01-01

    Recently, research related to molecules in stars has rapidly expanded because of progress in related fields. For this reason, it is almost impossible to cover all the topics related to molecules in stars. Thus, here the authors focus their attention on molecules in the atmospheres of cool stars and do not cover in any detail topics related to circumstellar molecules originating from expanding envelopes located far from the stellar surface. However, the authors do discuss molecules in quasi-static circumstellar envelopes (a recently discovered new component of circumstellar envelopes) located near the stellar surface, since molecular lines originating from such envelopes show little velocity shift relative to photospheric lines, and hence they directly affect the interpretation and analysis of stellar spectra

  12. Theory of polyelectrolytes in solvents.

    Science.gov (United States)

    Chitanvis, Shirish M

    2003-12-01

    Using a continuum description, we account for fluctuations in the ionic solvent surrounding a Gaussian, charged chain and derive an effective short-ranged potential between the charges on the chain. This potential is repulsive at short separations and attractive at longer distances. The chemical potential can be derived from this potential. When the chemical potential is positive, it leads to a meltlike state. For a vanishingly low concentration of segments, this state exhibits scaling behavior for long chains. The Flory exponent characterizing the radius of gyration for long chains is calculated to be approximately 0.63, close to the classical value obtained for second order phase transitions. For short chains, the radius of gyration varies linearly with N, the chain length, and is sensitive to the parameters in the interaction potential. The linear dependence on the chain length N indicates a stiff behavior. The chemical potential associated with this interaction changes sign, when the screening length in the ionic solvent exceeds a critical value. This leads to condensation when the chemical potential is negative. In this state, it is shown using the mean-field approximation that spherical and toroidal condensed shapes can be obtained. The thickness of the toroidal polyelectrolyte is studied as a function of the parameters of the model, such as the ionic screening length. The predictions of this theory should be amenable to experimental verification.

  13. An implicit boundary integral method for computing electric potential of macromolecules in solvent

    Science.gov (United States)

    Zhong, Yimin; Ren, Kui; Tsai, Richard

    2018-04-01

    A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equation that arises in mathematical models for the electrostatics of molecules in solvent. The proposed method uses an implicit boundary integral formulation to derive a linear system defined on Cartesian nodes in a narrowband surrounding the closed surface that separates the molecule and the solvent. The needed implicit surface is constructed from the given atomic description of the molecules, by a sequence of standard level set algorithms. A fast multipole method is applied to accelerate the solution of the linear system. A few numerical studies involving some standard test cases are presented and compared to other existing results.

  14. Wave equation of a nonlinear triatomic molecule and the adiabatic correction to the Born--Oppenheimer approximation

    International Nuclear Information System (INIS)

    Bardo, R.D.; Wolfsberg, M.

    1977-01-01

    The wave equation for a nonlinear polyatomic molecule is formulated in molecule-fixed coordinates by a method originally due to Hirschfelder and Wigner. Application is made to a triatomic molecule, and the wave equation is explicitly presented in a useful molecule-fixed coordinate system. The formula for the adiabatic correction to the Born--Oppenheimer approximation for a triatomic molecule is obtained. The extension of the present formulation to larger polyatomic molecules is pointed out. Some terms in the triatomic molecule wave equation are discussed in detail

  15. Towards a theoretical foundation for explicitation and implicitation

    OpenAIRE

    De Metsenaere, Hinde; Vandepitte, Sonia

    2017-01-01

    Explicitation and implicitation are two translation studies concepts that have given rise to a vast array of studies. These studies are, however, often difficult to compare, primarily because explicitation and implicitation have been interpreted differently, not rarely intuitively, by many translation studies researchers. This is due to the fact that the underlying concepts of explicitness and implicitness have not yet been satisfactorily defined for translation studies purposes. It is there...

  16. Quantum mechanical force field for water with explicit electronic polarization.

    Science.gov (United States)

    Han, Jaebeom; Mazack, Michael J M; Zhang, Peng; Truhlar, Donald G; Gao, Jiali

    2013-08-07

    A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across

  17. Effect of dynamic surface polarization on the oxidative stability of solvents in nonaqueous Li-O 2 batteries

    Science.gov (United States)

    Khetan, Abhishek; Pitsch, Heinz; Viswanathan, Venkatasubramanian

    2017-09-01

    Polarization-induced renormalization of the frontier energy levels of interacting molecules and surfaces can cause significant shifts in the excitation and transport behavior of electrons. This phenomenon is crucial in determining the oxidative stability of nonaqueous electrolytes in high-energy density electrochemical systems such as the Li-O2 battery. On the basis of partially self-consistent first-principles Sc G W0 calculations, we systematically study how the electronic energy levels of four commonly used solvent molecules, namely, dimethylsulfoxide (DMSO), dimethoxyethane (DME), tetrahydrofuran (THF), and acetonitrile (ACN), renormalize when physisorbed on the different stable surfaces of Li2O2 , the main discharge product. Using band level alignment arguments, we propose that the difference between the solvent's highest occupied molecular orbital (HOMO) level and the surface's valence-band maximum (VBM) is a refined metric of oxidative stability. This metric and a previously used descriptor, solvent's gas phase HOMO level, agree quite well for physisorbed cases on pristine surfaces where ACN is oxidatively most stable followed by DME, THF, and DMSO. However, this effect is intrinsically linked to the surface chemistry of the solvent's interaction with the surface states and defects, and depends strongly on their nature. We conclusively show that the propensity of solvent molecules to oxidize will be significantly higher on Li2O2 surfaces with defects as compared to pristine surfaces. This suggests that the oxidative stability of a solvent is dynamic and is a strong function of surface electronic properties. Thus, while gas phase HOMO levels could be used for preliminary solvent candidate screening, a more refined picture of solvent stability requires mapping out the solvent stability as a function of the state of the surface under operating conditions.

  18. Effects of Solvent and Ion Source Pressure on the Analysis of Anabolic Steroids by Low Pressure Photoionization Mass Spectrometry

    Science.gov (United States)

    Liu, Chengyuan; Zhu, Yanan; Yang, Jiuzhong; Zhao, Wan; Lu, Deen; Pan, Yang

    2017-04-01

    Solvent and ion source pressure were two important factors relating to the photon induced ion-molecule reactions in low pressure photoionization (LPPI). In this work, four anabolic steroids were analyzed by LPPI mass spectrometry. Both the ion species present and their relative abundances could be controlled by switching the solvent and adjusting the ion source pressure. Whereas M•+, MH+, [M - H2O]+, and solvent adducts were observed in positive LPPI, [M - H]- and various oxidation products were abundant in negative LPPI. Changing the solvent greatly affected formation of the ion species in both positive and negative ion modes. The ion intensities of the solvent adduct and oxygen adduct were selectively enhanced when the ion source pressure was elevated from 68 to 800 Pa. The limit of detection could be decreased by increasing the ion source pressure.

  19. Effects of Solvent and Ion Source Pressure on the Analysis of Anabolic Steroids by Low Pressure Photoionization Mass Spectrometry.

    Science.gov (United States)

    Liu, Chengyuan; Zhu, Yanan; Yang, Jiuzhong; Zhao, Wan; Lu, Deen; Pan, Yang

    2017-04-01

    Solvent and ion source pressure were two important factors relating to the photon induced ion-molecule reactions in low pressure photoionization (LPPI). In this work, four anabolic steroids were analyzed by LPPI mass spectrometry. Both the ion species present and their relative abundances could be controlled by switching the solvent and adjusting the ion source pressure. Whereas M •+ , MH + , [M - H 2 O] + , and solvent adducts were observed in positive LPPI, [M - H] - and various oxidation products were abundant in negative LPPI. Changing the solvent greatly affected formation of the ion species in both positive and negative ion modes. The ion intensities of the solvent adduct and oxygen adduct were selectively enhanced when the ion source pressure was elevated from 68 to 800 Pa. The limit of detection could be decreased by increasing the ion source pressure. Graphical Abstract ᅟ.

  20. Comparison of the Behaviour of Polymers in Supercritical Fluids and Organic Solvents Via Small Angle Neutron Scattering

    International Nuclear Information System (INIS)

    Melnichenko, Y.B.; Kiran, E.; Heath, K.D.; Salaniwal, S.; Cochran, H.D.; Stamm, M.; Van Hook, W.A.; Wignall, G.D.

    1999-01-01

    Small-angle neutron scattering has been used to study the effect of temperature and pressure on the phase behavior of semidilute solutions of polymers dissolved in organic and supercritical solvents. Above the theta temperature (To), these systems exhibit a ''good solvent'' domain, where the molecules expand beyond the unperturbed dimensions in both organic solvents and in COZ. However, this transition can be made to occur at a critical ''theta pressure'' (PO) in CO2 and this represents a new concept in the physics of polymer-solvent systems. For T < To, and P < Po, the system enters the ''poor solvent'' domain where diverging concentration fluctuations prevent the chains from collapsing and allow them to maintain their unperturbed dimensions

  1. Transitions of tethered chain molecules under tension.

    Science.gov (United States)

    Luettmer-Strathmann, Jutta; Binder, Kurt

    2014-09-21

    An applied tension force changes the equilibrium conformations of a polymer chain tethered to a planar substrate and thus affects the adsorption transition as well as the coil-globule and crystallization transitions. Conversely, solvent quality and surface attraction are reflected in equilibrium force-extension curves that can be measured in experiments. To investigate these effects theoretically, we study tethered chains under tension with Wang-Landau simulations of a bond-fluctuation lattice model. Applying our model to pulling experiments on biological molecules we obtain a good description of experimental data in the intermediate force range, where universal features dominate and finite size effects are small. For tethered chains in poor solvent, we observe the predicted two-phase coexistence at transitions from the globule to stretched conformations and also discover direct transitions from crystalline to stretched conformations. A phase portrait for finite chains constructed by evaluating the density of states for a broad range of solvent conditions and tensions shows how increasing tension leads to a disappearance of the globular phase. For chains in good solvents tethered to hard and attractive surfaces we find the predicted scaling with the chain length in the low-force regime and show that our results are well described by an analytical, independent-bond approximation for the bond-fluctuation model for the highest tensions. Finally, for a hard or slightly attractive surface the stretching of a tethered chain is a conformational change that does not correspond to a phase transition. However, when the surface attraction is sufficient to adsorb a chain it will undergo a desorption transition at a critical value of the applied force. Our results for force-induced desorption show the transition to be discontinuous with partially desorbed conformations in the coexistence region.

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

    Science.gov (United States)

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

    2005-10-01

    Time series analysis tools are employed on the principal modes obtained from the Cα trajectories from two independent molecular-dynamics simulations of α-amylase inhibitor (tendamistat). Fluctuations inside an energy minimum (intraminimum motions), transitions between minima (interminimum motions), and relaxations in different hierarchical energy levels are investigated and compared with those encountered in vacuum by using different sampling window sizes and intervals. The low-frequency low-indexed mode relationship, established in vacuum, is also encountered in water, which shows the reliability of the important dynamics information offered by principal components analysis in water. It has been shown that examining a short data collection period (100ps) may result in a high population of overdamped modes, while some of the low-frequency oscillations (memory: future conformations are less dependent on previous conformations due to the lowering of energy barriers in hierarchical levels of the energy landscape. In short-time dynamics (sight contradicts. However, this comes about because water enhances the transitions between minima and forces the protein to reduce its already inherent inability to maintain oscillations observed in vacuum. Some of the frequencies lower than 10cm-1 are found to be overdamped, while those higher than 20cm-1 are slightly increased. As for the long-time dynamics in water, it is found that random-walk motion is maintained for approximately 200ps (about five times of that in vacuum) in the low-indexed modes, showing the lowering of energy barriers between the higher-level minima.

  3. Structure formation in bis(terpyridine) derivative adlayers: molecule-substrate versus molecule-molecule interactions.

    Science.gov (United States)

    Hoster, Harry E; Roos, Matthias; Breitruck, Achim; Meier, Christoph; Tonigold, Katrin; Waldmann, Thomas; Ziener, Ulrich; Landfester, Katharina; Behm, R Jürgen

    2007-11-06

    The influence of the substrate and the deposition conditions-vapor deposition versus deposition from solution-on the structures formed upon self-assembly of deposited bis(terpyridine) derivative (2,4'-BTP) monolayers on different hexagonal substrates, including highly oriented pyrolytic graphite (HOPG), Au(111), and (111)-oriented Ag thin films, was investigated by high-resolution scanning tunneling microscopy and by model calculations of the intermolecular energies and the lateral corrugation of the substrate-adsorbate interaction. Similar quasi-quadratic network structures with almost the same lattice constants obtained on all substrates are essentially identical to the optimum configuration expected from an optimization of the adlayer structure with C-H...N-type bridging bonds as a structure-determining factor, which underlines a key role of the intermolecular interactions in adlayer order. Slight distortions from the optimum values to form commensurate adlayer structures on the metal substrates and the preferential orientation of the adlayer with respect to the substrate are attributed to the substrate-adsorbate interactions, specifically, the lateral corrugation in the substrate-adsorbate interaction upon lateral displacement and rotation of the adsorbed BTP molecules. The fact that similar adlayer structures are obtained on HOPG under ultrahigh vacuum conditions (solid|gas interface) and on HOPG in trichlorobenzene (solid|liquid interface) indicates that the intermolecular interactions are not severely affected by the solvent.

  4. Sustainable development of gree solvent separation process

    OpenAIRE

    Lisickov, Kiril; Fidancevska, Emilija; Grujic, Radoslav; Srebrenkoska, Vineta; Kuvendziev, Stefan

    2011-01-01

    Solvents defi ne a major part of the environmental performance of processes in the chemical industry and impact on cost, safety and health issues. The idea of green solvents expresses the goal to minimize the environmental impact resulting from the use of solvents in chemical production. In spite of conventional separation methods, precise process green technologies are based on the application of modern processes and process equipment as well as control and management...

  5. Supercritical solvent extraction of oil sand bitumen

    Science.gov (United States)

    Imanbayev, Ye. I.; Ongarbayev, Ye. K.; Tileuberdi, Ye.; Mansurov, Z. A.; Golovko, A. K.; Rudyk, S.

    2017-08-01

    The supercritical solvent extraction of bitumen from oil sand studied with organic solvents. The experiments were performed in autoclave reactor at temperature above 255 °C and pressure 29 atm with stirring for 6 h. The reaction resulted in the formation of coke products with mineral part of oil sands. The remaining products separated into SARA fractions. The properties of the obtained products were studied. The supercritical solvent extraction significantly upgraded extracted natural bitumen.

  6. Canyon solvent cleaning with activated alumina

    International Nuclear Information System (INIS)

    Reif, D.J.

    1987-01-01

    This paper presents recent work at SRL concerning the cleaning of solvent extraction solvent used at SRP. The paper explains why we undertook the work, and some laboratory studies on two approaches to solvent cleaning, namely extended carbonate washing and use of solid adsorbents. The paper then discusses scale-up of the preferred method and the results of the full-scale cleaning. 19 figs

  7. Comparative Assessment of Nonlocal Continuum Solvent Models Exhibiting Overscreening

    Directory of Open Access Journals (Sweden)

    Ren Baihua

    2017-01-01

    Full Text Available Nonlocal continua have been proposed to offer a more realistic model for the electrostatic response of solutions such as the electrolyte solvents prominent in biology and electrochemistry. In this work, we review three nonlocal models based on the Landau-Ginzburg framework which have been proposed but not directly compared previously, due to different expressions of the nonlocal constitutive relationship. To understand the relationships between these models and the underlying physical insights from which they are derive, we situate these models into a single, unified Landau-Ginzburg framework. One of the models offers the capacity to interpret how temperature changes affect dielectric response, and we note that the variations with temperature are qualitatively reasonable even though predictions at ambient temperatures are not quantitatively in agreement with experiment. Two of these models correctly reproduce overscreening (oscillations between positive and negative polarization charge densities, and we observe small differences between them when we simulate the potential between parallel plates held at constant potential. These computations require reformulating the two models as coupled systems of local partial differential equations (PDEs, and we use spectral methods to discretize both problems. We propose further assessments to discriminate between the models, particularly in regards to establishing boundary conditions and comparing to explicit-solvent molecular dynamics simulations.

  8. Dynamics of Activated Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Mullin, Amy S. [Univ. of Maryland, College Park, MD (United States)

    2016-11-16

    Experimental studies have been performed to investigate the collisional energy transfer processes of gas-phase molecules that contain large amounts of internal energy. Such molecules are prototypes for molecules under high temperature conditions relevant in combustion and information about their energy transfer mechanisms is needed for a detailed understanding and modeling of the chemistry. We use high resolution transient IR absorption spectroscopy to measure the full, nascent product distributions for collisions of small bath molecules that relax highly vibrationally excited pyrazine molecules with E=38000 cm-1 of vibrational energy. To perform these studies, we developed new instrumentation based on modern IR light sources to expand our experimental capabilities to investigate new molecules as collision partners. This final report describes our research in four areas: the characterization of a new transient absorption spectrometer and the results of state-resolved collision studies of pyrazine(E) with HCl, methane and ammonia. Through this research we have gained fundamental new insights into the microscopic details of relatively large complex molecules at high energy as they undergo quenching collisions and redistribute their energy.

  9. Kinetic isotope effects and tunnelling in the proton-transfer reaction between 4-nitrophenylnitromethane and tetramethylguanidine in various aprotic solvents

    International Nuclear Information System (INIS)

    Caldin, E.F.; Mateo, S.

    1975-01-01

    Rates and equilibrium constants have been determined for the proton-transfer reaction of 4-nitrophenylnitromethane, NO 2 C 6 H 4 CH 2 NO 2 , and its αα-deuterated analogue NO 2 C 6 H 4 CD 2 NO 2 , with the strong base tetramethylguanidine [HN=C(NMe 2 ) 2 ), at temperatures between -60 0 C and +65 0 in a range of aprotic solvents. Spectrophotometry and the stopped-flow technique were used. The reaction is a simple proton-transfer process leading to an ion-pair. The kinetic isotope effects are correlated with the polarity of the solvents, as measured by the dielectric constant or by the empirical parameter Esub(T). In the less polar solvents they are exceptionally large. In toluene, for example, at 25 0 C the rate ratio ksup(H)/ksup(D) = 45 +- 2, the activation energy difference Esub(a)sup(D) - Esub(a)sup(H) =4.3 +- 0.3 kcal molsup(-1) (16 kJ molsup(-1), and the ratio of the pre-exponential factors logsub(10) (Asup(D)/Asup(H)) = 1.5 +- 0.2+ and even larger values of logsub(10)(Asup(D)/Asup(H)) are found for mesitylene (1.94 +- 0.06) and cyclohexane (2.4 +- 0.2). Positive deviations from linear Arrhenius plots are found for these solvents. Tunnelling is the only interpretation that cannot account for these results. For the more polar solvents (dielectric constant 7 to 37), the isotope effects are closer to the range predicted by semi-classical theory. The isotope effects in all solvents have been fitted to Bell's equation for a parabolic barrier, and the barrier dimensions calculated for each solvent. The suggested interpretation of the results is that the solvent-solute interactions affect the height of the barrier and that motions of solvent molecules are coupled with the motion of the proton in the more polar solvents but not in the less polar ones; reorganization of solvent molecules accompanies the proton-transfer in the more polar solvents, but only electron-polarization in the less polar. Tunnelling has large effects in the less polar solvents, where the

  10. Effect of Viscosity and Polar Properties of Solvent on Dynamics of Photoinduced Charge Transfer in BTA-1 Cation — Derivative of Thioflavin T

    Science.gov (United States)

    Gogoleva, S. D.; Stsiapura, V. I.

    2018-05-01

    It was found that the spectral and fluorescent properties of BTA-1C cation in protic and aprotic solvents differ. It was shown that for solutions in long-chain alcohols viscosity is the main factor that determines the dynamics of intramolecular charge transfer in the excited state of the BTA-1C molecule. In the case of aprotic solvents a correlation was found between the rate constant of twisted intramolecular charge transfer (TICT) during rotation of fragments of the molecule in relation to each other in the excited state and the solvent relaxation rate: k TICT 1/τ S .

  11. Process for hydrogenating coal and coal solvents

    Energy Technology Data Exchange (ETDEWEB)

    Shridharani, K.G.; Tarrer, A.R.

    1983-02-15

    A novel process is described for the hydrogenation of coal by the hydrogenation of a solvent for the coal in which the hydrogenation of the coal solvent is conducted in the presence of a solvent hydrogenation catalyst of increased activity, wherein the hydrogenation catalyst is produced by reacting ferric oxide with hydrogen sulfide at a temperature range of 260/sup 0/ C to 315/sup 0/ C in an inert atmosphere to produce an iron sulfide hydrogenation catalyst for the solvent. Optimally, the reaction temperature is 275/sup 0/ C. Alternately, the reaction can be conducted in a hydrogen atmosphere at 350/sup 0/ C.

  12. Process for hydrogenating coal and coal solvents

    Science.gov (United States)

    Tarrer, Arthur R.; Shridharani, Ketan G.

    1983-01-01

    A novel process is described for the hydrogenation of coal by the hydrogenation of a solvent for the coal in which the hydrogenation of the coal solvent is conducted in the presence of a solvent hydrogenation catalyst of increased activity, wherein the hydrogenation catalyst is produced by reacting ferric oxide with hydrogen sulfide at a temperature range of 260.degree. C. to 315.degree. C. in an inert atmosphere to produce an iron sulfide hydrogenation catalyst for the solvent. Optimally, the reaction temperature is 275.degree. C. Alternately, the reaction can be conducted in a hydrogen atmosphere at 350.degree. C.

  13. Aminosilicone solvent recovery methods and systems

    Science.gov (United States)

    Spiry, Irina Pavlovna; Perry, Robert James; Wood, Benjamin Rue; Singh, Surinder Prabhjot; Farnum, Rachel Lizabeth; Genovese, Sarah Elizabeth

    2018-02-13

    The present invention is directed to aminosilicone solvent recovery methods and systems. The methods and systems disclosed herein may be used to recover aminosilicone solvent from a carbon dioxide containing vapor stream, for example, a vapor stream that leaves an aminosilicone solvent desorber apparatus. The methods and systems of the invention utilize a first condensation process at a temperature from about 80.degree. C. to about 150.degree. C. and a second condensation process at a temperature from about 5.degree. C. to about 75.degree. C. The first condensation process yields recovered aminosilicone solvent. The second condensation process yields water.

  14. Molecular Thermodynamic Modeling of Mixed Solvent Solubility

    DEFF Research Database (Denmark)

    Ellegaard, Martin Dela; Abildskov, Jens; O’Connell, John P.

    2010-01-01

    A method based on statistical mechanical fluctuation solution theory for composition derivatives of activity coefficients is employed for estimating dilute solubilities of 11 solid pharmaceutical solutes in nearly 70 mixed aqueous and nonaqueous solvent systems. The solvent mixtures range from...... nearly ideal to strongly nonideal. The database covers a temperature range from 293 to 323 K. Comparisons with available data and other existing solubility methods show that the method successfully describes a variety of observed mixed solvent solubility behaviors using solute−solvent parameters from...

  15. Dissociation in small molecules

    International Nuclear Information System (INIS)

    Dehmer, P.M.

    1982-01-01

    The study of molecular dissociation processes is one of the most interesting areas of modern spectroscopy owing to the challenges presented bt even the simplest of diatomic molecules. This paper reviews the commonly used descriptions of molecular dissociation processes for diatomic molecules, the selection rules for predissociation, and a few of the principles to be remembered when one is forced to speculate about dissociation mechanisms in a new molecule. Some of these points will be illustrated by the example of dissociative ionization in O 2

  16. Evidence for the TICT mediated nonradiative deexcitation process for the excited coumarin-1 dye in high polarity protic solvents

    Energy Technology Data Exchange (ETDEWEB)

    Barik, Atanu [Radiation Chemistry and Chemical Dynamics Division, Bhabha Atomic Research Center, Trombay, Mumbai 400 085 (India); Kumbhakar, Manoj [Radiation Chemistry and Chemical Dynamics Division, Bhabha Atomic Research Center, Trombay, Mumbai 400 085 (India); Nath, Sukhendu [Radiation Chemistry and Chemical Dynamics Division, Bhabha Atomic Research Center, Trombay, Mumbai 400 085 (India); Pal, Haridas [Radiation Chemistry and Chemical Dynamics Division, Bhabha Atomic Research Center, Trombay, Mumbai 400 085 (India)

    2005-08-29

    Photophysical properties of coumarin-1 (C1) dye in different protic solvents have been investigated using steady-state and time-resolved fluorescence measurements. Correlation of the Stokes' shifts ({delta}{nu}-bar ) with the solvent polarity ({delta}f) suggests the intramolecular charge transfer (ICT) character for the dye fluorescent state. Fluorescence quantum yields ({phi}{sub f}) and lifetimes ({tau}{sub f}) of the dye show an abrupt reduction in high polarity solvents having {delta}f >{approx}0.28. In these solvents {tau}{sub f} is seen to be strongly temperature dependent, though it is temperature independent in solvents with {delta}f <{approx}0.28. It is inferred that in high polarity protic solvents there is a participation of an additional nonradiative decay process via the involvement of twisted intramolecular charge transfer (TICT) state. Unlike present results, no involvement of TICT state was observed even in strongly polar aprotic solvent like acetonitrile. It is indicated that the intermolecular hydrogen bonding of the dye with protic solvents in addition with the solvent polarity helps in the stabilization of the TICT state for C1 dye. Unlike most TICT molecules, the activation barrier ({delta}E{sub a}) for the TICT mediated nonradiative process for C1 dye is seen to increase with solvent polarity. This is rationalized on the basis of the assumption that the TICT to ground state conversion is the activation-controlled rate-determining step for the present system than the usual ICT to TICT conversion as encountered for most other TICT molecules.

  17. Photoluminescence study of Congo red molecules under high pressure

    International Nuclear Information System (INIS)

    Wang, Z.P.; Zhang, Z.M.; Ding, Z.J.

    2007-01-01

    Pressure-induced changes on fluorescence spectra of Congo red molecules were examined up to 8.7 GPa using a diamond anvil cell at room temperature. The spectra changes are demonstrated to be sensitive to the pressure and solvent conditions. At hydrostatic pressure and with a solvent used as a pressure transmitting medium the fluorescence spectra show increase of intensity with elevated pressure up to about 2.3 GPa and then drop at higher pressures. For Congo red crystal under quasi-hydrostatic condition without solvent the fluorescence intensity decreases monotonically and the lower energy band becomes dominant with the pressure increasing. The three vibronic bands show red shifts with increase of pressure

  18. Solvent anode for plutonium purification

    International Nuclear Information System (INIS)

    Bowersox, D.F.; Fife, K.W.; Christensen, D.C.

    1986-01-01

    The purpose of this study is to develop a technique to allow complete oxidation of plutonium from the anode during plutonium electrorefining. This will eliminate the generation of a ''spent'' anode heel which requires further treatment for recovery. Our approach is to employ a solvent metal in the anode to provide a liquid anode pool throughout electrorefining. We use molten salts and metals in ceramic crucibles at 700 0 C. Our goal is to produce plutonium metal at 99.9% purity with oxidation and transfer of more than 98% of the impure plutonium feed metal from the anode into the salt and product phases. We have met these criteria in experiments on the 100 to 1000 g scale. We plan to scale our operations to 4 kg of feed plutonium and to optimize the process parameters

  19. Quantitation of buried contamination by use of solvents. [degradation of silicone polymers by amine solvents

    Science.gov (United States)

    Pappas, S. P.; Hsiao, Y. C.; Hill, L. W.

    1973-01-01

    Spore recovery form cured silicone potting compounds using amine solvents to degrade the cured polymers was investigated. A complete list of solvents and a description of the effect of each on two different silicone polymers is provided.

  20. Cleanup of 7.5% tributyl phosphate/n-paraffin solvent-extraction solvent

    International Nuclear Information System (INIS)

    Reif, D.J.

    1987-02-01

    The HM process at the Savannah River Plant uses 7.5% tributyl phosphate in n-paraffin as an extraction solvent. During use, the solvent is altered due to hydrolysis and radiolysis, forming materials which influence product losses, product decontamination, and separation efficiencies. Laboratory studies to improve online solvent cleaning have shown that carbonate washing, although removing residual solvent activity, does not remove binding ligands which hold fission products in the solvent. Treatment of solvent by an alumina adsorption process removes binding ligands and significantly improves recycle solvent performance. Both laboratory work defining a full-scale alumina adsorption process and the use of the process to clean HM process first cycle solvent is discussed

  1. Eliminating the domain error in local explicitly correlated second-order Møller-Plesset perturbation theory.

    Science.gov (United States)

    Werner, Hans-Joachim

    2008-09-14

    A new explicitly correlated local MP2-F12 method is proposed in which the error caused by truncating the virtual orbital space to pair-specific local domains is almost entirely removed. This is achieved by a simple modification of the ansatz for the explicitly correlated wave function, which makes it possible that the explicitly correlated terms correct both for the basis set incompleteness error as well as for the domain error in the LMP2. Benchmark calculations are presented for 21 molecules and 16 chemical reactions. The results demonstrate that the local approximations have hardly any effect on the accuracy of the computed correlation energies and reaction energies, and the LMP2-F12 reaction energies agree within 0.1-0.2 kcal/mol with estimated MP2 basis set limits.

  2. Single molecules and nanotechnology

    CERN Document Server

    Vogel, Horst

    2007-01-01

    This book focuses on recent advances in the rapidly evolving field of single molecule research. These advances are of importance for the investigation of biopolymers and cellular biochemical reactions, and are essential to the development of quantitative biology. Written by leading experts in the field, the articles cover a broad range of topics, including: quantum photonics of organic dyes and inorganic nanoparticles their use in detecting properties of single molecules the monitoring of single molecule (enzymatic) reactions single protein (un)folding in nanometer-sized confined volumes the dynamics of molecular interactions in biological cells The book is written for advanced students and scientists who wish to survey the concepts, techniques and results of single molecule research and assess them for their own scientific activities.

  3. Electron-molecule collisions

    CERN Document Server

    Takayanagi, Kazuo

    1984-01-01

    Scattering phenomena play an important role in modern physics. Many significant discoveries have been made through collision experiments. Amongst diverse kinds of collision systems, this book sheds light on the collision of an electron with a molecule. The electron-molecule collision provides a basic scattering problem. It is scattering by a nonspherical, multicentered composite particle with its centers having degrees of freedom of motion. The molecule can even disintegrate, Le., dissociate or ionize into fragments, some or all of which may also be molecules. Although it is a difficult problem, the recent theoretical, experimental, and computational progress has been so significant as to warrant publication of a book that specializes in this field. The progress owes partly to technical develop­ ments in measurements and computations. No less important has been the great and continuing stimulus from such fields of application as astrophysics, the physics of the earth's upper atmosphere, laser physics, radiat...

  4. Molecules to Materials

    Indian Academy of Sciences (India)

    evolved as a new line of thinking wherein a single molecule or perhaps a collection .... In photonic communication processes, laser light has to be modulated and .... The author wishes to thank G Rajaram for a critical reading of the manuscript.

  5. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    IAS Admin

    overall absorption spectrum of a molecule is a superposition of many such sharp lines .... dilute solution of the enzyme and the substrate over few drops of silicone oil placed ..... Near-field Scanning Optical Microscopy (NSOM): Development.

  6. Quantum dot molecules

    CERN Document Server

    Wu, Jiang

    2014-01-01

    This book reviews recent advances in the exciting and rapidly growing field of quantum dot molecules (QDMs). It offers state-of-the-art coverage of novel techniques and connects fundamental physical properties with device design.

  7. Molecule of the Month

    Indian Academy of Sciences (India)

    Molecule of the Month - Adamantane - A Plastic Piece of Diamond. J Chandrasekhar. Volume 16 Issue 12 ... Keywords. Adamantane; diamondoid systems; plastic crystals. ... Resonance – Journal of Science Education | News. © 2017 Indian ...

  8. Chinese Undergraduates' Explicit and Implicit Attitudes toward Persons with Disabilities

    Science.gov (United States)

    Chen, Shuang; Ma, Li; Zhang, Jian-Xin

    2011-01-01

    The present study is aimed at examining implicit and explicit attitudes toward persons with disabilities among Chinese college students. The "Implicit Association Test" was used to measure their implicit attitudes, whereas their explicit attitudes toward persons with disabilities were measured by using a scale of three items.…

  9. From Explicit to Symbolic Types for Communication Protocols in CCS

    DEFF Research Database (Denmark)

    Nielson, Hanne Riis; Nielson, Flemming; Kreiker, Jörg

    2012-01-01

    We study communication protocols having several rounds and expressed in value passing CCS. We develop a type-based analysis for providing an explicit record of all communications and show the usual subject reduction result. Since the explicit records can be infinitely large, we also develop a type...

  10. The Ms. Stereotype Revisited: Implicit and Explicit Facets

    Science.gov (United States)

    Malcolmson, Kelly A.; Sinclair, Lisa

    2007-01-01

    Implicit and explicit stereotypes toward the title Ms. were examined. Participants read a short description of a target person whose title of address varied (Ms., Mrs., Miss, Mr.). They then rated the person on agentic and communal traits and completed an Implicit Association Test. Replicating earlier research (Dion, 1987), at an explicit level,…

  11. Age and time effects on implicit and explicit learning

    NARCIS (Netherlands)

    Verneau, M.; Kamp, J. van der; Savelsbergh, G.J.P.; Looze, M.P. de

    2014-01-01

    Study Context: It has been proposed that effects of aging are more pronounced for explicit than for implicit motor learning. The authors evaluated this claim by comparing the efficacy of explicit and implicit learning of a movement sequence in young and older adults, and by testing the resilience

  12. Age and Time Effects on Implicit and Explicit Learning

    NARCIS (Netherlands)

    Verneau, M.M.N.; van der Kamp, J.; Savelsbergh, G.J.P.; de Looze, M.P.

    2014-01-01

    Study Context: It has been proposed that effects of aging are more pronounced for explicit than for implicit motor learning. The authors evaluated this claim by comparing the efficacy of explicit and implicit learning of a movement sequence in young and older adults, and by testing the resilience

  13. Explicitly solvable complex Chebyshev approximation problems related to sine polynomials

    Science.gov (United States)

    Freund, Roland

    1989-01-01

    Explicitly solvable real Chebyshev approximation problems on the unit interval are typically characterized by simple error curves. A similar principle is presented for complex approximation problems with error curves induced by sine polynomials. As an application, some new explicit formulae for complex best approximations are derived.

  14. Implicit versus explicit : An ACT-R learning perspective

    NARCIS (Netherlands)

    Taatgen, N.A.

    1999-01-01

    Dienes & Perner propose a theory of implicit and explicit knowledge that is not entirely complete. It does not address many of the empirical issues, nor does it explain the difference between implicit and explicit learning. It does, however, provide a possible unified explanation, as opposed to the

  15. The Development of Explicit Memory for Basic Perceptual Features.

    Science.gov (United States)

    Gulya, Michelle; Rossi-George, Alba; Hartshorn, Kristen; Vieira, Aurora; Rovee-Collier, Carolyn; Johnson, Marcia K.; Chalfonte, Barbara L.

    2002-01-01

    Three experiments with 164 individuals between 4 and 80 years old examined age-related changes in explicit memory for three perceptual features: item identity, color, and location. Findings indicated that performance on explicit memory tests was not a consistent inverted U-shaped function of age across various features, but depended on the…

  16. Gender Differences in Implicit and Explicit Memory for Affective Passages

    Science.gov (United States)

    Burton, Leslie A.; Rabin, Laura; Vardy, Susan Bernstein.; Frohlich, Jonathan; Wyatt, Gwinne; Dimitri, Diana; Constante, Shimon; Guterman, Elan

    2004-01-01

    Thirty-two participants were administered 4 verbal tasks, an Implicit Affective Task, an Implicit Neutral Task, an Explicit Affective Task, and an Explicit Neutral Task. For the Implicit Tasks, participants were timed while reading passages aloud as quickly as possible, but not so quickly that they did not understand. A target verbal passage was…

  17. On the Reliability of Implicit and Explicit Memory Measures.

    Science.gov (United States)

    Buchner, Axel; Wippich, Werner

    2000-01-01

    Studied the reliability of implicit and explicit memory tests in experiments involving these tests. Results with 168, 84, 120, and 128 undergraduates show that methodological artifacts may cause implicit memory tests to have lower reliability than explicit memory tests, but that implicit tests need not necessarily be less reliable. (SLD)

  18. Implicit vs. Explicit Trust in Social Matrix Factorization

    NARCIS (Netherlands)

    Fazeli, Soude; Loni, Babak; Bellogin, Alejandro; Drachsler, Hendrik; Sloep, Peter

    2014-01-01

    Incorporating social trust in Matrix Factorization (MF) methods demonstrably improves accuracy of rating prediction. Such approaches mainly use the trust scores explicitly expressed by users. However, it is often challenging to have users provide explicit trust scores of each other. There exist

  19. CDPOP: A spatially explicit cost distance population genetics program

    Science.gov (United States)

    Erin L. Landguth; S. A. Cushman

    2010-01-01

    Spatially explicit simulation of gene flow in complex landscapes is essential to explain observed population responses and provide a foundation for landscape genetics. To address this need, we wrote a spatially explicit, individual-based population genetics model (CDPOP). The model implements individual-based population modelling with Mendelian inheritance and k-allele...

  20. Panorama of explicit carbon pricing instruments around the world

    International Nuclear Information System (INIS)

    2016-09-01

    In September 2016, I4CE updated its database on carbon pricing policies and published a panorama of explicit carbon pricing policies. This panorama presents an implementation timeline, a world map and a table that together, provide information on the jurisdictions that have implemented or plan to implement explicit carbon pricing policies, the type of instrument chosen, the sectors covered and the carbon prices

  1. Moderators of Implicit-Explicit Exercise Cognition Concordance.

    Science.gov (United States)

    Berry, Tanya R; Rodgers, Wendy M; Markland, David; Hall, Craig R

    2016-12-01

    Investigating implicit-explicit concordance can aid in understanding underlying mechanisms and possible intervention effects. This research examined the concordance between implicit associations of exercise with health or appearance and related explicit motives. Variables considered as possible moderators were behavioral regulations, explicit attitudes, and social desirability. Participants (N = 454) completed measures of implicit associations of exercise with health and appearance and questionnaire measures of health and appearance motives, attitudes, social desirability, and behavioral regulations. Attitudes significantly moderated the relationship between implicit associations of exercise with health and health motives. Identified regulations significantly moderated implicit-explicit concordance with respect to associations with appearance. These results suggest that implicit and explicit exercise-related cognitions are not necessarily independent and their relationship to each other may be moderated by attitudes or some forms of behavioral regulation. Future research that takes a dual-processing approach to exercise behavior should consider potential theoretical moderators of concordance.

  2. Effect of pre-swelling of coal on its solvent extraction and liquefaction properties

    Energy Technology Data Exchange (ETDEWEB)

    Hengfu Shui; Zhicai Wang; Meixia Cao [Anhui University of Technology, Ma' anshan (China). School of Chemistry and Chemical Engineering

    2008-10-15

    Effects of pre-swelling of coal on solvent extraction and liquefaction properties were studied with Shenhua coal. It was found that pre-swelling treatments of the coal in three solvents, i.e., toluene (TOL), N-methyl-2-pyrrolidinone (NMP) and tetralin (THN) increased its extraction yield and liquefaction conversion, and differed the liquefied product distributions. The pre-swollen coals after removing the swelling solvents showed increased conversion in liquefaction compared with that of the swollen coals in the presence of swelling solvents. It was also found that the yields of (oil + gas) in liquefaction of the pre-swollen coals with NMP and TOL dramatically decreased in the presence of swelling solvent. TG and FTIR analyses of the raw coal, the swollen coals and the liquefied products were carried out in order to investigate the mechanism governing the effects of pre-swelling treatment on coal extraction and liquefaction. The results showed that the swelling pre-treatment could disrupt some non-covalent interactions of the coal molecules, relax its network structure and loosened the coal structure. It would thus benefit diffusion of a hydrogen donor solvent into the coal structure during liquefaction, and also enhance the hydrogen donating ability of the hydrogen-rich species derived from the coal. 21 refs., 4 figs., 3 tabs.

  3. Solvent-mediated pathways to gelation and phase separation in suspensions of grafted nanoparticles

    KAUST Repository

    Anyfantakis, Manos

    2009-01-01

    We explore the role of the solvent medium on the interplay between gelation and phase separation in suspensions of organosilicate planar hybrids grafted with hydrocarbon chains. We establish their phase diagram by means of dynamic light scattering, rheology and visual observations, and different routes to gelation, depending on the solvent used. In agreement with earlier works, the solvent quality for the grafted chains at a given temperature controls the balance between attractions and repulsions, and hence the phase diagram of the nanoparticles and their tendency to gel. Here we show how to tune the suspension state and hence its rheology. For decane, a good solvent for the hydrocarbon chains, gelation occurs at rather low volume fractions in the presence of phase separation. This is due to the interdigitation of solvent molecules with the grafted chains, resulting in their crystalline packing that promotes the attraction between particles. For toluene, a solvent of reduced quality for the hydrocarbon chains, no interdigitation takes place, and hence gelation is triggered by clustering at higher volume fractions before phase separation. Our results support the generic picture of complex kinetic arrest/phase separation interplay in soft matter, where phase separation can proceed, be interrupted or be completely inhibited. A number of interesting possibilities for tailoring the rheology of grafted colloidal systems emerge. © 2009 The Royal Society of Chemistry.

  4. Mapping the surface of Escherichia coli peptide deformylase by NMR with organic solvents.

    Science.gov (United States)

    Byerly, Douglas W; McElroy, Craig A; Foster, Mark P

    2002-07-01

    Identifying potential ligand binding sites on a protein surface is an important first step for targeted structure-based drug discovery. While performing control experiments with Escherichia coli peptide deformylase (PDF), we noted that the organic solvents used to solubilize some ligands perturbed many of the same resonances in PDF as the small molecule inhibitors. To further explore this observation, we recorded (15)N HSQC spectra of E. coli peptide deformylase (PDF) in the presence of trace quantities of several simple organic solvents (acetone, DMSO, ethanol, isopropanol) and identified their sites of interaction from local perturbation of amide chemical shifts. Analysis of the protein surface structure revealed that the ligand-induced shift perturbations map to the active site and one additional surface pocket. The correlation between sites of solvent and inhibitor binding highlights the utility of organic solvents to rapidly and effectively validate and characterize binding sites on proteins prior to designing a drug discovery screen. Further, the solvent-induced perturbations have implications for the use of organic solvents to dissolve candidate ligands in NMR-based screens.

  5. Rational Design of Molecular Gelator - Solvent Systems Guided by Solubility Parameters

    Science.gov (United States)

    Lan, Yaqi

    Self-assembled architectures, such as molecular gels, have attracted wide interest among chemists, physicists and engineers during the past decade. However, the mechanism behind self-assembly remains largely unknown and no capability exists to predict a priori whether a small molecule will gelate a specific solvent or not. The process of self-assembly, in molecular gels, is intricate and must balance parameters influencing solubility and those contrasting forces that govern epitaxial growth into axially symmetric elongated aggregates. Although the gelator-gelator interactions are of paramount importance in understanding gelation, the solvent-gelator specific (i.e., H-bonding) and nonspecific (dipole-dipole, dipole-induced and instantaneous dipole induced forces) intermolecular interactions are equally important. Solvent properties mediate the self-assembly of molecular gelators into their self-assembled fibrillar networks. Herein, solubility parameters of solvents, ranging from partition coefficients (logP), to Henry's law constants (HLC), to solvatochromic ET(30) parameters, to Kamlet-Taft parameters (beta, alpha and pi), to Hansen solubility parameters (deltap, deltad, deltah), etc., are correlated with the gelation ability of numerous classes of molecular gelators. Advanced solvent clustering techniques have led to the development of a priori tools that can identify the solvents that will be gelled and not gelled by molecular gelators. These tools will greatly aid in the development of novel gelators without solely relying on serendipitous discoveries.

  6. Measurement and correlation of solubility of ciclesonide in seven pure organic solvents

    International Nuclear Information System (INIS)

    Zhou, Lina; Yin, Qiuxiang; Guo, Zhiqiang; Lu, Haijiao; Liu, Mingyan; Chen, Wei; Hou, Baohong

    2017-01-01

    Highlights: • The solubility of ciclesonide in seven pure organic solvents was determined by gravimetric method. • The solubility order was interpreted by virtue of density function theory (DFT). • The experimental solubility of ciclesonide was correlated by four thermodynamic models. • Mixing thermodynamic properties of ciclesonide were calculated and discussed. - Abstract: The solubility of ciclesonide in seven organic solvents (ethanol, 2-propanol, 1-propanol, 1-butanol, acetonitrile, toluene and ethyl acetate) in the temperature range from 278.15 K to 313.15 K was measured by gravimetrical method under atmospheric pressure. The results indicate that the solubility of ciclesonide increases with elevating temperature in all investigated solvents. The solubility order in different solvents was interpreted through comparing interaction force between solute and solvent molecules by virtue of density function theory (DFT). Thermodynamic equations including the modified Apelblat equation, λh equation, Wilson equation and NRTL equation are all suitable to correlate the solubility results. Based on the Wilson equation, the thermodynamic parameters from the mixing process are calculated, and the results indicate the mixing process of ciclesonide in the selected pure solvents is spontaneous and entropy-driven.

  7. Systematic investigations of peak deformations due to co-solvent adsorption in preparative supercritical fluid chromatography.

    Science.gov (United States)

    Glenne, Emelie; Leek, Hanna; Klarqvist, Magnus; Samuelsson, Jörgen; Fornstedt, Torgny

    2017-05-05

    Strangely shaped overloaded bands were recently reported using a standard supercritical fluid chromatographic system comprising a diol column as the stationary phase and carbon dioxide with methanol as the mobile phase. Some of these overloaded elution profiles appeared strongly deformed and even had "anti-Langmuirian" shapes although their solute compounds had "Langmuirian" adsorption. To obtain a more complete understanding of the generality of these effects, the investigation was expanded to cover also other common co-solvents, such as ethanol, 2-propanol, and acetonitrile, as well as various stationary phase materials, such as silica, and 2-ethylpyridine. From this expanded study it could be confirmed that the effects of deformed overloaded solute band shapes, due to co-solvent adsorption, is general phenomena in supercritical fluid chromatographic. It could also be concluded that these effects as well as previously observed "solvent effects" or "plug effects" are entirely due to competition between the solute and solvent molecules for the adsorption sites on the stationary phase surface. Finally, guidelines were given for how to evaluate the risk of deformations occurring for a given solvent-column combination, based simply on testing retention times of solutes and co-solvent. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Dipole moments of molecules solvated in helium nanodroplets

    International Nuclear Information System (INIS)

    Stiles, Paul L.; Nauta, Klaas; Miller, Roger E.

    2003-01-01

    Stark spectra are reported for hydrogen cyanide and cyanoacetylene solvated in helium nanodroplets. The goal of this study is to understand the influence of the helium solvent on measurements of the permanent electric dipole moment of a molecule. We find that the dipole moments of the helium solvated molecules, calculated assuming the electric field is the same as in vacuum, are slightly smaller than the well-known gas-phase dipole moments of HCN and HCCCN. A simple elliptical cavity model quantitatively accounts for this difference, which arises from the dipole-induced polarization of the helium

  9. Solvent-vapor-assisted imprint lithography

    NARCIS (Netherlands)

    Voicu, Nicoleta E.; Ludwigs, Sabine; Crossland, Edward J. W.; Andrew, Piers; Steiner, Ullrich

    2007-01-01

    Sub-micrometer features are replicated into high-molecular-weight polymer resists by using solvent-assisted nanoimprint lithography (see figure). By swelling the polymer in a controlled solvent-vapor atmosphere, millibar pressures and ambient temperatures are sufficient to achieve high-fidelity

  10. Into the depths of deep eutectic solvents

    NARCIS (Netherlands)

    Rodriguez, N.; Alves da Rocha, M.A.; Kroon, M.C.

    2015-01-01

    Ionic liquids (ILs) have been successfully tested in a wide range of applications; however, their high price and complicated synthesis make them infeasible for large scale implementation. A decade ago, a new generation of solvents so called deep eutectic solvents (DESs) was reported for the first

  11. Remediation of Contaminated Soils by Solvent Flushing

    NARCIS (Netherlands)

    Augustijn, Dionysius C.M.; Jessup, Ron E.; Rao, P. Suresh C.; Wood, A. Lynn

    1994-01-01

    Solvent flushing is a potential technique for remediating a waste disposal/spill site contaminated with organic chemicals. This technique involves the injection of a solvent mixture (e.g., water plus alcohols) that enhances contaminant solubility, reduces the retardation factor, and increases the

  12. Structuring of polymer solutions upon solvent evaporation

    NARCIS (Netherlands)

    Schaefer, C.; van der Schoot, P.|info:eu-repo/dai/nl/102140618; Michels, J. J.

    2015-01-01

    The morphology of solution-cast, phase-separated polymers becomes finer with increasing solvent evaporation rate. We address this observation theoretically for a model polymer where demixing is induced by steady solvent evaporation. In contrast to what is the case for a classical, thermal quench

  13. Control of boiler temperature with explicit MPC; Panntemperaturreglering med explicit MPC

    Energy Technology Data Exchange (ETDEWEB)

    Slaetteke, Ola; Velut, Stefan; Raaberg, Martin

    2012-02-15

    MPC is the multivariable controller that has been most successful in the process industry and particularly the petrochemical industry. It has been described as one of the most significant developments in process control and the main reasons for this are: 1. It handles multivariable control problems in a natural manner. 2. It is relative easy to understand the structure of the controller, which is the same whether it is a simple loop or a multivariable system. 3. It handles limitations of both the process and other practical constraints in a systematic way. Examples of this is that a valve can only work between 0 and 100 %, but also that the CO-level in the flue gas must not exceed a certain level. 4. It allows for operating conditions near critical process boundaries, which in many cases is synonymous with increased production rates, reduced raw material consumption, better energy utilization, and faster process transitions. The aim of the project is to evaluate the potential of multivariable control in the form of explicit MPC in a boiler at Stora Enso Hylte Bruk. This research task can be divided into two sub-tasks: 1. General evaluation of explicit MPC. 2. Evaluation of multivariable control of boiler temperature The purpose of subtask one is to evaluate what is required of a facility owner to implement explicit MPC in a control system. This includes everything from available calculation tools, what is important to consider during the design phase of the controller, different pitfalls that exist, management of different operating modes, to how the controller should be implemented and commissioned. Subtask two is intended to evaluate the multivariable control of a boiler of CFB type (circulating fluidized bed). MPC controller will regulate the temperature in the boiler. In order to maintain the waste incineration directive, the temperature in the upper part of the boiler is controlled. This is done by means of changes in the flow of natural gas injection and

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

    Science.gov (United States)

    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.

  15. Investigating single molecule adhesion by atomic force spectroscopy.

    Science.gov (United States)

    Stetter, Frank W S; Kienle, Sandra; Krysiak, Stefanie; Hugel, Thorsten

    2015-02-27

    Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment.

  16. Certain Verbs Are Syntactically Explicit Quantifiers

    Directory of Open Access Journals (Sweden)

    Anna Szabolcsi

    2010-12-01

    Full Text Available Quantification over individuals, times, and worlds can in principle be made explicit in the syntax of the object language, or left to the semantics and spelled out in the meta-language. The traditional view is that quantification over individuals is syntactically explicit, whereas quantification over times and worlds is not. But a growing body of literature proposes a uniform treatment. This paper examines the scopal interaction of aspectual raising verbs (begin, modals (can, and intensional raising verbs (threaten with quantificational subjects in Shupamem, Dutch, and English. It appears that aspectual raising verbs and at least modals may undergo the same kind of overt or covert scope-changing operations as nominal quantifiers; the case of intensional raising verbs is less clear. Scope interaction is thus shown to be a new potential diagnostic of object-linguistic quantification, and the similarity in the scope behavior of nominal and verbal quantifiers supports the grammatical plausibility of ontological symmetry, explored in Schlenker (2006.ReferencesBen-Shalom, D. 1996. Semantic Trees. Ph.D. thesis, UCLA.Bittner, M. 1993. Case, Scope, and Binding. Dordrecht: Reidel.Cresswell, M. 1990. Entities and Indices. Dordrecht: Kluwer.Cresti, D. 1995. ‘Extraction and reconstruction’. Natural Language Semantics 3: 79–122.http://dx.doi.org/10.1007/BF01252885Curry, B. H. & Feys, R. 1958. Combinatory Logic I. Dordrecht: North-Holland.Dowty, D. R. 1988. ‘Type raising, functional composition, and non-constituent conjunction’. In Richard T. Oehrle, Emmon W. Bach & Deirdre Wheeler (eds. ‘Categorial Grammars and Natural Language Structures’, 153–197. Dordrecht: Reidel.Fox, D. 2002. ‘TOn Logical Form’. In Randall Hendrick (ed. ‘Minimalist Syntax’, 82–124. Oxford: Blackwell.Gallin, D. 1975. Intensional and higher-order modal logic: with applications to Montague semantics. North Holland Pub. Co.; American Elsevier Pub. Co., Amsterdam

  17. Solvent distillations studies for a reprocessing plant

    International Nuclear Information System (INIS)

    Ginisty, C.; Guillaume, B.

    1989-01-01

    The substantial amounts of solvent used in large reprocessing plants are such that considerable care must be paid to solvent management to limit the production of organic wastes. The installation of intensive treatment by chemical regeneration serves to increase the service life of the solvent. General solvent management, combined with a distillation unit under reduced pressure also helps to recycle the two components of the solvent at a low activity level. Distillation also serves to remove the heavy degradation products that are generally responsible for poor hydraulic behavior and for the holdup of radioactive products such as plutonium, zirconium and ruthenium. From the safety standpoint, the flashpoint of the distilled diluent tends to rise. It can therefore be recycled without risk

  18. Method of decomposing radioactive organic solvent wastes

    International Nuclear Information System (INIS)

    Uki, Kazuo; Ichihashi, Toshio; Hasegawa, Akira; Sato, Tatsuaki

    1986-01-01

    Purpose: To decompose radioactive organic solvent wastes or radioactive hydrocarbon solvents separated therefrom into organic materials under moderate conditions, as well as greatly decrease the amount of secondary wastes generated. Method: Radioactive organic solvent wastes comprising an organic phosphoric acid ester ingredient and a hydrocarbon ingredient as a diluent therefor, or radioactive hydrocarbon solvents separated therefrom are oxidatively decomposed by hydrogen peroxide in an aqueous phosphoric acid solution of phosphoric acid metal salts finally into organic materials to perform decomposing treatment for the radioactive organic solvent wastes. The decomposing reaction is carried out under relatively moderate conditions and cause less burden to facilities or the likes. Further, since the decomposed liquid after the treatment can be reused for the decomposing reaction as a catalyst solution secondary wastes can significantly be decreased. (Yoshihara, H.)

  19. Improving the industrial production of 6-APA: enzymatic hydrolysis of penicillin G in the presence of organic solvents.

    Science.gov (United States)

    Abian, Olga; Mateo, César; Fernández-Lorente, Gloria; Guisán, José M; Fernández-Lafuente, Roberto

    2003-01-01

    The hydrolysis of penicillin G in the presence of an organic solvent, used with the purpose of extracting it from the culture medium, may greatly simplify the industrial preparation of 6-APA. However, under these conditions, PGA immobilized onto Eupergit displays very low stability (half-life of 5 h in butanone-saturated water) and a significant degree of inhibition by the organic solvent (30%). The negative effect of the organic solvent strongly depended on the type of solvent utilized: water saturated with butanone (around 28% v/v) had a much more pronounced negative effect than that of methylisobutyl ketone (MIBK) (solubility in water was only 2%). These problems were sorted out by using a new penicillin G acylase derivative designed to work in the presence of organic solvents (with each enzyme molecule surrounded by an hydrophilic artificial environment) and a suitable organic solvent (MIBK). Using such solvent, this derivative kept its activity unaltered for 1 week at 32 degrees C. Moreover, the enzyme activity was hardly inhibited by the presence of the organic solvent. In this way, the new enzyme derivative thus prepared enables simplification of the industrial hydrolysis of penicillin G.

  20. Replica exchange with solute tempering: A method for sampling biological systems in explicit water

    Science.gov (United States)

    Liu, Pu; Kim, Byungchan; Friesner, Richard A.; Berne, B. J.

    2005-09-01

    An innovative replica exchange (parallel tempering) method called replica exchange with solute tempering (REST) for the efficient sampling of aqueous protein solutions is presented here. The method bypasses the poor scaling with system size of standard replica exchange and thus reduces the number of replicas (parallel processes) that must be used. This reduction is accomplished by deforming the Hamiltonian function for each replica in such a way that the acceptance probability for the exchange of replica configurations does not depend on the number of explicit water molecules in the system. For proof of concept, REST is compared with standard replica exchange for an alanine dipeptide molecule in water. The comparisons confirm that REST greatly reduces the number of CPUs required by regular replica exchange and increases the sampling efficiency. This method reduces the CPU time required for calculating thermodynamic averages and for the ab initio folding of proteins in explicit water. Author contributions: B.J.B. designed research; P.L. and B.K. performed research; P.L. and B.K. analyzed data; and P.L., B.K., R.A.F., and B.J.B. wrote the paper.Abbreviations: REST, replica exchange with solute tempering; REM, replica exchange method; MD, molecular dynamics.*P.L. and B.K. contributed equally to this work.

  1. The chemistry of nonaqueous solvents v.4 solution phenomena and aprotic solvents

    CERN Document Server

    Lagowski, J J

    1976-01-01

    The Chemistry of Nonaqueous Solvents, Volume IV: Solution Phenomena and Aprotic Solvents focuses on the chemistry of nonaqueous solvents, with emphasis on solution phenomena and aprotic solvents such as tetramethylurea, inorganic acid chlorides, cyclic carbonates, and sulfolane. This book is organized into seven chapters and begins with an overview of the theory of electrical conductivity and elementary experimental considerations, along with some of the interesting research on nonaqueous solvents. It then turns to a discussion on hydrogen bonding phenomena in nonaqueous systems as probed

  2. PARIS II: Computer Aided Solvent Design for Pollution Prevention

    Science.gov (United States)

    This product is a summary of U.S. EPA researchers' work developing the solvent substitution software tool PARIS II (Program for Assisting the Replacement of Industrial Solvents, version 2.0). PARIS II finds less toxic solvents or solvent mixtures to replace more toxic solvents co...

  3. Implicit and explicit memory for spatial information in Alzheimer's disease.

    Science.gov (United States)

    Kessels, R P C; Feijen, J; Postma, A

    2005-01-01

    There is abundant evidence that memory impairment in dementia in patients with Alzheimer's disease (AD) is related to explicit, conscious forms of memory, whereas implicit, unconscious forms of memory function remain relatively intact or are less severely affected. Only a few studies have been performed on spatial memory function in AD, showing that AD patients' explicit spatial memory is impaired, possibly related to hippocampal dysfunction. However, studies on implicit spatial memory in AD are lacking. The current study set out to investigate implicit and explicit spatial memory in AD patients (n=18) using an ecologically valid computer task, in which participants had to remember the locations of various objects in common rooms. The contribution of implicit and explicit memory functions was estimated by means of the process dissociation procedure. The results show that explicit spatial memory is impaired in AD patients compared with a control group (n=21). However, no group difference was found on implicit spatial function. This indicates that spared implicit memory in AD extends to the spatial domain, while the explicit spatial memory function deteriorates. Clinically, this finding might be relevant, in that an intact implicit memory function might be helpful in overcoming problems in explicit processing. Copyright (c) 2005 S. Karger AG, Basel.

  4. Measuring Explicit Word Learning of Preschool Children: A Development Study.

    Science.gov (United States)

    Kelley, Elizabeth Spencer

    2017-08-15

    The purpose of this article is to present preliminary results related to the development of a new measure of explicit word learning. The measure incorporated elements of explicit vocabulary instruction and dynamic assessment and was designed to be sensitive to differences in word learning skill and to be feasible for use in clinical settings. The explicit word learning measure included brief teaching trials and repeated fine-grained measurement of semantic knowledge and production of 3 novel words (2 verbs and 1 adjective). Preschool children (N = 23) completed the measure of explicit word learning; standardized, norm-referenced measures of expressive and receptive vocabulary; and an incidental word learning task. The measure of explicit word learning provided meaningful information about word learning. Performance on the explicit measure was related to existing vocabulary knowledge and incidental word learning. Findings from this development study indicate that further examination of the measure of explicit word learning is warranted. The measure may have the potential to identify children who are poor word learners. https://doi.org/10.23641/asha.5170738.

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

    Science.gov (United States)

    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.

  6. Electron-molecule collisions

    International Nuclear Information System (INIS)

    Shimamura, I.; Takayanagi, K.

    1984-01-01

    The study of collision processes plays an important research role in modern physics. Many significant discoveries have been made by means of collision experiments. Based on theoretical, experimental, and computational studies, this volume presents an overview detailing the basic processes of electron-molecule collisions. The editors have collected papers-written by a group of international experts-that consider a diverse range of phenomena occurring in electronmolecule collisions. The volume discusses first the basic formulation for scattering problems and then gives an outline of the physics of electron-molecule collisions. The main topics covered are rotational transitions, vibrational transitions, dissociation of molecules in slow collisions, the electron-molecule collision as a spectroscopic tool for studying molecular electronic structures, and experimental and computational techniques for determining the cross sections. These well-referenced chapters are self-contained and can be read independently or consecutively. Authoritative and up-to-date, Electron-Molecule Collisions is a useful addition to the libraries of students and researchers in the fields of atomic, molecular, and chemical physics, and physical chemistry

  7. Explicit strong stability preserving multistep Runge–Kutta methods

    KAUST Repository

    Bresten, Christopher; Gottlieb, Sigal; Grant, Zachary; Higgs, Daniel; Ketcheson, David I.; Né meth, Adrian

    2015-01-01

    High-order spatial discretizations of hyperbolic PDEs are often designed to have strong stability properties, such as monotonicity. We study explicit multistep Runge-Kutta strong stability preserving (SSP) time integration methods for use with such discretizations. We prove an upper bound on the SSP coefficient of explicit multistep Runge-Kutta methods of order two and above. Numerical optimization is used to find optimized explicit methods of up to five steps, eight stages, and tenth order. These methods are tested on the linear advection and nonlinear Buckley-Leverett equations, and the results for the observed total variation diminishing and/or positivity preserving time-step are presented.

  8. Explicit strong stability preserving multistep Runge–Kutta methods

    KAUST Repository

    Bresten, Christopher

    2015-10-15

    High-order spatial discretizations of hyperbolic PDEs are often designed to have strong stability properties, such as monotonicity. We study explicit multistep Runge-Kutta strong stability preserving (SSP) time integration methods for use with such discretizations. We prove an upper bound on the SSP coefficient of explicit multistep Runge-Kutta methods of order two and above. Numerical optimization is used to find optimized explicit methods of up to five steps, eight stages, and tenth order. These methods are tested on the linear advection and nonlinear Buckley-Leverett equations, and the results for the observed total variation diminishing and/or positivity preserving time-step are presented.

  9. Subliminal mere exposure and explicit and implicit positive affective responses.

    Science.gov (United States)

    Hicks, Joshua A; King, Laura A

    2011-06-01

    Research suggests that repeated subliminal exposure to environmental stimuli enhances positive affective responses. To date, this research has primarily concentrated on the effects of repeated exposure on explicit measures of positive affect (PA). However, recent research suggests that repeated subliminal presentations may increase implicit PA as well. The present study tested this hypothesis. Participants were either subliminally primed with repeated presentations of the same stimuli or only exposed to each stimulus one time. Results confirmed predictions showing that repeated exposure to the same stimuli increased both explicit and implicit PA. Implications for the role of explicit and implicit PA in attitudinal judgements are discussed.

  10. MOLECULES IN η CARINAE

    International Nuclear Information System (INIS)

    Loinard, Laurent; Menten, Karl M.; Güsten, Rolf; Zapata, Luis A.; Rodríguez, Luis F.

    2012-01-01

    We report the detection toward η Carinae of six new molecules, CO, CN, HCO + , HCN, HNC, and N 2 H + , and of two of their less abundant isotopic counterparts, 13 CO and H 13 CN. The line profiles are moderately broad (∼100 km s –1 ), indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO + do not appear to be underabundant in η Carinae. On the other hand, molecules containing nitrogen or the 13 C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of η Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

  11. Organic Solvent Tolerant Lipases and Applications

    Directory of Open Access Journals (Sweden)

    Shivika Sharma

    2014-01-01

    Full Text Available Lipases are a group of enzymes naturally endowed with the property of performing reactions in aqueous as well as organic solvents. The esterification reactions using lipase(s could be performed in water-restricted organic media as organic solvent(s not only improve(s the solubility of substrate and reactant in reaction mixture but also permit(s the reaction in the reverse direction, and often it is easy to recover the product in organic phase in two-phase equilibrium systems. The use of organic solvent tolerant lipase in organic media has exhibited many advantages: increased activity and stability, regiospecificity and stereoselectivity, higher solubility of substrate, ease of products recovery, and ability to shift the reaction equilibrium toward synthetic direction. Therefore the search for organic solvent tolerant enzymes has been an extensive area of research. A variety of fatty acid esters are now being produced commercially using immobilized lipase in nonaqueous solvents. This review describes the organic tolerance and industrial application of lipases. The main emphasis is to study the nature of organic solvent tolerant lipases. Also, the potential industrial applications that make lipases the biocatalysts of choice for the present and future have been presented.

  12. A class of explicitly soluble, local, many-center hamiltonians for one-particle quantum mechanics in two and three dimensions. I

    International Nuclear Information System (INIS)

    Grossmann, A.; Mebkhout, M.; Centre National de la Recherche Scientifique, 13 - Marseille

    1979-02-01

    An explicit formula for the resolvent of a class of one-particle, many-center, local Hamiltonians is derived. This formula gives, in particular, a full description of a model molecule given by point interactions at n arbitrarily placed fixed centers in three dimensions. It also gives a three-dimensional analogue of the Kronig-Penney model

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

    Science.gov (United States)

    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.

  14. Natural deep eutectic solvents as new potential media for green technology

    International Nuclear Information System (INIS)

    Dai, Yuntao; Spronsen, Jaap van; Witkamp, Geert-Jan; Verpoorte, Robert; Choi, Young Hae

    2013-01-01

    Highlights: ► Natural products were used as a source for deep eutectic solvents and ionic liquids. ► We define own chemical and physical properties of natural deep eutectic solvents. ► Interaction between natural deep eutectic solvents and solutes was confirmed by NMR. ► The developed natural deep eutectic solvents were applied as green media. - Abstract: Developing new green solvents is one of the key subjects in Green Chemistry. Ionic liquids (ILs) and deep eutectic solvents, thus, have been paid great attention to replace current harsh organic solvents and have been applied to many chemical processing such as extraction and synthesis. However, current ionic liquids and deep eutectic solvents have still limitations to be applied to a real chemical industry due to toxicity against human and environment and high cost of ILs and solid state of most deep eutectic solvents at room temperature. Recently we discovered that many plant abundant primary metabolites changed their state from solid to liquid when they were mixed in proper ratio. This finding made us hypothesize that natural deep eutectic solvents (NADES) play a role as alternative media to water in living organisms and tested a wide range of natural products, which resulted in discovery of over 100 NADES from nature. In order to prove deep eutectic feature the interaction between the molecules was investigated by nuclear magnetic resonance spectroscopy. All the tested NADES show clear hydrogen bonding between components. As next step physical properties of NADES such as water activity, density, viscosity, polarity and thermal properties were measured as well as the effect of water on the physical properties. In the last stage the novel NADES were applied to the solubilization of wide range of biomolecules such as non-water soluble bioactive natural products, gluten, starch, and DNA. In most cases the solubility of the biomolecules evaluated in this study was greatly higher than water. Based on the

  15. Natural deep eutectic solvents as new potential media for green technology

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Yuntao [Natural Products Laboratory, Institute of Biology, Leiden University, 2300 RA Leiden (Netherlands); Spronsen, Jaap van; Witkamp, Geert-Jan [Laboratory for Process Equipment, Delft University of Technology, Delft (Netherlands); Verpoorte, Robert [Natural Products Laboratory, Institute of Biology, Leiden University, 2300 RA Leiden (Netherlands); Choi, Young Hae, E-mail: y.choi@chem.leidenuniv.nl [Natural Products Laboratory, Institute of Biology, Leiden University, 2300 RA Leiden (Netherlands)

    2013-03-05

    Highlights: ► Natural products were used as a source for deep eutectic solvents and ionic liquids. ► We define own chemical and physical properties of natural deep eutectic solvents. ► Interaction between natural deep eutectic solvents and solutes was confirmed by NMR. ► The developed natural deep eutectic solvents were applied as green media. - Abstract: Developing new green solvents is one of the key subjects in Green Chemistry. Ionic liquids (ILs) and deep eutectic solvents, thus, have been paid great attention to replace current harsh organic solvents and have been applied to many chemical processing such as extraction and synthesis. However, current ionic liquids and deep eutectic solvents have still limitations to be applied to a real chemical industry due to toxicity against human and environment and high cost of ILs and solid state of most deep eutectic solvents at room temperature. Recently we discovered that many plant abundant primary metabolites changed their state from solid to liquid when they were mixed in proper ratio. This finding made us hypothesize that natural deep eutectic solvents (NADES) play a role as alternative media to water in living organisms and tested a wide range of natural products, which resulted in discovery of over 100 NADES from nature. In order to prove deep eutectic feature the interaction between the molecules was investigated by nuclear magnetic resonance spectroscopy. All the tested NADES show clear hydrogen bonding between components. As next step physical properties of NADES such as water activity, density, viscosity, polarity and thermal properties were measured as well as the effect of water on the physical properties. In the last stage the novel NADES were applied to the solubilization of wide range of biomolecules such as non-water soluble bioactive natural products, gluten, starch, and DNA. In most cases the solubility of the biomolecules evaluated in this study was greatly higher than water. Based on the

  16. Moderators of the Relationship between Implicit and Explicit Evaluation

    Science.gov (United States)

    Nosek, Brian A.

    2005-01-01

    Automatic and controlled modes of evaluation sometimes provide conflicting reports of the quality of social objects. This paper presents evidence for four moderators of the relationship between automatic (implicit) and controlled (explicit) evaluations. Implicit and explicit preferences were measured for a variety of object pairs using a large sample. The average correlation was r = .36, and 52 of the 57 object pairs showed a significant positive correlation. Results of multilevel modeling analyses suggested that: (a) implicit and explicit preferences are related, (b) the relationship varies as a function of the objects assessed, and (c) at least four variables moderate the relationship – self-presentation, evaluative strength, dimensionality, and distinctiveness. The variables moderated implicit-explicit correspondence across individuals and accounted for much of the observed variation across content domains. The resulting model of the relationship between automatic and controlled evaluative processes is grounded in personal experience with the targets of evaluation. PMID:16316292

  17. Recent Advances in Explicit Multiparametric Nonlinear Model Predictive Control

    KAUST Repository

    Domínguez, Luis F.; Pistikopoulos, Efstratios N.

    2011-01-01

    are derived. The performance of the explicit controllers are then tested and compared in a simulation example involving the operation of a continuous stirred-tank reactor (CSTR). © 2010 American Chemical Society.

  18. Two explicit formulas for the generalized Motzkin numbers

    Directory of Open Access Journals (Sweden)

    Jiao-Lian Zhao

    2017-02-01

    Full Text Available Abstract In the paper, by the Faà di Bruno formula, the authors establish two explicit formulas for the Motzkin numbers, the generalized Motzkin numbers, and the restricted hexagonal numbers.

  19. Explicit TE/TM scheme for particle beam simulations

    International Nuclear Information System (INIS)

    Dohlus, M.; Zagorodnov, I.

    2008-10-01

    In this paper we propose an explicit two-level conservative scheme based on a TE/TM like splitting of the field components in time. Its dispersion properties are adjusted to accelerator problems. It is simpler and faster than the implicit version. It does not have dispersion in the longitudinal direction and the dispersion properties in the transversal plane are improved. The explicit character of the new scheme allows a uniformly stable conformal method without iterations and the scheme can be parallelized easily. It assures energy and charge conservation. A version of this explicit scheme for rotationally symmetric structures is free from the progressive time step reducing for higher order azimuthal modes as it takes place for Yee's explicit method used in the most popular electrodynamics codes. (orig.)

  20. Explicit Solutions for One-Dimensional Mean-Field Games

    KAUST Repository

    Prazeres, Mariana

    2017-01-01

    In this thesis, we consider stationary one-dimensional mean-field games (MFGs) with or without congestion. Our aim is to understand the qualitative features of these games through the analysis of explicit solutions. We are particularly interested

  1. Explicit Nonlinear Model Predictive Control Theory and Applications

    CERN Document Server

    Grancharova, Alexandra

    2012-01-01

    Nonlinear Model Predictive Control (NMPC) has become the accepted methodology to solve complex control problems related to process industries. The main motivation behind explicit NMPC is that an explicit state feedback law avoids the need for executing a numerical optimization algorithm in real time. The benefits of an explicit solution, in addition to the efficient on-line computations, include also verifiability of the implementation and the possibility to design embedded control systems with low software and hardware complexity. This book considers the multi-parametric Nonlinear Programming (mp-NLP) approaches to explicit approximate NMPC of constrained nonlinear systems, developed by the authors, as well as their applications to various NMPC problem formulations and several case studies. The following types of nonlinear systems are considered, resulting in different NMPC problem formulations: Ø  Nonlinear systems described by first-principles models and nonlinear systems described by black-box models; �...

  2. Do quarks play an explicit role as nuclear constituents ?

    International Nuclear Information System (INIS)

    Yamazaki, Toshimitsu.

    1986-10-01

    Experimental signatures for explicit roles of quarks as nuclear constituents are looked for. It is stressed that hyperons in nuclei may reveal unique information on nuclear interior and possible quark deconfinement. Future directions of hypernuclear spectroscopy are discussed. (author)

  3. Solvent Handbook Database System user's manual

    International Nuclear Information System (INIS)

    1993-03-01

    Industrial solvents and cleaners are used in maintenance facilities to remove wax, grease, oil, carbon, machining fluids, solder fluxes, mold release, and various other contaminants from parts, and to prepare the surface of various metals. However, because of growing environmental and worker-safety concerns, government regulations have already excluded the use of some chemicals and have restricted the use of halogenated hydrocarbons because they affect the ozone layer and may cause cancer. The Solvent Handbook Database System lets you view information on solvents and cleaners, including test results on cleaning performance, air emissions, recycling and recovery, corrosion, and non-metals compatibility. Company and product safety information is also available

  4. Modeling of Salt Solubilities in Mixed Solvents

    DEFF Research Database (Denmark)

    Chiavone-Filho, O.; Rasmussen, Peter

    2000-01-01

    A method to correlate and predict salt solubilities in mixed solvents using a UNIQUAC+Debye-Huckel model is developed. The UNIQUAC equation is applied in a form with temperature-dependent parameters. The Debye-Huckel model is extended to mixed solvents by properly evaluating the dielectric...... constants and the liquid densities of the solvent media. To normalize the activity coefficients, the symmetric convention is adopted. Thermochemical properties of the salt are used to estimate the solubility product. It is shown that the proposed procedure can describe with good accuracy a series of salt...

  5. Solvent extraction in the nuclear fuel cycle

    International Nuclear Information System (INIS)

    Eccles, H.; Naylor, A.

    1987-01-01

    Solvent extraction techniques have been used in the uranium nuclear fuel cycle in three main areas; concentration of uranium from ore leach liquor, purification of ore concentrates and fuel reprocessing. Solvent extraction has been extended to the removal of transuranic elements from active waste liquor, the recovery of uranium from natural sources and the recovery of noble metals from active waste liquor. Schemes are presented for solvent extraction of uranium using the Amex or Dapex process; spent fuel reprocessing and the Purex process. Recent and future developments of the techniques are outlined. (UK)

  6. Chemical reactions in solvents and melts

    CERN Document Server

    Charlot, G

    1969-01-01

    Chemical Reactions in Solvents and Melts discusses the use of organic and inorganic compounds as well as of melts as solvents. This book examines the applications in organic and inorganic chemistry as well as in electrochemistry. Organized into two parts encompassing 15 chapters, this book begins with an overview of the general properties and the different types of reactions, including acid-base reactions, complex formation reactions, and oxidation-reduction reactions. This text then describes the properties of inert and active solvents. Other chapters consider the proton transfer reactions in

  7. Spreadsheet algorithm for stagewise solvent extraction

    International Nuclear Information System (INIS)

    Leonard, R.A.; Regalbuto, M.C.

    1994-01-01

    The material balance and equilibrium equations for solvent extraction processes have been combined with computer spreadsheets in a new way so that models for very complex multicomponent multistage operations can be setup and used easily. A part of the novelty is the way in which the problem is organized in the spreadsheet. In addition, to facilitate spreadsheet setup, a new calculational procedure has been developed. The resulting Spreadsheet Algorithm for Stagewise Solvent Extraction (SASSE) can be used with either IBM or Macintosh personal computers as a simple yet powerful tool for analyzing solvent extraction flowsheets. 22 refs., 4 figs., 2 tabs

  8. TRUEX process solvent cleanup with solid sorbents

    International Nuclear Information System (INIS)

    Tse, Pui-Kwan; Reichley-Yinger, L.; Vandegrift, G.F.

    1989-01-01

    Solid sorbents, alumina, silica gel, and Amberlyst A-26 have been tested for the cleanup of degraded TRUEX-NPH solvent. A sodium carbonate scrub alone does not completely remove acidic degradation products from highly degraded solvent and cannot restore the stripping performance of the solvent. By following the carbonate scrub with either neutral alumina or Amberlyst A-26 anion exchange resin, the performance of the TRUEX-NPH is substantially restored. The degraded TRUEX-NPH was characterized before and after treatment by supercritical fluid chromatography. Its performance was evaluated by americium distribution ratios, phase-separation times, and lauric acid distribution coefficients. 17 refs., 2 figs., 5 tabs

  9. Direct measurement for organic solvents diffusion using ultra-sensitive optical resonator

    Science.gov (United States)

    Ali, Amir R.; Elias, Catherine M.

    2017-06-01

    In this paper, novel techniques using ultra-sensitive chemical optical sensor based on whispering gallery modes (WGM) are proposed through two different configurations. The first one will use a composite micro-sphere, when the solvent interacts with the polymeric optical sensors through diffusion the sphere start to swallow that solvent. In turn, that leads to change the morphology and mechanical properties of the polymeric spheres. Also, these changes could be measured by tracking the WGM shifts. Several experiments were carried out to study the solvent induced WGM shift using microsphere immersed in a solvent atmosphere. It can be potentially used for sensing the trace organic solvents like ethanol and methanol. The second configuration will use a composite beam nitrocellulose composite (NC) structure that acts as a sensing element. In this configuration, a beam is anchored to a substrate in one end, and the other end is compressing the polymeric sphere causing a shift in its WGM. When a chemical molecule is attached to the beam, the resonant frequency of the cantilever will be changed for a certain amount. By sensing this certain resonant frequency change, the existence of a single chemical molecule can be detected. A preliminary experimental model is developed to describe the vibration of the beam structure. The resonant frequency change of the cantilever due to attached mass is examined imperially using acetone as an example. Breath diagnosis can use this configuration in diabetic's diagnosis. Since, solvent like acetone concentration in human breath leads to a quick, convenient, accurate and painless breath diagnosis of diabetics. These micro-optical sensors have been examined using preliminary experiments to fully investigate its response. The proposed chemical sensor can achieve extremely high sensitivity in molecular level.

  10. Uranium refining by solvent extraction

    International Nuclear Information System (INIS)

    Kraikaew, J.; Srinuttrakul, W.

    2014-01-01

    The solvent extraction process to produce higher purity uranium from yellowcake was studied in laboratory scale. Yellowcake, which the uranium purity is around 70% and the main impurity is thorium, was obtained from monazite processing pilot plant of Rare Earth Research and Development Center in Thailand. For uranium re-extraction process, the extractant chosen was Tributylphosphate (TBP) in kerosene. It was found that the optimum concentration of TBP was 10% in kerosene and the optimum nitric acid concentration in uranyl nitrate feed solution was 4 N. An increase in concentrations of uranium and thorium in feed solution resulted in a decrease in the distribution of both components in the extractant. However, the distribution of uranium into the extractant was found to be more than that of thorium. The equilibration study of the extraction system, UO_2(NO_3)/4N HNO_3 – 10%TBP/Kerosene, was also investigated. Two extraction stages were calculated graphically from 100,000 ppm uranium concentration in feed solution input with 90% extraction efficiency and the flow ratio of aqueous phase to organic phase was adjusted to 1.0. For thorium impurity scrubbing process, 10% TBP in kerosene was loaded with uranium and minor thorium from uranyl nitrate solution prepared from yellowcake and was scrubbed with different low concentration nitric acid. The results showed that at nitric acid normality was lower than 1 N, uranium distributed well to aqueous phase. As conclusion, optimum nitric acid concentration for scrubbing process should not less than 1 N and diluted nitric acid or de-ionized water should be applied to strip uranium from organic phase in the final refining process. (author)

  11. Explicit formula for a fundamental class of functions

    OpenAIRE

    Avdispahić, Muharem; Smajlović, Lejla

    2005-01-01

    The purpose of this paper is to prove an analogue of A. Weil's explicit formula for a fundamental class of functions, i.e. the class of meromorphic functions that have an Euler sum representation and satisfy certain a functional equation. The advance of this explicit formula is that it enlarges the class of allowed test functions, from the class of functions with bounded Jordan variation to the class of functions of $\\phi $-bounded variation. A condition posed to the test fu...

  12. Higgs pair production in the MSSM with explicit CP violation

    International Nuclear Information System (INIS)

    Demir, D.A.

    1999-07-01

    In the minimal supersymmetric standard model with explicit CP violation, associated production of the lightest Higgs boson with heavier ones is analyzed. Due to explicit CP violation, the Higgs bosons are no longer CP eigenstates so that both of the heavy Higgs bosons contribute to the process. While the radiative corrections in the Higgs sector turn out to be quite important, the vertex radiative corrections remain small as in the CP conserving theory. (author)

  13. Explicit and implicit reinforcement learning across the psychosis spectrum.

    Science.gov (United States)

    Barch, Deanna M; Carter, Cameron S; Gold, James M; Johnson, Sheri L; Kring, Ann M; MacDonald, Angus W; Pizzagalli, Diego A; Ragland, J Daniel; Silverstein, Steven M; Strauss, Milton E

    2017-07-01

    Motivational and hedonic impairments are core features of a variety of types of psychopathology. An important aspect of motivational function is reinforcement learning (RL), including implicit (i.e., outside of conscious awareness) and explicit (i.e., including explicit representations about potential reward associations) learning, as well as both positive reinforcement (learning about actions that lead to reward) and punishment (learning to avoid actions that lead to loss). Here we present data from paradigms designed to assess both positive and negative components of both implicit and explicit RL, examine performance on each of these tasks among individuals with schizophrenia, schizoaffective disorder, and bipolar disorder with psychosis, and examine their relative relationships to specific symptom domains transdiagnostically. None of the diagnostic groups differed significantly from controls on the implicit RL tasks in either bias toward a rewarded response or bias away from a punished response. However, on the explicit RL task, both the individuals with schizophrenia and schizoaffective disorder performed significantly worse than controls, but the individuals with bipolar did not. Worse performance on the explicit RL task, but not the implicit RL task, was related to worse motivation and pleasure symptoms across all diagnostic categories. Performance on explicit RL, but not implicit RL, was related to working memory, which accounted for some of the diagnostic group differences. However, working memory did not account for the relationship of explicit RL to motivation and pleasure symptoms. These findings suggest transdiagnostic relationships across the spectrum of psychotic disorders between motivation and pleasure impairments and explicit RL. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  14. Recent Advances in Explicit Multiparametric Nonlinear Model Predictive Control

    KAUST Repository

    Domínguez, Luis F.

    2011-01-19

    In this paper we present recent advances in multiparametric nonlinear programming (mp-NLP) algorithms for explicit nonlinear model predictive control (mp-NMPC). Three mp-NLP algorithms for NMPC are discussed, based on which novel mp-NMPC controllers are derived. The performance of the explicit controllers are then tested and compared in a simulation example involving the operation of a continuous stirred-tank reactor (CSTR). © 2010 American Chemical Society.

  15. Molecule of the Month

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 1; Issue 2. Molecule of the Month Isomers of Benzene - Still Pursuing Dreams. J Chandrasekhar. Feature Article Volume 1 Issue 2 February 1996 pp 80-83. Fulltext. Click here to view fulltext PDF. Permanent link:

  16. Atoms, Molecules, and Compounds

    CERN Document Server

    Manning, Phillip

    2007-01-01

    Explores the atoms that govern chemical processes. This book shows how the interactions between simple substances such as salt and water are crucial to life on Earth and how those interactions are predestined by the atoms that make up the molecules.

  17. Electrons in Molecules

    Indian Academy of Sciences (India)

    structure and properties (includingreactivt'ty) - both static (independent of time) and ... Furthermore, since the energy of H2 + in the ground state must be lower than that of .... (Figure 2b); note also that dp is positive in parts of the antibinding regions behind the two ... But, now both the sizes and shapes of molecules enter into.

  18. Molecule of the Month

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 16; Issue 12. Molecule of the Month - A Stable Dibismuthene - A Compound with a Bi-Bi Double Bond. V Chandrasekhar. Volume 16 ... Author Affiliations. V Chandrasekhar1. Department of Chemistry, Indian Institute of Technology, Kanpur 208 016, India.

  19. OMG: Open molecule generator

    NARCIS (Netherlands)

    Peironcely, J.E.; Rojas-Chertó, M.; Fichera, D.; Reijmers, T.; Coulier, L.; Faulon, J.-L.; Hankemeier, T.

    2012-01-01

    Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical

  20. Molecule-based magnets

    Indian Academy of Sciences (India)

    Administrator

    Employing self-assembly methods, it is possible to engineer a bulk molecular material ... synthesis of molecular magnets in 1986, a large variety of them have been synthesized, which can be catego- ... maintained stably per organic molecule, stabilization of a ..... rotating freely under an applied field because it is a magne-.

  1. Molecule of the Month

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 2; Issue 5. Molecule of the Month Molecular–Chameleon: Solvatochromism at its Iridescent Best! Photon Rao. Feature Article Volume 2 Issue 5 May 1997 pp 69-72. Fulltext. Click here to view fulltext PDF. Permanent link:

  2. Small Molecule Library Synthesis Using Segmented Flow

    Directory of Open Access Journals (Sweden)

    Christina M. Thompson

    2011-11-01

    Full Text Available Flow chemistry has gained considerable recognition as a simple, efficient, and safe technology for the synthesis of many types of organic and inorganic molecules ranging in scope from large complex natural products to silicon nanoparticles. In this paper we describe a method that adapts flow chemistry to the synthesis of libraries of compounds using a fluorous immiscible solvent as a spacer between reactions. The methodology was validated in the synthesis of two small heterocycle containing libraries. The reactions were performed on a 0.2 mmol scale, enabling tens of milligrams of material to be generated in a single 200 mL reaction plug. The methodology allowed library synthesis in half the time of conventional microwave synthesis while maintaining similar yields. The ability to perform multiple, potentially unrelated reactions in a single run is ideal for making small quantities of many different compounds quickly and efficiently.

  3. Direct single-molecule dynamic detection of chemical reactions.

    Science.gov (United States)

    Guan, Jianxin; Jia, Chuancheng; Li, Yanwei; Liu, Zitong; Wang, Jinying; Yang, Zhongyue; Gu, Chunhui; Su, Dingkai; Houk, Kendall N; Zhang, Deqing; Guo, Xuefeng

    2018-02-01

    Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.

  4. Intimate partner violence and preschoolers' explicit memory functioning.

    Science.gov (United States)

    Jouriles, Ernest N; Brown, Alan S; McDonald, Renee; Rosenfield, David; Leahy, Matthew M; Silver, Cheryl

    2008-06-01

    This research examines whether parents' intimate partner physical violence (IPV) relates to their preschoolers' explicit memory functioning, whether children's symptoms of hyperarousal mediate this relation, and whether mothers' positive parenting moderates this relation. Participants were 69 mothers and their 4- or 5-year-old child (34 girls). Mothers completed measures of IPV, children's hyperarousal symptoms, parent-child aggression, and positive parenting. Measures of explicit memory functioning were administered to preschoolers. As expected, IPV correlated negatively with preschoolers' performance on explicit memory tasks, even after controlling for parent-child aggression and demographic variables related to preschoolers' memory functioning. Preschoolers' hyperarousal symptoms did not mediate the relation between IPV and explicit memory functioning, but mothers' positive parenting moderated this relation. Specifically, the negative relation between IPV and preschoolers' performance on 2 of the 3 explicit memory tasks was weaker when mothers engaged in higher levels of positive parenting. These findings extend research on IPV and children's adjustment difficulties to explicit memory functioning in preschoolers and suggest that mothers can ameliorate the influence of IPV on preschoolers' memory functioning via their parenting. (c) 2008 APA, all rights reserved

  5. Implicit and explicit memory in survivors of chronic interpersonal violence.

    Science.gov (United States)

    Minshew, Reese; D'Andrea, Wendy

    2015-01-01

    We investigated the relationship of implicit and explicit memory to a range of symptoms in a sample of 27 women with exposure to chronic interpersonal violence (IPV). Participants viewed the first 3 letters ("stems") of trauma-related, general threat, and neutral words; valenced words were matched with neutral words with the same stem. Free recall and a word-stem completion task were used to test explicit and implicit memory, respectively. Participants exhibited increased implicit memory for trauma-related words as compared with both general threat words and neutral "match" words. They also showed increased explicit memory for both general threat and trauma-related words. Finally, although neither implicit nor explicit memory was correlated with PTSD symptoms, implicit memory for trauma-related words was significantly correlated with symptoms associated with ongoing IPV. Interpersonal sensitivity, hostility, and alexithymia were significantly correlated with implicit, but not explicit, memory for trauma words. Somatization, dissociation, and alexithymia were negatively correlated with explicit, but not implicit, memory for general-threat words. These findings suggest that memory processes in survivors of IPV are closely related to the symptom profile associated with complex trauma. Exploring memory processes in survivors of IPV may lend unique insight into the development and maintenance of the symptom profile associated with IPV. (c) 2015 APA, all rights reserved).

  6. Exotic helium molecules

    International Nuclear Information System (INIS)

    Portier, M.

    2007-12-01

    We study the photo-association of an ultracold cloud of magnetically trapped helium atoms: pairs of colliding atoms interact with one or two laser fields to produce a purely long range 4 He 2 (2 3 S 1 -2 3 P 0 ) molecule, or a 4 He 2 (2 3 S 1 -2 3 S 1 ) long range molecule. Light shifts in one photon photo-association spectra are measured and studied as a function of the laser polarization and intensity, and the vibrational state of the excited molecule. They result from the light-induced coupling between the excited molecule, and bound and scattering states of the interaction between two metastable atoms. Their analysis leads to the determination of the scattering length a = (7.2 ± 0.6) ruling collisions between spin polarized atoms. The two photon photo-association spectra show evidence of the production of polarized, long-range 4 He 2 (2 3 S 1 -2 3 S 1 ) molecules. They are said to be exotic as they are made of two metastable atoms, each one carrying a enough energy to ionize the other. The corresponding lineshapes are calculated and decomposed in sums and products of Breit-Wigner and Fano profiles associated to one and two photon processes. The experimental spectra are fit, and an intrinsic lifetime τ = (1.4 ± 0.3) μs is deduced. It is checked whether this lifetime could be limited by spin-dipole induced Penning autoionization. This interpretation requires that there is a quasi-bound state close to the dissociation threshold in the singlet interaction potential between metastable helium atoms for the theory to match the experiment. (author)

  7. OMG: Open Molecule Generator.

    Science.gov (United States)

    Peironcely, Julio E; Rojas-Chertó, Miguel; Fichera, Davide; Reijmers, Theo; Coulier, Leon; Faulon, Jean-Loup; Hankemeier, Thomas

    2012-09-17

    Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck.

  8. OMG: Open Molecule Generator

    Directory of Open Access Journals (Sweden)

    Peironcely Julio E

    2012-09-01

    Full Text Available Abstract Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG, which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck.

  9. Singlet oxygen reactivity in water-rich solvent mixtures

    Directory of Open Access Journals (Sweden)

    Cristina Sousa

    2008-01-01

    Full Text Available The 3-methylindole (3MI oxygenation sensitized by psoralen (PSO has been investigated in 100%, 20% and 5% O2-saturated water/dioxane (H2O/Dx mixtures. The lowering of the ¹O2* chemical rate when water (k chem∆3MI = 1.4 × 109 M-1 s-1 is replaced by deuterated water (k chem∆3MI = 1.9 × 108 M-1 s-1 suggests that hydrogen abstraction is involved in the rate determining step. A high dependence of the chemical rate constant on water concentration in H2O/Dx mixtures was found showing that water molecules are absolutely essential for the success of the 3MI substrate oxidation by ¹O2* in water-rich solvent mixtures.

  10. Comparison of Intermolecular Forces in Anhydrous Sorbitol and Solvent Cocrystals.

    Science.gov (United States)

    Dierks, Teresa M; Korter, Timothy M

    2017-08-03

    The hygroscopicity of solid sorbitol is important for its utilization as a sweetener in the pharmaceutical and food industries. The molecular foundations of sorbitol hydration characteristics are explored here using two solvated cocrystals, sorbitol-water and sorbitol-pyridine. In this work, solid-state density functional theory and terahertz time-domain spectroscopy were used to evaluate the relative stabilities of these cocrystals as compared to anhydrous sorbitol in terms of conformational and cohesive energies. The modification of the hydrogen-bonding network in crystalline sorbitol by solvent molecules gives new insight into the origins of the notable stability of sorbitol-water as compared to similar solids such as mannitol-water. In particular, the energy analysis reveals that the relative instability of the mannitol hydrate is based primarily in the lack of water-water interactions which provide considerable stabilization in the sorbitol-water crystal.

  11. Cyclodextrin Films with Fast Solvent Transport and Shape-Selective Permeability

    KAUST Repository

    Villalobos, Luis Francisco

    2017-04-24

    This study describes the molecular-level design of a new type of filtration membrane made of crosslinked cyclodextrins-inexpensive macrocycles of glucose, shaped like hollow truncated cones. The channel-like cavities of cyclodextrins spawn numerous paths of defined aperture in the separation layer that can effectively discriminate between molecules. The transport of molecules through these membranes is highly shape-sensitive. In addition, the presence of hydrophobic (cavity) and hydrophilic (ester-crosslinked outer part) domains in these films results in high permeances for both polar and nonpolar solvents.

  12. Interaction between like-charged colloidal particles in aqueous electrolyte solution: Attractive component arising from solvent granularity

    Directory of Open Access Journals (Sweden)

    R.Akiyama

    2007-12-01

    Full Text Available The potential of mean force (PMF between like-charged colloidal particles immersed in aqueous electrolyte solution is studied using the integral equation theory. Solvent molecules are modeled as neutral hard spheres, and ions and colloidal particles are taken to be charged hard spheres. The Coulomb potentials for ion-ion, ion-colloidal particle, and colloidal particle-colloidal particle pairs are divided by the dielectric constant of water. This simple model is employed to account for the effects of solvent granularity neglected in the so-called primitive model. The van der Waals attraction between colloidal particles, which is an essential constituent of conventional DLVO theory, is omitted in the present model. Nevertheless, when the electrolyte concentration is sufficiently high, attractive regions appear in the PMF. In particular, the interaction at small separations is significantly attractive and the contact of colloidal particles is stabilized. This interesting behavior arises from the effects of the translational motion of solvent molecules.

  13. Characterizing DNA condensation and conformational changes in organic solvents.

    Directory of Open Access Journals (Sweden)

    Fuyou Ke

    Full Text Available Organic solvents offer a new approach to formulate DNA into novel structures suitable for gene delivery. In this study, we examined the in situ behavior of DNA in N, N-dimethylformamide (DMF at low concentration via laser light scattering (LLS, TEM, UV absorbance and Zeta potential analysis. Results revealed that, in DMF, a 21bp oligonucleotide remained intact, while calf thymus DNA and supercoiled plasmid DNA were condensed and denatured. During condensation and denaturation, the size was decreased by a factor of 8-10, with calf thymus DNA forming spherical globules while plasmid DNA exhibited a toroid-like conformation. In the condensed state, DNA molecules were still able to release the counterions to be negatively charged, indicating that the condensation was mainly driven by the excluded volume interactions. The condensation induced by DMF was reversible for plasmid DNA but not for calf thymus DNA. When plasmid DNA was removed from DMF and resuspended in an aqueous solution, the DNA was quickly regained a double stranded configuration. These findings provide further insight into the behavior and condensation mechanism of DNA in an organic solvent and may aid in developing more efficient non-viral gene delivery systems.

  14. Wetting behavior of nonpolar nanotubes in simple dipolar liquids for varying nanotube diameter and solute-solvent interactions

    Energy Technology Data Exchange (ETDEWEB)

    Rana, Malay Kumar; Chandra, Amalendu, E-mail: amalen@iitk.ac.in [Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016 (India)

    2015-01-21

    Atomistic simulations of model nonpolar nanotubes in a Stockmayer liquid are carried out for varying nanotube diameter and nanotube-solvent interactions to investigate solvophobic interactions in generic dipolar solvents. We have considered model armchair type single-walled nonpolar nanotubes with increasing radii from (5,5) to (12,12). The interactions between solute and solvent molecules are modeled by the well-known Lennard-Jones and repulsive Weeks-Chandler-Andersen potentials. We have investigated the density profiles and microscopic arrangement of Stockmayer molecules, orientational profiles of their dipole vectors, time dependence of their occupation, and also the translational and rotational motion of solvent molecules in confined environments of the cylindrical nanopores and also in their external peripheral regions. The present results of structural and dynamical properties of Stockmayer molecules inside and near atomistically rough nonpolar surfaces including their wetting and dewetting behavior for varying interactions provide a more generic picture of solvophobic effects experienced by simple dipolar liquids without any specific interactions such as hydrogen bonds.

  15. [Chemical hazards when working with solvent glues].

    Science.gov (United States)

    Domański, Wojciech; Makles, Zbigniew

    2012-01-01

    Solvent glues are used in a wide variety of industries, e.g., textile, footwear and rubber. The problem of workers' exposure to solvent vapors is rarely tackled within the area of occupational safety and health in small and medium-sized enterprises. In order to assess exposure to solvents, organic solvents emitted by glues were identified in the samples of workplace air. The concentration of acetone, benzene, cyclohexane, ethylbenzene, n-hexane, methylcyclohexane, butyl acetate and toluene were determined. The obtained results evidenced the presence of cyclohexane, ethylbenzene, ethylcyclohexane, heptane, n-hexane, o-xylene, methylcyclohexane, methylcyclopentane, butyl acetate and toluene in workplace air. The concentration of those compounds in workplace air was low, usually below 0.15 of MAC. At some workstations the presence of benzene was also observed. Occupational risk was assessed at workstations where gluing took place. It showed that the risk at those workstations was medium or low.

  16. Organic solvents from sugar cane molasses

    Energy Technology Data Exchange (ETDEWEB)

    Oeser, H

    1970-01-01

    The production of organic solvents by fermentation of low priced cane molasses is discussed. Processes described and illustrated in detail include the production of acetone, butanol, ethanol, acetic acid, ethyl acetate and butyl acetate.

  17. Solvent induced supramolecular anisotropy in molecular gels

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, Michael A., E-mail: mroger09@uoguelph.ca [Department of Food Science, University of Guelph, Guelph, Ontario, N3C3X9 (Canada); Corradini, Maria G. [Department of Food Science, University of Massachusetts Amherst, Amherst, MA, 01003 (United States); Emge, Thomas [Department of Chemistry and Biochemistry, Rutgers University, New Brunswick, NJ, 08901 (United States)

    2017-06-15

    Herein is the first report of solvent induced anisotropy in 12-hydroxystearic acid self-assembled fibrillar networks. Increasing the chain length of polar solvent, such as nitriles and ketones, tailored the anisotropy of the fibrillar aggregates. 12HSA molecular gels, comprised of alkanes, exhibited an isotropic fibrillar network irrespective of the alkane chain length. In polar solvents, anisotropy, observed using 2D powder x-ray diffraction profiles, is correlated to a fibrillar supramolecular morphologies in long chain nitriles and ketones while sphereulitic crystals are correlated to x-ray diffraction patterns with an isotropic scatter intensity in short chain ketones and nitriles. These changes directly modify the final physical properties of the gels. - Highlights: • 12-HSA self-assembles into crystalline supramolecular morphologies depending on the solvent. • Alkanes, short chain nitriles and ketones led to 12-HSA displaying supramolecular isotropy. • In long chain nitriles and ketones, 12-HSA displays supramolecular anisotropy.

  18. Solvent induced supramolecular anisotropy in molecular gels

    International Nuclear Information System (INIS)

    Rogers, Michael A.; Corradini, Maria G.; Emge, Thomas

    2017-01-01

    Herein is the first report of solvent induced anisotropy in 12-hydroxystearic acid self-assembled fibrillar networks. Increasing the chain length of polar solvent, such as nitriles and ketones, tailored the anisotropy of the fibrillar aggregates. 12HSA molecular gels, comprised of alkanes, exhibited an isotropic fibrillar network irrespective of the alkane chain length. In polar solvents, anisotropy, observed using 2D powder x-ray diffraction profiles, is correlated to a fibrillar supramolecular morphologies in long chain nitriles and ketones while sphereulitic crystals are correlated to x-ray diffraction patterns with an isotropic scatter intensity in short chain ketones and nitriles. These changes directly modify the final physical properties of the gels. - Highlights: • 12-HSA self-assembles into crystalline supramolecular morphologies depending on the solvent. • Alkanes, short chain nitriles and ketones led to 12-HSA displaying supramolecular isotropy. • In long chain nitriles and ketones, 12-HSA displays supramolecular anisotropy.

  19. Full scale solvent extraction remedial results

    International Nuclear Information System (INIS)

    Cash, A.B.

    1992-01-01

    Sevenson Extraction Technology, Inc. has completed the development of the Soil Restoration Unit (initially developed by Terra-Kleen Corporation), a mobile, totally enclosed solvent extraction treatment facility for the removal of organic contaminated media is greater by a closed loop, counter current process that recycles all solvents. The solvents used are selected for the individual site dependant upon the contaminants, such as PCB's, oil, etc. and the soil conditions. A mixture of up to fourteen non-toxic solvents can be used for complicated sites. The full scale unit has been used to treat one superfund site, the Traband Site in Tulsa, Oklahoma, and is currently treating another superfund site, the Pinette's Salvage Yard Site in Washburn, Maine. The full scale Soil Restoration Unit has also been used at a non-superfund site, as part of a TSCA Research and Development permit. The results from these sites will be discussed in brief herein, and in more detail in the full paper

  20. Enantioselective solvent-free Robinson annulation reactions

    Indian Academy of Sciences (India)

    Unknown

    solvents to effect an asymmetric synthesis is an important step forward towards ... In continuation of our preliminary communication 2, we wish to ..... formation of chiral enamine 74 from the reaction of S-proline with pro-R carbonyl group.

  1. STUDIES ON SOLVENT EXTRACTION OF FREE HYDROGEN ...

    African Journals Online (AJOL)

    synthesized through glucose degradation (glycolysis) to lactic acid. ... g sample into a well stoppered plastic bottle and mixed with 20 mL of distilled .... Recovery of used solvent is necessary because methylchloroform is toxic to the bacteria.

  2. Green and Bio-Based Solvents.

    Science.gov (United States)

    Calvo-Flores, Francisco G; Monteagudo-Arrebola, María José; Dobado, José A; Isac-García, Joaquín

    2018-04-24

    Chemical reactions and many of the procedures of separation and purification employed in industry, research or chemistry teaching utilize solvents massively. In the last decades, with the birth of Green Chemistry, concerns about the employment of solvents and the effects on human health, as well as its environmental impacts and its dependence on non-renewable raw materials for manufacturing most of them, has drawn the attention of the scientific community. In this work, we review the concept of green solvent and the properties and characteristics to be considered green. Additionally, we discuss the different possible routes to prepare many solvents from biomass, as an alternative way to those methods currently applied in the petrochemical industry.

  3. Activity coefficients of solutes in binary solvents

    International Nuclear Information System (INIS)

    Gokcen, N.A.

    1982-01-01

    The activity coefficients in dilute ternary systems are discussed in detail by using the Margules equations. Analyses of some relevant data at high temperatures show that the sparingly dissolved solutes in binary solvents follow complex behavior even when the binary solvents are very nearly ideal. It is shown that the activity data on the solute or the binary system cannot permit computation of the remaining activities except for the regular solutions. It is also shown that a fourth-order equation is usually adequate in expressing the activity coefficient of a solute in binary solvents at high temperatures. When the activity data for a binary solvent are difficult to obtain in a certain range of composition, the activity data for a sparingly dissolved solute can be used to supplement determination of the binary activities

  4. Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

    Directory of Open Access Journals (Sweden)

    Clarisse Gravina Ricci

    2018-02-01

    Full Text Available Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes.

  5. Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

    Science.gov (United States)

    Ricci, Clarisse Gravina; Li, Bo; Cheng, Li-Tien; Dzubiella, Joachim; McCammon, J. Andrew

    2018-01-01

    Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed) solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes. PMID:29484300

  6. Conformational analysis of glutamic acid: a density functional approach using implicit continuum solvent model.

    Science.gov (United States)

    Turan, Başak; Selçuki, Cenk

    2014-09-01

    Amino acids are constituents of proteins and enzymes which take part almost in all metabolic reactions. Glutamic acid, with an ability to form a negatively charged side chain, plays a major role in intra and intermolecular interactions of proteins, peptides, and enzymes. An exhaustive conformational analysis has been performed for all eight possible forms at B3LYP/cc-pVTZ level. All possible neutral, zwitterionic, protonated, and deprotonated forms of glutamic acid structures have been investigated in solution by using polarizable continuum model mimicking water as the solvent. Nine families based on the dihedral angles have been classified for eight glutamic acid forms. The electrostatic effects included in the solvent model usually stabilize the charged forms more. However, the stability of the zwitterionic form has been underestimated due to the lack of hydrogen bonding between the solute and solvent; therefore, it is observed that compact neutral glutamic acid structures are more stable in solution than they are in vacuum. Our calculations have shown that among all eight possible forms, some are not stable in solution and are immediately converted to other more stable forms. Comparison of isoelectronic glutamic acid forms indicated that one of the structures among possible zwitterionic and anionic forms may dominate over the other possible forms. Additional investigations using explicit solvent models are necessary to determine the stability of charged forms of glutamic acid in solution as our results clearly indicate that hydrogen bonding and its type have a major role in the structure and energy of conformers.

  7. Solvent effects on ion-receptor interactions in the presence of an external electric field.

    Science.gov (United States)

    Novák, Martin; Foroutan-Nejad, Cina; Marek, Radek

    2016-11-09

    In this work we investigated the influence of an external electric field on the arrangement of the solvent shells around ions interacting with a carbon-based receptor. Our survey reveals that the mechanism of interaction between a monoatomic ion and a π-type ion receptor varies by the variation in the solvent polarity, the nature of the ion, and the strength of the external field. The characteristics of the ion-surface interaction in nonpolar solvents are similar to those observed in a vacuum. However, in water, we identified two mechanisms. Soft and polarizable ions preferentially interact with the π-receptor. In contrast, two bonded states were found for hard ions. A fully solvated ion, weakly interacting with the receptor at weak field, and a strong π-complex at the strong-field regime were identified. An abrupt variation in the potential energy surface (PES) associated with the rearrangement of the solvation shell on the surface of the receptor induced by an external field was observed both in implicit and explicit solvent environments. The electric field at which the solvation shell breaks is proportional to the hardness of the ion as has been suggested recently based on experimental observations.

  8. Relationship of the Williams-Poulios and Manning-Rosen Potential Energy Models for Diatomic Molecules

    Science.gov (United States)

    Jia, Chun-Sheng; Liang, Guang-Chuan; Peng, Xiao-Long; Tang, Hong-Ming; Zhang, Lie-Hui

    2014-06-01

    By employing the dissociation energy and the equilibrium bond length for a diatomic molecule as explicit parameters, we generate an improved form of the Williams-Poulios potential energy model. It is found that the negative Williams-Poulios potential model is equivalent to the Manning-Rosen potential model for diatomic molecules. We observe that the Manning-Rosen potential is superior to the Morse potential in reproducing the interaction potential energy curves for the {{a}3 Σu+} state of the 6Li2 molecule and the {{X}1 sum+} state of the SiF+ molecule.

  9. An overview of industrial solvent use or is there life after chlorinated solvents?

    International Nuclear Information System (INIS)

    Green, B.

    1991-01-01

    Everyone using industrial chemicals has been affected by the fire- storm of new regulations governing solvent use. How will companies currently using hazardous solvents prepare for the changes ahead? What will the impact be on commonly used industrial solvents? What effect are environmental pressures having on solvent use and disposal? Are the responsible individuals in your company up-to-date on phase-out schedules? This paper is written for an audience of compliance coordinators, consultants, production engineers and corporate management. In it, the either addresses the above questions and discusses the specific products affected. The author reviews currently available alternatives to chlorinated and hazardous solvents and introduces a simple system for rating alternatives. The program also includes a discussion of solvent minimization programs and worker reeducation

  10. Occupational exposure to solvents and bladder cancer

    DEFF Research Database (Denmark)

    Hadkhale, Kishor; Martinsen, Jan Ivar; Weiderpass, Elisabete

    2017-01-01

    logistic regression model was used to estimate hazard ratios (HR) and their 95% confidence intervals (95% CI). Increased risks were observed for trichloroethylene (HR 1.23, 95% 95% CI 1.12-1.40), toluene (HR 1.20, 95% CI 1.00-1.38), benzene (HR 1.16, 95% CI 1.04-1.31), aromatic hydrocarbon solvents (HR 1...... of occupational exposure to trichloroethylene, perchloroethylene, aromatic hydrocarbon solvents, benzene and toluene and the risk of bladder cancer....

  11. Computer-Aided Solvent Screening for Biocatalysis

    DEFF Research Database (Denmark)

    Abildskov, Jens; Leeuwen, M.B. van; Boeriu, C.G.

    2013-01-01

    constrained properties related to chemical reaction equilibrium, substrate and product solubility, water solubility, boiling points, toxicity and others. Two examples are provided, covering the screening of solvents for lipase-catalyzed transesterification of octanol and inulin with vinyl laurate....... Esterification of acrylic acid with octanol is also addressed. Solvents are screened and candidates identified, confirming existing experimental results. Although the examples involve lipases, the method is quite general, so there seems to be no preclusion against application to other biocatalysts....

  12. Solvent management in a reprocessing plant

    International Nuclear Information System (INIS)

    Guillaume, B.; Germain, M.; Puyou, M.; Rouyer, H.

    1987-01-01

    Solvent management in large capacity reprocessing plant is studied to limit production of organic wastes. Chemical processing increases life time of solvent. Low pressure distillation allows the recycling of TBP and diluent at a low activity level. Besides heavy degradation products are eliminated. For the safety the flash point of distillated diluent increases slightly. Tests on an industrial scale started in 1985 and since more than 500 cubic meters were treated [fr

  13. Effect of high donor number solvent and cathode morphology on interfacial processes in Li-air batteries

    Science.gov (United States)

    Kislenko, S. A.

    2018-01-01

    The work is focused on the investigation of the effect of solvent and carbon cathode morphology on the performance of Li-air batteries. Molecular dynamics simulation was used to explore the interfacial behavior of the main reactants (O2 and Li+) of the oxygen reduction reaction in high donor number solvent dimethyl sulfoxide (DMSO) at the following carbon surfaces: graphene plane, graphene edge, nanotube. It was shown that the adsorption barrier of O2 molecules decreases in the order graphene plane > nanotube > graphene edge, leading to the fastest adsorption kinetics on graphene edges. Strong solvation of Li+ in DMSO prevents ions adsorption on defect-free graphene planes and nanotubes, which is qualitatively different from low donor number solvents, such as acetonitrile. It can be concluded from these results, that nucleation and growth of discharge products in DMSO is shifted from the surface towards the solvent bulk that, in turn, leads to capacity increase of Li-air batteries.

  14. The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank

    OpenAIRE

    Westbrook, John D.; Shao, Chenghua; Feng, Zukang; Zhuravleva, Marina; Velankar, Sameer; Young, Jasmine

    2014-01-01

    Summary: The Chemical Component Dictionary (CCD) is a chemical reference data resource that describes all residue and small molecule components found in Protein Data Bank (PDB) entries. The CCD contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, chemical descriptors, systematic chemical names and idealize...

  15. Study on infrared multiphoton excitation of the linear triatomic molecule by the Lie-algebra approach

    International Nuclear Information System (INIS)

    Feng, H.; Zheng, Y.; Ding, S.

    2007-01-01

    Infrared multiphoton vibrational excitation of the linear triatomic molecule has been studied using the quadratic anharmonic Lie-algebra model, unitary transformations, and Magnus approximation. An explicit Lie-algebra expression for the vibrational transition probability is obtained by using a Lie-algebra approach. This explicit Lie-algebra expressions for time-evolution operator and vibrational transition probabilities make the computation clearer and easier. The infrared multiphoton vibrational excitation of the DCN linear tri-atomic molecule is discussed as an example

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

    Science.gov (United States)

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

    2016-09-13

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

  17. Hazardous Solvent Substitution Data System reference manual

    International Nuclear Information System (INIS)

    Branham-Haar, K.A.; Twitchell, K.E.

    1993-07-01

    Concern for the environment, in addition to Federal regulation, mandate the replacement of hazardous solvents with safer cleaning agents. Manufacturers are working to produce these replacement solvents. As these products are developed, potential users need to be informed of their availability. To promote the use of these new products instead of traditional solvents, the Idaho National Engineering Laboratory (INEL) has developed the Hazardous Solvent Substitution Data System (HSSDS). The HSSDS provides a comprehensive system of information on alternatives to hazardous solvents and related subjects, and it makes that information available to solvent users, industrial hygienists, and process engineers. The HSSDS uses TOPIC reg-sign, a text retrieval system produced by Verity, Inc., to allow a user to search for information on a particular subject. TOPIC reg-sign produces a listing of the retrieved documents and allows the use to examine the documents individually and to use the information contained in them. This reference manual does not replace the comprehensive TOPIC reg-sign user documentation (available from Verity, Inc.), or the HSSDS Tutorial (available from the INEL). The purpose of this reference manual is to provide enough instruction on TOPIC reg-sign so the user may begin accessing the data contained in the HSSDS

  18. Caustic-Side Solvent Extraction: Chemical and Physical Properties of the Optimized Solvent

    Energy Technology Data Exchange (ETDEWEB)

    Delmau, L.H.

    2002-10-08

    This work was undertaken to optimize the solvent used in the Caustic Side Solvent Extraction (CSSX) process and to measure key chemical and physical properties related to its performance in the removal of cesium from the alkaline high-level salt waste stored in tanks at the Savannah River Site. The need to adjust the solvent composition arose from the prior discovery that the previous baseline solvent was supersaturated with respect to the calixarene extractant. The following solvent-component concentrations in Isopar{reg_sign} L diluent are recommended: 0.007 M calix[4]arene-bis(tert-octylbenzo-crown-6) (BOBCalixC6) extractant, 0.75 M 1-(2,2,3,3-tetrafluoropropoxy)-3-(4-sec-butylphenoxy)-2-propanol (Cs-7SB) phase modifier, and 0.003 M tri-n-octylamine (TOA) stripping aid. Criteria for this selection included BOBCalixC6 solubility, batch cesium distribution ratios (D{sub Cs}), calculated flowsheet robustness, third-phase formation, coalescence rate (dispersion numbers), and solvent density. Although minor compromises within acceptable limits were made in flowsheet robustness and solvent density, significant benefits were gained in lower risk of third-phase formation and lower solvent cost. Data are also reported for the optimized solvent regarding the temperature dependence of D{sub Cs} in extraction, scrubbing, and stripping (ESS); ESS performance on recycle; partitioning of BOBCalixC6, Cs-7SB, and TOA to aqueous process solutions; partitioning of organic anions; distribution of metals; solvent phase separation at low temperatures; solvent stability to elevated temperatures; and solvent density and viscosity. Overall, the technical risk of the CSSX process has been reduced by resolving previously identified issues and raising no new issues.

  19. Interaction forces between nanoparticles in Lennard-Jones (L-J) solvents

    International Nuclear Information System (INIS)

    Sinha, Indrajit; Mukherjee, Ashim K

    2014-01-01

    Molecular simulations, such as Monte Carlo (MC) and molecular dynamics (MD) have been recently used for understanding the forces between colloidal nanoparticles that determine the dispersion and stability of nanoparticle suspensions. Herein we review the current status of research in the area of nanoparticles immersed in L-J solvents. The first study by Shinto et al. used large smooth spheres to depict nanoparticles in L-J and soft sphere solvents. The nanoparticles were held fixed at a particular interparticle distance and only the solvents were allowed to equilibrate. Both Van-der-waals and solvation forces were computed at different but fixed interparticle separation. Later Qin and Fitchthorn improved on this model by considering the nanoparticles as collection of molecules, thus taking into the account the effect of surface roughness of nanoparticles. Although the inter particle distance was fixed, the rotation of such nanoparticles with respect to each other was also investigated. Recently, in keeping with the experimental situation, we modified this model by allowing the nanoparticles to move and rotate freely. Solvophilic, neutral and solvophobic interactions between the solvent atoms and those that make up the nanoparticles were modelled. While neutral and solvophobic nanoparticles coalesce even at intermediate distances, solvophilic nanoparticles are more stable in solution due to the formation of a solvent shield

  20. Investigating the solvent and temperature effects on the cyclohexadienyl radical in an ionic liquid

    International Nuclear Information System (INIS)

    Taylor, Becky; Cormier, P.J.; Lauzon, J.M.; Ghandi, Khashayar

    2009-01-01

    The cyclohexadienyl radical was studied in a novel green solvent; tetradecyl (trihexyl) phosphonium chloride ionic liquid (IL 101). Both the solvent effects and how the hyperfine coupling changes with respect to temperature have been examined and compared to literature. This was done through experimental muon techniques at the TRIUMF National Laboratory in Canada as well as through ab initio calculations. The ionic liquid solvent effects were found to be consistent with other solvents, when assuming ionic liquids to be a combination of ion pairs. In ionic liquid the hyperfine coupling constants of the proton and reduced muon decreased linearly with increasing temperature. The analysis showed that the majority of this relationship is due to a vibrational effect, although the solvent density plays a role too. The temperature effect on the entropy of the system was determined to be negligible. The temperature coefficient of the reduced muon hyperfine coupling was larger than that of the proton in IL 101 due to the effects of nearby ionic liquid molecules.

  1. Investigating the solvent and temperature effects on the cyclohexadienyl radical in an ionic liquid

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, Becky; Cormier, P.J.; Lauzon, J.M. [Department of Chemistry, Mount Allison University, Sackville, New Brunswick, E4L 1G3 (Canada); Ghandi, Khashayar, E-mail: kghandi@mta.c [Department of Chemistry, Mount Allison University, Sackville, New Brunswick, E4L 1G3 (Canada)

    2009-04-15

    The cyclohexadienyl radical was studied in a novel green solvent; tetradecyl (trihexyl) phosphonium chloride ionic liquid (IL 101). Both the solvent effects and how the hyperfine coupling changes with respect to temperature have been examined and compared to literature. This was done through experimental muon techniques at the TRIUMF National Laboratory in Canada as well as through ab initio calculations. The ionic liquid solvent effects were found to be consistent with other solvents, when assuming ionic liquids to be a combination of ion pairs. In ionic liquid the hyperfine coupling constants of the proton and reduced muon decreased linearly with increasing temperature. The analysis showed that the majority of this relationship is due to a vibrational effect, although the solvent density plays a role too. The temperature effect on the entropy of the system was determined to be negligible. The temperature coefficient of the reduced muon hyperfine coupling was larger than that of the proton in IL 101 due to the effects of nearby ionic liquid molecules.

  2. Thermodynamics of 4’-bromomethyl-2-cyanobiphenyl in different solvents

    International Nuclear Information System (INIS)

    Yang, Jingxiang; Wu, Hong; Wang, Yongli; Luan, Qinghua; Zhang, Jie; Wang, Guan; Hao, Hongxun

    2015-01-01

    Highlights: • The melting properties of OTBNBr were investigated. • The solubility of OTBNBr in eight selected organic solvents has been determined. • The interaction of solvents molecules plays a dominated role in the dissolving behavior. • The experimental solubility data in pure solvents were well correlated by four models. • The activity coefficient and temperature dependence of van’t Hoff enthalpy were investigated. - Abstract: The melting properties and the heat capacity of the solid state and the melt state 4’-bromomethyl-2-cyanobiphenyl (OTBNBr) were determined. The enthalpy, entropy and Gibbs free energy of fusion were also calculated. The solubility of OTBNBr in eight organic solvents was experimentally measured at temperatures from (283.15 to 323.15) K by using a static method. The reasons for the differences of the solubility of OTBNBr in various solvents are discussed by using the intermolecular interaction. Furthermore, the experimental solubility values were well correlated by the modified Apelblat equation, the λh equation, the Wilson model and the van’t Hoff equation. Finally, the temperature dependence of the activity coefficient and the van’t Hoff enthalpy in the tested solutions was investigated and is discussed

  3. Characterization and antioxidant activity of bovine serum albumin and sulforaphane complex in different solvent systems

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Xueyan; Zhou, Rui; Jing, Hao, E-mail: h200521@cau.edu.cn

    2014-02-15

    Modes and influencing factors of bovine serum albumin (BSA) and sulforaphane (SFN) interaction will help us understand the interaction mechanisms and functional changes of bioactive small molecule and biomacromolecule. This study investigated interaction mechanisms of BSA and SFN and associated antioxidant activity in three solvent systems of deionized water (dH{sub 2}O), dimethyl sulfoxide (DMSO) and ethanol (EtOH), using Fourier transform infrared spectroscopy (FT-IR), fluorescence spectroscopy, synchronous fluorescence spectroscopy, DPPH and ABTS radical scavenging assays. The results revealed that SFN had ability to quench BSA's fluorescence in static modes, and to interact with BSA at both tyrosine (Tyr) and tryptophan (Trp) residues, while the Trp residues were highly sensitive, which was demonstrated by fluorescence at 340 nm. Hydrophobic forces, hydrogen bonds and van der Waals interactions were all involved in BSA and SFN interaction, which were not significantly changed by three solvents. The binding constant values and binding site numbers were in a descending order of dH{sub 2}O>DMSO>EtOH. The values of free energy change were in a descending order of dH{sub 2}O>DMSO>EtOH, which indicated that the binding forces were in a descending order of dH{sub 2}O>DMSO>EtOH. There was no significant difference in antioxidant activity between SFN and BSA–SFN. Moreover, three solvents had not significant influence on antioxidant activity of SFN and BSA–SFN. -- Highlights: • We report interaction mechanisms of BSA and sulforaphane in three solvent systems. • We report antioxidant activity of BSA–sulforaphane complex in three solvent systems. • Decreasing the solvent polarity will decrease the binding of BSA and sulforaphane. • Three solvents had not influence on antioxidant activity of BSA–sulforaphane.

  4. Single-Molecule Nanomagnets

    Science.gov (United States)

    Friedman, Jonathan R.; Sarachik, Myriam P.

    2010-04-01

    Single-molecule magnets straddle the classical and quantum mechanical worlds, displaying many fascinating phenomena. They may have important technological applications in information storage and quantum computation. We review the physical properties of two prototypical molecular nanomagnets, Mn12-acetate and Fe8: Each behaves as a rigid, spin-10 object and exhibits tunneling between up and down directions. As temperature is lowered, the spin-reversal process evolves from thermal activation to pure quantum tunneling. At low temperatures, magnetic avalanches occur in which the magnetization of an entire sample rapidly reverses. We discuss the important role that symmetry-breaking fields play in driving tunneling and in producing Berry-phase interference. Recent experimental advances indicate that quantum coherence can be maintained on timescales sufficient to allow a meaningful number of quantum computing operations to be performed. Efforts are under way to create monolayers and to address and manipulate individual molecules.

  5. Superexcited states of molecules

    International Nuclear Information System (INIS)

    Nakamura, Hiroki; Takagi, Hidekazu.

    1990-01-01

    The report addresses the nature and major features of molecule's superexcited states, focusing on their involvement in dynamic processes. It also outlines the quantum defect theory which allows various processes involving these states to be treated in a unified way. The Rydberg state has close relation with an ionized state with a positive energy. The quantum defect theory interprets such relation. Specifically, the report first describes the quantum defect theory focusing on its basic principle. The multi-channel quantum defect theory is then outlined centering on how to describe a Rydberg-type superexcited state. Description of a dissociative double-electron excited state is also discussed. The quantum defect theory is based on the fact that the physics of the motion of a Rydberg electron vary with the region in the electron's coordinate space. Finally, various molecular processes that involve a superexcited state are addressed focusing on autoionization, photoionization, dissociative recombination and bonding ionization of diatomic molecules. (N.K.)

  6. Modeling the Dispersibility of Single Walled Carbon Nanotubes in Organic Solvents by Quantitative Structure-Activity Relationship Approach

    Science.gov (United States)

    Yilmaz, Hayriye; Rasulev, Bakhtiyor; Leszczynski, Jerzy

    2015-01-01

    The knowledge of physico-chemical properties of carbon nanotubes, including behavior in organic solvents is very important for design, manufacturing and utilizing of their counterparts with improved properties. In the present study a quantitative structure-activity/property relationship (QSAR/QSPR) approach was applied to predict the dispersibility of single walled carbon nanotubes (SWNTs) in various organic solvents. A number of additive descriptors and quantum-chemical descriptors were calculated and utilized to build QSAR models. The best predictability is shown by a 4-variable model. The model showed statistically good results (R2training = 0.797, Q2 = 0.665, R2test = 0.807), with high internal and external correlation coefficients. Presence of the X0Av descriptor and its negative term suggest that small size solvents have better SWCNTs solubility. Mass weighted descriptor ATS6m also indicates that heavier solvents (and small in size) most probably are better solvents for SWCNTs. The presence of the Dipole Z descriptor indicates that higher polarizability of the solvent molecule increases the solubility. The developed model and contributed descriptors can help to understand the mechanism of the dispersion process and predictorganic solvents that improve the dispersibility of SWNTs. PMID:28347035

  7. Modeling the Dispersibility of Single Walled Carbon Nanotubes in Organic Solvents by Quantitative Structure-Activity Relationship Approach

    Directory of Open Access Journals (Sweden)

    Hayriye Yilmaz

    2015-05-01

    Full Text Available The knowledge of physico-chemical properties of carbon nanotubes, including behavior in organic solvents is very important for design, manufacturing and utilizing of their counterparts with improved properties. In the present study a quantitative structure-activity/property relationship (QSAR/QSPR approach was applied to predict the dispersibility of single walled carbon nanotubes (SWNTs in various organic solvents. A number of additive descriptors and quantum-chemical descriptors were calculated and utilized to build QSAR models. The best predictability is shown by a 4-variable model. The model showed statistically good results (R2training = 0.797, Q2 = 0.665, R2test = 0.807, with high internal and external correlation coefficients. Presence of the X0Av descriptor and its negative term suggest that small size solvents have better SWCNTs solubility. Mass weighted descriptor ATS6m also indicates that heavier solvents (and small in size most probably are better solvents for SWCNTs. The presence of the Dipole Z descriptor indicates that higher polarizability of the solvent molecule increases the solubility. The developed model and contributed descriptors can help to understand the mechanism of the dispersion process and predictorganic solvents that improve the dispersibility of SWNTs.

  8. Effect of Solvent Additives on the Solution Aggregation of Phenyl-C61-Butyl Acid Methyl Ester (PCBM)

    KAUST Repository

    Tummala, Naga Rajesh

    2015-11-24

    High-boiling-point solvent additives, employed during the solution processing of active-layer formulations, impact the efficiency of bulk hetero-junction (BHJ) organic solar cells by influencing the morphological / topological features of the multicomponent thin film. Here, we aim at a better understanding of how these additives change the aggregation landscape in the casting solution prior to film deposition via a multi-scale computational study of the aggregation phenomena of phenyl-C61-butyric-acid methyl ester (PCBM) in various solutions. The energetic landscape of PCBM-solvent / solvent-additive intermolecular interactions is evaluated at the electronic-structure level through symmetry-adapted perturbation theory to determine the nature and strength of non-covalent forces important to aggregation. Molecular dynamics simulations highlight how the choice of solvent and solvent additives control the formation of molecular aggregates. Our results indicate that high-boiling-point solvent additives change the effective interactions among the PCBM and casting-solvent molecules and alter the equilibrium PCBM aggregate sizes in solution.

  9. AGOA: A Hydration Procedure and Its Application to the 1-Phenyl-beta-Carboline Molecule

    OpenAIRE

    Hernandes, Marcelo Z.; Silva, João B. P. da; Longo, Ricardo L.

    2002-01-01

    A new procedure, named AGOA, has been developed and implemented in a computer program written in FORTRAN 77 to explore the hydration structures of polar solutes using its molecular electrostatic potential (MEP). This procedure can be generalized to polar solvents other than water. It has been tested for several small molecules, and applied to complex molecules of pharmacological interest, such as the beta-carbolinic systems derived from indole. This is a stringent, but not general, test of th...

  10. Atoms, molecules & elements

    CERN Document Server

    Graybill, George

    2007-01-01

    Young scientists will be thrilled to explore the invisible world of atoms, molecules and elements. Our resource provides ready-to-use information and activities for remedial students using simplified language and vocabulary. Students will label each part of the atom, learn what compounds are, and explore the patterns in the periodic table of elements to find calcium (Ca), chlorine (Cl), and helium (He) through hands-on activities.

  11. Molecular modeling study of agglomeration of [6,6]-phenyl-C61-butyric acid methyl ester in solvents.

    Science.gov (United States)

    Mortuza, S M; Banerjee, Soumik

    2012-12-28

    The molecular interactions between solvent and nanoparticles during photoactive layer formation in organic photovoltaic (OPV) cells influence the morphology of the photoactive layer and hence determine the power conversion efficiency. Prediction of optimal synthesis parameters in OPVs, such as choice of solvent, processing temperature, and nanoparticle concentration, requires fundamental understanding of the mechanisms that govern the agglomeration of nanoparticles in solvents. In this study, we used molecular dynamics simulations to simulate a commonly used organic nanoparticle, [6,6]-phenyl-C61-butyric acid methyl ester (PCBM), in various solvents to correlate solvent-nanoparticle interactions with the size of the agglomerate structure of PCBM. We analyzed the effects of concentration of PCBM and operating temperature on the molecular rearrangement and agglomeration of PCBM in three solvents: (i) toluene, (ii) indane, and (iii) toluene-indane mixture. We evaluated the agglomeration behavior of PCBM by determining sizes of the largest clusters of PCBM and the corresponding size distributions. To obtain further insight into the agglomerate structure of PCBMs, we evaluated radial distribution functions (RDFs) and coordination numbers of the various moieties of PCBMs with respect to solvent atoms as well as with respect to that of other PCBMs. Our simulations demonstrate that PCBMs form larger clusters in toluene while they are relatively dispersed in indane, which indicates the greater solubility of PCBM in indane than in toluene. In toluene-indane mixture, PCBMs are clustered to a greater extent than in indane and less than that in toluene. To correlate agglomerate size to nanoparticle-solvent interactions, we also evaluated the potential of mean force (PMF) of the fullerene moiety of PCBM in toluene and indane. Our results also show that the cluster size of PCBM molecules increases with the increase of concentration of PCBM and the processing temperature. To

  12. Photonic Molecule Lasers Revisited

    Science.gov (United States)

    Gagnon, Denis; Dumont, Joey; Déziel, Jean-Luc; Dubé, Louis J.

    2014-05-01

    Photonic molecules (PMs) formed by coupling two or more optical resonators are ideal candidates for the fabrication of integrated microlasers, photonic molecule lasers. Whereas most calculations on PM lasers have been based on cold-cavity (passive) modes, i.e. quasi-bound states, a recently formulated steady-state ab initio laser theory (SALT) offers the possibility to take into account the spectral properties of the underlying gain transition, its position and linewidth, as well as incorporating an arbitrary pump profile. We will combine two theoretical approaches to characterize the lasing properties of PM lasers: for two-dimensional systems, the generalized Lorenz-Mie theory will obtain the resonant modes of the coupled molecules in an active medium described by SALT. Not only is then the theoretical description more complete, the use of an active medium provides additional parameters to control, engineer and harness the lasing properties of PM lasers for ultra-low threshold and directional single-mode emission. We will extend our recent study and present new results for a number of promising geometries. The authors acknowledge financial support from NSERC (Canada) and the CERC in Photonic Innovations of Y. Messaddeq.

  13. Interstellar molecules and masers

    International Nuclear Information System (INIS)

    Nguyen-Q-Rieu; Guibert, J.

    1978-01-01

    The study of dense and dark clouds, in which hydrogen is mostly in molecular form, became possible since the discovery of interstellar molecules, emitting in the centimeter and millimeter wavelengths. The molecular lines are generally not in local thermal equilibrium (LTE). Their intensity can often be explained by invoking a population inversion mechanism. Maser emission lines due to OH, H 2 O and SiO molecules are among the most intense molecular lines. The H 2 CO molecule, detected in absorption in front of the cold cosmic background radiation of 2.7 K, illustrates the inverse phenomenon, the antimaser absorption. For a radio transition of frequency v, the inversion rate Δn (relative population difference between the upper and lower level) as well as the maser gain can be determined from the radio observations. In the case of the OH lines in the 2 PIsub(3/2), J=3/2 state, the inversion rates approximately 1 to 2% derived from the observations, are comparable with those obtained in the laboratory. The determination of the excitation mechanisms of the masers, through the statistical equilibrium and radiative transfer equations, implies the knowledge of collisional and radiative transition probabilities. A pumping model, which can satisfactorily explain the radio observations of some interstellar OH clouds, will be discussed [fr

  14. Solvent-Dependent Self-Assembly of 4,7-Dibromo-5,6-bis(octyloxybenzo[c][1,2,5] Thiadiazole on Graphite Surface by Scanning Tunneling Microscopy

    Directory of Open Access Journals (Sweden)

    Bao Zha

    2013-01-01

    Full Text Available Solvent effect on self-assembly of 4,7-dibromo-5,6-bis(octyloxybenzo[c][1,2,5] thiadiazole (DBT on a highly oriented graphite (HOPG surface was investigated by scanning tunneling microscopy (STM by using 1-phenyloctane, 1-octanoic acid, and 1-octanol as the solvents. Two different patterns were obtained in 1-phenyloctane and 1-octanoic acid, suggesting that the self-assembly of DBT was solvent dependent. At the 1-phenyloctane/HOPG interface, a linear structure was revealed due to the intermolecular halogen bonding. When 1-octanoic acid and 1-octanol are used as the solvents, the coadsorption of solvent molecules resulting from the hydrogen bonding between DBT and solvent made an important contribution to the formation of a lamellar structure. The results demonstrate that solvents could affect the molecular self-assembly according to the variational intermolecular interactions.

  15. Synthesis of single-molecule nanocars.

    Science.gov (United States)

    Vives, Guillaume; Tour, James M

    2009-03-17

    p-carborane- and ruthenium-based wheels with greater solubility in organic solvents. Although fullerene wheels must be attached in the final synthetic step, p-carborane- and ruthenium-based wheels do not inhibit organometallic coupling reactions, which allows a more convergent synthesis of molecular machines. We also prepared functional nanotrucks for the transport of atoms and molecules, as well as self-assembling nanocars and nanotrains. Although engineering challenges such as movement over long distance and non-atomically flat surfaces remain, the greatest current research challenge is imaging. The detailed study of nanocars requires complementary single molecule imaging techniques such as STM, AFM, TEM, or single-molecule fluorescence microscopy. Further developments in engineering and synthesis could lead to enzyme-like manipulation and assembly of atoms and small molecules in nonbiological environments.

  16. Post monitoring of a cyclodextrin remeditated chlorinated solvent contaminated aquifer

    Science.gov (United States)

    Blanford, W. J.

    2006-12-01

    Hydroxypropyl-â-cyclodextrin (HPâCD) has been tested successfully in the laboratory and in the field for enhanced flushing of low-polarity contaminants from aquifers. The cyclodextrin molecule forms a toroidal structure, which has a hydrophobic cavity. Within this cavity, organic compounds of appropriate shape and size can form inclusion complexes, which is the basis for the use of cyclodextrin in groundwater remediation. The hydrophilic exterior of the molecule makes cyclodextrin highly water-soluble. The solubility of cyclodextrins can be further enhanced by adding functional groups, such as hydroxypropyl groups, to the cyclodextrin core. The aqueous solubility of HPâCD exceeds 950 g/L. These high solubilities are advantageous for field applications because they permit relatively high concentrations of the flushing agent. In order for cyclodextrin to become a feasible remediative alternative, it must be demonstrate a short term resistance to biodegradation during field application, but ultimately biodegrade so as not to pose a long term presence in the aquifer. The potential for degradation of cyclodextrin as well as changes in the chlorinated solvents and groundwater geochemistry were examined during the post monitoring of a field demonstration in a shallow aquifer at Little Creek Naval Amphibious Base in Virginia. It was found that a portion of the cyclodextrin remaining in the aquifer after the cessation of field activities biodegraded during the 425 days of post monitoring. This degradation also led to the degradation of the chlorinated solvents trichloroethylene and 1,1-trichloroethane through both biological and chemical processes. The aquifer remained anaerobic with average dissolved oxygen levels below 0.5 mg/L. Dissolved nitrate and sulfate concentrations within the cyclodextrin plume decreased due their being used as terminal electron acceptors during the degradation of the cyclodextrin. The concentrations of total iron at the field site showed no

  17. EdgeMaps: visualizing explicit and implicit relations

    Science.gov (United States)

    Dörk, Marian; Carpendale, Sheelagh; Williamson, Carey

    2011-01-01

    In this work, we introduce EdgeMaps as a new method for integrating the visualization of explicit and implicit data relations. Explicit relations are specific connections between entities already present in a given dataset, while implicit relations are derived from multidimensional data based on shared properties and similarity measures. Many datasets include both types of relations, which are often difficult to represent together in information visualizations. Node-link diagrams typically focus on explicit data connections, while not incorporating implicit similarities between entities. Multi-dimensional scaling considers similarities between items, however, explicit links between nodes are not displayed. In contrast, EdgeMaps visualize both implicit and explicit relations by combining and complementing spatialization and graph drawing techniques. As a case study for this approach we chose a dataset of philosophers, their interests, influences, and birthdates. By introducing the limitation of activating only one node at a time, interesting visual patterns emerge that resemble the aesthetics of fireworks and waves. We argue that the interactive exploration of these patterns may allow the viewer to grasp the structure of a graph better than complex node-link visualizations.

  18. Insight of solvent extraction process: Reassessment of trace level determinations

    Energy Technology Data Exchange (ETDEWEB)

    Chandramouleeswaran, S. [Analytical Chemistry Division, Bhabha Atomic Research Centre, Mumbai, 400094 (India); Ramkumar, Jayshree, E-mail: jrk@barc.gov.in [Analytical Chemistry Division, Bhabha Atomic Research Centre, Mumbai, 400094 (India); Basu, M. [Chemistry Division, Bhabha Atomic Research Centre, Mumbai, 400094 (India)

    2016-09-28

    Solvent extraction is hoary yet modern technique with great scope of research due to the various intriguing phenomena in the system. Tri-n-butyl phosphate (TBP) is a well known extractant which has been extensively used for separation of uranium matrix prior to elemental profiling. In this paper, one of the impurities namely Fe is being considered as it posed a challenge to the separation due to its co-extraction with TBP along with uranium. In these studies, for the first time, the existence of cation-cation inner sphere complexes between the UO{sub 2}{sup 2+}and Fe{sup 3+} ions in both aqueous and organic phases have been establisted in addition to the selective separation of iron from uranium sample matrix using only TBP. The data from both spectrophotometric and thermophysical studies corroborated one another confirming the presence of cation-cation interactions (CCIs). The developed solvent extraction with only TBP showed almost no interferences on the iron extraction from matrix uranium and other co-ions like aluminum and copper. This has been the first time application of pure TBP for selective removal of iron from uranium samples. The procedure possessed excellent reproducibility and robustness. - Graphical abstract: Spectrophotometric studies indicate a possibility of cation-cation inner sphere complex formation between the ions (UO{sub 2}{sup 2+} and Fe{sup 3+}) in aqueous phase to a great extent but it is reduced in the organic phase due to the solvation of ions by TBP molecules. These results are corroborated by those of thermophysical studies. Solvent extraction procedure suitably modified to ensure selective and complete removal of iron from uranium matrix prior to its analysis by ICP-OES. The developed methodology was applied to analysis of uranium samples. - Highlights: • The presence of cation – cation inner sphere complexes between UO{sub 2}{sup 2+} and Fe{sup 3+} established. • A decreased tendency in organic layer due to TBP solvation.

  19. Morphology versus vertical phase segregation in solvent annealed small molecule bulk heterojunction organic solar cells

    Czech Academy of Sciences Publication Activity Database

    Kovalenko, A.; Stoyanova, V.; Pospisil, J.; Zhivkov, I.; Fekete, Ladislav; Karashanova, D.; Kratochvílová, Irena; Vala, M.; Weiter, M.

    2015-01-01

    Roč. 2015, Oct (2015), s. 238981 ISSN 1110-662X R&D Projects: GA ČR(CZ) GA15-05095S; GA TA ČR TA04020156; GA MŠk LO1409 Institutional support: RVO:68378271 Keywords : organic solar cells Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.226, year: 2015

  20. Cyanide single-molecule magnets exhibiting solvent dependent reversible "on" and "off" exchange bias behavior

    DEFF Research Database (Denmark)

    Pinkowicz, Dawid; Southerland, Heather I.; Avendaño, Carolina

    2015-01-01

    The syntheses, structures, and magnetic properties of four new complex salts, (PPN){[Mn(III)(salphen)(MeOH)]2[M(III)(CN)6]}·7MeOH (Mn2M·7MeOH) (M = Fe, Ru, Os and Co; PPN(+) = bis(triphenylphosphoranylidene)ammonium cation; H2salphen = N,N'-bis(salicylidene)-1,2-diaminobenzene), and a mixed metal...