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Sample records for chemistry solvation dynamics

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

    Energy Technology Data Exchange (ETDEWEB)

    Wishart, J.F.

    2011-06-12

    Ionic liquids (ILs) are a rapidly expanding family of condensed-phase media with important applications in energy production, nuclear fuel and waste processing, improving the efficiency and safety of industrial chemical processes, and pollution prevention. ILs generally have low volatilities and are combustion-resistant, highly conductive, recyclable and capable of dissolving a wide variety of materials. They are finding new uses in chemical synthesis, catalysis, separations chemistry, electrochemistry and other areas. Ionic liquids have dramatically different properties compared to conventional molecular solvents, and they provide a new and unusual environment to test our theoretical understanding of primary radiation chemistry, charge transfer and other reactions. We are interested in how IL properties influence physical and dynamical processes that determine the stability and lifetimes of reactive intermediates and thereby affect the courses of reactions and product distributions. We study these issues by characterization of primary radiolysis products and measurements of their yields and reactivity, quantification of electron solvation dynamics and scavenging of electrons in different states of solvation. From this knowledge we wish to learn how to predict radiolytic mechanisms and control them or mitigate their effects on the properties of materials used in nuclear fuel processing, for example, and to apply IL radiation chemistry to answer questions about general chemical reactivity in ionic liquids that will aid in the development of applications listed above. Very early in our radiolysis studies it became evident that the slow solvation dynamics of the excess electron in ILs (which vary over a wide viscosity range) increase the importance of pre-solvated electron reactivity and consequently alter product distributions and subsequent chemistry. This difference from conventional solvents has profound effects on predicting and controlling radiolytic yields

  2. IONIC LIQUIDS: RADIATION CHEMISTRY, SOLVATION DYNAMICS AND REACTIVITY PATTERNS

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

  4. IONIC LIQUIDS: RADIATION CHEMISTRY, SOLVATION DYNAMICS AND REACTIVITY PATTERNS.

    Energy Technology Data Exchange (ETDEWEB)

    WISHART,J.F.

    2007-10-01

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

  5. Ionic liquids: radiation chemistry, solvation dynamics and reactivity patterns

    International Nuclear Information System (INIS)

    Ionic liquids (ILs) are a rapidly expanding family of condensed-phase media with important applications in energy production, nuclear fuel and waste processing, improving the efficiency and safety of industrial chemical processes, and pollution prevention. ILs are nonvolatile, noncombustible, highly conductive, recyclable and capable of dissolving a wide variety of materials. They are finding new uses in chemical synthesis, catalysis, separations chemistry, electrochemistry and other areas. Ionic liquids have dramatically different properties compared to conventional molecular solvents, and they provide a new and unusual environment to test our theoretical understanding of charge transfer and other reactions. We are interested in how IL properties influence physical and dynamical processes that determine the stability and lifetimes of reactive intermediates and thereby affect the courses of chemical reactions and product distributions. Successful use of ionic liquids in radiation-filled environments, where their safety advantages could be significant, requires an understanding of ionic liquid radiation chemistry. For example, characterizing the primary steps of IL radiolysis will reveal radiolytic degradation pathways and suggest ways to prevent them or mitigate their effects on the properties of the material. An understanding of ionic liquid radiation chemistry will also facilitate pulse radiolysis studies of general chemical reactivity in ILs, which will aid in the development of energy production, chemical industry and environmental applications. Pulse radiolysis of [R4N][NTf2] [R4N][N(CN)2], and [R4P][N(CN)2] ionic liquids produces solvated electrons that absorb over a broad range in the near infrared and persisting for hundreds of nanoseconds. Systematic cation variation shows that solvated electron's spectroscopic properties depend strongly on the lattice structure of the ionic liquid. Very early in our radiolysis studies it became evident that slow solvation

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

    Science.gov (United States)

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

    2016-07-01

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

  7. Femtosecond resolved solvation dynamics in polar solvents

    Science.gov (United States)

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

    1989-01-01

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

  8. Solvation!

    Energy Technology Data Exchange (ETDEWEB)

    Ivana Adamovic

    2004-12-19

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

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

    Science.gov (United States)

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

    2015-10-01

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

  10. Solvation dynamics of lithium salts in wet nitrobenzene

    Czech Academy of Sciences Publication Activity Database

    Moakes, G.; Gelbaum, L. T.; Leisen, J.; Janata, J.; Mareček, Vladimír

    2006-01-01

    Roč. 593, 1-2 (2006), s. 111-118. ISSN 0022-0728 R&D Projects: GA ČR GA203/03/0822 Grant ostatní: Georgia Research Alliance(US) GRA.CG06.D Institutional research plan: CEZ:AV0Z40400503 Keywords : solvation * NMR * FTIR * nitrobenzene/water * solvatomers Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.339, year: 2006

  11. Ultrafast solvation dynamics at internal site of staphylococcal nuclease investigated by site-directed mutagenesis

    CERN Document Server

    Guang-yu, Gao; Wei, Wang; Shu-feng, Wang; Zhong, Dongping; Qi-huang, Gong

    2014-01-01

    Solvation is essential for protein activities. To study internal solvation of protein, site-directed mutagenesis is applied. Intrinsic fluorescent probe, tryptophan, is inserted into desired position inside protein molecule for ultrafast spectroscopic study. Here we review this unique method for protein dynamics researches. We introduce the frontiers of protein solvation, site-directed mutagenesis, protein stability and characteristics, and the spectroscopic methods. Then we present time-resolved spectroscopic dynamics of solvation dynamics inside caves of active sites. The studies are carried out on a globular protein, staphylococcal nuclease. The solvation at internal sites of the caves indicate clear characteristics of local environment. These solvation behaviors correlated to the enzyme activity directly.

  12. I. Cognitive and instructional factors relating to students' development of personal models of chemical systems in the general chemistry laboratory II. Solvation in supercritical carbon dioxide/ethanol mixtures studied by molecular dynamics simulation

    Science.gov (United States)

    Anthony, Seth

    likely to appear in students' post-laboratory refined models. These discussions during the laboratory period are primarily prompted by factors external to the students or their laboratory groups such as questions posed by the instructor or laboratory materials. Part II. Solvation of polar molecules within non-polar supercritical carbon dioxide is often facilitated by the introduction of polar cosolvents as entrainers, which are believed to preferentially surround solute molecules. Molecular dynamics simulations of supercritical carbon dioxide/ethanol mixtures reveal that ethanol molecules form hydrogen-bonded aggregates of varying sizes and structures, with cyclic tetramers and pentamers being unusually prevalent. The dynamics of ethanol molecules within these mixtures at a range of thermodynamic conditions can largely be explained by differences in size and structure in these aggregates. Simulations that include solute molecules reveal enhancement of the polar cosolvent around hydrogen-bonding sites on the solute molecules, corroborating and helping to explain previously reported experimental trends in solute mobility.

  13. Solvation dynamics of biomolecules: modeling and terahertz experiments.

    Science.gov (United States)

    Leitner, David M; Gruebele, Martin; Havenith, Martina

    2008-12-01

    The role of water in biomolecule dynamics has attracted much interest over the past decade, due in part to new probes of biomolecule-water interactions and developments in molecular simulations. Terahertz (THz) spectroscopy, among the most recent experimental methods brought to bear on this problem, is able to detect even small solute induced changes of the collective water network dynamics at the biomolecule-water interface. THz measurements reveal that proteins influence up to 1000 water molecules in their surroundings, and that even small saccharides influence the dynamics of hundreds of surrounding water molecules. The THz spectrum of a protein is sensitive to mutation and depends on the surface charge and flexibility of the protein. Influence on the solvation shell appears most pronounced for native wildtype proteins and decreases upon partial unfolding or mutation. THz spectra of solvated saccharides reveal that the number of water molecules coupled dynamically to a saccharide, forming a dynamical hydration shell around it, is related to the number of exposed oxygen atoms on the solute. The thickness of this layer appears correlated with the bioprotection efficiency of the saccharide. All findings support the thesis of a long-range dynamic coupling between biomolecule and solvent. PMID:19436490

  14. Ultrafast Solvation Dynamics of Subtilisin-Polyethylene Glycol Interaction for Protein Crystallization

    Institute of Scientific and Technical Information of China (English)

    DING Qing; MENG Geng; WANG Shu-Feng; ZHENG Xiao-Feng; YANG Hong; GONG Qi-Huang

    2011-01-01

    We study the ultrafast solvation dynamics of protein-precipitant complexes. Protein subtilisin carlsberg (SC) was mixed with several polyethylene glycol (PEG) precipitants for protein crystallization. Picosecond-resolved emission spectra from single intrinsic tryptophan residue (Trp-113) are recorded to construct solvation correlation functions. For precipitant concentrations with various crystallization effects, we observe drastically different solvation relaxation processes. These differences in solvation dynamics are correlated with the local protein structural integrity and water-network stability upon interaction with the precipitants. The solvation dynamics at the protein surface is proposed as a new perspective to study precipitant-protein interactions.%@@ We study the ultrafast solvation dynamics of protein-precipitant complexes.Protein subtilisin earlsberg (SC) was mixed with several polyethylene glycol (PEG) precipitants for protein crystallization.Picosecond-resolved emission spectra from single intrinsic tryptophan residue (Trp-113) are recorded to construct solvation correlation functions.For precipitant concentrations with various crystallization effects, we observe drastically different solvation relaxation processes.These differences in solvation dynamics are correlated with the local protein structural integrity and water-network stability upon interaction with the precipitants.The solvation dynamics at the protein surface is proposed as a new perspective to study precipitant-protein interactions.

  15. Quantum Chemistry for Solvated Molecules on Graphical Processing Units (GPUs)using Polarizable Continuum Models

    CERN Document Server

    Liu, Fang; Kulik, Heather J; Martínez, Todd J

    2015-01-01

    The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale biomolecular systems can be limited by computational expense of both the gas phase electronic structure and the solvation interaction. We have previously used graphical processing units (GPUs) to accelerate the first of these steps. Here, we extend the use of GPUs to accelerate electronic structure calculations including C-PCM solvation. Implementation on the GPU leads to significant acceleration of the generation of the required integrals for C-PCM. We further propose two strategies to improve the solution of the required linear equations: a dynamic convergence threshold and a randomized block-Jacobi preconditioner. These strategies are not specific to GPUs and are expected to be beneficial for both CPU and GPU implementations. We benchmark the performance of the new implementat...

  16. Quantum Chemistry for Solvated Molecules on Graphical Processing Units Using Polarizable Continuum Models.

    Science.gov (United States)

    Liu, Fang; Luehr, Nathan; Kulik, Heather J; Martínez, Todd J

    2015-07-14

    The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale biomolecular systems can be limited by computational expense of both the gas phase electronic structure and the solvation interaction. We have previously used graphical processing units (GPUs) to accelerate the first of these steps. Here, we extend the use of GPUs to accelerate electronic structure calculations including C-PCM solvation. Implementation on the GPU leads to significant acceleration of the generation of the required integrals for C-PCM. We further propose two strategies to improve the solution of the required linear equations: a dynamic convergence threshold and a randomized block-Jacobi preconditioner. These strategies are not specific to GPUs and are expected to be beneficial for both CPU and GPU implementations. We benchmark the performance of the new implementation using over 20 small proteins in solvent environment. Using a single GPU, our method evaluates the C-PCM related integrals and their derivatives more than 10× faster than that with a conventional CPU-based implementation. Our improvements to the linear solver provide a further 3× acceleration. The overall calculations including C-PCM solvation require, typically, 20-40% more effort than that for their gas phase counterparts for a moderate basis set and molecule surface discretization level. The relative cost of the C-PCM solvation correction decreases as the basis sets and/or cavity radii increase. Therefore, description of solvation with this model should be routine. We also discuss applications to the study of the conformational landscape of an amyloid fibril. PMID:26575750

  17. Competitive lithium solvation of linear and cyclic carbonates from quantum chemistry.

    Science.gov (United States)

    Borodin, Oleg; Olguin, Marco; Ganesh, P; Kent, Paul R C; Allen, Joshua L; Henderson, Wesley A

    2016-01-01

    The composition of the lithium cation (Li(+)) solvation shell in mixed linear and cyclic carbonate-based electrolytes has been re-examined using Born-Oppenheimer molecular dynamics (BOMD) as a function of salt concentration and cluster calculations with ethylene carbonate:dimethyl carbonate (EC:DMC)-LiPF6 as a model system. A coordination preference for EC over DMC to a Li(+) was found at low salt concentrations, while a slightly higher preference for DMC over EC was found at high salt concentrations. Analysis of the relative binding energies of the (EC)n(DMC)m-Li(+) and (EC)n(DMC)m-LiPF6 solvates in the gas-phase and for an implicit solvent (as a function of the solvent dielectric constant) indicated that the DMC-containing Li(+) solvates were stabilized relative to (EC4)-Li(+) and (EC)3-LiPF6 by immersing them in the implicit solvent. Such stabilization was more pronounced in the implicit solvents with a high dielectric constant. Results from previous Raman and IR experiments were reanalyzed and reconciled by correcting them for changes of the Raman activities, IR intensities and band shifts for the solvents which occur upon Li(+) coordination. After these correction factors were applied to the results of BOMD simulations, the composition of the Li(+) solvation shell from the BOMD simulations was found to agree well with the solvation numbers extracted from Raman experiments. Finally, the mechanism of the Li(+) diffusion in the dilute (EC:DMC)LiPF6 mixed solvent electrolyte was studied using the BOMD simulations. PMID:26601903

  18. Molecular dynamics study of the solvation of an alpha-helical transmembrane peptide by DMSO

    NARCIS (Netherlands)

    Duarte, A.M.; Mierlo, van C.P.M.; Hemminga, M.A.

    2008-01-01

    10-ns molecular dynamics study of the solvation of a hydrophobic transmembrane helical peptide in dimethyl sulfoxide (DMSO) is presented. The objective is to analyze how this aprotic polar solvent is able to solvate three groups of amino acid residues (i.e., polar, apolar, and charged) that are loca

  19. XI International conference Problems of solvation and complex formation in solutions, and VI Conference of young scientists Theoretical and experimental chemistry of liquid-phase systems (Krestovsky readings). Summary of reports

    International Nuclear Information System (INIS)

    The collection contains materials of plenary, sectional and poster sessions, presented at the XI International conference Problems of solvation and complex formation in solutions, and VI Conference of young scientists Theoretical and experimental chemistry of liquid-phase systems (Krestovsky readings). Theoretical questions and new experimental methods of chemistry of solutions, structure and dynamics of molecular and ion-molecular systems in solution and at the phase boundary; modern aspects of applied chemistry of solutions are discussed

  20. Dynamic Combinatorial Chemistry

    DEFF Research Database (Denmark)

    Lisbjerg, Micke

    This thesis is divided into seven chapters, which can all be read individually. The first chapter, however, contains a general introduction to the chemistry used in the remaining six chapters, and it is therefore recommended to read chapter one before reading the other chapters. Chapter 1...... is a general introductory chapter for the whole thesis. The history and concepts of dynamic combinatorial chemistry are described, as are some of the new and intriguing results recently obtained. Finally, the properties of a broad range of hexameric macrocycles are described in detail. Chapter 2 gives...

  1. Solvation of sodium octanoate micelles in concentrated urea solution studied by means of molecular dynamics simulations.

    Science.gov (United States)

    de Moura, André Farias; Bernardino, Kalil; de Oliveira, Osmair Vital; Freitas, Luiz Carlos Gomide

    2011-12-15

    The effects of urea on self-assembling remains a challenging topic on surface chemistry, and computational modeling may have a role on the unraveling of the molecular mechanisms underlying these effects. Bearing that in mind, we performed a set of molecular dynamics simulations to assess the effects of urea on the self-assembling properties of sodium octanoate, an anionic surfactant, as compared to the aggregation of the same surfactant in pure water as the solvent. The concentration of free monomers increased 3-fold in the presence of urea, in agreement with the accepted view that urea should increase monomer solubility. Regarding the size distribution of micellar aggregates, the urea solution favored smaller micelles and a narrower distribution. Preferential solvation by either water or urea changed along the surfactant molecules, from urea-rich shells around apolar atoms at the end of the hydrophobic tails to nearly no urea at the polar headgroups. This solvation profile is consistent with two different hypotheses from the literature: on one hand, urea molecules interact directly with apolar atoms from the hydrophobic tails, acting as a surfactant, and on the other hand the presence of urea molecules increases the hydration of polar sites. Another important observation regards the solvent structure, which exhibits a complex composition profile around both water and urea molecules. Although the solvent structure was appreciably different in each case, the free energy calculations for the dissociation of a pair of octanoate molecules pointed to a purely enthalpic free energy loss in urea solution, a finding that does not lend support to the third hypothesis that is often claimed as accounting for the urea effects, namely, that urea disrupts water structure and that this structural change decreases the hydrophobic effect due to an entropy change. The presence of urea had no significant effect on the molecular structure of the surfactant molecules, although it

  2. Femtosecond solvation dynamics in a neat ionic liquid and ionic liquid microemulsion: excitation wavelength dependence.

    Science.gov (United States)

    Adhikari, Aniruddha; Sahu, Kalyanasis; Dey, Shantanu; Ghosh, Subhadip; Mandal, Ujjwal; Bhattacharyya, Kankan

    2007-11-01

    Solvation dynamics in a neat ionic liquid, 1-pentyl-3-methyl-imidazolium tetra-flouroborate ([pmim][BF4]) and its microemulsion in Triton X-100 (TX-100)/benzene is studied using femtosecond up-conversion. In both the neat ionic liquid and the microemulsion, the solvation dynamics is found to depend on excitation wavelength (lambda(ex)). The lambda(ex) dependence is attributed to structural heterogeneity in neat ionic liquid (IL) and in IL microemulsion. In neat IL, the heterogeneity arises from clustering of the pentyl groups which are surrounded by a network of cation and anions. Such a nanostructural organization is predicted in many recent simulations and observed recently in an X-ray diffraction study. In an IL microemulsion, the surfactant (TX-100) molecules aggregate in form of a nonpolar peripheral shell around the polar pool of IL. The micro-environment in such an assembly varies drastically over a short distance. The dynamic solvent shift (and average solvation time) in neat IL as well as in IL microemulsions decreases markedly as lambda(ex) increases from 375 to 435 nm. In a [pmim][BF4]/water/TX-100/benzene quaternary microemulsion, the solvation dynamics is slower than that in a microemulsion without water. This is ascribed to the smaller size of the water containing microemulsion. The anisotropy decay in an IL microemulsion is found to be faster than that in neat IL. PMID:17944511

  3. [Experimental and computation studies of polar solvation

    International Nuclear Information System (INIS)

    This report from the Pennsylvania State University contains seven sections: (1) radiative rate effects in solvatlvatochromic probes; (2) intramolecular charge transfer reactions; (3) Solvation dynamics in low temperature alcohols; (4) Ionic solvation dynamics; (5) solvation and proton-transfer dynamics in 7-azaindole; (6) computer simulations of solvation dynamics; (7) solvation in supercritical fluids. 20 refs., 11 figs

  4. Observing Solvation Dynamics with Simultaneous Femtosecond X-ray Emission Spectroscopy and X-ray Scattering

    DEFF Research Database (Denmark)

    Haldrup, Kristoffer; Gawelda, Wojciech; Abela, Rafael;

    2016-01-01

    and structural changes, and local solvent structural changes are desired. We have studied the intra- and intermolecular dynamics of a model chromophore, aqueous [Fe(bpy)3]2+, with complementary X-ray tools in a single experiment exploiting intense XFEL radiation as a probe. We monitored the ultrafast structural...... solute. By simultaneous combination of both methods only, we can extract new information about the solvation dynamic processes unfolding during the first picosecond (ps). The measured bulk solvent density increase of 0.2% indicates a dramatic change of the solvation shell around each photoexcited solute......, confirming previous ab initio molecular dynamics simulations. Structural changes in the aqueous solvent associated with density and temperature changes occur with similar to 1 ps time constants, characteristic for structural dynamics in water. This slower time scale of the solvent response allows us...

  5. Quantum solvation dynamics of HCN in a helium-4 droplet

    International Nuclear Information System (INIS)

    Ultracold nanodroplets of helium-4, containing several thousands of He atoms, offer considerable promise as microscopic cryogenic chambers. Potential applications include the creation of tailor-made chemical or biomolecular complexes and studies of superfluidity in nanoscale systems. Recent experiments have succeeded in interrogating droplets of quantum solvent which consist of as few as 1-20 helium-4 atoms and which contain a single solute molecule. This allows the transition from a floppy, but essentially molecular, complex to a dissolved molecule to be followed and, surprisingly, the transition is found to occur quite rapidly, in some cases for as few as N=7-20 solvent atoms. For example, in experiments on helium-4 droplets seeded with CO molecules [Tang and McKellar, J. Chem. Phys. 119, 754 (2003)], two series of transitions are observed which correlate with the a-type (ΔK=0) and b-type (ΔK=±1) lines of the binary complex, CO-He (K is the quantum number associated with the projection of the total angular momentum onto the vector connecting the atom and the molecular center of mass). The a-type series, which evolves from the end-over-end rotational motion of the CO-He binary complex, saturates to the nanodroplet limit for as few as 10-15 helium-4 atoms, i.e., the effective moment of inertia of the molecule converges to its asymptotic (solvated) value quite rapidly. In contrast, the b-type series, which evolves from the free-molecule rotational mode, disappears altogether for N≅7 atoms. Similar behavior is observed in recent computational studies of HCN(4He)N droplets [Paolini et al., J. Chem. Phys. 123, 114306 (2005)]. In this article the quantum solvation of HCN in small helium-4 droplets is studied using a new fixed-node diffusion Monte Carlo (DMC) procedure. In this approach a Born-Oppenheimer-type separation of radial and angular motions is introduced as a means of computing nodal surfaces of the many-body wave functions which are required in the fixed

  6. Picosecond solvation dynamics--a potential viewer of DMSO-water binary mixtures.

    Science.gov (United States)

    Banik, Debasis; Kundu, Niloy; Kuchlyan, Jagannath; Roy, Arpita; Banerjee, Chiranjib; Ghosh, Surajit; Sarkar, Nilmoni

    2015-02-01

    In this work, we have investigated the composition dependent anomalous behavior of dimethyl sulfoxide (DMSO)-water binary mixture by collecting the ultrafast solvent relaxation response around a well known solvation probe Coumarin 480 (C480) by using a femtosecond fluorescence up-conversion spectrometer. Recent molecular dynamics simulations have predicted two anomalous regions of DMSO-water binary mixture. Particularly, these studies encourage us to investigate the anomalies from experimental background. DMSO-water binary mixture has repeatedly given evidences of its dual anomalous nature in front of our systematic investigation through steady-state and time-resolved measurements. We have calculated average solvation times of C480 by two individual well-known methods, among them first one is spectral-reconstruction method and another one is single-wavelength measurement method. The results of both the methods roughly indicate that solvation time of C480 reaches maxima in the mole fraction of DMSO XD = 0.12-0.17 and XD = 0.27-0.35, respectively. Among them, the second region (XD = 0.27-0.35) is very common as most of the thermodynamic properties exhibit deviation in this range. Most probably, the anomalous solvation trend in this region is fully guided by the shear viscosity of the medium. However, the first region is the most interesting one. In this region due to formation of strongly hydrogen bonded 1DMSO:2H2O complexes, hydration around the probe C480 decreases, as a result of which solvation time increases. PMID:25662652

  7. Solvated Positron Chemistry. Competitive Positron Reactions with Halide Ions in Water

    DEFF Research Database (Denmark)

    Christensen, Palle; Pedersen, Niels Jørgen; Andersen, J. R.;

    1979-01-01

    It is shown by means of the angular correlation technique that the binding of positrons to halides is strongly influenced by solvation effects. For aqueous solutions we find increasing values for the binding energies between the halide and the positron with increasing mass of the halide. This is...

  8. Solvation thermodynamics

    CERN Document Server

    Ben-Naim, Arieh

    1987-01-01

    This book deals with a subject that has been studied since the beginning of physical chemistry. Despite the thousands of articles and scores of books devoted to solvation thermodynamics, I feel that some fundamen­ tal and well-established concepts underlying the traditional approach to this subject are not satisfactory and need revision. The main reason for this need is that solvation thermodynamics has traditionally been treated in the context of classical (macroscopic) ther­ modynamics alone. However, solvation is inherently a molecular pro­ cess, dependent upon local rather than macroscopic properties of the system. Therefore, the starting point should be based on statistical mechanical methods. For many years it has been believed that certain thermodynamic quantities, such as the standard free energy (or enthalpy or entropy) of solution, may be used as measures of the corresponding functions of solvation of a given solute in a given solvent. I first challenged this notion in a paper published in 1978 b...

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

    Science.gov (United States)

    Schmollngruber, Michael; Schröder, Christian; Steinhauser, Othmar

    2013-05-01

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

  10. Dynamic Processes in Prochiral Solvating Agents (pro-CSAs Studied by NMR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Jan Labuta

    2014-05-01

    Full Text Available Several dynamic processes, including tautomerism and macrocyclic inversion, in 1H-NMR prochiral solvating agents (pro-CSAs are investigated. Various features of pro-CSA, including modes of interaction for complex formation, stoichiometry, binding strength and temperature effects were compared for three representative pro-CSA molecules. Structural effects of conjugated tetrapyrrole pro-CSA on the mechanism of enantiomeric excess determination are also discussed. Detailed analysis of species (complexes and dynamic processes occurring in solution and their 1H-NMR spectral manifestations at various temperatures is presented.

  11. The Aqueous Solvation of Water A Comparison of Continuum Methods with Molecular Dynamics

    CERN Document Server

    Rick, S W; Rick, Steven W.

    1994-01-01

    The calculation of the solvation properties of a single water molecule in liquid water is carried out in two ways. In the first, the water molecule is placed in a cavity and the solvent is treated as a dielectric continuum. This model is analyzed by numerically solving the Poisson equation using the DelPhi program. The resulting solvation properties depend sensitively on the shape and size of the cavity. In the second method, the solvent and solute molecules are treated explicitly in molecular dynamics simulations using Ewald boundary conditions. We find a 2 kcal/mole difference in solvation free energies predicted by these two methods when standard cavity radii are used. In addition, dielectric continuum theory assumes that the solvent reacts solely by realigning its electric moments linearly with the strength of the solute's electric field; the results of the molecular simulation show important non-linear effects. Non-linear solvent effects are generally of two types: dielectric saturation, due to solvent-s...

  12. Ultrafast UV photon echo peak shift and fluorescence up conversion studies of non-polar solvation dynamics

    International Nuclear Information System (INIS)

    We present photon echo peak shift and femtosecond fluorescence up-conversion studies of non-polar solvation dynamics of a simple non-polar dye p-terphenyl in ethanol and cyclohexane, using excitation in the UV range at 290 nm. The UV fluorescence up-conversion experiments were combined with a polychromatic detection and the results highlight the high sensitivity of this approach to fully characterize the excited state dynamics of the dye. We also demonstrate the feasibility of UV photon echo and transient grating and its sensitivity for the detection of non-polar solvation dynamics by measuring the frequency correlation function of the dye in the ground state. While solvation dynamics in the picosecond regime is observed in ethanol, electronic coherence dephasing occurs on timescales faster than 100 fs in ethanol as well as in the non-polar solvent cyclohexane

  13. Ultrafast UV photon echo peak shift and fluorescence up conversion studies of non-polar solvation dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Oskouei, A. Ajdarzadeh; Braem, O.; Cannizzo, A.; Mourik, F. van; Tortschanoff, A. [Ecole Polytechnique Federale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, FSB, BSP CH-1015 Lausanne (Switzerland); Chergui, M. [Ecole Polytechnique Federale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, FSB, BSP CH-1015 Lausanne (Switzerland)], E-mail: Majed.Chergui@epfl.ch

    2008-06-23

    We present photon echo peak shift and femtosecond fluorescence up-conversion studies of non-polar solvation dynamics of a simple non-polar dye p-terphenyl in ethanol and cyclohexane, using excitation in the UV range at 290 nm. The UV fluorescence up-conversion experiments were combined with a polychromatic detection and the results highlight the high sensitivity of this approach to fully characterize the excited state dynamics of the dye. We also demonstrate the feasibility of UV photon echo and transient grating and its sensitivity for the detection of non-polar solvation dynamics by measuring the frequency correlation function of the dye in the ground state. While solvation dynamics in the picosecond regime is observed in ethanol, electronic coherence dephasing occurs on timescales faster than 100 fs in ethanol as well as in the non-polar solvent cyclohexane.

  14. Simulated solvation of organic ions: protonated methylamines in water nanodroplets. Convergence toward bulk properties and the absolute proton solvation enthalpy.

    Science.gov (United States)

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

    2014-06-12

    We applied an alternative, purely theoretical route to estimate thermodynamical properties of organic ions in bulk solution. The method performs a large ensemble of simulations of ions solvated in water nanodroplets of different sizes, using a polarizable molecular dynamics approach. We consider protonated ammonia and methylamines, and K(+) for comparison, solvated in droplets of 50-1000 water molecules. The parameters of the model are assigned from high level quantum computations of small clusters. All the bulk phase results extrapolated from droplet simulations match, and confirm independently, the relative and absolute experiment-based ion solvation energies. Without using experiment-based parameters or assumptions, the results confirm independently the solvation enthalpy of the proton, as -270.3 ± 1.1 kcal mol(-1). The calculated relative solvation enthalpies of these ions are constant from small water clusters, where only the ionic headgroups are solvated, up to bulk solution. This agrees with experimental thermochemistry, that the relative solvation energies of alkylammonium ions by only four H2O molecules reproduce the relative bulk solvation energies, although the small clusters lack major bulk solvation factors. The droplet results also show a slow convergence of ion solvation properties toward their bulk limit, and predict that the stepwise solvation enthalpies of ion/water droplets are very close to those of pure neutral water droplets already after 50 water molecules. Both the ionic and neutral clusters approach the bulk condensation energy very gradually up to 10,000 water molecules, consistent with the macroscopic liquid drop model for pure water droplets. Compared to standard computational methods based on infinite periodic systems, our protocol represents a new purely theoretical approach to investigate the solvation properties of ions. It is applicable to the solvation of organic ions, which are pivotal in environmental, industrial, and

  15. Solvation Structure and Dynamics of Ni(2+)(aq) from First Principles.

    Science.gov (United States)

    Mareš, Jiří; Liimatainen, Helmi; Laasonen, Kari; Vaara, Juha

    2011-09-13

    The aqueous solution of Ni(2+) was investigated using first principles molecular dynamics (FPMD) simulation based on periodic density-functional theory (DFT) calculations. The experimental structural parameters of the Ni(aq) complex are reproduced well by the simulation. An exchange event of the water molecule in the first solvation shell is observed, supporting the proposed dissociative mechanism of exchange. The calculated dynamic characteristics of the surrounding water molecules indicate too slow translational diffusion in comparison to experimental results, in agreement with other FPMD studies employing a similar level of theory. We also find that the reorientational dynamics of water are an order of magnitude slower as compared to experimental data. On the other hand, the angular momentum dynamics are in better agreement with the experimental data than the previously reported results from MD simulations employing empirical force fields. The obtained MD trajectory can supply accurate structures for the calculation of magnetic properties. PMID:26605483

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

    Science.gov (United States)

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

    2010-04-01

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

  17. On the origin of the anomalous ultraslow solvation dynamics in heterogeneous environments

    Indian Academy of Sciences (India)

    Kankan Bhattacharyya; Biman Bagchi

    2007-03-01

    Many recent experimental studies have reported a surprising ultraslow component (even >10 ns) in the solvation dynamics of a polar probe in an organized assembly, the origin of which is not understood at present. Here we propose two molecular mechanisms in explanation. The first one involves the motion of the `buried water’ molecules (both translation and rotation), accompanied by cooperative relaxation (‘local melting’) of several surfactant chains. An estimate of the time is obtained by using an effective Rouse chain model of chain dynamics, coupled with a mean first passage time calculation. The second explanation invokes self-diffusion of the (di)polar probe itself from a less polar to a more polar region. This may also involve cooperative motion of the surfactant chains in the hydrophobic core, if the probe has a sizeable distribution inside the core prior to excitation, or escape of the probe to the bulk from the surface of the self-assembly. The second mechanism should result in the narrowing of the full width of the emission spectrum with time, which has indeed been observed in recent experiments. It is argued that both the mechanisms may give rise to an ultraslow time constant and may be applicable to different experimental situations. The effectiveness of solvation as a dynamical probe in such complex systems has been discussed.

  18. Solvation Dynamics in Different Phases of the Lyotropic Liquid Crystalline System.

    Science.gov (United States)

    Roy, Bibhisan; Satpathi, Sagar; Gavvala, Krishna; Koninti, Raj Kumar; Hazra, Partha

    2015-09-01

    Reverse hexagonal (HII) liquid crystalline material based on glycerol monooleate (GMO) is considered as a potential carrier for drugs and other important biomolecules due to its thermotropic phase change and excellent morphology. In this work, the dynamics of encapsulated water, which plays important role in stabilization and formation of reverse hexagonal mesophase, has been investigated by time dependent Stokes shift method using Coumarin-343 as a solvation probe. The formation of the reverse hexagonal mesophase (HII) and transformation to the L2 phase have been monitored using small-angle X-ray scattering and polarized light microscopy experiments. REES studies suggest the existence of different polar regions in both HII and L2 systems. The solvation dynamics study inside the reverse hexagonal (HII) phase reveals the existence of two different types of water molecules exhibiting dynamics on a 120-900 ps time scale. The estimated diffusion coefficients of both types of water molecules obtained from the observed dynamics are in good agreement with the measured diffusion coefficient collected from the NMR study. The calculated activation energy is found to be 2.05 kcal/mol, which is associated with coupled rotational-translational water relaxation dynamics upon the transition from "bound" to "quasi-free" state. The observed ∼2 ns faster dynamics of the L2 phase compared to the HII phase may be associated with both the phase transformation as well as thermotropic effect on the relaxation process. Microviscosities calculated from time-resolved anisotropy studies infer that the interface is almost ∼22 times higher viscous than the central part of the cylinder. Overall, our results reveal the unique dynamical features of water inside the cylinder of reverse hexagonal and inverse micellar phases. PMID:26258397

  19. Ab Initio Molecular Dynamics Study of Aqueous Solvation of Ethanol and Ethylene

    CERN Document Server

    Van Erp, T S; Erp, Titus S. van; Meijer, Evert Jan

    2002-01-01

    The structure and dynamics of aqueous solvation of ethanol and ethylene are studied by DFT-based Car-Parrinello molecular dynamics. We did not find an enhancement of the structure of the hydrogen bonded network of hydrating water molecules. Both ethanol and ethylene can easily be accommodated in the hydrogen-bonded network of water molecules without altering its structure. This is supports the conclusion from recent neutron diffraction experiments that there is no hydrophobic hydration around small hydrophobic groups. Analysis of the electronic charge distribution using Wannier functions shows that the dipole moment of ethanol increases from 1.8 D to 3.1 D upon solvation, while the apolar ethylene molecule attains an average dipole moment of 0.5 D. For ethylene, we identified configurations with $\\pi$-H bonded water molecules, that have rare four-fold hydrogen-bonded water coordination, yielding instantaneous dipole moments of ethylene of up to 1 D. The results provide valuable information for the improvement...

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

    Science.gov (United States)

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

    2016-09-01

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

  1. Dynamics of solvation and desolvation of rubidium attached to He nanodroplets

    CERN Document Server

    von Vangerow, J; Stienkemeier, andF; Mudrich, M

    2015-01-01

    The real-time dynamics of photoexcited and photoionized rubidium (Rb) atoms attached to helium (He) nanodroplets is studied by femtosecond pump-probe mass spectrometry. While excited Rb atoms in the perturbed 6p-state (Rb*) desorb off the He droplets, Rb^+ photoions tend to sink into the droplet interior when created near the droplet surface. The transition from Rb^+ solvation to full Rb* desorption is found to occur at a delay time t~600 fs for Rb* in the 6pSigma-state and t~1200 fs for the 6pPi-state. Rb^+He ions are found to be created by directly exciting bound Rb*He exciplex states as well as by populating bound Rb^+He-states in an photoassociative ionization process.

  2. A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water

    Science.gov (United States)

    Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul

    2016-03-01

    The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a "first-principles" DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.

  3. A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water.

    Science.gov (United States)

    Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul

    2016-03-21

    The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a "first-principles" DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand. PMID:27004884

  4. Dynamics of forest soil chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Alveteg, M.

    1998-11-01

    Acidification caused by emissions of nitrogen and sulphur and associated adverse effects on forest ecosystems has been an issue on the political agenda for decades. Temporal aspects of soil acidification and/or recovery can be investigated using the soil chemistry model SAFE, a dynamic version of the steady-state model PROFILE used in critical loads assessment on the national level, e.g. for Sweden. In this thesis, possibilities to replace the use of apparent gibbsite solubility coefficients with a more mechanistic Al sub-model are investigated and a reconstruction model, MAKEDEP, is presented which makes hindcasts and forecasts of atmospheric deposition and nutrient uptake and cycling. A regional application of SAFE/MAKEDEP based on 622 sites in Switzerland is also presented. It is concluded that the quantitative information on pools and fluxes of Al in forest ecosystems is very limited and that there currently exists no mechanistic alternative in modelling soil solution Al. MAKEDEP is a valuable and operational tool for deriving input to dynamic soil chemistry models such as SMART, MAGIC and SAFE. For multi-layer models, e.g. the SAFE model, including nutrient cycling in MAKEDEP is shown to be important. The strength of the regional assessment strategy presented in this thesis lies in its transparency and modularity. All sub-modules, including models, transfer functions, assumptions in the data acquisition strategy, etc., can be checked and replaced individually. As the presented assessment strategy is based on knowledge and data from a wide range of scientists and fields it is of vital importance that the research community challenge the assumptions made. The many measurable intermediate results produced by the included models will hopefully encourage scientists to challenge the models through additional measurements at the calculation sites. It is concluded that current reduction plans are not sufficient for all forest ecosystems in Switzerland to recover from

  5. Free Energy Barriers for the N-Terminal Asparagine to Succinimide Conversion: Quantum Molecular Dynamics Simulations for the Fully Solvated Model.

    Science.gov (United States)

    Kaliman, Ilya; Nemukhin, Alexander; Varfolomeev, Sergei

    2010-01-12

    Deamidation of asparagine residues represents one of the main routes for the post-translational modification of protein sequences. We computed the estimates of the free energy barriers for three stages of the deamidation process, deprotonation, cyclization, and deamination, of the conversion of asparagine to the succinimide intermediate within the fully solvated model with explicit water molecules. The Born-Oppenheimer molecular dynamics in the Gaussian and Plane Wave (GPW) approximation as implemented in the CP2K quantum chemistry package was utilized to sample the configurational space. By applying the metadynamics technique, the estimates of the free energy barriers were obtained for three separated stages of the reaction. In agreement with the experimental kinetic measurements, the estimated activation barriers do not exceed 21 kcal/mol. We demonstrate that the use of fully solvated models is the critical issue in theoretical studies of these reactions. We also conclude that more extensive sampling is necessary to obtain full free energy profiles and accurate barriers for the reaction stages. PMID:26614331

  6. A coordination chemistry study of hydrated and solvated cationic vanadium ions in oxidation states +III, +IV, and +V in solution and solid state.

    Science.gov (United States)

    Krakowiak, Joanna; Lundberg, Daniel; Persson, Ingmar

    2012-09-17

    The coordination chemistry of hydrated and solvated vanadium(III), oxovanadium(IV), and dioxovanadium(V) ions in the oxygen-donor solvents water, dimethyl sulfoxide (DMSO), and N,N'-dimethylpropyleneurea (DMPU) has been studied in solution by extended X-ray absorption fine structure (EXAFS) and large-angle X-ray scattering (LAXS) and in the solid state by single-crystal X-ray diffraction and EXAFS. The hydrated vanadium(III) ion has a regular octahedral configuration with a mean V-O bond distance of 1.99 Å. In the hydrated and DMSO-solvated oxovanadium(IV) ions, vanadium binds strongly to an oxo group at ca. 1.6 Å. The solvent molecule trans to the oxo group is very weakly bound, at ca. 2.2 Å, while the remaining four solvent molecules, with a mean V-O bond distance of 2.0 Å, form a plane slightly below the vanadium atom; the mean O═V-O(perp) bond angle is ca. 98°. In the DMPU-solvated oxovanadium(IV) ion, the space-demanding properties of the DMPU molecule leave no solvent molecule in the trans position to the oxo group, which reduces the coordination number to 5. The O═V-O bond angle is consequently much larger, 107°, and the mean V═O and V-O bond distances decrease to 1.58 and 1.97 Å, respectively. The hydrated and DMSO-solvated dioxovanadium(V) ions display a very distorted octahedral configuration with the oxo groups in the cis position with a mean V═O bond distance of 1.6 Å and a O═V═O bond angle of ca. 105°. The solvent molecules trans to the oxo groups are weakly bound, at ca. 2.2 Å, while the remaining two have bond distances of 2.02 Å. The experimental studies of the coordination chemistry of hydrated and solvated vanadium(III,IV,V) ions are complemented by summarizing previously reported crystal structures to yield a comprehensive description of the coordination chemistry of vanadium with oxygen-donor ligands. PMID:22950803

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

    Science.gov (United States)

    Chaban, Vitaly V; Prezhdo, Oleg V

    2016-03-10

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

  8. Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

    Science.gov (United States)

    Carnevale, V.; Raugei, S.

    2009-12-01

    Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

  9. Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

    International Nuclear Information System (INIS)

    Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

  10. Ultrafast vectorial and scalar dynamics of ionic clusters: Azobenzene solvated by oxygen

    Science.gov (United States)

    Paik, D. Hern; Baskin, J. Spencer; Kim, Nam Joon; Zewail, Ahmed H.

    2006-10-01

    The ultrafast dynamics of clusters of trans-azobenzene anion (A-) solvated by oxygen molecules was investigated using femtosecond time-resolved photoelectron spectroscopy. The time scale for stripping off all oxygen molecules from A- was determined by monitoring in real time the transient of the A- rise, following an 800nm excitation of A- (O2)n, where n =1-4. A careful analysis of the time-dependent photoelectron spectra strongly suggests that for n >1 a quasi-O4 core is formed and that the dissociation occurs by a bond cleavage between A- and conglomerated (O2)n rather than a stepwise evaporation of O2. With time and energy resolutions, we were able to capture the photoelectron signatures of transient species which instantaneously rise (rupture of the A--(O2)n nuclear coordinate and a slower component (1.6-36ps, increasing with n) attributed to an indirect channel exhibiting a quasistatistical behavior. The photodetachment transients exhibit a change in the transition dipole direction as a function of time delay. Rotational dephasing occurs on a time scale of 2-3ps, with a change in the sign of the transient anisotropy between A-O2 and the larger clusters. This behavior is a key indicator of an evolving cluster structure and is successfully modeled by calculations based on the structures and inertial motion of the parent clusters.

  11. Nanostructure, solvation dynamics, and nanotemplating of plasmonically active SERS substrate in reverse vesicles

    Energy Technology Data Exchange (ETDEWEB)

    Saha, Ranajay; Rakshit, Surajit [S.N. Bose National Centre for Basic Sciences, Department of Chemical, Biological and Macromolecular Sciences (India); Majumdar, Dipanwita; Singha, Achintya [Bose Institute, Department of Physics (India); Mitra, Rajib Kumar; Pal, Samir Kumar, E-mail: skpal@bose.res.in [S.N. Bose National Centre for Basic Sciences, Department of Chemical, Biological and Macromolecular Sciences (India)

    2013-04-15

    Reverse vesicles (RVs) are the organic counterparts to vesicles and are spherical containers in oils consisting of an oily core surrounded by reverse bilayers with water layers present in between. We present here a facile route for forming stable RV from nontoxic surfactants and oil components. The RV formation is characterized by dynamic light scattering and further confirmed by transmission electron microscopic (TEM) techniques. The water channels present in between the bilayers are found to be a potential template for inorganic nanoparticles' (NPs) synthesis. Both the UV-Vis absorption spectroscopy and the TEM study reveal successful formation of highly clustered silver NPs within the water layers of the RVs. X-ray powder diffraction analyzes the crystalline nature of the NPs. FTIR spectroscopy shows the signature of different kinds of water molecules in between the RV bilayers. The dynamical description of the templating water, dictating the controlled formation of the NPs in the RV, is well revealed in the picosecond-resolved solvation dynamics study of a hydrophilic fluorescence probe 2 Prime -(4-hydroxyphenyl)-5-[5-(4-methylpiperazine-1-yl) -benzimidazo-2-yl-benzimidazole] (H258). The rotational anisotropy study successfully describes geometrical restriction of the probe molecule in the RV. Notably, this study provides the first proof-of-concept data for the ability of the RV to be a template of synthesizing metal NPs. The as-prepared NP clusters are evaluated to be potential surface-enhanced Raman scattering substrate in solution using crystal violet as a model analyte. The present study offers a new RV, which is a prospective nontoxic nanotemplate and is believed to contribute potentially in the emerging NP-vesicle hybrid assembly-based plasmonic applications.Nanotemplating of metal clusters for the efficient SERS detection in liquid phase is reported in a new nontoxic reverse vesicle.

  12. Nanostructure, solvation dynamics, and nanotemplating of plasmonically active SERS substrate in reverse vesicles

    International Nuclear Information System (INIS)

    Reverse vesicles (RVs) are the organic counterparts to vesicles and are spherical containers in oils consisting of an oily core surrounded by reverse bilayers with water layers present in between. We present here a facile route for forming stable RV from nontoxic surfactants and oil components. The RV formation is characterized by dynamic light scattering and further confirmed by transmission electron microscopic (TEM) techniques. The water channels present in between the bilayers are found to be a potential template for inorganic nanoparticles’ (NPs) synthesis. Both the UV–Vis absorption spectroscopy and the TEM study reveal successful formation of highly clustered silver NPs within the water layers of the RVs. X-ray powder diffraction analyzes the crystalline nature of the NPs. FTIR spectroscopy shows the signature of different kinds of water molecules in between the RV bilayers. The dynamical description of the templating water, dictating the controlled formation of the NPs in the RV, is well revealed in the picosecond-resolved solvation dynamics study of a hydrophilic fluorescence probe 2′-(4-hydroxyphenyl)-5-[5-(4-methylpiperazine-1-yl) -benzimidazo-2-yl-benzimidazole] (H258). The rotational anisotropy study successfully describes geometrical restriction of the probe molecule in the RV. Notably, this study provides the first proof-of-concept data for the ability of the RV to be a template of synthesizing metal NPs. The as-prepared NP clusters are evaluated to be potential surface-enhanced Raman scattering substrate in solution using crystal violet as a model analyte. The present study offers a new RV, which is a prospective nontoxic nanotemplate and is believed to contribute potentially in the emerging NP-vesicle hybrid assembly-based plasmonic applications.Nanotemplating of metal clusters for the efficient SERS detection in liquid phase is reported in a new nontoxic reverse vesicle.

  13. A coordination chemistry study of hydrated and solvated cationic vanadium ions in oxidation states +III, +IV, and +V in solution and solid state

    OpenAIRE

    Krakowiak, Joanna; Lundberg, Daniel; Persson, Ingmar

    2012-01-01

    The coordination chemistry of hydrated and solvated vanadium(III), oxovanadium(IV), and dioxovanadium(V) ions in the oxygen donor solvents water, dimethylsulfoxide (dmso) and N,N′-dimethylpropyleneurea (dmpu) has been studied in solution by EXAFS and large angle X-ray scattering (LAXS) and in solid state by single crystal X-ray diffraction and EXAFS. The hydrated vanadium(III) ion has a regular octahedral configuration with a mean V-O bond distance of 1.99 Å. In the hydrated and dimethylsulfo...

  14. Dynamic combinatorial libraries : new opportunities in systems chemistry

    NARCIS (Netherlands)

    Hunt, Rosemary A. R.; Otto, Sijbren; Hunt, Rosemary A.R.

    2011-01-01

    Combinatorial chemistry is a tool for selecting molecules with special properties. Dynamic combinatorial chemistry started off aiming to be just that. However, unlike ordinary combinatorial chemistry, the interconnectedness of dynamic libraries gives them an extra dimension. An understanding of thes

  15. Dynamics of solvation and rotational relaxation of Coumarin 153 in ionic liquid confined nanometer-sized microemulsions.

    Science.gov (United States)

    Chakrabarty, Debdeep; Seth, Debabrata; Chakraborty, Anjan; Sarkar, Nilmoni

    2005-03-31

    The effects of confinement of the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate on solvation dynamics and rotational relaxation of Coumarin 153 (C-153) in Triton X-100/cyclohexane microemulsions have been explored using steady-state and picosecond time-resolved emission spectroscopy. The steady-state and rotational relaxation data indicate that C-153 molecules are incorporated in the core of the microemulsions. The average rotational relaxation time increases with increase in w ([bmim][BF(4)]/[TX-100]) values. The solvent relaxation in the core of the microemulsion occurs on two different time scales and is almost insensitive to the increase in w values. The solvent relaxation is retarded in the pool of the microemulsions compared to the neat solvent. Though, the retardation is very small compared to several-fold retardation of the solvation time of the conventional solvent inside the pool of the microemulsions. PMID:16851624

  16. Materials Properties and Solvated Electron Dynamics of Isolated Nanoparticles and Nanodroplets Probed with Ultrafast Extreme Ultraviolet Beams.

    Science.gov (United States)

    Ellis, Jennifer L; Hickstein, Daniel D; Xiong, Wei; Dollar, Franklin; Palm, Brett B; Keister, K Ellen; Dorney, Kevin M; Ding, Chengyuan; Fan, Tingting; Wilker, Molly B; Schnitzenbaumer, Kyle J; Dukovic, Gordana; Jimenez, Jose L; Kapteyn, Henry C; Murnane, Margaret M

    2016-02-18

    We present ultrafast photoemission measurements of isolated nanoparticles in vacuum using extreme ultraviolet (EUV) light produced through high harmonic generation. Surface-selective static EUV photoemission measurements were performed on nanoparticles with a wide array of compositions, ranging from ionic crystals to nanodroplets of organic material. We find that the total photoelectron yield varies greatly with nanoparticle composition and provides insight into material properties such as the electron mean free path and effective mass. Additionally, we conduct time-resolved photoelectron yield measurements of isolated oleylamine nanodroplets, observing that EUV photons can create solvated electrons in liquid nanodroplets. Using photoemission from a time-delayed 790 nm pulse, we observe that a solvated electron is produced in an excited state and subsequently relaxes to its ground state with a lifetime of 151 ± 31 fs. This work demonstrates that femotosecond EUV photoemission is a versatile surface-sensitive probe of the properties and ultrafast dynamics of isolated nanoparticles. PMID:26807653

  17. Solvated Positron Chemistry. II

    DEFF Research Database (Denmark)

    Mogensen, O. E.

    1979-01-01

    The reaction of the hydrated positron, eaq+ with Cl−, Br−, and I− ions in aqueous solutions was studied by means of positron The measured angular correlation curves for [Cl−, e+], [Br−, e+, and [I−, e+] bound states were in good agreement with th Because of this agreement and the fact that the ca...

  18. Anion Solvation in Carbonate Electrolytes

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Zhengcheng

    2015-11-16

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

  19. Solvation dynamics and enzyme catalysis in a designed enzyme undergoing directed evolution

    Science.gov (United States)

    Schreck, Carl; Head-Gordon, Teresa

    2014-03-01

    We explore whether catalysis of a de novo designed enzyme-substrate complex is correlated to necessary solvent fluctuations to induce a chemical reaction. By studying a designed KEMP Eliminase as it goes through rounds of directed evolution to improve it's catalytic activity, we have found that catalytic activity correlates with an increase in density and structure of water near the active site. This suggests fluctuations in the solvation water near the active site couple to fluctuations in KEMP Eliminase to facilitate the catalytic process. To flesh this idea out, we are studying the progression of vibrational properties and cooperative fluctuations of solvation water by simulating the terahertz observable.

  20. A THz/FTIR fingerprint of the solvated proton: evidence for Eigen structure and Zundel dynamics.

    Science.gov (United States)

    Decka, Dominique; Schwaab, Gerhard; Havenith, Martina

    2015-05-01

    In continuation of earlier work on La(III), Ni(II) and Mn(II) halides, we present low frequency (30-400 cm(-1)) spectra of solvated HCl and HBr as a function of solute concentration. This frequency range provides direct access to water network modes and changes induced by solvated solutes. We were able to dissect the spectra into components associated to solvated ions and ion pairs using a chemical equilibrium model in combination with principal component analysis. While the Cl(-) rattling mode at 190 cm(-1) is found to be unchanged, the Br(-) resonance around 90 cm(-1) is decreased in intensity below the detection threshold when replacing the divalent or trivalent metal ions by a proton. The solvated proton shows two resonances: a solvation water mode around 140 cm(-1) and a high frequency resonance at 325 cm(-1) that we assign to the rattling motion of an Eigen structure H3O(+) in its solvation cage. This assignment is corroborated by isotopic substitution measurements which show a redshift of the high frequency peak when HCl/H2O is replaced by DCl/D2O. The linewidth of the H3O(+) rattling mode corresponds to a relaxation time of the oscillatory process of τ ≈ 60 fs, considerably faster than the relaxation time of τ ≈ 160 fs for Cl(-). In addition, we find a broad background that we attribute to fast non-oscillatory motions of a proton in a Zundel-like complex. Our results are in agreement with an Eigen-Zundel-Eigen (EZE) model of proton transport. Upon ion pairing the broad background is strongly reduced indicating a reduction of fast proton transfer processes. The Cl(-) resonance blueshifts by 20 cm(-1) which indicates a transition from free ions to a solvent shared ion pair. Surprisingly, the center frequency of the Eigen complex does not change upon ion pairing. This can be rationalized in terms of an unchanged local solvation structure. PMID:25872169

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

    Science.gov (United States)

    Debolt, Stephen Edward

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

  2. Nonequilibrium versus equilibrium molecular dynamics studies of solvation dynamics after photoexcitation of OClO

    Science.gov (United States)

    Gunnerson, Kim N.; Brooksby, Craig; Prezhdo, Oleg V.; Reid, Philip J.

    2007-10-01

    The results of our earlier work [C. Brooksby, O. V. Prezhdo, and P. J. Reid, J. Chem. Phys. 119, 9111 (2003)] rationalizing the surprisingly weak solvent dependence of the dynamics following photoexcitation of chlorine dioxide in water, chloroform, and cyclohexane are thoroughly tested. Comparisons are made between equilibrium and nonequilibrium solvent response, equilibrium response in the ground and excited electronic states, as well as the cumulant and direct evaluation of the optical response function. In general, the linear response and cumulant approximations are found to hold, although minor deviations are found with all solvents. The ground state, linear response, and cumulant data show best agreement with experiment, most likely due to the better tested ground-state force field and the robust behavior of the linear response and cumulant approximations. The main conclusion of our earlier work explaining the weak solvent dependence by the domination of the van der Waals interaction component remains intact within the more advanced treatments. However, the molecular origin of this surprising experimental observation is different in water and chloroform compared to cyclohexane.

  3. Structure and dynamics of the hydrated magnesium ion and of the solvated magnesium carbonates: insights from first principles simulations.

    Science.gov (United States)

    Di Tommaso, Devis; de Leeuw, Nora H

    2010-01-28

    We report first principles molecular dynamics simulations based on the density functional theory and the Car-Parrinello method to study the structures and dynamics of the hydrated Mg(2+) ion and of the solvated MgHCO(3)(+) and MgCO(3) complexes in aqueous solution. According to these simulations, the first hydration shell of the hydrated magnesium ion consists of six water molecules, whereas in the solvated magnesium bicarbonate and magnesium carbonate complexes the Mg(2+) is mostly five-coordinated, which indicates that when coordinated to magnesium the HCO(3)(-) and CO(3)(2-) anions reduce its the coordination sphere. Our simulations show that the structures of the most stable monomers of magnesium bi-carbonate and magnesium carbonate in solution are Mg[eta(1)-HCO(3)](H(2)O)(4)(+) and Mg[eta(1)-CO(3)](H(2)O)(4), i.e. the preferred hydration number is four, while the (bi-)carbonate is coordinated to the magnesium in a monodentate mode. The analysis of the exchange processes of the water molecules in the first and second hydration shell of Mg(2+) shows that the HCO(3)(-) or CO(3)(2-) ligands affect the dynamics of the magnesium coordination spheres by making its hydration shell more "labile". Furthermore, molecular dynamics simulations of the non-associated Mg(2+)/Cl(-) pair in water suggest that, despite negligible differences in the coordination spheres of Mg(2+), the chloride anion has a significant influence on the water exchange rates in the second hydration shell of Mg(2+). PMID:20066374

  4. Controlling Chemistry in Dynamic Nanoscale Systems

    DEFF Research Database (Denmark)

    Jesorka, Aldo; Lizana, Ludvig; Konkoli, Zoran; Czolkos, Ilja; Orwar, Owe

    Spatial organization and shape dynamics are inherent properties of biological cells and cell interiors. There are strong indications that these features are important for the in vivo control of reaction parameters in biochemical transformations. Nanofluidic model devices founded on surfactant...... concept. Controlled release of chol-DNA molecules from SU-8 surfaces gives the possibility to dynamically change surface and/or solution properties in micro and nanoreactor applications, opening access to stable 2D chemistry on surface-based devices with potential for easy interfacing with conventional...

  5. Propensities in the solvation of M+–Benzene systems (M = Na, K, Rb) investigated by cluster dynamics

    International Nuclear Information System (INIS)

    Highlights: ► A semiempirical interaction potential is used to model intermolecular interactions. ► The model is based on the decomposition of the molecular polarizability. ► The model uses an improved Lennard Jones function. ► The solvation characteristics depend on the size of the cation. - Abstract: The study of size-specific interactions of alkali ions (M+) with aromatic compounds is crucial to understand the mechanisms governing the selectivity in protein channels. In particular, the investigation of the aqueous solvent effect on M+–π systems is of fundamental importance. The related processes are typically governed by several intermolecular interaction contributions as hydrogen bonds, dispersion, induction and electrostatics, which are often weak and difficult to evaluate in detail. In the present paper, the behavior of the M+–Benzene (M = Na, K, Rb, Benzene = Bz) aggregates surrounded by water molecules is analyzed performing molecular dynamics (MD) simulations. As the accuracy of such simulations depends on the reliability of the used intermolecular potential energy formulation we adopt a potential model based on a combination of electrostatic and non electrostatic components, whose reliability has been previously tested on some prototype systems by comparing predictions of the model with both accurate ab initio calculations and/or high level experimental data, has been used. The non electrostatic component has been described as sum of improved Lennard Jones (ILJ) functions, whose parameters have been derived from polarizabilities of atoms, groups of atoms and/or molecules. The electrostatic contribution has been calculated as a sum of Coulombic potentials arising from the interaction between permanent ion charge and/or permanent molecular charge distributions, which, at long range, for M+–Bz, H2O–Bz and M+–H2O reproduces the ion-quadrupole, dipole-quadrupole and the ion-dipole interactions, respectively. Energetics and structure of the

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

    Indian Academy of Sciences (India)

    Surjit B Dixit; Mihaly Mezei; David L Beveridge

    2012-07-01

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

  7. Direct Observation of Cascade of Photoinduced Ultrafast Intramolecular Charge Transfer Dynamics in Diphenyl Acetylene Derivatives: Via Solvation and Intramolecular Relaxation.

    Science.gov (United States)

    Karunakaran, Venugopal; Das, Suresh

    2016-07-21

    Interaction of light with electron donor-acceptor π-conjugated systems leading to intramolecular charge transfer (ICT) plays an essential role in transformation of light energy. Here the cascade of photoinduced ICT processes is directly observed by investigating the excited state relaxation dynamics of cyano and mono/di methoxy substituted diphenyl acetylene derivatives using femtosecond pump-probe spectroscopy and nanosecond laser flash photolysis. The femtosecond transient absorption spectra of the chromophores upon ultrafast excitation reveal the dynamics of intermediates involved in transition from initially populated Frank-Condon state to local excited state (LE). It also provides the dynamic details of the transition from the LE to the charge transfer state yielding the formation of the radical ions. Finally, the charge transfer state decays to the triplet state by geminate charge recombination. The latter dynamics are observed in the nanosecond transient absorption spectra. It is found that excited state relaxation pathways are controlled by different stages of solvation and intramolecular relaxation depending on the solvent polarity. The twisted ICT state is more stabilized (978 ps) in acetonitrile than cyclohexane where major components of transient absorption originate from the S1 state. PMID:27347705

  8. Optimization of molecular and crystalline forms of drugs, agrochemicals, pesticides in relation to activity, bioavailability, patentability and to the fabrication of polymorphs, solvates, co-crystals with green chemistry methods

    OpenAIRE

    Nanna, Saverio

    2015-01-01

    This doctorate was funded by the Regione Emilia Romagna, within a Spinner PhD project coordinated by the University of Parma, and involving the universities of Bologna, Ferrara and Modena. The aim of the project was: - Production of polymorphs, solvates, hydrates and co-crystals of active pharmaceutical ingredients (APIs) and agrochemicals with green chemistry methods; - Optimization of molecular and crystalline forms of APIs and pesticides in relation to activity, bioavailability an...

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

    Science.gov (United States)

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

    2015-01-22

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

  10. Solvation dynamics monitored by combined X-ray spectroscopies and scattering: photoinduced spin transition in aqueous [Fe(bpy)3]2+

    DEFF Research Database (Denmark)

    Bressler, C.; Gawelda, W.; Galler, A.;

    2014-01-01

    between intramolecular dynamics and the intermolecular caging solvent response with 100 ps time resolution. On this time scale the ultrafast spin transition including intramolecular geometric structure changes as well as the concomitant bulk solvent heating process due to energy dissipation from the...... the number of free parameters in the XDS analysis, and both combined permit extraction of information about the structural dynamics of the first solvation shell....

  11. Freezing hot electrons. Electron transfer and solvation dynamics at D{sub 2}O and NH{sub 3}-metal interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Staehler, A.J.

    2007-05-15

    The present work investigates the electron transfer and solvation dynamics at the D{sub 2}O/Cu(111), D{sub 2}O/Ru(001), and NH{sub 3}/Cu(111) interfaces using femtosecond time-resolved two-photon photoelectron spectroscopy. Within this framework, the influence of the substrate, adsorbate structure and morphology, solvation site, coverage, temperature, and solvent on the electron dynamics are studied, yielding microscopic insight into the underlying fundamental processes. Transitions between different regimes of ET, substrate-dominated, barrier-determined, strong, and weak coupling are observed by systematic variation of the interfacial properties and development of empirical model descriptions. It is shown that the fundamental steps of the interfacial electron dynamics are similar for all investigated systems: Metal electrons are photoexcited to unoccupied metal states and transferred into the adlayer via the adsorbate's conduction band. The electrons localize at favorable sites and are stabilized by reorientations of the surrounding polar solvent molecules. Concurrently, they decay back two the metal substrate, as it offers a continuum of unoccupied states. However, the detailed characteristics vary for the different investigated interfaces: For amorphous ice-metal interfaces, the electron transfer is initially, right after photoinjection, dominated by the substrate's electronic surface band structure. With increasing solvation, a transient barrier evolves at the interface that increasingly screens the electrons from the substrate. Tunneling through this barrier becomes the rate-limiting step for ET. The competition of electron decay and solvation leads to lifetimes of the solvated electrons in the order of 100 fs. Furthermore, it is shown that the electrons bind in the bulk of the ice layers, but on the edges of adsorbed D{sub 2}O clusters and that the ice morphology strongly influences the electron dynamics. For the amorphous NH{sub 3}/Cu(111

  12. Application of X-ray absorption spectroscopy and molecular dynamics simulation to study the atomistic solvation structure of tetraglyme:KSCN electrolytes

    International Nuclear Information System (INIS)

    The atomistic solvation structure of tetraglyme:KSCN (TET:KSCN) electrolytes with various K+:ether oxygen (M:O) ratio were studied by a combination of molecular dynamic (MD) simulation and Extended X-Ray Absorption Fine Structure (EXAFS) called “MD-EXAFS” method. This method gives useful information at the atomistic scale including the average distance between atom pair around the probed ion (R0) and Coordination Number (N). MD simulation results suggest that K+ ions are mostly coordinated to ether oxygen and the conformation around C–C bond prefer the gauche state and TET becomes more compact shape. K+ ions are also coordinated to thiocyanate (SCN−) anion at both nitrogen and sulfur atoms due to strong electron delocalization over three atoms in SCN− (S, C and N). A comparison between MD-EXAFS with the experimental spectra gives an overall good agreement for both frequency and amplitude of the oscillations. - Graphical abstract: A snapshot from MD simulation of TET:KSCN complex that represent the solvation structure of K+ ion by TET oxygens and SCN− anion. The most probable case is the solvation by 1 TET chain with 3 oxygen atoms and 2 SCN− anion. - Highlights: • This work combines MD simulation and XAS to study polymer electrolytes. • Doping KSCN can slightly induce the conformational change of TET chain. • Both polymer and anions are included in first solvation shell of cation

  13. Theoretical Investigation of the Vibrational Dynamics of Ag+CO Solvated in the Ne Matrix

    Czech Academy of Sciences Publication Activity Database

    Šilhan, Martin; Nachtigall, Petr; Bludský, Ota

    2003-01-01

    Roč. 375, 1/2 (2003), s. 54-58. ISSN 0009-2614 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : density-functional * calculations * metal-carbonyl cations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.438, year: 2003

  14. Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling.

    Science.gov (United States)

    Hansen, Halvor S; Daura, Xavier; Hünenberger, Philippe H

    2010-09-14

    A new method, fragment-based local elevation umbrella sampling (FB-LEUS), is proposed to enhance the conformational sampling in explicit-solvent molecular dynamics (MD) simulations of solvated polymers. The method is derived from the local elevation umbrella sampling (LEUS) method [ Hansen and Hünenberger , J. Comput. Chem. 2010 , 31 , 1 - 23 ], which combines the local elevation (LE) conformational searching and the umbrella sampling (US) conformational sampling approaches into a single scheme. In LEUS, an initial (relatively short) LE build-up (searching) phase is used to construct an optimized (grid-based) biasing potential within a subspace of conformationally relevant degrees of freedom, which is then frozen and used in a (comparatively longer) US sampling phase. This combination dramatically enhances the sampling power of MD simulations but, due to computational and memory costs, is only applicable to relevant subspaces of low dimensionalities. As an attempt to expand the scope of the LEUS approach to solvated polymers with more than a few relevant degrees of freedom, the FB-LEUS scheme involves an US sampling phase that relies on a superposition of low-dimensionality biasing potentials optimized using LEUS at the fragment level. The feasibility of this approach is tested using polyalanine (poly-Ala) and polyvaline (poly-Val) oligopeptides. Two-dimensional biasing potentials are preoptimized at the monopeptide level, and subsequently applied to all dihedral-angle pairs within oligopeptides of 4,  6,  8, or 10 residues. Two types of fragment-based biasing potentials are distinguished: (i) the basin-filling (BF) potentials act so as to "fill" free-energy basins up to a prescribed free-energy level above the global minimum; (ii) the valley-digging (VD) potentials act so as to "dig" valleys between the (four) free-energy minima of the two-dimensional maps, preserving barriers (relative to linearly interpolated free-energy changes) of a prescribed magnitude

  15. DFT Molecular Dynamics (DFTMD) Simulations of Carbohydrates: I. COSMO Solvated Alpha-maltose

    Science.gov (United States)

    Density functional molecular dynamics (DFTMD) is carried out on low-energy conformations of alpha-maltose. Finite temperature molecular dynamics trajectories are generated with forces obtained from B3LYP/6-31+G* electronic structure calculations. The implicit solvent method COSMO is applied to sim...

  16. Estimation of abraham solvation equation coefficients for hydrogen bond formation from abraham solvation parameters for solute activity and basicity

    NARCIS (Netherlands)

    Noort, van P.C.M.

    2013-01-01

    Abraham solvation equations find widespread use in environmental chemistry and pharmaco-chemistry. The coefficients in these equations, which are solvent (system) descriptors, are usually determined by fitting experimental data. To simplify the determination of these coefficients in Abraham solvatio

  17. Solvation structure and dynamics of Ni{sup 2+}(aq) from a polarizable force field

    Energy Technology Data Exchange (ETDEWEB)

    Mareš, Jiří, E-mail: jiri.mares@oulu.fi; Vaara, Juha

    2014-10-31

    Highlights: • We parameterize the Ni{sup 2+} ion within the AMOEBA polarizable forcefield. • Besides vdW parameters, we fit also polarizability, Thole damping and charge. • We use an empirical adjustment to account for the transition into condensed phase. • Very good structural and dynamical properties of Ni{sup 2+}(aq) are demonstrated. - Abstract: An aqueous solution of Ni{sup 2+} has often been used as a prototypic transition-metal system for experimental and theoretical studies in nuclear and electron-spin magnetic resonance (NMR and ESR). Molecular dynamics (MD) simulation of Ni{sup 2+}(aq) has been a part of many of these studies. As a transition metal complex, its MD simulation is particularly difficult using common force fields. In this work, we parameterize the Ni{sup 2+} ion for a simulation of the aqueous solution within the modern polarizable force field AMOEBA. We show that a successful parameterization is possible for this specific case when releasing the physical interpretation of the electrostatic and polarization parameters of the force field. In doing so, particularly the Thole damping parameter and also the ion charge and polarizability were used as fitting parameters. The resulting parameterizations give in a MD simulation good structural and dynamical properties of the [Ni(H{sub 2}O){sub 6}]{sup 2+} complex, along with the expected excellent performance of AMOEBA for the water solvent. The presented parameterization is appropriate for high-accuracy simulations of both structural and dynamic properties of Ni{sup 2+}(aq). This work documents possible approaches of parameterization of a transition metal within the AMOEBA force field.

  18. Solvation structure and dynamics of Ni2+(aq) from a polarizable force field

    International Nuclear Information System (INIS)

    Highlights: • We parameterize the Ni2+ ion within the AMOEBA polarizable forcefield. • Besides vdW parameters, we fit also polarizability, Thole damping and charge. • We use an empirical adjustment to account for the transition into condensed phase. • Very good structural and dynamical properties of Ni2+(aq) are demonstrated. - Abstract: An aqueous solution of Ni2+ has often been used as a prototypic transition-metal system for experimental and theoretical studies in nuclear and electron-spin magnetic resonance (NMR and ESR). Molecular dynamics (MD) simulation of Ni2+(aq) has been a part of many of these studies. As a transition metal complex, its MD simulation is particularly difficult using common force fields. In this work, we parameterize the Ni2+ ion for a simulation of the aqueous solution within the modern polarizable force field AMOEBA. We show that a successful parameterization is possible for this specific case when releasing the physical interpretation of the electrostatic and polarization parameters of the force field. In doing so, particularly the Thole damping parameter and also the ion charge and polarizability were used as fitting parameters. The resulting parameterizations give in a MD simulation good structural and dynamical properties of the [Ni(H2O)6]2+ complex, along with the expected excellent performance of AMOEBA for the water solvent. The presented parameterization is appropriate for high-accuracy simulations of both structural and dynamic properties of Ni2+(aq). This work documents possible approaches of parameterization of a transition metal within the AMOEBA force field

  19. Triplex hydration: nanosecond molecular dynamics simulation of the solvated triplex formed by mixed sequences

    OpenAIRE

    Ojha, Rajendra P.; Tiwari, Rakesh K.

    2003-01-01

    A theoretical model for the hydration pattern and motion of ions around the triple helical DNA with mixed sequences d(GACTGGTGAC)d(GTCACCAGTC)*d(GACTGGTGAC) in solution, during MD simulation, using the particle mesh Ewald sum method, is elaborated here. The AMBER 5.0 force field has been used during the simulation in solvent. The simulation studies support a dynamically stable atmosphere around the DNA triplex in solution over the entire length of the trajectory. The results have been compare...

  20. Molecular dynamics study of solvation effects on acid dissociation in aprotic media

    OpenAIRE

    Laria, Daniel; Kapral, Raymond; Estrin, Dario; Ciccotti, Giovanni

    1996-01-01

    Acid ionization in aprotic media is studied using Molecular Dynamics techniques. In particular, models for HCl ionization in acetonitrile and dimethylsulfoxide are investigated. The proton is treated quantum mechanically using Feynman path integral methods and the remaining molecules are treated classically. Quantum effects are shown to be essential for the proper treatment of the ionization. The potential of mean force is computed as a function of the ion pair separation and the local solven...

  1. Solvation structure and dynamics of Ni2+(aq) from a polarizable force field

    Science.gov (United States)

    Mareš, Jiří; Vaara, Juha

    2014-10-01

    An aqueous solution of Ni2+ has often been used as a prototypic transition-metal system for experimental and theoretical studies in nuclear and electron-spin magnetic resonance (NMR and ESR). Molecular dynamics (MD) simulation of Ni2+(aq) has been a part of many of these studies. As a transition metal complex, its MD simulation is particularly difficult using common force fields. In this work, we parameterize the Ni2+ ion for a simulation of the aqueous solution within the modern polarizable force field AMOEBA. We show that a successful parameterization is possible for this specific case when releasing the physical interpretation of the electrostatic and polarization parameters of the force field. In doing so, particularly the Thole damping parameter and also the ion charge and polarizability were used as fitting parameters. The resulting parameterizations give in a MD simulation good structural and dynamical properties of the [Ni(H2O)6 ] 2 + complex, along with the expected excellent performance of AMOEBA for the water solvent. The presented parameterization is appropriate for high-accuracy simulations of both structural and dynamic properties of Ni2+(aq). This work documents possible approaches of parameterization of a transition metal within the AMOEBA force field.

  2. Dithioacetal Exchange: A New Reversible Reaction for Dynamic Combinatorial Chemistry.

    Science.gov (United States)

    Orrillo, A Gastón; Escalante, Andrea M; Furlan, Ricardo L E

    2016-05-10

    Reversibility of dithioacetal bond formation is reported under acidic mild conditions. Its utility for dynamic combinatorial chemistry was explored by combining it with orthogonal disulfide exchange. In such a setup, thiols are positioned at the intersection of both chemistries, constituting a connecting node between temporally separated networks. PMID:26990904

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

    Science.gov (United States)

    van Noort, Paul

    2013-01-01

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

  4. Molecular dynamics study of solvation effects on acid dissociation in aprotic media

    CERN Document Server

    Laria, D; Estrin, D A; Ciccotti, G; Laria, Daniel; Kapral, Raymond; Estrin, Dario; Ciccotti, Giovanni

    1996-01-01

    Acid ionization in aprotic media is studied using Molecular Dynamics techniques. In particular, models for HCl ionization in acetonitrile and dimethylsulfoxide are investigated. The proton is treated quantum mechanically using Feynman path integral methods and the remaining molecules are treated classically. Quantum effects are shown to be essential for the proper treatment of the ionization. The potential of mean force is computed as a function of the ion pair separation and the local solvent structure is examined. The computed dissociation constants in both solvents differ by several orders of magnitude which are in reasonable agreement with experimental results. Solvent separated ion pairs are found to exist in dimethylsulfoxide but not in acetonitrile. Dissociation mechanisms in small clusters are also investigated. Solvent separated ion pairs persist even in aggregates composed of rather few molecules, for instance, as few as thirty molecules. For smaller clusters or for large ion pair separations cluste...

  5. Applications of Molecular Dynamics in Atmospheric and Solution Chemistry

    OpenAIRE

    Li, Xin

    2011-01-01

    This thesis focuses on the applications of molecular dynamics simulation techniques in the fields of solution chemistry and atmospheric chemistry. The work behind the thesis takes account of the fast development of computer hardware, which has made computationally intensive simulations become more and more popular in disciplines like pharmacy, biology and materials science. In molecular dynamics simulations using classical force fields, the atoms are represented by mass points with partial ch...

  6. Where do ions solvate?

    Indian Academy of Sciences (India)

    Yan Levin

    2005-06-01

    We study a simple model of ionic solvation inside a water cluster. The cluster is modeled as a spherical dielectric continuum. It is found that unpolarizable ions always prefer the bulk solvation. On the other hand, for polarizable ions, there exists a critical value of polarization above which surface solvation becomes energetically favorable for large enough water clusters.

  7. Proton solvation in protic and aprotic solvents.

    Science.gov (United States)

    Rossini, Emanuele; Knapp, Ernst-Walter

    2016-05-01

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

  8. Dynamic combinatorial chemistry with diselenides and disulfides in water

    DEFF Research Database (Denmark)

    Rasmussen, Brian; Sørensen, Anne; Gotfredsen, Henrik;

    2014-01-01

    Diselenide exchange is introduced as a reversible reaction in dynamic combinatorial chemistry in water. At neutral pH, diselenides are found to mix with disulfides and form dynamic combinatorial libraries of diselenides, disulfides, and selenenylsulfides. This journal is © the Partner Organisations...

  9. Promote Chemistry Learning with Dynamic Visualizations: Generation, Selection, and Critique

    OpenAIRE

    Zhang, Zhihui

    2011-01-01

    Dynamic visualizations can strengthen chemistry instruction by illustrating atomic level phenomena. Visualizations can help students add ideas about unseen phenomena involving atomic particles. They allow students to interact with phenomena that cannot be investigated in hands-on laboratories. Connecting dynamic, atomic representations with associated observable phenomena and symbolic representations has the potential to increase the coherence and comprehensiveness of student understanding. C...

  10. Dynamic Combinatorial Chemistry with Diselenides, Disulfides, Imines and Metal Coordination

    DEFF Research Database (Denmark)

    Sørensen, Anne

    10 or 1.0 mol% diselenide was sufficient to catalyse the library formation while 0.1 mol% catalyst had little effect on the reaction. Next, it was proven possible to introduce the diselenide exchange reaction as a reversible reaction for dynamic combinatorial chemistry in water at physiological p......The design and preparation of strong and selective artificial receptors, especially biomi-metic receptors that function in aqueous solution, has proved truly challenging. In this thesis it will be described how the strengths of dynamic combinatorial chemistry can be used to great advantage in this...... field. The aim of this project has therefore been to develop new ways of using dynamic combinatorial libraries for molecular recognition in aqueous media. The focus has been on using what has been learned from the well-established di-sulfide exchange chemistry to incorporate a new reaction into dynamic...

  11. Organoactinide chemistry: synthesis, structure, and solution dynamics

    International Nuclear Information System (INIS)

    This thesis considers three aspects of organoactinide chemistry. In chapter one, a bidentate phosphine ligand was used to kinetically stabilize complexes of the type Cp2MX2. Ligand redistribution processes are present throughout the synthetic work, as has often been observed in uranium cyclopentadienyl chemistry. The effects of covalent M-L bonding on the solution and solid state properties of U(III) coordination complexes are considered. In particular, the nature of the more subtle interaction between the metal and the neutral ligand are examined. Using relative basicity data obtained in solution, and solid state structural data (and supplemented by gas phase photoelectron measurements), it is demonstrated that the more electron rich U(III) centers engage in significant U → L π-donation. Trivalent uranium is shown to be capable of acting either as a one- or two-electron reducing agent toward a wide variety of unsaturated organic and inorganic molecules, generating molecular classes unobtainable via traditional synthetic approaches, as well as offering an alternative synthetic approach to molecules accessible via metathesis reactions. Ligand redistribution processes are again observed, but given the information concerning ligand lability, this reactivity pattern is applied to the synthesis of pure materials inaccessible from redox chemistry. 214 refs., 33 figs., 10 tabs

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

    Science.gov (United States)

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

    2014-11-01

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

  13. Halide anion solvation and recognition by a macro tri-cyclic tetra-ammonium host in an ionic liquid: a molecular dynamics stud

    International Nuclear Information System (INIS)

    We report a molecular dynamics study of halide anions X- and their inclusion complexes X- - L4+ with a macro-tri-cyclic tetrahedral host L4+ built from four quaternary ammonium sites, in an ionic liquid (IL) based on the 1-butyl-3-methyl-imidazolium (BMI+) cation and the PF6- anion. The 'dry' and 'humid' forms of the [BMI][PF6] IL are compared, showing the importance of IL ions in the 'dry' IL and, in some cases, of water molecules in the 'humid' IL. In the 'dry' IL the F-, Cl-, Br- and I- un-complexed halides are surrounded by 4-5 BMI+ cations whose binding mode evolves from hydrogen bonding to facial coordination along this series. Solvent humidity has the largest impact on the solvation of F- whose first shell BMI+ cations are all displaced by H2O molecules, while the first solvation shell of Cl-, Br- and I- comprises 3-4 BMI+ cations plus ca. 4 H2O molecules. The solvation of the L4+ host and of its X- - L4+ complex mainly involves PF6- anions in the 'dry' IL, and additional H2O molecules in the 'humid' IL. The question of anion binding selectivity is addressed by free energy perturbation calculations which predict that, in the 'dry' liquid, F- is preferred over Cl-, Br- and I-, which contrasts with the aqueous solution where L4+ is selective for Cl-. In the 'humid' liquid however, there is no F-/Cl- discrimination, showing the importance of small amounts of water on the complexation selectivity. (authors)

  14. Ion solvation thermodynamics from simulation with a polarizable force field.

    Science.gov (United States)

    Grossfield, Alan; Ren, Pengyu; Ponder, Jay W

    2003-12-17

    Thermodynamic measurements of the solvation of salts and electrolytes are relatively straightforward, but it is not possible to separate total solvation free energies into distinct cation and anion contributions without reference to an additional extrathermodynamic assumption. The present work attempts to resolve this difficulty using molecular dynamics simulations with the AMOEBA polarizable force field and perturbation techniques to directly compute absolute solvation free energies for potassium, sodium, and chloride ions in liquid water and formamide. Corresponding calculations are also performed with two widely used nonpolarizable force fields. The simulations with the polarizable force field accurately reproduce in vacuo quantum mechanical results, experimental ion-cluster solvation enthalpies, and experimental solvation free energies for whole salts, while the other force fields do not. The results indicate that calculations with a polarizable force field can capture the thermodynamics of ion solvation and that the solvation free energies of the individual ions differ by several kilocalories from commonly cited values. PMID:14664617

  15. System dynamics modeling: from mechanics to chemistry

    OpenAIRE

    D’Anna, Michele; Fuchs, Hans; Lubini, Paolo

    2008-01-01

    In this paper, we discuss a contribution toward the use of analogical reasoning by explicit system dynamics modeling of physical processes. The relational structures found in simple models are transferred to an example of chemical processes leading to chemical equilibrium. We present an experiment on the mutarotation of D-glucose. A dynamical model will be built that makes use of amount of substance and chemical potential differences in analogy to quantities of fluid and pressure ...

  16. Stimulated Photon Echo Studies of Protein-Matrix Solvation Dynamics and Interexciton-State Radiationless Decay in Allophycocyanin and α Phycocyanin

    Science.gov (United States)

    Beck, Warren F.; Homoelle, Bradley J.; Diffey, William M.

    1998-03-01

    We have employed two third-order femtosecond spectroscopic methods, stimulated-photon-echo peak-shift (3PEPS) and transient-grating (TG) spectroscopy, to characterize solvation dynamics at physiological temperatures in phycobiliprotein systems, the α subunit of C-phycocyanin and allophycocyanin in the trimeric aggregation state. Both systems exhibit a biphasic solvation response: an inertial phase, arising from librational motions of the amino acids or included water molecules in the chromophore-binding site, contributes a 80--100-fs component to the 3PEPS profile and appears as a rapidly-damped 72-cm-1 modulation of the TG signal; the diffusive phase, arising from collective protein-matrix motions, exhibits a component in the TG signal and 3PEPS profile on the 5--20-ps and longer time scales. The 3PEPS profile observed with allophycocyanin exhibits additional fast decay components, with time constants of 56 fs and 220 fs, that report the additional contributions to electronic dephasing that arise from interexciton-state radiationless decay and vibrational relaxation in the lower exciton state, respectively. These results, taken along with those of previous transient hole-burning experiments, show that the exciton states in allophycocyanin are imperfectly correlated.

  17. Controlling Chemistry in Dynamic Nanoscale Systems

    DEFF Research Database (Denmark)

    Jesorka, Aldo; Lizana, Ludvig; Konkoli, Zoran;

    2011-01-01

    Spatial organization and shape dynamics are inherent properties of biological cells and cell interiors. There are strong indications that these features are important for the in vivo control of reaction parameters in biochemical transformations. Nanofluidic model devices founded on surfactant sys...

  18. Ab Initio Molecular Dynamics Simulations of an Excess Proton in a Triethylene Glycol-Water Solution: Solvation Structure, Mechanism, and Kinetics.

    Science.gov (United States)

    McDonnell, Marshall T; Xu, Haixuan; Keffer, David J

    2016-06-16

    We investigate the solvation shell structures, the distribution of protonic defects, mechanistic details, kinetics, and dynamics of proton transfer for an excess proton in bulk water and for an excess proton in an aqueous solution of triethylene glycol (TEG) via Car-Parrinello molecular dynamics simulations. The PW91, PBE, and PBE with the Tkatchenko-Scheffler (TS) density-dependent dispersion functionals were used and compared for bulk water and the TEG-water mixtures. The excess proton is found to reside predominantly on water molecules but also resides on hydroxyl groups of TEG. The lifetimes associated with structural diffusion time scales of the protonated water were found to be on the order of ∼1 ps. All three functionals studied support the presolvation requirement for structural diffusion. The highest level of theory shows a reduction in the free energy barrier for water-water proton transfer in TEG-water mixtures compared to bulk water. The effect of TEG shows no strong change in the kinetics for TEG-water mixtures compared to bulk water for this same level of theory. The excess proton displays burst-rest behavior in the presence of TEG, similar to that found in bulk water. We find that the TEG chain disrupts the hydrogen-bond network, causing the solvation shell around water to be populated by TEG chain groups instead of other waters, reducing the rigidity of the hydrogen-bond network. Methylene is a dominant hydrogen bond donor for the protonated water in hydrogen-bond networks associated with proton transfer and structural diffusion. This is consistent with previous studies that have found the hydronium ion to be amphiphilic in nature and to have higher proton mobility at oil-water interfaces. PMID:27218455

  19. Free-radical chemistry of thiourea in aqueous solution, induced by OH radical, H atom, α-hydroxyalkyl radicals, photoexcited maleimide, and the solvated electron

    International Nuclear Information System (INIS)

    Hydroxyl radicals react with thiourea (and its tetramethyl derivative) yielding dimeric radical cations which are characterized by strong absorptions at 400 nm (450 nm). An analysis of the kinetics of the buildup of these absorptions gives evidence for the intermediacy of OH-adducts and the monomeric radical cations. The dimeric radical cations are also generated in the reactions of triplet-excited maleimide with those thioureas. Moreover, in acidic solutions even reducing radicals such as the H atom and α-hydroxy alkyl radicals give rise to these intermediates in full yields, albeit displaying different kinetics. Potential mechanistic implications are discussed. The dimeric thiourea radical cations are strong oxidants and readily oxidize the anions of phenol and 2'-deoxyguanosine. The solvated electron gives rise to an intermediate which is rapidly protonated by water (pKa > 11). Quantum mechanical calculations support the assignment of the 400 nm (450 nm) absorption to the respective dimeric thiourea radical cation. (author)

  20. Dynamic combinatorial and protein-templated click chemistry in medicinal chemistry

    OpenAIRE

    Mondal, Milon

    2016-01-01

    We have highlighted throughout this thesis that fragment-based drug design (FBDD) and structure-based drug design (SBDD) still constitute a number of challenges such as the risk associated with de novo SBDD and are time-consuming as they involve synthesis and validation of the binding mode of each derivative in the fragment/hit-optimization cycle. To overcome these hurdles, we combined FBDD or de novo SBDD projects with dynamic combinatorial chemistry (DCC) or protein-templated click chemistr...

  1. Parameter optimization in differential geometry based solvation models.

    Science.gov (United States)

    Wang, Bao; Wei, G W

    2015-10-01

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

  2. Complex Dynamics in Nonequilibrium Economics and Chemistry

    Science.gov (United States)

    Wen, Kehong

    Complex dynamics provides a new approach in dealing with economic complexity. We study interactively the empirical and theoretical aspects of business cycles. The way of exploring complexity is similar to that in the study of an oscillatory chemical system (BZ system)--a model for modeling complex behavior. We contribute in simulating qualitatively the complex periodic patterns observed from the controlled BZ experiments to narrow the gap between modeling and experiment. The gap between theory and reality is much wider in economics, which involves studies of human expectations and decisions, the essential difference from natural sciences. Our empirical and theoretical studies make substantial progress in closing this gap. With the help from the new development in nonequilibrium physics, i.e., the complex spectral theory, we advance our technique in detecting characteristic time scales from empirical economic data. We obtain correlation resonances, which give oscillating modes with decays for correlation decomposition, from different time series including S&P 500, M2, crude oil spot prices, and GNP. The time scales found are strikingly compatible with business experiences and other studies in business cycles. They reveal the non-Markovian nature of coherent markets. The resonances enhance the evidence of economic chaos obtained by using other tests. The evolving multi-humped distributions produced by the moving-time -window technique reveal the nonequilibrium nature of economic behavior. They reproduce the American economic history of booms and busts. The studies seem to provide a way out of the debate on chaos versus noise and unify the cyclical and stochastic approaches in explaining business fluctuations. Based on these findings and new expectation formulation, we construct a business cycle model which gives qualitatively compatible patterns to those found empirically. The soft-bouncing oscillator model provides a better alternative than the harmonic oscillator

  3. An ab initio Molecular Dynamics study of the solvated OHCl- complex. Implications for the atmospheric oxidation of (Cl-)aq to (Cl2)g

    Energy Technology Data Exchange (ETDEWEB)

    D' Auria, R; Kuo, I W; Tobias, D J

    2007-07-26

    We have studied the OHCl{sup -} complex in a six water cluster and in bulk liquid water by means of generalized gradient-corrected BLYP density functional theory based Born-Oppenheimer molecular dynamics. Self-interaction corrected results, that predict an H-bonded OH...Cl{sup -} complex, are compared to the uncorrected ones, that predict a bonded (HO-Cl){sup -}. A second order Moeller-Plesset potential energy landscape of the gas-phase complex in its ground state was computed to determine which of the two configurations represents the true nature of the bond. Since no evidence of a local minimum was found in the vicinity of the geometry corresponding to the (HO-Cl){sup -} we conclude that the complex is held together by a H-bond like interaction in both an asymmetric solvation environment, as represented by the cluster, and in a symmetric solvation environment, as represented by the bulk system. In the limits of the present results we postulate that the mechanism that governs the atmospheric oxidation of (Cl{sup -}){sub int} to (Cl{sub 2}){sub gas} on the surface of marine aerosols [Knipping et al. 2000] is initiated by the formation of an H-bonded OH...Cl{sup -} complex. Furthermore, since no evidence of charge transfer mechanism from Cl{sup -} to OH was found, in the liquid as well as in the cluster environments, a likely second step toward the oxidation of Cl{sup -} should consist in the reaction of the complex with a second Cl{sup -} that would result in the formation of the species Cl{sup -2} and OH{sup -}. (Cl{sub 2}){sub g} could then be formed upon charge exchange reaction with an impinging OH molecule.

  4. Solvation of uranyl-CMPO complexes in dry vs. humid forms of the [BMI][PF6] ionic liquid. A molecular dynamics study.

    Science.gov (United States)

    Chaumont, Alain; Wipff, Georges

    2006-01-28

    The solvation of the [UO(2)(NO(3))(CMPO)](+) and [UO(2)(NO(3))(2)(CMPO)(2)] complexes (CMPO = octyl(phenyl)-N,N-diisobutylmethylcarbamoyl phosphine oxide) is investigated by molecular dynamics in the "dry" and "humid" forms of a room temperature ionic liquid (IL) based on the 1-butyl-3-methylimidazolium (BMI(+)) cation and the hexafluorophosphate (PF(6)(-)) anion. The simulations reveal the importance of the solvent anions in "dry" conditions and of water molecules in the "humid" solvent. For the [UO(2)(NO(3))(CMPO)](+) complex, the monodentate vs. bidentate coordination modes of CMPO are compared, and the first solvation shell of uranyl is completed by 1-3 PF(6)(-) anions in the dry IL and by 2-3 water molecules in the humid IL, leading to a total coordination number close to 5. The energy analysis shows that interactions with the IL stabilize the [UO(2)(NO(3))(bi)(CMPO)(mono)](+) form (with bidentate nitrate and monodentate CMPO) in the dry IL and the [UO(2)(NO(3))(mono)(CMPO)(mono)](+) form (with monodentate nitrate and CMPO) in the humid IL. The extracted compound characterized by EXAFS is thus proposed to be the [UO(2)(NO(3))(mono)(CMPO)(mono)(H(2)O)(3)](+) species. Furthermore we compare the [UO(2)(NO(3))(2)(CMPO)(2)] complex in its associated and dissociated forms ([UO(2)(NO(3))(mono)(CMPO)(mono)](+) + CMPO + NO(3)(-)) and discuss the results in the context of uranyl extraction by CMPO to ionic liquids. PMID:16482292

  5. Acceleration of the chemistry solver for modeling DI engine combustion using dynamic adaptive chemistry (DAC) schemes

    Science.gov (United States)

    Shi, Yu; Liang, Long; Ge, Hai-Wen; Reitz, Rolf D.

    2010-03-01

    Acceleration of the chemistry solver for engine combustion is of much interest due to the fact that in practical engine simulations extensive computational time is spent solving the fuel oxidation and emission formation chemistry. A dynamic adaptive chemistry (DAC) scheme based on a directed relation graph error propagation (DRGEP) method has been applied to study homogeneous charge compression ignition (HCCI) engine combustion with detailed chemistry (over 500 species) previously using an R-value-based breadth-first search (RBFS) algorithm, which significantly reduced computational times (by as much as 30-fold). The present paper extends the use of this on-the-fly kinetic mechanism reduction scheme to model combustion in direct-injection (DI) engines. It was found that the DAC scheme becomes less efficient when applied to DI engine simulations using a kinetic mechanism of relatively small size and the accuracy of the original DAC scheme decreases for conventional non-premixed combustion engine. The present study also focuses on determination of search-initiating species, involvement of the NOx chemistry, selection of a proper error tolerance, as well as treatment of the interaction of chemical heat release and the fuel spray. Both the DAC schemes were integrated into the ERC KIVA-3v2 code, and simulations were conducted to compare the two schemes. In general, the present DAC scheme has better efficiency and similar accuracy compared to the previous DAC scheme. The efficiency depends on the size of the chemical kinetics mechanism used and the engine operating conditions. For cases using a small n-heptane kinetic mechanism of 34 species, 30% of the computational time is saved, and 50% for a larger n-heptane kinetic mechanism of 61 species. The paper also demonstrates that by combining the present DAC scheme with an adaptive multi-grid chemistry (AMC) solver, it is feasible to simulate a direct-injection engine using a detailed n-heptane mechanism with 543 species

  6. Examination of the formation process of pre-solvated and solvated electron in n-alcohol using femtosecond pulse radiolysis

    Science.gov (United States)

    Toigawa, Tomohiro; Gohdo, Masao; Norizawa, Kimihiro; Kondoh, Takafumi; Kan, Koichi; Yang, Jinfeng; Yoshida, Yoichi

    2016-06-01

    The formation process of pre-solvated and solvated electron in methanol (MeOH), ethanol (EtOH), n-butanol (BuOH), and n-octanol (OcOH) were investigated using a fs-pulse radiolysis technique by observing the pre-solvated electron at 1400 nm. The formation time constants of the pre-solvated electrons were determined to be 1.2, 2.2, 3.1, and 6.3 ps for MeOH, EtOH, BuOH, and OcOH, respectively. The formation time constants of the solvated electrons were determined to be 6.7, 13.6, 22.2, and 32.9 ps for MeOH, EtOH, BuOH, and OcOH, respectively. The formation dynamics and structure of the pre-solvated and solvated electrons in n-alcohols were discussed based on relation between the obtained time constant and dielectric relaxation time constant from the view point of kinetics. The observed formation time constants of the solvated electrons seemed to be strongly correlated with the second component of the dielectric relaxation time constants, which are related to single molecule motion. On the other hand, the observed formation time constants of the pre-solvated electrons seemed to be strongly correlated with the third component of the dielectric relaxation time constants, which are related to dynamics of hydrogen bonds.

  7. Solvation in supercritical water

    International Nuclear Information System (INIS)

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

  8. Forcing of stratospheric chemistry and dynamics during the Dalton Minimum

    Science.gov (United States)

    Anet, J. G.; Muthers, S.; Rozanov, E.; Raible, C. C.; Peter, T.; Stenke, A.; Shapiro, A. I.; Beer, J.; Steinhilber, F.; Brönnimann, S.; Arfeuille, F.; Brugnara, Y.; Schmutz, W.

    2013-11-01

    The response of atmospheric chemistry and dynamics to volcanic eruptions and to a decrease in solar activity during the Dalton Minimum is investigated with the fully coupled atmosphere-ocean chemistry general circulation model SOCOL-MPIOM (modeling tools for studies of SOlar Climate Ozone Links-Max Planck Institute Ocean Model) covering the time period 1780 to 1840 AD. We carried out several sensitivity ensemble experiments to separate the effects of (i) reduced solar ultra-violet (UV) irradiance, (ii) reduced solar visible and near infrared irradiance, (iii) enhanced galactic cosmic ray intensity as well as less intensive solar energetic proton events and auroral electron precipitation, and (iv) volcanic aerosols. The introduced changes of UV irradiance and volcanic aerosols significantly influence stratospheric dynamics in the early 19th century, whereas changes in the visible part of the spectrum and energetic particles have smaller effects. A reduction of UV irradiance by 15%, which represents the presently discussed highest estimate of UV irradiance change caused by solar activity changes, causes global ozone decrease below the stratopause reaching as much as 8% in the midlatitudes at 5 hPa and a significant stratospheric cooling of up to 2 °C in the mid-stratosphere and to 6 °C in the lower mesosphere. Changes in energetic particle precipitation lead only to minor changes in the yearly averaged temperature fields in the stratosphere. Volcanic aerosols heat the tropical lower stratosphere, allowing more water vapour to enter the tropical stratosphere, which, via HOx reactions, decreases upper stratospheric and mesospheric ozone by roughly 4%. Conversely, heterogeneous chemistry on aerosols reduces stratospheric NOx, leading to a 12% ozone increase in the tropics, whereas a decrease in ozone of up to 5% is found over Antarctica in boreal winter. The linear superposition of the different contributions is not equivalent to the response obtained in a simulation

  9. Solvation of Magnesium Dication: Molecular Dynamics Simulation and Vibrational Spectroscopic Study of Magnesium Chloride in Aqueous Solutions

    Czech Academy of Sciences Publication Activity Database

    Callahan, K. M.; Casillas-Ituarte, N. N.; Roeselová, Martina; Allen, H. C.; Tobias, D. J.

    2010-01-01

    Roč. 114, č. 15 (2010), s. 5141-5148. ISSN 1089-5639 R&D Projects: GA MŠk LC512; GA MŠk ME09064 Institutional research plan: CEZ:AV0Z40550506 Keywords : potential of mean force * ion pairing Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.732, year: 2010

  10. Dynamic light scattering with applications to chemistry, biology, and physics

    CERN Document Server

    Berne, Bruce J

    2000-01-01

    Lasers play an increasingly important role in a variety of detection techniques, making inelastic light scattering a tool of growing value in the investigation of dynamic and structural problems in chemistry, biology, and physics. Until the initial publication of this work, however, no monograph treated the principles behind current developments in the field.This volume presents a comprehensive introduction to the principles underlying laser light scattering, focusing on the time dependence of fluctuations in fluid systems; it also serves as an introduction to the theory of time correlation f

  11. Excitons in a Photosynthetic Light-Harvesting System A Combined Molecular Dynamics\\/Quantum Chemistry and Polaron Model Study

    CERN Document Server

    Damjanovic, A; Schulten, K; Damjanovic, Ana; Kosztin, Ioan; Schulten, Klaus

    2001-01-01

    The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with a novel approach which combines molecular dynamics (MD) simulations with quantum chemistry (QC) calculations. The MD simulations of an LH-II complex, solvated and embedded in a lipid bilayer at physiological conditions (with total system size of 87,055 atoms) revealed a pathway of a water molecule into the B800 binding site, as well as increased dimerization within the B850 BChl ring, as compared to the dimerization found for the crystal structure. The fluctuations of pigment (B850 BChl) excitation energies, as a function of time, were determined via ab initio QC calculations based on the geometries that emerged from the MD simulations. From the results of these calculations we constructed a time-dependent Hamiltonian of the B850 exciton system from which we determined the linear absorption spectrum. Finally, a polaron model is introduced to describe quantum mechanically both the excitonic and vibrat...

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

    Science.gov (United States)

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

  13. Interior and interfacial aqueous solvation of benzene dicarboxylate dianions and their methylated analogues: A combined molecular dynamics and photoelectron spectroscopy study

    Czech Academy of Sciences Publication Activity Database

    Minofar, B.; Vrbka, Luboš; Mucha, Martin; Jungwirth, Pavel; Yang, X.; Wang, X. B.; Fu, Y. J.; Wang, L. S.

    2005-01-01

    Roč. 109, - (2005), s. 5042-5049. ISSN 1089-5639 R&D Projects: GA MŠk(CZ) ME 644; GA MŠk(CZ) LC512 Grant ostatní: NSF(US) CHE041312; NSF(US) CHE0209719 Institutional research plan: CEZ:AV0Z40550506 Keywords : benzene dicarboxylate dianions * molecular dynamics * photoelectron spectroscopy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.898, year: 2005

  14. Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure

    Science.gov (United States)

    Piquemal, Jean-Philip; Perera, Lalith; Cisneros, G. Andrés; Ren, Pengyu; Pedersen, Lee G.; Darden, Thomas A.

    2006-08-01

    Molecular dynamics simulations were performed using a modified amoeba force field to determine hydration and dynamical properties of the divalent cations Ca2+ and Mg2+. The extension of amoeba to divalent cations required the introduction of a cation specific parametrization. To accomplish this, the Tholé polarization damping model parametrization was modified based on the ab initio polarization energy computed by a constrained space orbital variation energy decomposition scheme. Excellent agreement has been found with condensed phase experimental results using parameters derived from gas phase ab initio calculations. Additionally, we have observed that the coordination of the calcium cation is influenced by the size of the periodic water box, a recurrent issue in first principles molecular dynamics studies.

  15. Femtosecond X-Ray Scattering Study of Ultrafast Photoinduced Structural Dynamics in Solvated [Co(terpy)2]2+

    DEFF Research Database (Denmark)

    Biasin, Elisa; Brandt van Driel, Tim; Kjær, Kasper Skov;

    2016-01-01

    We study the structural dynamics of photoexcited [Co(terpy)2]2+ in an aqueous solution with ultrafast x-ray diffuse scattering experiments conducted at the Linac Coherent Light Source. Through direct comparisons with density functional theory calculations, our analysis shows that the...

  16. Natural Abundance 17O, 6Li NMR and Molecular Modeling Studies of the Solvation Structures of Lithium bis(fluorosulfonyl)imide/1,2-dimethoxyethane Liquid Electrolytes

    Energy Technology Data Exchange (ETDEWEB)

    Wan, Chuan; Hu, Mary Y.; Borodin, Oleg; Qian, Jiangfeng; Qin, Zhaohai; Zhang, Jiguang; Hu, Jian Z.

    2016-03-01

    Natural abundance 17O and 6Li NMR experiments, quantum chemistry and molecular dynamics studies were employed to investigate the solvation structures of Li+ at various concentrations of LiFSI in DME electrolytes in an effort to solve this puzzle. It was found that the chemical shifts of both 17O and 6Li changed with the concentration of LiFSI, indicating the changes of solvation structures with concentration. For the quantum chemistry calculations, the coordinated cluster LiFSI(DME)2 forms at first, and its relative ratio increases with increasing LiFSI concentration to 1 M. Then the solvation structure LiFSI(DME) become the dominant component. As a result, the coordination of forming contact ion pairs between Li+ and FSI- ion increases, but the association between Li+ and DME molecule decreases. Furthermore, at LiFSI concentration of 4 M the solvation structures associated with Li+(FSI-)2(DME), Li+2(FSI-)(DME)4 and (LiFSI)2(DME)3 become the dominant components. For the molecular dynamics simulation, with increasing concentration, the association between DME and Li+ decreases, and the coordinated number of FSI- increases, which is in perfect accord with the DFT results. These results provide more insight on the fundamental mechanism on the very high CE of Li deposition in these electrolytes, especially at high current density conditions.

  17. Colour chemistry and mini-review on hadron dynamics

    International Nuclear Information System (INIS)

    This paper consists of two parts, colour chemistry and mini-review on hadron dynamics. Colour is now popularly believed to be the basis of strong interaction. Unfortunately, the empirical evidence for colour remains as yet limited. It is necessary to seek an entirely new class of phenomena qualitatively different from those in a colourless world. Diquoniums are the simplest example. There are two types of diquoniums such as T-diquoniums and M-diquoniums. The spectrum, the decay pattern and the production mechanism are discussed. The existence of M-diquoniums would be verification of colour. The experimental situation is not yet very clear. Generalization to other multiquark states is discussed. The mini-review on hadron dynamics covers what is now known as soft hadron collision or small transverse momentum physics. There are some new results on standard Regge phenomenology, and it can be said that the standard Regge model for quantum number exchanges continues to be useful. The recent interest on the spectroscopy of multiquark states is reflected in the search for Regge exchanges of multiquark trajectories, and extends to the study of duality. A fair amount of effort was devoted to reconciling duality with unitarity, based on the dual topological unitarisation (DTU). The main result in this scheme is the calculation of the crossed meson loop with the topology of a cylinder. Asymptotic problems can be studied in Regge field theory without reference to DTU. The progress made in this Tokyo Conference on soft hadron dynamics is not dramatic. (Kato, T.)

  18. Inertial solvation in femtosecond 2D spectra

    Science.gov (United States)

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

    2001-03-01

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

  19. Molecular Dynamics Simulations on the solvation and interfacial behaviour of hydrophobic species. Applications to the TATB hypothesis and to the liquid/liquid extraction of cations to supercritical CO2

    International Nuclear Information System (INIS)

    We report molecular dynamics studies on the solvation of charged hydrophobic molecules in pure liquids and at liquid / liquid interfaces. The first part of the thesis deals with the TATB hypothesis according to which the Asφ4+ (TA+) and Bφ4- (TB-) ions have the same free energy of solvation in any solvent. The two ions are found to be solvated differently in pure liquids (water, chloroform, acetonitrile) as at a chloroform / water interface. These results are confirmed by free energy calculations and by simulations on iso-volume spherical S+ and S- ions, which perfectly meet the TATB criteria. The many methodological tests performed show the importance of (i) the corrected treatment of 'long range interactions' (ii) the precise repartition of atomic charges (iii) the solvent models, especially for water, on the + / - charge discrimination by solvent. In the second part, in relation to the liquid / liquid extraction of cations from water to supercritical CO2, we report the behaviour of ions (Cs+, UO22+, Eu3+), of un-complexed extractants molecules (tri-n-butylphosphate, calixarene), of their complexes with the cations and nitric acid at a preformed chloroform / water interface and during de-mixing simulations which started from a perfectly mixed CO2 / water solutions. These studies demonstrate the importance of interfacial phenomena, of simulation conditions and acid and extractant concentrations, in assisted ion extraction to supercritical CO2. (author)

  20. Femtosecond X-Ray Scattering Study of Ultrafast Photoinduced Structural Dynamics in Solvated [Co(terpy)2]2+

    CERN Document Server

    Biasin, Elisa; Kjær, Kasper S; Dohn, Asmus O; Christensen, Morten; Harlang, Tobias; Chabera, Pavel; Liu, Yizhu; Uhlig, Jens; Pápai, Mátyás; Németh, Zoltán; Hartsock, Robert; Liang, Winnie; Zhang, Jianxin; Alonso-Mori, Roberto; Chollet, Matthieu; Glownia, James M; Nelson, Silke; Sokaras, Dimosthenis; Assefa, Tadesse A; Britz, Alexander; Galler, Andreas; Gawelda, Wojciech; Bressler, Christian; Gaffney, Kelly J; Lemke, Henrik T; Møller, Klaus B; Nielsen, Martin M; Sundström, Villy; Vankó, György; Wärnmark, Kenneth; Canton, Sophie E; Haldrup, Kristoffer

    2016-01-01

    We study the structural dynamics of photoexcited [Co(terpy)2]2+ in an aqueous solution with ultrafast x-ray diffuse scattering experiments conducted at the Linac Coherent Light Source. Through direct comparisons with density functional theory calculations, our analysis shows that the photoexcitation event leads to elongation of the Co-N bonds, followed by coherent Co-N bond length oscillations arising from the impulsive excitation of a vibrational mode dominated by the symmetrical stretch of all six Co-N bonds. This mode has a period of 0.33 ps and decays on a subpicosecond time scale. We find that the equilibrium bond-elongated structure of the high spin state is established on a single-picosecond time scale and that this state has a lifetime of ~ 7 ps.

  1. Femtosecond soft x-ray spectroscopy of solvated transition metal complexes: Deciphering the interplay of electronic and structural dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Huse, Nils; Cho, Hana; Hong, Kiryong; Jamula, Lindsey; de Groot, Frank M. F.; Kim, Tae Kyu; McCusker, James K.; Schoenlein, Robert W.

    2011-03-09

    We present the first implementation of femtosecond soft X-ray spectroscopy as an ultrafast direct probe of the excited-state valence orbitals in solution-phase molecules. This method is applied to photoinduced spin crossover of [Fe(tren(py)3)]2+, where the ultrafast spinstate conversion of the metal ion, initiated by metal-to-ligand charge-transfer excitation, is directly measured using the intrinsic spin-state selectivity of the soft X-ray L-edge transitions. Our results provide important experimental data concerning the mechanism of ultrafast spin-state conversion and subsequent electronic and structural dynamics, highlighting the potential of this technique to study ultrafast phenomena in the solution phase.

  2. Femtosecond X-Ray Scattering Study of Ultrafast Photoinduced Structural Dynamics in Solvated [Co (terpy)2]2 +

    Science.gov (United States)

    Biasin, Elisa; van Driel, Tim Brandt; Kjær, Kasper S.; Dohn, Asmus O.; Christensen, Morten; Harlang, Tobias; Chabera, Pavel; Liu, Yizhu; Uhlig, Jens; Pápai, Mátyás; Németh, Zoltán; Hartsock, Robert; Liang, Winnie; Zhang, Jianxin; Alonso-Mori, Roberto; Chollet, Matthieu; Glownia, James M.; Nelson, Silke; Sokaras, Dimosthenis; Assefa, Tadesse A.; Britz, Alexander; Galler, Andreas; Gawelda, Wojciech; Bressler, Christian; Gaffney, Kelly J.; Lemke, Henrik T.; Møller, Klaus B.; Nielsen, Martin M.; Sundström, Villy; Vankó, György; Wärnmark, Kenneth; Canton, Sophie E.; Haldrup, Kristoffer

    2016-07-01

    We study the structural dynamics of photoexcited [Co (terpy)2]2 + in an aqueous solution with ultrafast x-ray diffuse scattering experiments conducted at the Linac Coherent Light Source. Through direct comparisons with density functional theory calculations, our analysis shows that the photoexcitation event leads to elongation of the Co-N bonds, followed by coherent Co-N bond length oscillations arising from the impulsive excitation of a vibrational mode dominated by the symmetrical stretch of all six Co-N bonds. This mode has a period of 0.33 ps and decays on a subpicosecond time scale. We find that the equilibrium bond-elongated structure of the high spin state is established on a single-picosecond time scale and that this state has a lifetime of ˜7 ps .

  3. Femtosecond X-Ray Scattering Study of Ultrafast Photoinduced Structural Dynamics in Solvated [Co(terpy)_{2}]^{2+}.

    Science.gov (United States)

    Biasin, Elisa; van Driel, Tim Brandt; Kjær, Kasper S; Dohn, Asmus O; Christensen, Morten; Harlang, Tobias; Chabera, Pavel; Liu, Yizhu; Uhlig, Jens; Pápai, Mátyás; Németh, Zoltán; Hartsock, Robert; Liang, Winnie; Zhang, Jianxin; Alonso-Mori, Roberto; Chollet, Matthieu; Glownia, James M; Nelson, Silke; Sokaras, Dimosthenis; Assefa, Tadesse A; Britz, Alexander; Galler, Andreas; Gawelda, Wojciech; Bressler, Christian; Gaffney, Kelly J; Lemke, Henrik T; Møller, Klaus B; Nielsen, Martin M; Sundström, Villy; Vankó, György; Wärnmark, Kenneth; Canton, Sophie E; Haldrup, Kristoffer

    2016-07-01

    We study the structural dynamics of photoexcited [Co(terpy)_{2}]^{2+} in an aqueous solution with ultrafast x-ray diffuse scattering experiments conducted at the Linac Coherent Light Source. Through direct comparisons with density functional theory calculations, our analysis shows that the photoexcitation event leads to elongation of the Co-N bonds, followed by coherent Co-N bond length oscillations arising from the impulsive excitation of a vibrational mode dominated by the symmetrical stretch of all six Co-N bonds. This mode has a period of 0.33 ps and decays on a subpicosecond time scale. We find that the equilibrium bond-elongated structure of the high spin state is established on a single-picosecond time scale and that this state has a lifetime of ∼7  ps. PMID:27419566

  4. Collective excitations in liquid DMSO : FIR spectrum, Low frequency vibrational density of states and ultrafast dipolar solvation dynamics

    CERN Document Server

    Hazra, Milan

    2016-01-01

    Valuable dynamical and structural information about neat liquid DMSO at ambient conditions can be obtained through study of low frequency vibrations in the far infrared (FIR), that is, terahertz regime. For DMSO, collective excitations as well as single molecule stretches and bends have been measured by different kinds of experiments such as OHD-RIKES and terahertz spectroscopy. In the present work we investigate the intermolecular vibrational spectrum of DMSO through three different computational techniques namely (i) the far-infra red spectrum obtained through Fourier transform of total dipole moment auto time correlation function, (ii) from Fourier transform of the translational and angular velocity time autocorrelation functions and a (iii) quenched normal mode analysis of the parent liquid at 300K. The three spectrum, although exhibit differences among each other, reveal similar features which are in good, semi-quantitative, agreement with experimental results. Study of participation ratio of the density...

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

    Science.gov (United States)

    Sonu; Kumari, Sunita; Saha, Subit K

    2016-01-21

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

  6. Vesper - Venus Chemistry and Dynamics Orbiter - A NASA Discovery Mission Proposal: Submillimeter Investigation of Atmospheric Chemistry and Dynamics

    Science.gov (United States)

    Chin, Gordon

    2011-01-01

    Vesper conducts a focused investigation of the chemistry and dynamics of the middle atmosphere of our sister planet- from the base of the global cloud cover to the lower thermosphere. The middle atmosphere controls the stability of the Venus climate system. Vesper determines what processes maintain the atmospheric chemical stability, cause observed variability of chemical composition, control the escape of water, and drive the extreme super-rotation. The Vesper science investigation provides a unique perspective on the Earth environment due to the similarities in the middle atmosphere processes of both Venus and the Earth. Understanding key distinctions and similarities between Venus and Earth will increase our knowledge of how terrestrial planets evolve along different paths from nearly identical initial conditions.

  7. Competitive Solvation of the Imidazolium Cation by Water and Methanol

    CERN Document Server

    Chaban, Vitaly

    2014-01-01

    Imidazolium-based ionic liquids are widely used in conjunction with molecular liquids for various applications. Solvation, miscibility and similar properties are of fundamental importance for successful implementation of theoretical schemes. This work reports competitive solvation of the 1,3-dimethylimidazolium cation by water and methanol. Employing molecular dynamics simulations powered by semiempirical Hamiltonian (electronic structure level of description), the local structure nearly imidazolium cation is described in terms of radial distribution functions. Although water and methanol are chemically similar, water appears systematically more successful in solvating the 1,3-dimethylimidazolium cation. This result fosters construction of future applications of the ternary ion-molecular systems.

  8. Design of a Dynamic Undergraduate Green Chemistry Course

    Science.gov (United States)

    Kennedy, Sarah A.

    2016-01-01

    The green chemistry course taught at Westminster College (PA) incorporates nontraditional teaching techniques and texts to educate future chemists about the importance of using green chemistry principles. The course is designed to introduce green chemistry concepts and demonstrate their inherent necessity by discussing historical missteps by the…

  9. Quantifying solvated electrons' delocalization.

    Science.gov (United States)

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

    2015-07-28

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

  10. Theoretical study of reaction dynamics in radiation chemistry

    International Nuclear Information System (INIS)

    The period from late 1950's to early 1970's was golden age of radiation chemistry. During this period the hydrated electron was discovered, various new phenomena were found in ionic processes in liquid hydrocarbons, and the trapped electron and electron tunneling were discovered in organic glasses. In those days radiation chemistry was a vast treasure-house of theoretical problems. We could find not only problems special to radiation chemistry but also many problems interesting as general physical chemistry. In this review I explain how some theoretical problems discovered in the field of radiation chemistry have evolved into those of general physical chemistry, with special emphasis on my own work. (author)

  11. Accurate modeling of molecular optical properties by a combination of molecular dynamics and quantum chemistry

    Czech Academy of Sciences Publication Activity Database

    Andrushchenko, Valery; Bouř, Petr

    Katowice : University of Silesia, 2014. O6. [Chemistry towards Biology. Central Europe Conference /7./. 09.09.2014-12.09.2014, Katowice] R&D Projects: GA ČR(CZ) GA14-03564S Grant ostatní: AV ČR(CZ) M200550902 Institutional support: RVO:61388963 Keywords : molecular dynamics * quantum chemistry * multi-scale spectra Subject RIV: CF - Physical ; Theoretical Chemistry

  12. Hydrophobic Solvation: Aqueous Methane Solutions

    Science.gov (United States)

    Konrod, Oliver; Lankau, Timm

    2007-01-01

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

  13. Hydrophobic solvation of nonspherical solutes

    International Nuclear Information System (INIS)

    The theory of hydrophobic effects presented by Pratt and Chandler is generalized to include nonpolar solutes which are distinctly aspherical. The theory is used to study the solvation of simple aspherical hydrocarbon solutes in liquid water. The radial solvation of each component of diatomiclike solutes is studied as a function of their separation, or bond length. From these results it is found that when the bond length is large enough that one water molecule can fit between the apolar pair, the radial solvation of each is the same as that when the bond length approaches infinity. The solvation of the various sites of the homologous series methane, ethane, propane, and n-butane is also studied, and effects of the geometrical structure of the solutes on their solvation is discussed

  14. Chemistry

    International Nuclear Information System (INIS)

    The chemical research and development efforts related to the design and ultimate operation of molten-salt breeder reactor systems are concentrated on fuel- and coolant-salt chemistry, including the development of analytical methods for use in these systems. The chemistry of tellurium in fuel salt is being studied to help elucidate the role of this element in the intergranular cracking of Hastelloy N. Studies were continued of the effect of oxygen-containing species on the equilibrium between dissolved UF3 and dissolved UF4, and, in some cases, between the dissolved uranium fluorides and graphite, and the UC2. Several aspects of coolant-salt chemistry are under investigation. Hydroxy and oxy compounds that could be formed in molten NaBF4 are being synthesized and characterized. Studies of the chemistry of chromium (III) compounds in fluoroborate melts were continued as part of a systematic investigation of the corrosion of structural alloys by coolant salt. An in-line voltammetric method for determining U4+/U3+ ratios in fuel salt was tested in a forced-convection loop over a six-month period. (LK)

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

    Science.gov (United States)

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

    2016-07-01

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

  16. Lithium solvation in dimethyl sulfoxide-acetonitrile mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Semino, Rocío; Zaldívar, Gervasio; Calvo, Ernesto J. [Departamento de Química Inorgánica Analítica y Química-Física e INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, 1428 Buenos Aires (Argentina); Laria, Daniel, E-mail: dhlaria@cnea.gov.ar [Departamento de Química Inorgánica Analítica y Química-Física e INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, 1428 Buenos Aires (Argentina); Departamento de Física de la Materia Condensada, Comisión Nacional de Energía Atómica, Avenida Libertador 8250, 1429 Buenos Aires (Argentina)

    2014-12-07

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

  17. Lithium solvation in dimethyl sulfoxide-acetonitrile mixtures

    International Nuclear Information System (INIS)

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

  18. Chemistry

    International Nuclear Information System (INIS)

    Research progress is reported in programs on fuel-salt chemistry, properties of compounds in the Li--Te system, Te spectroscopy UF4--H equilibria, porous electrode studies of molten salts, fuel salt-coolant salt reactions, thermodynamic properties of transition-metal fluorides, and properties of sodium fluoroborate. Developmental work on analytical methods is summarized including in-line analysis of molten MSBR fuel, analysis of coolant-salts for tritium, analysis of molten LiF--BeF2--ThF4 for Fe and analysis of LiF--BeF--ThF4 for Te

  19. Beyond Problem-Based Learning: Using Dynamic PBL in Chemistry

    Science.gov (United States)

    Overton, Tina L.; Randles, Christopher A.

    2015-01-01

    This paper describes the development and implementation of a novel pedagogy, dynamic problem-based learning. The pedagogy utilises real-world problems that evolve throughout the problem-based learning activity and provide students with choice and different data sets. This new dynamic problem-based learning approach was utilised to teach…

  20. Viscosity and Solvation

    Science.gov (United States)

    Robertson, C. T.

    1973-01-01

    Discusses theories underlying the phenomena of solution viscosities, involving the Jones and Dole equation, B-coefficient determination, and flickering cluster model. Indicates that viscosity measurements provide a basis for the study of the structural effects of ions in aqueous solutions and are applicable in teaching high school chemistry. (CC)

  1. Introduction to dynamic spin chemistry magnetic field effects on chemical and biochemical reactions

    CERN Document Server

    Hayashi, Hisaharu

    2004-01-01

    This book presents a detailed account of one of the most mysterious problems in science - whether ordinary magnetic fields can exert an appreciable influence on chemical and biochemical reactions. The first aim of the book is to introduce this research, through theoretical and dynamic spin chemistry, to graduate students and researchers, by means of detailed theoretical and experimental descriptions. The second aim is to review typical recent investigations, which will stimulate new interest and applications in the 21st century. Because dynamic spin chemistry is based on established science, i

  2. Dynamic sulfur chemistry as a key tool in the design of self-healing polymers

    Science.gov (United States)

    Martin, Roberto; Rekondo, Alaitz; Ruiz de Luzuriaga, Alaitz; Casuso, Pablo; Dupin, Damien; Cabañero, Germán; Grande, Hans J.; Odriozola, Ibon

    2016-08-01

    The rich variety of reversible or dynamic covalent chemistries based on sulfur offers a unique opportunity for the design of self-healing polymer networks. The reversibility of such chemical bonds can be used to create soft systems which can self-mend at ambient conditions. Here we focus on the mechanism of three different dynamic sulfur chemistries which have been used for the development of self-healing elastomers and hydrogels: thiolate/nanoparticle exchange, aromatic disulfide exchange and gold(I)-thiolate/disulfide exchange.

  3. Gas dynamics, optics and chemistry of an aircraft condensable wake

    Energy Technology Data Exchange (ETDEWEB)

    Grinats, E.S.; Kashevarov, A.V.; Stasenko, A.L. [Central Aerohydrodynamic Inst., Zhukovsky (Russian Federation)

    1997-12-31

    Prediction of the properties of a jet-and-vortex wake from an individual airplane is of great interest as the first step to assessment of the possible global changes in the atmosphere due to the world civil aviation. Several mathematical models of the different regions of an aircraft wake and corresponding numerical results are presented. The axisymmetric exhaust jet was simulated on the base of the well-known k-{epsilon} model of turbulence. Jet chemistry was investigated on the base of kinetic scheme of the gas phase reactions of enriched by including chemisorption by water droplets of several species and by taking into account of the photochemical processes. In the 3D far wake model, the numerical results for distribution of species exhausted by the engines and entrapped by the velocity field of two parallel vortices are shown. (R.P.) 7 refs.

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

    Science.gov (United States)

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

    2015-04-01

    The present special issue presents exciting experimental and theoretical results in the topic of "Solvation Science", a topic that emerges from physical, theoretical, and industrial chemistry, and is also of interest to a multitude of neighboring fields, such as inorganic and organic chemistry, biochemistry, physics and engineering. We hope that the articles will be highly useful for researchers who would like to enter this newly emerging area, and that it is a valuable source for the nucleation of new ideas and collaborations to better understand the active role of the solvent in reactions. PMID:25660560

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

    Science.gov (United States)

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

    2016-10-12

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

  6. Molecular Dynamics Simulations on the solvation and interfacial behaviour of hydrophobic species. Applications to the TATB hypothesis and to the liquid/liquid extraction of cations to supercritical CO{sub 2}; Simulations par dynamique moleculaire de la solvatation et du comportement interfacial d'especes hydrophobes: application a l'hypothese TATB et a l'extraction liquide/liquide de cations par le CO{sub 2} supercritique

    Energy Technology Data Exchange (ETDEWEB)

    Schurhammer, R

    2001-12-15

    We report molecular dynamics studies on the solvation of charged hydrophobic molecules in pure liquids and at liquid / liquid interfaces. The first part of the thesis deals with the TATB hypothesis according to which the As{phi}{sub 4}{sup +} (TA{sup +}) and B{phi}{sub 4}{sup -} (TB{sup -}) ions have the same free energy of solvation in any solvent. The two ions are found to be solvated differently in pure liquids (water, chloroform, acetonitrile) as at a chloroform / water interface. These results are confirmed by free energy calculations and by simulations on iso-volume spherical S{sup +} and S{sup -} ions, which perfectly meet the TATB criteria. The many methodological tests performed show the importance of (i) the corrected treatment of 'long range interactions' (ii) the precise repartition of atomic charges (iii) the solvent models, especially for water, on the + / - charge discrimination by solvent. In the second part, in relation to the liquid / liquid extraction of cations from water to supercritical CO{sub 2}, we report the behaviour of ions (Cs{sup +}, UO{sub 2}{sup 2+}, Eu{sup 3+}), of un-complexed extractants molecules (tri-n-butylphosphate, calixarene), of their complexes with the cations and nitric acid at a preformed chloroform / water interface and during de-mixing simulations which started from a perfectly mixed CO{sub 2} / water solutions. These studies demonstrate the importance of interfacial phenomena, of simulation conditions and acid and extractant concentrations, in assisted ion extraction to supercritical CO{sub 2}. (author)

  7. A Systematic Study of Chloride Ion Solvation in Water using van der Waals Inclusive Hybrid Density Functional Theory

    OpenAIRE

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

    2015-01-01

    In this work, the solvation and electronic structure of the aqueous chloride ion solution was investigated using Density Functional Theory (DFT) based \\textit{ab initio} molecular dynamics (AIMD). From an analysis of radial distribution functions, coordination numbers, and solvation structures, we found that exact exchange ($E_{\\rm xx}$) and non-local van der Waals (vdW) interactions effectively \\textit{weaken} the interactions between the Cl$^-$ ion and the first solvation shell. With a Cl-O...

  8. Preparation of cerium halide solvate complexes

    Science.gov (United States)

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

    2013-08-06

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

  9. Localized Template-Driven Functionalization of Nanoparticles by Dynamic Combinatorial Chemistry

    NARCIS (Netherlands)

    Nowak, Piotr; Saggiomo, Vittorio; Salehian, Fatemeh; Colomb-Delsuc, Mathieu; Han, Yang; Otto, Sijbren

    2015-01-01

    We have developed a method for the localized functionalization of gold nanoparticles using imine-based dynamic combinatorial chemistry. By using DNA templates, amines were grafted on the aldehyde-functionalized nanoparticles only if and where the nanoparticles interacted with the template molecules.

  10. Combined effects of surface conditions, boundary layer dynamics and chemistry on diurnal SOA evolution

    NARCIS (Netherlands)

    Janssen, R.H.H.; Vilà-Guerau de Arellano, J.; Ganzeveld, L.N.; Kabat, P.; Jimenez, J.L.; Farmer, D.K.; Heerwaarden, van C.C.; Mammarella, I.

    2012-01-01

    We study the combined effects of land surface conditions, atmospheric boundary layer dynamics and chemistry on the diurnal evolution of biogenic secondary organic aerosol in the atmospheric boundary layer, using a model that contains the essentials of all these components. First, we evaluate the mod

  11. Chemistry

    International Nuclear Information System (INIS)

    Research and development activities dealing with the chemical problems related to design and ultimate operation of molten-salt reactor systems are described. An experimental test stand was constructed to expose metallurgical test specimens to Te2 vapor at defined temperatures and deposition rates. To better define the chemistry of fluoroborate coolant, several aspects are being investigated. The behavior of hydroxy and oxy compounds in molten NaBF4 is being investigated to define reactions and compounds that may be involved in corrosion and/or could be involved in methods for trapping tritium. Two corrosion products of Hastelloy N, Na3CrF6 and Na5Cr3F14, were identified from fluoroborate systems. The evaluation of fluoroborate and alternate coolants continued. Research on the behavior of hydrogen and its isotopes is summarized. The solubilities of hydrogen, deuterium, and helium in Li2BeF4 are very low. The sorption of tritium on graphite was found to be significant (a few milligrams of tritium per kilogram of graphite), possibly providing a means of sequestering a portion of the tritium produced. Development of analytical methods continued with emphasis on voltammetric and spectrophotometric techniques for the in-line analysis of corrosion products such as Fe2+ and Cr3+ and the determination of the U3+/U4+ ratio in MSBR fuel salt. Similar studies were conducted with the NaBF4--NaF coolant salt. Information developed during the previous operation of the CSTF has been assessed and used to formulate plans for evaluation of in-line analytical methods in future CSTF operations. Electroanalytical and spectrophotometric research suggests that an electroactive protonic species is present in molten NaBF4--NaF, and that this species rapidly equilibrates with a volatile proton-containing species. Data obtained from the CSTF indicated that tritium was concentrated in the volatile species. (JGB)

  12. Aqueous vanadium ion dynamics relevant to bioinorganic chemistry: A review.

    Science.gov (United States)

    Kustin, Kenneth

    2015-06-01

    Aqueous solutions of the four highest vanadium oxidation states exhibit four diverse colors, which only hint at the diverse reactions that these ions can undergo. Cationic vanadium ions form complexes with ligands; anionic vanadium ions form complexes with ligands and self-react to form isopolyanions. All vanadium species undergo oxidation-reduction reactions. With a few exceptions, elucidation of the dynamics of these reactions awaited the development of fast reaction techniques before the kinetics of elementary ligation, condensation, reduction, and oxidation of the aqueous vanadium ions could be investigated. As the biological roles played by endogenous and therapeutic vanadium expand, it is appropriate to bring the results of the diverse kinetics studies under one umbrella. To achieve this goal this review presents a systematic examination of elementary aqueous vanadium ion dynamics. PMID:25578410

  13. Surface Effects on Aqueous Ionic Solvation: A Molecular Dynamics Simulation Study of NaCl at the Air/Water Interface from Infinite Dilution to Saturation

    Czech Academy of Sciences Publication Activity Database

    Jungwirth, Pavel; Tobias, D. J.

    2000-01-01

    Roč. 104, č. 32 (2000), s. 7702-7706. ISSN 1089-5647 Grant ostatní: NATO Science Program(XE) CLG-974459 Institutional research plan: CEZ:AV0Z4040901; CEZ:A54/98:Z4-040-9-ii Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.386, year: 2000

  14. Metascalable molecular dynamics simulation of nano-mechano-chemistry

    Science.gov (United States)

    Shimojo, F.; Kalia, R. K.; Nakano, A.; Nomura, K.; Vashishta, P.

    2008-07-01

    We have developed a metascalable (or 'design once, scale on new architectures') parallel application-development framework for first-principles based simulations of nano-mechano-chemical processes on emerging petaflops architectures based on spatiotemporal data locality principles. The framework consists of (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms, (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these scalable algorithms onto hardware. The EDC-STEP-HCD framework exposes and expresses maximal concurrency and data locality, thereby achieving parallel efficiency as high as 0.99 for 1.59-billion-atom reactive force field molecular dynamics (MD) and 17.7-million-atom (1.56 trillion electronic degrees of freedom) quantum mechanical (QM) MD in the framework of the density functional theory (DFT) on adaptive multigrids, in addition to 201-billion-atom nonreactive MD, on 196 608 IBM BlueGene/L processors. We have also used the framework for automated execution of adaptive hybrid DFT/MD simulation on a grid of six supercomputers in the US and Japan, in which the number of processors changed dynamically on demand and tasks were migrated according to unexpected faults. The paper presents the application of the framework to the study of nanoenergetic materials: (1) combustion of an Al/Fe2O3 thermite and (2) shock initiation and reactive nanojets at a void in an energetic crystal.

  15. Dynamic coupling of bulk chemistry, trace elements and mantle flow

    Science.gov (United States)

    Davies, J. H.; Heck, H. V.; Nowacki, A.; Wookey, J. M.; Elliott, T.; Porcelli, D.

    2015-12-01

    Fully dynamical models that not only track the evolution of chemical heterogeneities through the mantle, but also incorporate the effect of chemical heterogeneities on the dynamics of mantle convection are now emerging. Since in general analytical solutions to these complex problems are lacking, careful testing and investigations of the effect and usefulness of these models is needed. We extend our existing numerical mantle convection code that can track fluid flow in 3D spherical geometry and tracks both bulk chemical components (basal fraction) and different trace elements. The chemical components fractionate upon melting when and where the solidus is crossed. Now, the chemical information will effect the flow of the fluid in the following ways: The bulk composition will link to density and the (radioactive) trace element abundance to heat production. Results will be reported of the effect of different density structures; either starting with a primordial dense layer at the base of the mantle, having all density variation originate from melting (basalt production), or a combination between these two end-member scenarios. In particular we will focus on the connection between large scale bulk chemical structures in the (deep) mantle and the evolution of the distribution of noble gasses (He and Ar). The distribution of noble gasses depend upon 1) assumptions on the initial distributions in the mantle, 2) the mantle flow, 3) radioactive production and, 4) outgassing to the atmosphere upon melting close to the surface.

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

    Science.gov (United States)

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

    2005-01-01

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

  17. Dynamics and Disequilibrium Carbon Chemistry in HD 209458b's Atmosphere

    CERN Document Server

    Cooper, C S; Cooper, Curtis S.; Showman, Adam P.

    2006-01-01

    Chemical equilibrium considerations suggest that, assuming solar elemental abundances, carbon on HD 209458b is sequestered primarily as carbon monoxide (CO) and methane (CH4). The relative mole fractions of CO(g) and CH4(g) in chemical equilibrium are expected to vary greatly according to variations in local temperature and pressure. We show, however, that in the p = 1--1000 mbar range, chemical equilibrium does not hold. To explore disequilibrium effects, we couple the chemical kinetics of CO and CH4 to a three-dimensional numerical model of HD 209458b's atmospheric circulation. These simulations show that vigorous dynamics caused by uneven heating of this tidally locked planet homogenize the CO and CH4 concentrations at p < 1 bar, even in the presence of lateral temperature variations of ~500--1000 K. In the 1--1000 mbar pressure range, we find that over 98% of the carbon is in CO. This is true even in cool regions where CH4 is much more stable thermodynamically. Our work shows furthermore that planets 3...

  18. Coupling dynamics and chemistry in the air pollution modelling of street canyons: A review.

    Science.gov (United States)

    Zhong, Jian; Cai, Xiao-Ming; Bloss, William James

    2016-07-01

    Air pollutants emitted from vehicles in street canyons may be reactive, undergoing mixing and chemical processing before escaping into the overlying atmosphere. The deterioration of air quality in street canyons occurs due to combined effects of proximate emission sources, dynamical processes (reduced dispersion) and chemical processes (evolution of reactive primary and formation of secondary pollutants). The coupling between dynamics and chemistry plays a major role in determining street canyon air quality, and numerical model approaches to represent this coupling are reviewed in this article. Dynamical processes can be represented by Computational Fluid Dynamics (CFD) techniques. The choice of CFD approach (mainly the Reynolds-Averaged Navier-Stokes (RANS) and Large-Eddy Simulation (LES) models) depends on the computational cost, the accuracy required and hence the application. Simplified parameterisations of the overall integrated effect of dynamics in street canyons provide capability to handle relatively complex chemistry in practical applications. Chemical processes are represented by a chemical mechanism, which describes mathematically the chemical removal and formation of primary and secondary species. Coupling between these aspects needs to accommodate transport, dispersion and chemical reactions for reactive pollutants, especially fast chemical reactions with time scales comparable to or shorter than those of typical turbulent eddies inside the street canyon. Different approaches to dynamical and chemical coupling have varying strengths, costs and levels of accuracy, which must be considered in their use for provision of reference information concerning urban canopy air pollution to stakeholders considering traffic and urban planning policies. PMID:27149146

  19. Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

    Science.gov (United States)

    Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

  20. Electron solvation in aqueous reverse micelles: Equilibrium properties

    Science.gov (United States)

    Laria, Daniel; Kapral, Raymond

    2002-10-01

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

  1. Atomic hydration potentials using a Monte Carlo Reference State (MCRS) for protein solvation modeling

    OpenAIRE

    Makeev Vsevolod J; Rakhmanov Sergei V

    2007-01-01

    Abstract Background Accurate description of protein interaction with aqueous solvent is crucial for modeling of protein folding, protein-protein interaction, and drug design. Efforts to build a working description of solvation, both by continuous models and by molecular dynamics, yield controversial results. Specifically constructed knowledge-based potentials appear to be promising for accounting for the solvation at the molecular level, yet have not been used for this purpose. Results We dev...

  2. Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene

    International Nuclear Information System (INIS)

    The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories

  3. Electron transfer theory revisit: Quantum solvation effect

    CERN Document Server

    Han, P; Cui, P; Mo, Y; He, G; Yan, Y J; Han, Ping; Xu, Rui-Xue; Cui, Ping; Mo, Yan; He, Guozhong; Yan, YiJing

    2006-01-01

    The effect of solvation on the electron transfer (ET) rate processes is investigated on the basis of the exact theory constructed in J. Phys. Chem. B Vol. 110, (2006); quant-ph/0604071. The nature of solvation is studied in a close relation with the mechanism of ET processes. The resulting Kramers' turnover and Marcus' inversion characteristics are analyzed accordingly. The classical picture of solvation is found to be invalid when the solvent longitudinal relaxation time is short compared with the inverse temperature.

  4. Dynamics and mechanisms of catalytic processes and hot chemistry. Final report, March 1, 1972-October 31, 1984

    International Nuclear Information System (INIS)

    General areas of research addressed are recoil chemistry of halogens, tritium, and sulfur, radiotracer methods for studies of chemical dynamics, thermal and photochemistry of sulfur dioxide, and photochemistry and photoassistance in catalytic systems

  5. Systematic solvate screening of trospium chloride: discovering hydrates of a long-established pharmaceutical

    Czech Academy of Sciences Publication Activity Database

    Sládková, V.; Skalická, T.; Skořepová, E.; Čejka, J.; Eigner, Václav; Kratochvíl, B.

    2015-01-01

    Roč. 17, č. 25 (2015), s. 4712-4721. ISSN 1466-8033 R&D Projects: GA ČR(CZ) GA14-03276S Institutional support: RVO:68378271 Keywords : trospium chloride * solvate screening * x-ray crystallography * Jana2006 Subject RIV: CC - Organic Chemistry Impact factor: 4.034, year: 2014

  6. Constant energy DFT molecular dynamics simulations of solvated carbohydrates at the B3LYP/6-31+G* level of theory

    Science.gov (United States)

    The disaccharide, alpha/beta-maltose, has been studied using constant energy ab initio molecular dynamics at the B3LYP/6-31+G* COSMO (solvent) level of theory. Maltose is of particular interest as the variation in glycosidic dihedral angles is dependent upon the starting hydroxyl conformation. Tha...

  7. Simulated solvation of organic ions II: Study of linear alkylated

    OpenAIRE

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

    2015-01-01

    We investigated the solvation of carboxylate ions from formate to hexanoate, in droplets of 50 to 1000 water molecules and neat water, by computations using standard molecular dynamics and sophisticated polarizable models. The carboxylate ions from methanoate to hexanoate show strong propensity for the air/water interface in small droplets. Only the ions larger than propanoate retain propensity for the interface in larger droplets, where their enthalpic stabilization by ion/water dispersion i...

  8. 3D radiative hydrodynamic simulations of protostellar collapse with H-C-O dynamical chemistry

    CERN Document Server

    Dzyurkevich, Natalia; Lesaffre, Pierre; Semenov, Dimitry

    2016-01-01

    Combining the co-evolving chemistry, hydrodynamics and radiative transfer is an important step for star formation studies. It allows both a better link to observations and a self-consistent monitoring of the magnetic dissipation in the collapsing core. Our aim is to follow a chemo-dynamical evolution of collapsing dense cores with a reduced gas-grain chemical network. We present the results of radiative hydrodynamic (RHD) simulations of 1 M$_\\odot$ isolated dense core collapse. The physical setup includes RHD and dynamical evolution of a chemical network. To perform those simulations, we merged the multi-dimensional adaptive-mesh-refinement code RAMSES and the thermo-chemistry Paris-Durham shock code. We simulate the formation of the first hydro-static core (FHSC) and the co-evolution of 56 species describing mainly H-C-O chemistry. Accurate benchmarking is performed, testing the reduced chemical network against a well-establiched complex network. We show that by using a compact set of reactions, one can matc...

  9. Parameterization and evaluation of sulfate adsorption in a dynamic soil chemistry model

    International Nuclear Information System (INIS)

    Including sulfate adsorption improves the dynamic behavior of the SAFE model. - Sulfate adsorption was implemented in the dynamic, multi-layer soil chemistry model SAFE. The process is modeled by an isotherm in which sulfate adsorption is considered to be fully reversible and dependent on sulfate concentration as well as pH in soil solution. The isotherm was parameterized by a site-specific series of simple batch experiments at different pH (3.8-5.0) and sulfate concentration (10-260 μmol l-1) levels. Application of the model to the Lake Gaardsjoen roof covered site shows that including sulfate adsorption improves the dynamic behavior of the model and sulfate adsorption and desorption delay acidification and recovery of the soil. The modeled adsorbed pool of sulfate at the site reached a maximum level of 700 mmol/m2 in the late 1980s, well in line with experimental data

  10. Impact Of Geo-engineered Aerosols On Stratospheric Chemistry And Dynamics

    Science.gov (United States)

    Tilmes, S.; Garcia, R. R.; Kinnison, D. E.; Gettelman, A.; Rasch, P. J.

    2008-12-01

    Geo-engineering schemes have been proposed to alleviate the consequences of global warming; one proposed scheme is to inject sulfur into the stratosphere so as to mimic the effects of large volcanic eruptions. Past volcanic eruptions have shown that strongly enhanced sulfate aerosols in the stratosphere result in a higher planetary albedo, leading to surface cooling. However, the increase of sulfate aerosol surface area enhances heterogeneous reactions in the stratosphere that lead to ozone loss. The potential for high Arctic ozone depletion in the context of geo-engineering is known. On the other hand, halogen compounds are now decreasing in the atmosphere as a result of the enforcement of the Montreal Protocol and its amendments, and this is expected to bring about the recovery of the ozone layer and to lessen the potential impact of aerosols. In this study we present results of calculations made with NCAR's Whole Atmosphere Community Climate Model (WACCM), focusing on the impact of Geo-engineering on stratospheric chemistry and dynamics. Aside from changes in heterogeneous reactions, changes in stratospheric dynamics have a significant impact on ozone. On average, changes of both chemistry and dynamics result in a slowdown of the recovery of ozone for mid- and high latitudes. An increase of ozone depletion as a result of geo-engineering was found in both polar regions for the period between 2040-2050.

  11. Topical Review: Molecular reaction and solvation visualized by time-resolved X-ray solution scattering: Structure, dynamics, and their solvent dependence

    Directory of Open Access Journals (Sweden)

    Kyung Hwan Kim

    2014-01-01

    Full Text Available Time-resolved X-ray solution scattering is sensitive to global molecular structure and can track the dynamics of chemical reactions. In this article, we review our recent studies on triiodide ion (I3– and molecular iodine (I2 in solution. For I3–, we elucidated the excitation wavelength-dependent photochemistry and the solvent-dependent ground-state structure. For I2, by combining time-slicing scheme and deconvolution data analysis, we mapped out the progression of geminate recombination and the associated structural change in the solvent cage. With the aid of X-ray free electron lasers, even clearer observation of ultrafast chemical events will be made possible in the near future.

  12. Aespoe project. Hydrogeology and hydro-chemistry used to indicate present flow dynamics

    International Nuclear Information System (INIS)

    Major development in hydrogeological and hydrochemical groundwater modelling have been used independently to describe the present flow dynamics prior to and following the construction of the Aespoe Hard Rock Laboratory. Groundwater flow models used in calculating flow paths in the rock mass can be compared to the geochemical groundwater mixing and mass balance modelling in order to provide useful information on flow paths and transport times. However, there is still much work to be done to improve the integration between models on groundwater flow, groundwater chemistry and transport of solutes. (author)

  13. A molecular density functional theory to study solvation in water

    CERN Document Server

    Jeanmairet, Guillaume

    2014-01-01

    A classical density functional theory is applied to study solvation of solutes in water. An approx- imate form of the excess functional is proposed for water. This functional requires the knowledge of pure solvent direct correlation functions. Those functions can be computed by using molecular simulations such as molecular dynamic or Monte Carlo. It is also possible to use functions that have been determined experimentally. The functional minimization gives access to the solvation free energy and to the equilibrium solvent density. Some correction to the functional are also proposed to get the proper tetrahedral order of solvent molecules around a charged solute and to reproduce the correct long range hydrophobic behavior of big apolar solutes. To proceed the numerical minimization of the functional, the theory has been discretized on two tridimensional grids, one for the space coordinates, the other for the angular coordinates, in a functional minimization code written in modern Fortran, mdft. This program i...

  14. Triazolinediones enable ultrafast and reversible click chemistry for the design of dynamic polymer systems

    Science.gov (United States)

    Billiet, Stijn; de Bruycker, Kevin; Driessen, Frank; Goossens, Hannelore; van Speybroeck, Veronique; Winne, Johan M.; Du Prez, Filip E.

    2014-09-01

    With its focus on synthetic reactions that are highly specific and reliable, ‘click’ chemistry has become a valuable tool for many scientific research areas and applications. Combining the modular, covalently bonded nature of click-chemistry linkages with an ability to reverse these linkages and reuse the constituent reactants in another click reaction, however, is a feature that is not found in most click reactions. Here we show that triazolinedione compounds can be used in click-chemistry applications. We present examples of simple and ultrafast macromolecular functionalization, polymer-polymer linking and polymer crosslinking under ambient conditions without the need for a catalyst. Moreover, when triazolinediones are combined with indole reaction partners, the reverse reaction can also be induced at elevated temperatures, and the triazolinedione reacted with a different reaction partner, reversibly or irreversibly dependent on its exact nature. We have used this ‘transclick’ reaction to introduce thermoreversible links into polyurethane and polymethacrylate materials, which allows dynamic polymer-network healing, reshaping and recycling.

  15. Dynamic Combinatorial Chemistry and Organocatalysis with Thiosemicarbazones and Organocatalysts for Hydrazone and Oxime Bioconjugations

    DEFF Research Database (Denmark)

    Larsen, Dennis

    The first part of this thesis describes the use of thiosemicarbazones for dynamic combinatorial chemistry. Building blocks incorporating thiosemicarbazides and acetalprotected aldehydes were synthesised and conditions where these building blocks formed dynamic combinatorial libraries under...... of this thesis describes the development of new bifunctional organocatalysts for the formation of hydrazones and oximes at neutral pH. New effective variants of the previously known anthranilic acid-based catalysts were discovered, and via a virtual breakdown of the structure of already identified...... catalysts, two new types of catalysts were discovered: The 2-aminophenols and the 2-(aminomethyl)benzimidazoles. With aldehyde substrates none of the newly discovered catalysts were as effective as a previously discovered benzenephosphonic acid, but with aromatic ketones, an otherwise challenging class of...

  16. Spatiotemporal dynamics of spring and stream water chemistry in a high-mountain area

    International Nuclear Information System (INIS)

    The present study deals with the application of the self-organizing map (SOM) technique in the exploration of spatiotemporal dynamics of spring and stream water samples collected in the Chocholowski Stream Basin located in the Tatra Mountains (Poland). The SOM-based classification helped to uncover relationships between physical and chemical parameters of water samples and factors determining the quality of water in the studied high-mountain area. In the upper part of the Chocholowski Stream Basin, located on the top of the crystalline core of the Tatras, concentrations of the majority of ionic substances were the lowest due to limited leaching. Significantly higher concentration of ionic substances was detected in spring and stream samples draining sedimentary rocks. The influence of karst-type springs on the quality of stream water was also demonstrated. - Highlights: → We use SOM approach to explore physiochemical data for mountain waters. → Geologic structure and hydrological events impact water chemistry. → Limited leaching, typical of crystalline core, reflects in low water mineralization. → Sedimentary rocks are susceptible for leaching. → Eutrophication has not been shown to be a threat in the Chocholowska Valley. - Spatiotemporal dynamics of spring and stream water chemistry in unique high-mountain area was evaluated by the self-organizing map technique.

  17. Coordination Chemistry and Structural Dynamics of a Long and Flexible Piperazine-Derived Ligand.

    Science.gov (United States)

    Hawes, Chris S; Hamilton, Sophie E; Hicks, Jamie; Knowles, Gregory P; Chaffee, Alan L; Turner, David R; Batten, Stuart R

    2016-07-01

    A long and highly flexible internally functionalized dipyridyl ligand α,α'-p-xylylenebis(1-(4-pyridylmethylene)-piper-4-azine), L, has been employed in the synthesis of a series of coordination polymer materials with Co(II), Cd(II), and Ag(I) ions. In poly-[Cd(L)(TPA)] 1 and poly-[Co(L)(IPA)], 2, (TPA = terephthalate, IPA = isophthalate) the ligand adopts a similar linear conformation to that seen in the structure of the unbound molecule and provides a long (2.6 nm) metal-metal bridging distance. Due to the mismatch of edge lengths with that provided by the carboxylate coligands, geometric distortions from the regular dia and (4,4) network geometries for 1 and 2, respectively, are observed. In poly-[Ag2(CF3SO3)2(L)], 3, the ligand coordinates through both pyridine groups and two of the four piperazine nitrogen donors, forming a high-connectivity 2-dimensional network. The compound poly-[Ag2(L)](BF4)2·2MeCN, 4, a porous 3-dimensional cds network, undergoes a fascinating and rapid single-crystal-to-single-crystal rearrangement on exchange of the acetonitrile guests for water in ambient air, forming a nonporous hydrated network poly-[Ag2(L)](BF4)2·2H2O, 5, in which the well-ordered guest water molecules mediate the rearrangement of the tetrafluoroborate anions and the framework itself through hydrogen bonding. The dynamics of the system are examined in greater detail through the preparation of a kinetic product, the dioxane-solvated species poly-[Ag2(L)](BF4)2·2C4H8O2, 6, which undergoes a slow conversion to 5 over the course of approximately 16 h, a transition which can be monitored in real time. The reverse transformation can also be observed on immersing the hydrate 5 in dioxane. The structural features and physical properties of each of the materials can be rationalized based on the flexible and multifunctional nature of the ligand molecule, as well as the coordination behavior of the chosen metal ions. PMID:27328206

  18. Segue between Favorable and Unfavorable Solvation

    Energy Technology Data Exchange (ETDEWEB)

    Maibaum, Lutz; Chandler, David

    2007-03-21

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

  19. Segue Between Favorable and Unfavorable Solvation

    OpenAIRE

    Maibaum, Lutz; Chandler, David

    2007-01-01

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

  20. Statistical analysis of cellular detonation dynamics from numerical simulations: one-step chemistry

    Science.gov (United States)

    Sharpe, G. J.; Radulescu, M. I.

    2011-10-01

    In this paper, two methods are developed for statistically analysing the nonlinear cellular dynamics from numerical simulations of gaseous detonations, one use of which is the systematic determination of detonation cell sizes from such simulations. Both these methods rely on signed vorticity records in which the individual families of transverse waves are captured independently. The first method involves an automated extraction of the main triple-point tracks from the vorticity records, allowing statistical analysis of the spacings between neighbouring tracks. The second method uses the autocorrelation function to spectrally analyse the vorticity records. These methods are then employed for a preliminary analysis of the cellular dynamics of the standard, idealized one-step chemistry model. Evidence is found for 'cell size doubling' bifurcations in the one-step model as the cellular dynamics become more irregular (e.g. as the activation is increased). It is also shown that the statistical models converge slowly due to systematic 'shot-to-shot' variation in the cellular dynamics for fixed parameters with different initial perturbations. Instead, it appears that a range of equally probable cell sizes can be obtained for given parameters.

  1. Hydroxide Solvation and Transport in Anion Exchange Membranes

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Chen [Univ. of Chicago, IL (United States); Wuhan Univ. (China); Tse, Ying-Lung Steve [Univ. of Chicago, IL (United States); Lindberg, Gerrick E. [Northern Arizona Univ., Flagstaff, AZ (United States); Knight, Chris [Argonne National Lab. (ANL), Argonne, IL (United States); Voth, Gregory A. [Univ. of Chicago, IL (United States)

    2016-01-27

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

  2. Development and evaluation of the aerosol dynamic and gas phase chemistry model ADCHEM

    Directory of Open Access Journals (Sweden)

    P. Roldin

    2010-08-01

    Full Text Available The aim of this work was to develop a model ideally suited for detailed studies on aerosol dynamics, gas and particle phase chemistry within urban plumes, from local scale (1×1 km2 to regional or global scale. This article describes and evaluates the trajectory model for Aerosol Dynamics, gas and particle phase CHEMistry and radiative transfer (ADCHEM, which has been developed and used at Lund University since 2007. The model treats both vertical and horizontal dispersion perpendicular to an air mass trajectory (2-space dimensions, which is not treated in Lagrangian box-models (0-space dimensions. The Lagrangian approach enables a more detailed representation of the aerosol dynamics, gas and particle phase chemistry and a finer spatial and temporal resolution compared to that of available regional 3D-CTMs. These features make it among others ideally suited for urban plume studies. The aerosol dynamics model includes Brownian coagulation, dry deposition, wet deposition, in-cloud processing, condensation, evaporation, primary particle emissions and homogeneous nucleation. The gas phase chemistry model calculates the gas phase concentrations of 63 different species, using 119 different chemical reactions. Daily isoprene and monoterpene emissions from European forests were simulated separately with the vegetation model LPJ-GUESS, and included as input to ADCHEM. ADCHEM was used to simulate the ageing of the urban plumes from the city of Malmö in Southern Sweden (280 000 inhabitants. Several sensitivity tests were performed concerning the number of size bins, size structure method, coupled or uncoupled condensation, the volatility basis set (VBS or traditional 2-product model for secondary organic aerosol formation, different aerosol dynamic processes and vertical and horizontal mixing. The simulations show that the full-stationary size structure gives accurate results with little numerical diffusion when more than 50 size bins are used

  3. Amplification without instability: applying fluid dynamical insights in chemistry and biology

    International Nuclear Information System (INIS)

    While amplification of small perturbations often arises from instability, transient amplification is possible locally even in asymptotically stable systems. That is, knowledge of a system's stability properties can mislead one's intuition for its transient behaviors. This insight, which has an interesting history in fluid dynamics, has more recently been rediscovered in ecology. Surprisingly, many nonlinear fluid dynamical and ecological systems share linear features associated with transient amplification of noise. This paper aims to establish that these features are widespread in many other disciplines concerned with noisy systems, especially chemistry, cell biology and molecular biology. Here, using classic nonlinear systems and the graphical language of network science, we explore how the noise amplification problem can be reframed in terms of activatory and inhibitory interactions between dynamical variables. The interaction patterns considered here are found in a great variety of systems, ranging from autocatalytic reactions and activator–inhibitor systems to influential models of nerve conduction, glycolysis, cell signaling and circadian rhythms. (paper)

  4. Development of a computational fluid dynamics and chemistry model for the fouling of jet fuels

    Science.gov (United States)

    Krazinski, J. L.; Vanka, S. P.; Pearce, J. A.; Roquemore, W. M.

    1990-03-01

    A new approach has been devised in which Computational Fluid Dynamic and Chemistry (CFDC) models are employed to predict the fluid mechanics, heat transfer, and deposition in fuel system components. The structure of this model is such that it has the potential of being used as a tool for research or to assist in the design of heat exchangers or other fuel system components. The model contains several unknown parameters that must be calibrated using experimental data for a particular fuel. This paper describes the development of the model, a method of calibrating the model, and a sensitivity analysis of the effects of different model parameters on predicted deposition rates in a heated tube.

  5. Understanding solvation in the low global warming hydrofluoroolefin HFO-1234ze propellant.

    Science.gov (United States)

    Yang, Lin; da Rocha, Sandro R P

    2014-09-11

    Hydrofluoroolefins (HFOs), with zero ozone-depleting effect and very low global warming potential, are considered to be the next-generation high-pressure working fluids. They have industrial relevance in areas including refrigeration and medical aerosols. One major challenge expected in the replacement of existing working fluids with HFOs is the solubility and solvation of additives in such hydrophobic and oleophobic low dielectric semifluorinated solvents. The study of the solvation of chemistries that represent those additives by HFOs is, therefore, of great relevance. In this work, we systematically investigate how the polarity and structure of fragments (the tail, t) that represent those additives affect their binding energy (Eb) with HFO-1234ze (1,1,1,3-tetrafluoropropene) (the solvent, s; Eb(st)). We also compare and contrast those results with those for the working fluids that are most widely used in the industry, the hydrofluoroalkanes (HFAs) HFA-134a and HFA-227. Three main chemistries were investigated: alkanes, ethers, and esters. It was found that HFO-1234ze interacts quite favorably with ethers and esters, as indicated by their Eb(st), while Eb(st) with alkanes was much lower. While ether and ester groups showed little difference in Eb(st), the much lower self-interaction energy between ether tail-tail fragments (Eb(tt)) is expected to result in improved solubility/solvation of those groups in HFO-1234ze when compared with the more polar ester groups. The ratio Eb(st)/Eb(tt) is defined as the enhancement factor (Eenh) and is expected to be a better predictor of solubility/solvation of the tail fragments. The branching of the tail groups upon the addition of pendant CH3 groups did not significantly affect the solvation by the propellant. At low branching density (one CH3 pendant group), it did not affect tail-tail self-interaction either. However, at high enough branching (two CH3 groups), steric hindrance caused a significant decrease in Eb(tt) and

  6. Implementation of a Research-Based Lab Module in a High School Chemistry Curriculum: A Study of Classroom Dynamics

    Science.gov (United States)

    Pilarz, Matthew

    2013-01-01

    For this study, a research-based lab module was implemented in two high school chemistry classes for the purpose of examining classroom dynamics throughout the process of students completing the module. A research-based lab module developed for use in undergraduate laboratories by the Center for Authentic Science Practice in Education (CASPiE) was…

  7. Solvation structure and transport properties of alkali cations in dimethyl sulfoxide under exogenous static electric fields

    Energy Technology Data Exchange (ETDEWEB)

    Kerisit, Sebastien [Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Vijayakumar, M., E-mail: Vijay@pnnl.gov, E-mail: karl.mueller@pnnl.gov [Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Joint Center for Energy Storage Research, Fundamental and Computational Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Han, Kee Sung [Joint Center for Energy Storage Research, Fundamental and Computational Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Mueller, Karl T., E-mail: Vijay@pnnl.gov, E-mail: karl.mueller@pnnl.gov [Joint Center for Energy Storage Research, Fundamental and Computational Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802 (United States)

    2015-06-14

    A combination of molecular dynamics simulations and pulsed field gradient nuclear magnetic resonance spectroscopy is used to investigate the role of exogenous electric fields on the solvation structure and dynamics of alkali ions in dimethyl sulfoxide (DMSO) and as a function of temperature. Good agreement was obtained, for select alkali ions in the absence of an electric field, between calculated and experimentally determined diffusion coefficients normalized to that of pure DMSO. Our results indicate that temperatures of up to 400 K and external electric fields of up to 1 V nm{sup −1} have minimal effects on the solvation structure of the smaller alkali cations (Li{sup +} and Na{sup +}) due to their relatively strong ion-solvent interactions, whereas the solvation structures of the larger alkali cations (K{sup +}, Rb{sup +}, and Cs{sup +}) are significantly affected. In addition, although the DMSO exchange dynamics in the first solvation shell differ markedly for the two groups, the drift velocities and mobilities are not significantly affected by the nature of the alkali ion. Overall, although exogenous electric fields induce a drift displacement, their presence does not significantly affect the random diffusive displacement of the alkali ions in DMSO. System temperature is found to have generally a stronger influence on dynamical properties, such as the DMSO exchange dynamics and the ion mobilities, than the presence of electric fields.

  8. Atomistic simulation of ion solvation in water explains surface preference of halides

    OpenAIRE

    Caleman, C.; Hub, J. S.; van Maaren, P.; van der Spoel, D

    2011-01-01

    Water is a demanding partner. It strongly attracts ions, yet some halide anions—chloride, bromide, and iodide—are expelled to the air/water interface. This has important implications for chemistry in the atmosphere, including the ozone cycle. We present a quantitative analysis of the energetics of ion solvation based on molecular simulations of all stable alkali and halide ions in water droplets. The potentials of mean force for Cl-, Br-, and I- have shallow minima near the surface. We demons...

  9. Strain-Induced Reactivity in the Dynamic Covalent Chemistry of Macrocyclic Imines.

    Science.gov (United States)

    Ratjen, Lars; Vantomme, Ghislaine; Lehn, Jean-Marie

    2015-07-01

    The displacement of molecular structures from their thermodynamically most stable state by imposition of various types of electronic and conformational constraints generates highly strained entities that tend to release the accumulated strain energy by undergoing either structural changes or chemical reactions. The latter case amounts to strain-induced reactivity (SIR) that may enforce specific chemical transformations. A particular case concerns dynamic covalent chemistry which may present SIR, whereby reversible reactions are activated by coupling to a high-energy state. We herewith describe such a dynamic covalent chemical (DCC) system involving the reversible imine formation reaction. It is based on the formation of strained macrocyclic bis-imine metal complexes in which the macrocyclic ligand is in a high energy form enforced by the coordination of the metal cation. Subsequent demetallation generates a highly strained free macrocycle that releases its accumulated strain energy by hydrolysis and reassembly into a resting state. Specifically, the metal-templated condensation of a dialdehyde with a linear diamine leads to a bis-imine [1+1]-macrocyclic complex in which the macrocyclic ligand is in a coordination-enforced strained conformation. Removal of the metal cation by a competing ligand yields a highly reactive [1+1]-macrocycle, which then undergoes hydrolysis to transient non-cyclic aminoaldehyde species, which then recondense to a strain-free [2+2]-macrocyclic resting state. The process can be monitored by (1) H NMR spectroscopy. Energy differences between different conformational states have been evaluated by Hartree-Fock (HF) computations. One may note that the stabilisation of high-energy molecular forms by metal ion coordination followed by removal of the latter, offers a general procedure for producing out-of-equilibrium molecular states, the fate of which may then be examined, in particular when coupled to dynamic covalent chemical processes. PMID

  10. Spatial and Temporal Dynamics of Carbonate Chemistry in the Northwestern Hawaiian Islands

    Science.gov (United States)

    Coughlin, C.; Winn, C. D.; Kahng, S.

    2014-12-01

    The rapid increase in atmospheric and surface ocean CO2 concentrations has the potential to drastically alter the metabolic processes particularly in nearshore ecosystems. However, much of what is known about carbonate chemistry is based on observations and analysis of surface waters of the open ocean where spatial and temporal variability is far less dynamic than in nearshore coral reef ecosystems. Carbon system dynamics data from four consecutive years has been examined in the coastal and nearshore waters of the Papahānaumokuākea Marine National Monument in the Northwest Hawaiian Islands. This data has been collected for the purpose of improving our understanding of the carbon system dynamics in this unique and pristine environment. The data collected includes continuous CTD data and discrete bottle samples, as well as continuous underway measurements. In addition to standard hydrographic profile data, water column alkalinity and pH have been measured on discrete water samples, and continuous underway measurements of pCO2 and pH have been obtained. This data is used to investigate the impact of NWHI coral reef ecosystems on the carbon system in and surrounding the archipelago. The data demonstrates that a significant "island mass effect" with respect to the oceanographic carbon system exists around the islands within the archipelago. In addition, spatial and temporal variability of several oceanographic features that exhibit a radial, latitudinal, or longitudinal gradient in the nearshore waters of the NWHI islands, islets, and atolls will be described. Finally, a shallow pH maximum coincident with the shallow oxygen maximum is observed, which suggests an open ocean feature substantially influenced by turbulence surrounding the islands within the monument. The data analysis and coral reef ecosystem monitoring will aid in developing a long-term plan to assist in the sustainability of Papahānaumokuākea Marine National Monument.

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

    Science.gov (United States)

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

  12. Solvation pressure as real pressure: I. Ethanol and starch under negative pressure

    CERN Document Server

    Uden, N W A V; Faux, D A; Tanczos, A C; Howlin, B; Dunstan, D J

    2003-01-01

    The reality of the solvation pressure generated by the cohesive energy density of liquids is demonstrated by three methods. Firstly, the Raman spectrum of ethanol as a function of cohesive energy density (solvation pressure) in ethanol-water and ethanol-chloroform mixtures is compared with the Raman spectrum of pure ethanol under external hydrostatic pressure and the solvation pressure and hydrostatic pressure are found to be equivalent for some transitions. Secondly, the bond lengths of ethanol are calculated by molecular dynamics modelling for liquid ethanol under pressure and for ethanol vapour. The difference in bond lengths between vapour and liquid are found to be equivalent to the solvation pressure for the C-H sub 3 , C-H sub 2 and O-H bond lengths, with discrepancies for the C-C and C-O bond lengths. Thirdly, the pressure-induced gelation of potato starch is measured in pure water and in mixtures of water and ethanol. The phase transition pressure varies in accordance with the change in solvation pre...

  13. Picosecond solvation dynamics—A potential viewer of DMSO—Water binary mixtures

    Science.gov (United States)

    Banik, Debasis; Kundu, Niloy; Kuchlyan, Jagannath; Roy, Arpita; Banerjee, Chiranjib; Ghosh, Surajit; Sarkar, Nilmoni

    2015-02-01

    In this work, we have investigated the composition dependent anomalous behavior of dimethyl sulfoxide (DMSO)-water binary mixture by collecting the ultrafast solvent relaxation response around a well known solvation probe Coumarin 480 (C480) by using a femtosecond fluorescence up-conversion spectrometer. Recent molecular dynamics simulations have predicted two anomalous regions of DMSO-water binary mixture. Particularly, these studies encourage us to investigate the anomalies from experimental background. DMSO-water binary mixture has repeatedly given evidences of its dual anomalous nature in front of our systematic investigation through steady-state and time-resolved measurements. We have calculated average solvation times of C480 by two individual well-known methods, among them first one is spectral-reconstruction method and another one is single-wavelength measurement method. The results of both the methods roughly indicate that solvation time of C480 reaches maxima in the mole fraction of DMSO XD = 0.12-0.17 and XD = 0.27-0.35, respectively. Among them, the second region (XD = 0.27-0.35) is very common as most of the thermodynamic properties exhibit deviation in this range. Most probably, the anomalous solvation trend in this region is fully guided by the shear viscosity of the medium. However, the first region is the most interesting one. In this region due to formation of strongly hydrogen bonded 1DMSO:2H2O complexes, hydration around the probe C480 decreases, as a result of which solvation time increases.

  14. Determination of Kamlet-Taft parameters for selected solvate ionic liquids.

    Science.gov (United States)

    Eyckens, Daniel J; Demir, Baris; Walsh, Tiffany R; Welton, Tom; Henderson, Luke C

    2016-05-11

    The normalised polarity E and Kamlet-Taft parameters of recently described solvate ionic liquids, composed of lithium bis(trifluoromethyl)sulfonimide (LiTFSI) in tri- () or tetraglyme () have been determined and compared to the parent glyme ( and ). We show that these solvate ionic liquids have a high polarity (, (E) = 1.03; , (E) = 1.03) and display very high electron pair accepting characteristics (, α = 1.32; , α = 1.35). Molecular dynamics simulations suggest that the chelated lithium cation is responsible for this observation. The relatively small hydrogen bond acceptor (β) values for these systems (, β = 0.41; , β = 0.37) are thought to be due primarily to the TFSI anion, which is supplemented slightly by the glyme oxygen atom. In addition, these solvate ionic liquids are found to have a high polarisability (, π* = 0.94; , π* = 0.90). PMID:27122349

  15. Solvation of monovalent anions in formamide and methanol: Parameterization of the IEF-PCM model

    International Nuclear Information System (INIS)

    The thermodynamics of solvation for a series of monovalent anions in formamide and methanol has been studied using the polarizable continuum model (PCM). The parameterization of this continuum model was guided by molecular dynamics simulations. The parameterized PCM model predicts the Gibbs free energies of solvation for 13 anions in formamide and 16 anions in methanol in very good agreement with experimental data. Two sets of atomic radii were tested in the definition of the solute cavities in the PCM and their performances are evaluated and discussed. Mean absolute deviations of the calculated free energies of solvation from the experimental values are in the range of 1.3-2.1 kcal/mol

  16. Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST.

    Science.gov (United States)

    Ramsey, Steven; Nguyen, Crystal; Salomon-Ferrer, Romelia; Walker, Ross C; Gilson, Michael K; Kurtzman, Tom

    2016-08-01

    The expulsion of water from surfaces upon molecular recognition and nonspecific association makes a major contribution to the free energy changes of these processes. In order to facilitate the characterization of water structure and thermodynamics on surfaces, we have incorporated Grid Inhomogeneous Solvation Theory (GIST) into the CPPTRAJ toolset of AmberTools. GIST is a grid-based implementation of Inhomogeneous Fluid Solvation Theory, which analyzes the output from molecular dynamics simulations to map out solvation thermodynamic and structural properties on a high-resolution, three-dimensional grid. The CPPTRAJ implementation, called GIST-cpptraj, has a simple, easy-to-use command line interface, and is open source and freely distributed. We have also developed a set of open-source tools, called GISTPP, which facilitate the analysis of GIST output grids. Tutorials for both GIST-cpptraj and GISTPP can be found at ambermd.org. © 2016 Wiley Periodicals, Inc. PMID:27317094

  17. Theoretical oxidation state analysis of Ru-(bpy)3: Influence of water solvation and Hubbard correction in first-principles calculations

    International Nuclear Information System (INIS)

    Oxidation state is a powerful concept that is widely used in chemistry and materials physics, although the concept itself is arguably ill-defined quantum mechanically. In this work, we present impartial comparison of four, well-recognized theoretical approaches based on Lowdin atomic orbital projection, Bader decomposition, maximally localized Wannier function, and occupation matrix diagonalization, for assessing how well transition metal oxidation states can be characterized. Here, we study a representative molecular complex, tris(bipyridine)ruthenium. We also consider the influence of water solvation through first-principles molecular dynamics as well as the improved electronic structure description for strongly correlated d-electrons by including Hubbard correction in density functional theory calculations

  18. Tuning structure and mobility of solvation shells surrounding tracer additives.

    Science.gov (United States)

    Carmer, James; Jain, Avni; Bollinger, Jonathan A; van Swol, Frank; Truskett, Thomas M

    2015-03-28

    Molecular dynamics simulations and a stochastic Fokker-Planck equation based approach are used to illuminate how position-dependent solvent mobility near one or more tracer particle(s) is affected when tracer-solvent interactions are rationally modified to affect corresponding solvation structure. For tracers in a dense hard-sphere fluid, we compare two types of tracer-solvent interactions: (1) a hard-sphere-like interaction, and (2) a soft repulsion extending beyond the hard core designed via statistical mechanical theory to enhance tracer mobility at infinite dilution by suppressing coordination-shell structure [Carmer et al., Soft Matter 8, 4083-4089 (2012)]. For the latter case, we show that the mobility of surrounding solvent particles is also increased by addition of the soft repulsive interaction, which helps to rationalize the mechanism underlying the tracer's enhanced diffusivity. However, if multiple tracer surfaces are in closer proximity (as at higher tracer concentrations), similar interactions that disrupt local solvation structure instead suppress the position-dependent solvent dynamics. PMID:25833590

  19. Use of semantic technologies for the development of a dynamic trajectories generator in a Semantic Chemistry eLearning platform

    CERN Document Server

    Huber, Richard; Todor, Alexandru; Krebs, Sebastian; Heese, Ralf; Paschke, Adrian

    2010-01-01

    ChemgaPedia is a multimedia, webbased eLearning service platform that currently contains about 18.000 pages organized in 1.700 chapters covering the complete bachelor studies in chemistry and related topics of chemistry, pharmacy, and life sciences. The eLearning encyclopedia contains some 25.000 media objects and the eLearning platform provides services such as virtual and remote labs for experiments. With up to 350.000 users per month the platform is the most frequently used scientific educational service in the German spoken Internet. In this demo we show the benefit of mapping the static eLearning contents of ChemgaPedia to a Linked Data representation for Semantic Chemistry which allows for generating dynamic eLearning paths tailored to the semantic profiles of the users.

  20. From ab initio quantum chemistry to molecular dynamics: The delicate case of hydrogen bonding in ammonia

    CERN Document Server

    Boese, A D; Martin, J M L; Marx, D; Chandra, Amalendu; Martin, Jan M.L.; Marx, Dominik

    2003-01-01

    The ammonia dimer (NH3)2 has been investigated using high--level ab initio quantum chemistry methods and density functional theory (DFT). The structure and energetics of important isomers is obtained to unprecedented accuracy without resorting to experiment. The global minimum of eclipsed C_s symmetry is characterized by a significantly bent hydrogen bond which deviates from linearity by about 20 degrees. In addition, the so-called cyclic C_{2h} structure is extremely close in energy on an overall flat potential energy surface. It is demonstrated that none of the currently available (GGA, meta--GGA, and hybrid) density functionals satisfactorily describe the structure and relative energies of this nonlinear hydrogen bond. We present a novel density functional, HCTH/407+, designed to describe this sort of hydrogen bond quantitatively on the level of the dimer, contrary to e.g. the widely used BLYP functional. This improved functional is employed in Car-Parrinello ab initio molecular dynamics simulations of liq...

  1. Influence of a Carrington-like event on the atmospheric chemistry, temperature and dynamics

    Directory of Open Access Journals (Sweden)

    M. Calisto

    2012-06-01

    Full Text Available We have modeled the atmospheric impact of a major solar energetic particle event similar in intensity to what is thought of the Carrington Event of 1–2 September 1859. Ionization rates for the August 1972 solar proton event, which had an energy spectrum comparable to the Carrington Event, were scaled up in proportion to the fluence estimated for both events. We have assumed such an event to take place in the year 2020 in order to investigate the impact on the modern, near future atmosphere. Effects on atmospheric chemistry, temperature and dynamics were investigated using the 3-D Chemistry Climate Model SOCOL v2.0. We find significant responses of NOx, HOx, ozone, temperature and zonal wind. Ozone and NOx have in common an unusually strong and long-lived response to this solar proton event. The model suggests a 3-fold increase of NOx generated in the upper stratosphere lasting until the end of November, and an up to 10-fold increase in upper mesospheric HOx. Due to the NOx and HOx enhancements, ozone reduces by up to 60–80% in the mesosphere during the days after the event, and by up to 20–40% in the middle stratosphere lasting for several months after the event. Total ozone is reduced by up to 20 DU in the Northern Hemisphere and up to 10 DU in the Southern Hemisphere. Free tropospheric and surface air temperatures show a significant cooling of more than 3 K and zonal winds change significantly by 3–5 m s−1 in the UTLS region. In conclusion, a solar proton event, if it took place in the near future with an intensity similar to that ascribed to of the Carrington Event of 1859, must be expected to have a major impact on atmospheric composition throughout the middle atmosphere, resulting in significant and persistent decrease in total ozone.

  2. Influence of a Carrington-like event on the atmospheric chemistry, temperature and dynamics

    Directory of Open Access Journals (Sweden)

    M. Calisto

    2012-09-01

    Full Text Available We have modeled the atmospheric impact of a major solar energetic particle event similar in intensity to what is thought of the Carrington Event of 1–2 September 1859. Ionization rates for the August 1972 solar proton event, which had an energy spectrum comparable to the Carrington Event, were scaled up in proportion to the fluence estimated for both events. We have assumed such an event to take place in the year 2020 in order to investigate the impact on the modern, near future atmosphere. Effects on atmospheric chemistry, temperature and dynamics were investigated using the 3-D Chemistry Climate Model SOCOL v2.0. We find significant responses of NOx, HOx, ozone, temperature and zonal wind. Ozone and NOx have in common an unusually strong and long-lived response to this solar proton event. The model suggests a 3-fold increase of NOx generated in the upper stratosphere lasting until the end of November, and an up to 10-fold increase in upper mesospheric HOx. Due to the NOx and HOx enhancements, ozone reduces by up to 60–80% in the mesosphere during the days after the event, and by up to 20–40% in the middle stratosphere lasting for several months after the event. Total ozone is reduced by up to 20 DU in the Northern Hemisphere and up to 10 DU in the Southern Hemisphere. Free tropospheric and surface air temperatures show a significant cooling of more than 3 K and zonal winds change significantly by 3–5 m s−1 in the UTLS region. In conclusion, a solar proton event, if it took place in the near future with an intensity similar to that ascribed to of the Carrington Event of 1859, must be expected to have a major impact on atmospheric composition throughout the middle atmosphere, resulting in significant and persistent decrease in total ozone.

  3. Solvation and Reaction in Ionic Liquids

    Energy Technology Data Exchange (ETDEWEB)

    Maroncelli, Mark

    2015-01-15

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

  4. FAST MOLECULAR SOLVATION ENERGETICS AND FORCE COMPUTATION.

    Science.gov (United States)

    Bajaj, Chandrajit; Zhao, Wenqi

    2010-01-20

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

  5. Zirconium isopropoxide solvate solubility in isopropanol

    International Nuclear Information System (INIS)

    Stability of zirconium isopropoxide solvate was measured in isopropanol at 20-70 deg. The solubility increased with temperature elevation and depended on product part history. Solubility enthalpy was equal to 9±1 kJ/mol in the range of stable values of solubility

  6. Groundwater phosphate dynamics in a river riparian zone: effects of hydrologic flowpaths, lithology and redox chemistry

    Science.gov (United States)

    Carlyle, G. C.; Hill, A. R.

    2001-07-01

    This study examines the influence of riparian zone hydrology, lithology and redox chemistry on groundwater phosphate dynamics. Patterns of soluble reactive phosphorus (SRP), dissolved oxygen (DO) and ferrous iron (Fe 2+) in combination with hydrologic data and sediment characteristics were studied in a forested floodplain connected to a large upland sand aquifer in an agricultural region of southern Ontario, Canada. Groundwater discharge from the upland aquifer flowed laterally beneath peat in a 2-4 m thick zone of permeable sands across the floodplain to the river. Within the sands, low SRP concentrations (3 mg L -1 and Fe 2+ concentrations <0.2 mg L -1 which extended for a horizontal distance of 100-140 m across the riparian zone. High SRP concentrations (50-950 μg L -1) were associated with low DO and high Fe 2+ concentrations which exceeded 1 mg L -1 in buried channel sediments near the river bank. Sediment P fractionation indicated that the buried channel sediments contained a much higher pool of total P and Fe+Al-P than the sands. Groundwater SRP concentrations at the river bank were 25-80 μg L -1 compared to <10 μg L -1 in river water indicating that the floodplain was a source of SRP to the river. Areas of elevated SRP and Fe 2+ within the floodplain expanded in August when DO concentrations in groundwater were lower than in late spring or autumn. These data suggest that the microbial reduction of Fe 3+ to soluble Fe 2+ in anaerobic conditions influences groundwater SRP concentrations in the riparian zone. This study shows that well-organized patterns of groundwater SRP concentrations occur in riparian zones which reflect the interaction of hydrologic flowpaths and environments of different redox state. Internal sources of P associated with buried channel sediments can also influence subsurface SRP transport and release to streams.

  7. Incorporating excluded solvent volume and physical dipoles for computing solvation free energy.

    Science.gov (United States)

    Yang, Pei-Kun

    2015-07-01

    The solvation free energy described using the Born equation depends on the solute charge, solute radius, and solvent dielectric constant. However, the dielectric polarization derived from Gauss's law used in the Born equation differs from that obtained from molecular dynamics simulations. Therefore, the adjustment of Born radii is insufficient for fitting the solvation free energy to various solute conformations. In order to mimic the dielectric polarization surrounding a solute in molecular dynamics simulations, the water molecule in the first coordination shell is modeled as a physical dipole in a van der Waals sphere, and the intermediate water is treated as a bulk solvent. The electric dipole of the first-shell water is modeled as positive and negative surface charge layers with fixed charge magnitudes, but with variable separation distance as derived from the distributions of hydrogen and oxygen atoms of water dictated by their orientational distribution functions. An equation that describes the solvation free energy of ions using this solvent scheme with a TIP3P water model is derived, and the values of the solvation free energies of ions estimated from this derived equation are found to be similar to those obtained from the experimental data. PMID:26113115

  8. The spring 2011 final stratospheric warming above Eureka: anomalous dynamics and chemistry

    Directory of Open Access Journals (Sweden)

    C. Adams

    2012-08-01

    Full Text Available In spring 2011, the Arctic polar vortex was stronger than in any other year on record. As the polar vortex started to break up in April, ozone and NO2 columns were measured with UV-visible spectrometers above the Polar Environment Atmospheric Research Laboratory (PEARL in Eureka, Canada (80.05° N, 86.42° W using the differential optical absorption spectroscopy (DOAS technique. These ground-based column measurements were complemented by Ozone Monitoring Instrument (OMI and Optical Spectrograph and Infra-Red Imager System (OSIRIS satellite measurements, Global Modeling Initiative (GMI simulations, and dynamical parameters. On 8 April 2011, NO2 columns above PEARL from the DOAS, OMI, and GMI datasets were approximately twice as large as in previous years. On this day, temperatures and ozone volume mixing ratios above Eureka were high, suggesting enhanced chemical production of NO2 from NO. Additionally, GMI NOx and N2O fields suggest that downward transport along the vortex edge and horizontal transport from lower latitudes also contributed to the enhanced NO2. The anticyclone that transported lower-latitude NOx above PEARL became frozen-in and persisted in dynamical and GMI N2O fields until the end of the measurement period on 31 May 2011. Ozone isolated within this frozen-in anticyclone (FrIAC in the middle stratosphere was depleted due to reactions with the enhanced NOx. Ozone loss was calculated using the passive tracer technique, with passive ozone profiles from the Lagrangian Chemistry and Transport Model, ATLAS. At 600 K, ozone losses between 1 December 2010 and 20 May 2011 reached 4.2 parts per million by volume (ppmv (58% and 4.4 ppmv (61%, when calculated using GMI and OSIRIS ozone profiles, respectively. This middle-stratosphere gas-phase ozone loss led to a more rapid decrease in ozone column amounts in April/May 2011 compared with

  9. Identification of Di(oxymethylene)glycol in the Raman Spectrum of Formaldehyde Aqueous Solutions by ab lnitio Molecular Dynamics Simulations and Quantum Chemistry Calculations

    Czech Academy of Sciences Publication Activity Database

    Delcroix, Pauline; Pagliai, M.; Cardini, G.; Bégué, D.; Hanoune, B.

    2015-01-01

    Roč. 119, č. 38 (2015), s. 9785-9793. ISSN 1089-5639 Institutional support: RVO:61388963 Keywords : hydrogen bond dynamics * chemical equilibria * liquid water Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.693, year: 2014

  10. Consequences of unburned hydrocarbons on microstreamer dynamics and chemistry during plasma remediation of NOx using dielectric barrier discharges

    International Nuclear Information System (INIS)

    Atmospheric pressure plasmas, and dielectric barrier discharges (DBDs) in particular, are being investigated for their use in the remediation of nitrogen oxides (NOx) from automotive exhausts. In their normal mode of operation, DBDs consist of a large density of short-lived filamentary microdischarges. Localized energy deposition results in spatially nonuniform gas temperatures and species densities which initiate advective and diffusive transport. Diesel exhausts, one of the major sources of NOx, typically contain unburned hydrocarbons (UHCs) which significantly influence the NOx chemistry during plasma remediation. In this paper, we discuss results from a computational investigation of the consequences of UHC chemistry on radial transport dynamics and remediation of NOx. In the presence of UHCs, radicals such as O and OH are dominantly consumed in the microstreamer region and their transport to larger radii is reduced. As a result, the conversion of NO to NO2 is mainly restricted to the core of the microstreamer

  11. Consequences of unburned hydrocarbons on microstreamer dynamics and chemistry during plasma remediation of NO sub x using dielectric barrier discharges

    CERN Document Server

    Dorai, R

    2003-01-01

    Atmospheric pressure plasmas, and dielectric barrier discharges (DBDs) in particular, are being investigated for their use in the remediation of nitrogen oxides (NO sub x) from automotive exhausts. In their normal mode of operation, DBDs consist of a large density of short-lived filamentary microdischarges. Localized energy deposition results in spatially nonuniform gas temperatures and species densities which initiate advective and diffusive transport. Diesel exhausts, one of the major sources of NO sub x , typically contain unburned hydrocarbons (UHCs) which significantly influence the NO sub x chemistry during plasma remediation. In this paper, we discuss results from a computational investigation of the consequences of UHC chemistry on radial transport dynamics and remediation of NO sub x. In the presence of UHCs, radicals such as O and OH are dominantly consumed in the microstreamer region and their transport to larger radii is reduced. As a result, the conversion of NO to NO sub 2 is mainly restricted t...

  12. The DACCIWA Project: Dynamics-Aerosol-Chemistry-Cloud interactions in West Africa

    Science.gov (United States)

    Knippertz, Peter

    2014-05-01

    Massive economic and population growth and urbanisation are expected to lead to a tripling of anthropogenic emissions from southern West Africa (SWA) between 2000 and 2030, the impacts of which on human health, ecosystems, food security and the regional climate are largely unknown. An assessment of these impacts is complicated by (a) a superposition with effects of global climate change, (b) the strong dependence of SWA on the sensitive West African monsoon, (c) incomplete scientific understanding of interactions between emissions, clouds, radiation, precipitation and regional circulations and (d) by a lack of observations to advance our understanding and improve predictions. The purpose of this contribution is to introduce the research consortium DACCIWA (Dynamics-Aerosol-Chemistry-Cloud interactions in West Africa), which comprises 16 partners in six European and West African countries. The interdisciplinary DACCIWA team will build on the scientific and logistical foundations established by the African Monsoon Multidisciplinary Analysis (AMMA) project and collaborate closely with operational centres. DACCIWA will receive funding of about M8.75€ from the European Commission as part of Framework Programme 7 from 2015 until 2018. The DACCIWA project will conduct extensive fieldwork in SWA to collect high-quality observations, spanning the entire process chain from surface-based natural and anthropogenic emissions to impacts on health, ecosystems and climate. This will include a major field campaign in summer 2015 with three research aircrafts and two ground-based supersites. Combining the resulting benchmark dataset with a wide range of modelling activities will allow us: (a) to assess all relevant physical and chemical processes, (b) to improve the monitoring of climate and compositional parameters from space, (c) to determine health impacts from air pollution, and (d) to develop the next generation of weather and climate models capable of representing coupled

  13. The spring 2011 final stratospheric warming above Eureka: anomalous dynamics and chemistry

    Science.gov (United States)

    Adams, C.; Strong, K.; Zhao, X.; Bourassa, A. E.; Daffer, W. H.; Degenstein, D.; Drummond, J. R.; Farahani, E. E.; Fraser, A.; Lloyd, N. D.; Manney, G. L.; McLinden, C. A.; Rex, M.; Roth, C.; Strahan, S. E.; Walker, K. A.; Wohltmann, I.

    2013-01-01

    In spring 2011, the Arctic polar vortex was stronger than in any other year on record. As the polar vortex started to break up in April, ozone and NO2 columns were measured with UV-visible spectrometers above the Polar Environment Atmospheric Research Laboratory (PEARL) in Eureka, Canada (80.05° N, 86.42° W) using the differential optical absorption spectroscopy (DOAS) technique. These ground-based column measurements were complemented by Ozone Monitoring Instrument (OMI) and Optical Spectrograph and Infra-Red Imager System (OSIRIS) satellite measurements, Global Modeling Initiative (GMI) simulations, and meteorological quantities. On 8 April 2011, NO2 columns above PEARL from the DOAS, OMI, and GMI datasets were approximately twice as large as in previous years. On this day, temperatures and ozone volume mixing ratios above Eureka were high, suggesting enhanced chemical production of NO2 from NO. Additionally, GMI NOx (NO + NO2) and N2O fields suggest that downward transport along the vortex edge and horizontal transport from lower latitudes also contributed to the enhanced NO2. The anticyclone that transported lower-latitude NOx above PEARL became frozen-in and persisted in dynamical and GMI N2O fields until the end of the measurement period on 31 May 2011. Ozone isolated within this frozen-in anticyclone (FrIAC) in the middle stratosphere was lost due to reactions with the enhanced NOx. Below the FrIAC (from the tropopause to 700 K), NOx driven ozone loss above Eureka was larger than in previous years, according to GMI monthly average ozone loss rates. Using the passive tracer technique, with passive ozone profiles from the Lagrangian Chemistry and Transport Model, ATLAS, ozone losses since 1 December 2010 were calculated at 600 K. In the air mass that was above Eureka on 20 May 2011, ozone losses reached 4.2 parts per million by volume (ppmv) (58%) and 4.4 ppmv (61%), when calculated using GMI and OSIRIS ozone profiles, respectively. This gas-phase ozone loss

  14. Ligand Exchange Processes on Solvated Lithium Cations

    OpenAIRE

    Pasgreta, Ewa Maria

    2007-01-01

    In this work the solvation process of Li+ ion, as well as solvent and ligand exchange reactions on Li+ ion were studied. Li+ ions possess interesting properties and like other alkali metal ions are known to form complexes with macrocyclic ligands called cryptands. In this summary, an overview over the insights gained in the factors that control the reactivity of Li+ complexes with respect to the solvent and cryptand properties is presented. Three main questions were addressed: • How does the ...

  15. Distinctive Solvation Patterns Make Renal Osmolytes Diverse

    OpenAIRE

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

    2013-01-01

    The kidney uses mixtures of five osmolytes to counter the stress induced by high urea and NaCl concentrations. The individual roles of most of the osmolytes are unclear, and three of the five have not yet been thermodynamically characterized. Here, we report partial molar volumes and activity coefficients of glycerophosphocholine (GPC), taurine, and myo-inositol. We derive their solvation behavior from the experimental data using Kirkwood-Buff theory. We also provide their solubility data, in...

  16. On the coupling between molecular diffusion and solvation shell exchange

    DEFF Research Database (Denmark)

    Møller, Klaus Braagaard; Rey, Rossend; Masia, Marco;

    2005-01-01

    formulas are derived which quantitatively estimate this effect, and which are of general applicability to molecular diffusion in any thermal fluid. Despite the simplicity of the kinematic considerations, they are shown to well describe many aspects of solvent exchange/diffusion coupling features for......The connection between diffusion and solvent exchanges between first and second solvation shells is studied by means of molecular dynamics simulations and analytic calculations, with detailed illustrations for water exchange for the Li+ and Na+ ions, and for liquid argon. First, two methods are...... proposed which allow, by means of simulation;to extract the quantitative speed-up in diffusion induced by the exchange events. Second,. it is shown by simple kinematic considerations that the instantaneous velocity of the solute conditions to a considerable extent the character of the exchanges. Analytic...

  17. Ultrafast solvation dynamics of 12'-apo-{beta}-carotenoic-12'-acid in [C{sub 6}mim]{sup +}[Tf{sub 2}N]{sup -}

    Energy Technology Data Exchange (ETDEWEB)

    Lohse, Peter W.; Ehlers, Florian [Georg-August-Universitaet Goettingen, Institut fuer Physikalische Chemie, Tammannstr. 6, D-37077 Goettingen (Germany); Oum, Kawon, E-mail: koum@gwdg.de [Georg-August-Universitaet Goettingen, Institut fuer Physikalische Chemie, Tammannstr. 6, D-37077 Goettingen (Germany); Scholz, Mirko [Georg-August-Universitaet Goettingen, Institut fuer Physikalische Chemie, Tammannstr. 6, D-37077 Goettingen (Germany); Lenzer, Thomas, E-mail: tlenzer@gwdg.de [Georg-August-Universitaet Goettingen, Institut fuer Physikalische Chemie, Tammannstr. 6, D-37077 Goettingen (Germany)

    2010-07-19

    Intra- and intermolecular relaxation pathways of 12'-apo-{beta}-carotenoic-12'-acid, an apocarotenoid with terminal carbonyl substitution, were identified after photoexcitation using ultrafast pump-supercontinuum probe spectroscopy in the 350-750 nm range. The apocarotenoid was dissolved in 1-n-hexyl-3-methylimidazolium-bis(trifluoromethylsulfonyl)amide and excited to the S{sub 2} state at 482 nm. Internal conversion occurred within 170 fs to a single S{sub 1}/ICT state with intramolecular charge transfer character. This state exhibits characteristic excited state absorption band-shifts due to time-dependent solvation, which appears to be a general feature of carbonyl apocarotenoids with polarity-dependent S{sub 1}/ICT lifetimes. We also demonstrate that higher pump beam energies open a route for the clean preparation of long-lived radical cations by resonant one-color two-photon excitation using S{sub 2} as the intermediate state. The radical cations are easily identified by a characteristic absorption peak in the region 700-750 nm and an absorption tail towards shorter wavelengths.

  18. Electron solvation in liquid alcohols. Effect of microscopic liquid structure

    International Nuclear Information System (INIS)

    Complete text of publication follows. Numerous theoretical works show that excess electrons in polar liquids can localize in cavities in which the surrounding solvent molecules create an attractive potential well. These cavities are called the pre-existing traps. Existence of the preformed traps in liquids is also suggested by results of the femtosecond time-resolved studies on the solvated electron. Thus, theoretical description of the pre-existing traps in various liquids is important for understanding the process of primary electron localization in these media. In the present work the structure of liquid alcohols, obtained by computer simulation, has been analyzed in order to identify the regions that can serve as pre-existing sites for primary localization of an excess electron. The calculations were performed for two alcohols: 1-propanol and 2-propanol, at 298 K. Configurations of molecules for each liquid sample were generated in a classical Molecular Dynamics Simulations. The static and dynamical properties of the traps have been investigated and described in terms of the statistical distributions of their geometrical parameters and their lifetimes, respectively. Moreover, we have connected these properties with the local structure of the medium around the traps. Our general conclusions are as follows: (1) electron traps in 1-propanol (generally in primary alcohols) are deeper in comparison with traps in 2-propanol (secondary alcohols), (2) electron solvation process in 1-propanol, in contrast to 2-propanol, does not involve breaking of hydrogen bonding net, (3) and they are consistent with the experimental results of Zhang et al. (Radiat. Phys. Chem., 1999, 54, 433) for electrons localized in those matrices

  19. Molecular correlations and solvation in simple fluids.

    Science.gov (United States)

    Barbosa, Marco A A; Widom, B

    2010-06-01

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

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

    Science.gov (United States)

    Wu, X W; Sung, S S

    1999-02-15

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

  1. Do High School Chemistry Examinations Inhibit Deeper Level Understanding of Dynamic Reversible Chemical Reactions?

    Science.gov (United States)

    Wheeldon, R.; Atkinson, R.; Dawes, A.; Levinson, R.

    2012-01-01

    Background and purpose: Chemistry examinations can favour the deployment of algorithmic procedures like Le Chatelier's Principle (LCP) rather than reasoning using chemical principles. This study investigated the explanatory resources which high school students use to answer equilibrium problems and whether the marks given for examination answers…

  2. Virtual Laboratory in the Role of Dynamic Visualisation for Better Understanding of Chemistry in Primary School

    Science.gov (United States)

    Herga, Nataša Rizman; Cagran, Branka; Dinevski, Dejan

    2016-01-01

    Understanding chemistry includes the ability to think on three levels: the macroscopic level, the symbolic level, and the level of particles--sub-microscopic level. Pupils have the most difficulty when trying to understand the sub-microscopic level because it is outside their range of experience. A virtual laboratory enables a simultaneous…

  3. Exploring Interactive and Dynamic Simulations Using a Computer Algebra System in an Advanced Placement Chemistry Course

    Science.gov (United States)

    Matsumoto, Paul S.

    2014-01-01

    The article describes the use of Mathematica, a computer algebra system (CAS), in a high school chemistry course. Mathematica was used to generate a graph, where a slider controls the value of parameter(s) in the equation; thus, students can visualize the effect of the parameter(s) on the behavior of the system. Also, Mathematica can show the…

  4. Minimalistic predictor of protein binding energy: contribution of solvation factor to protein binding.

    Science.gov (United States)

    Choi, Jeong-Mo; Serohijos, Adrian W R; Murphy, Sean; Lucarelli, Dennis; Lofranco, Leo L; Feldman, Andrew; Shakhnovich, Eugene I

    2015-02-17

    It has long been known that solvation plays an important role in protein-protein interactions. Here, we use a minimalistic solvation-based model for predicting protein binding energy to estimate quantitatively the contribution of the solvation factor in protein binding. The factor is described by a simple linear combination of buried surface areas according to amino-acid types. Even without structural optimization, our minimalistic model demonstrates a predictive power comparable to more complex methods, making the proposed approach the basis for high throughput applications. Application of the model to a proteomic database shows that receptor-substrate complexes involved in signaling have lower affinities than enzyme-inhibitor and antibody-antigen complexes, and they differ by chemical compositions on interfaces. Also, we found that protein complexes with components that come from the same genes generally have lower affinities than complexes formed by proteins from different genes, but in this case the difference originates from different interface areas. The model was implemented in the software PYTHON, and the source code can be found on the Shakhnovich group webpage: http://faculty.chemistry.harvard.edu/shakhnovich/software. PMID:25692584

  5. The spring 2011 final stratospheric warming above Eureka: anomalous dynamics and chemistry

    Directory of Open Access Journals (Sweden)

    C. Adams

    2013-01-01

    Full Text Available In spring 2011, the Arctic polar vortex was stronger than in any other year on record. As the polar vortex started to break up in April, ozone and NO2 columns were measured with UV-visible spectrometers above the Polar Environment Atmospheric Research Laboratory (PEARL in Eureka, Canada (80.05° N, 86.42° W using the differential optical absorption spectroscopy (DOAS technique. These ground-based column measurements were complemented by Ozone Monitoring Instrument (OMI and Optical Spectrograph and Infra-Red Imager System (OSIRIS satellite measurements, Global Modeling Initiative (GMI simulations, and meteorological quantities. On 8 April 2011, NO2 columns above PEARL from the DOAS, OMI, and GMI datasets were approximately twice as large as in previous years. On this day, temperatures and ozone volume mixing ratios above Eureka were high, suggesting enhanced chemical production of NO2 from NO. Additionally, GMI NOx (NO + NO2 and N2O fields suggest that downward transport along the vortex edge and horizontal transport from lower latitudes also contributed to the enhanced NO2. The anticyclone that transported lower-latitude NOx above PEARL became frozen-in and persisted in dynamical and GMI N2O fields until the end of the measurement period on 31 May 2011. Ozone isolated within this frozen-in anticyclone (FrIAC in the middle stratosphere was lost due to reactions with the enhanced NOx. Below the FrIAC (from the tropopause to 700 K, NOx driven ozone loss above Eureka was larger than in previous years, according to GMI monthly average ozone loss rates. Using the passive tracer technique, with passive ozone profiles from the Lagrangian Chemistry and Transport Model, ATLAS, ozone losses since 1 December 2010 were calculated at 600 K. In the air mass that was above Eureka on 20 May 2011, ozone losses reached 4.2 parts per million by

  6. Picosecond solvation dynamics—A potential viewer of DMSO—Water binary mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Banik, Debasis; Kundu, Niloy; Kuchlyan, Jagannath; Roy, Arpita; Banerjee, Chiranjib; Ghosh, Surajit; Sarkar, Nilmoni, E-mail: nilmoni@chem.iitkgp.ernet.in [Department of Chemistry, Indian Institute of Technology, Kharagpur, WB 721302 (India)

    2015-02-07

    In this work, we have investigated the composition dependent anomalous behavior of dimethyl sulfoxide (DMSO)-water binary mixture by collecting the ultrafast solvent relaxation response around a well known solvation probe Coumarin 480 (C480) by using a femtosecond fluorescence up-conversion spectrometer. Recent molecular dynamics simulations have predicted two anomalous regions of DMSO-water binary mixture. Particularly, these studies encourage us to investigate the anomalies from experimental background. DMSO-water binary mixture has repeatedly given evidences of its dual anomalous nature in front of our systematic investigation through steady-state and time-resolved measurements. We have calculated average solvation times of C480 by two individual well-known methods, among them first one is spectral-reconstruction method and another one is single-wavelength measurement method. The results of both the methods roughly indicate that solvation time of C480 reaches maxima in the mole fraction of DMSO X{sub D} = 0.12–0.17 and X{sub D} = 0.27–0.35, respectively. Among them, the second region (X{sub D} = 0.27–0.35) is very common as most of the thermodynamic properties exhibit deviation in this range. Most probably, the anomalous solvation trend in this region is fully guided by the shear viscosity of the medium. However, the first region is the most interesting one. In this region due to formation of strongly hydrogen bonded 1DMSO:2H{sub 2}O complexes, hydration around the probe C480 decreases, as a result of which solvation time increases.

  7. Ligand Conformational and Solvation/Desolvation Free Energy in Protein-Ligand Complex Formation

    Czech Academy of Sciences Publication Activity Database

    Kolář, Michal; Fanfrlík, Jindřich; Hobza, Pavel

    2011-01-01

    Roč. 115, č. 16 (2011), s. 4718-4724. ISSN 1520-6106 R&D Projects: GA MŠk LC512; GA ČR GAP208/11/0295 Grant ostatní: Korea Science and Engineering Foundation(KR) R32-2008-000-10180-0; European Science Fund(XE) CZ.1.05/2.1.00/03.0058 Institutional research plan: CEZ:AV0Z40550506 Keywords : solvation free energy * SMD * HIV protease inhibitors Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.696, year: 2011

  8. Seasonal Dynamics in the Chemistry and Structure of the Fat Bodies of Bumblebee Queens

    Czech Academy of Sciences Publication Activity Database

    Votavová, A.; Tomčala, Aleš; Kofroňová, Edita; Kudzejová, Michaela; Šobotník, J.; Jiroš, Pavel; Komzáková, O.; Valterová, Irena

    2015-01-01

    Roč. 10, č. 11 (2015), e0142261/1-e0142261/14. E-ISSN 1932-6203 R&D Projects: GA ČR(CZ) GA14-04291S Institutional support: RVO:61388963 Keywords : transmission electron microscopy * triacylglycerols * phospholipids * fatty acid composition * glycogen Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 3.234, year: 2014 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142261

  9. Abacavir methanol 2.5-solvate

    Directory of Open Access Journals (Sweden)

    Phuong-Truc T. Pham

    2009-08-01

    Full Text Available The structure of abacavir (systematic name: {(1S,4R-4-[2-amino-6-(cyclopropylamino-9H-purin-9-yl]cyclopent-2-en-1-yl}methanol, C14H18N6O·2.5CH3OH, consists of hydrogen-bonded ribbons which are further held together by additional hydrogen bonds involving the hydroxyl group and two N atoms on an adjacent purine. The asymmetric unit also contains 2.5 molecules of methanol solvate which were grossly disordered and were excluded using SQUEEZE subroutine in PLATON [Spek, (2009. Acta Cryst. D65, 148–155].

  10. Abacavir methanol 2.5-solvate

    OpenAIRE

    Pham, Phuong-Truc T

    2009-01-01

    The structure of abacavir (systematic name: {(1S,4R)-4-[2-amino-6-(cyclopropylamino)-9H-purin-9-yl]cyclopent-2-en-1-yl}methanol), C14H18N6O·2.5CH3OH, consists of hydrogen-bonded ribbons which are further held together by additional hydrogen bonds involving the hydroxyl group and two N atoms on an adjacent purine. The asymmetric unit also contains 2.5 molecules of methanol solvate which were grossly disordered and were excluded using SQUEEZE subroutine in PLATON [Spek, (2009...

  11. Acetoguanamine N,N-dimethylformamide solvate

    Directory of Open Access Journals (Sweden)

    Gustavo Portalone

    2008-09-01

    Full Text Available The structure of acetoguanamine (or 2,4-diamino-6-methyl-1,3,5-triazine has been determined as the N,N-dimethylformamide solvate, C4H7N5·C3H7NO. The molecular components are associated in the crystal structure to form ribbons stabilized by three N—H...N and one N—H...O hydrogen bonds which involve NH groups as donors and the N atoms of the heterocyclic ring and the carbonyl O atom of the solvent as acceptors.

  12. A Synthesis of Fluid Dynamics and Quantum Chemistry for the Design of Nanoelectronics

    Science.gov (United States)

    MacDougall, Preston J.

    1998-01-01

    In 1959, during a famous lecture entitled "There's Plenty of Room at the Bottom", Richard Feynman focused on the startling technical possibilities that would exist at the limit of miniaturization, that being atomically precise devices with dimensions in the nanometer range. A nanometer is both a convenient unit of length for medium to large sized molecules, and the root of the name of the new interdisciplinary field of "nanotechnology". Essentially, "nanoelectronics" denotes the goal of shrinking electronic devices, such as diodes and transistors, as well as integrated circuits of such devices that can perform logical operations, down to dimensions in the range of 100 nanometers. The thirty-year hiatus in the development of nanotechnology can figuratively be seen as a period of waiting for the bottom-up and atomically precise construction skills of synthetic chemistry to meet the top-down reductionist aspirations of device physics. The sub-nanometer domain of nineteenth-century classical chemistry has steadily grown, and state-of-the-art supramolecular chemistry can achieve atomic precision in non-repeating molecular assemblies of the size desired for nanotechnology. For nanoelectronics in particular, a basic understanding of the electron transport properties of molecules must also be developed. Quantum chemistry provides powerful computational methods that can accurately predict the properties of small to medium sized molecules on a desktop workstation, and those of large molecules if one has access to a supercomputer. Of the many properties of a molecule that quantum chemistry routinely predicts, the ability to carry a current is one that had not even been considered until recently. "Currently", there is a controversy over just how to define this key property. Reminiscent of the situation in high-Tc superconductivity, much of the difficulty arises from the different models that are used to simplify the complex electronic structure of real materials. A model

  13. Solvatation eines Coumarinfarbstoffes in Gemischen aus Alkanen und Alkoholen

    OpenAIRE

    Cichos, Frank

    1998-01-01

    Diese Arbeit charakterisiert die Solvatation des organischen Farbstoffes Coumarin 153 in Gemischen aus jeweils einem Alkan und einem Alkohol. Dabei werden Methoden der statischen und zeitaufgeloesten optischen Spektroskopie sowie klassische molekulardynamische Simulationen fuer die Untersuchungen angewendet. Die experimentellen Ergebnisse zeigen, dass der Farbstoff im Gemisch selektiv durch den Alkohol solvatisiert ist. Die Staerke dieser Solvatation ist für den ...

  14. Extended Lagrangian quantum molecular dynamics simulations of shock-induced chemistry in hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Sanville, Edward J [Los Alamos National Laboratory; Bock, Nicolas [Los Alamos National Laboratory; Challacombe, William M [Los Alamos National Laboratory; Cawkwell, Marc J [Los Alamos National Laboratory; Niklasson, Anders M N [Los Alamos National Laboratory; Dattelbaum, Dana M [Los Alamos National Laboratory; Sheffield, Stephen [Los Alamos National Laboratory; Sewell, Thomas D [UNIV OF MISSOURI

    2010-01-01

    A set of interatomic potentials for hydrocarbons that are based upon the self-consistent charge transfer tight-binding approximation to density functional theory have been developed and implemented into the quantum molecular dynamics code ''LATTE''. The interatomic potentials exhibit an outstanding level of transferability and have been applied in molecular dynamics simulations of tert-butylacetylene under thermodynamic conditions that correspond to its single-shock Hugoniot. We have achieved precise conservation of the total energy during microcanonical molecular dynamics trajectories under incomplete convergence via the extended Lagrangian Born-Oppenheimer molecular dynamics formalism. In good agreement with the results of a series of flyer-plate impact experiments, our SCC-TB molecular dynamics simulations show that tert-butylactylene molecules polymerize at shock pressures around 6.1 GPa.

  15. Solvation structure around ruthenium(II tris(bipyridine in lithium halide solutions

    Directory of Open Access Journals (Sweden)

    Ida Josefsson

    2016-03-01

    Full Text Available The solvation of the ruthenium(II tris(bipyridine ion ([Ru(bpy3]2+ is investigated with molecular dynamics simulations of lithium halide solutions in polar solvents. The anion distribution around the [Ru(bpy3]2+ complex exhibits a strong solvent dependence. In aqueous solution, the iodide ion forms a solvent shared complex with [Ru(bpy3]2+, but not in the other solvents. Between Cl– and [Ru(bpy3]2+, the strong hydration of the chloride ion results in a solvent separated complex where more than one solvent molecule separates the anion from the metal center. Hence, tailored solvation properties in electrolytes is a route to influence ion-ion interactions and related electron transfer processes.

  16. Solvation structure around ruthenium(II) tris(bipyridine) in lithium halide solutions

    Science.gov (United States)

    Josefsson, Ida; Eriksson, Susanna K.; Rensmo, Håkan; Odelius, Michael

    2016-01-01

    The solvation of the ruthenium(II) tris(bipyridine) ion ([Ru(bpy)3]2+) is investigated with molecular dynamics simulations of lithium halide solutions in polar solvents. The anion distribution around the [Ru(bpy)3]2+ complex exhibits a strong solvent dependence. In aqueous solution, the iodide ion forms a solvent shared complex with [Ru(bpy)3]2+, but not in the other solvents. Between Cl– and [Ru(bpy)3]2+, the strong hydration of the chloride ion results in a solvent separated complex where more than one solvent molecule separates the anion from the metal center. Hence, tailored solvation properties in electrolytes is a route to influence ion-ion interactions and related electron transfer processes. PMID:26798838

  17. Electrolyte Solvation and Ionic Association. VI. Acetonitrile-Lithium Salt Mixtures. Highly Associated Salts Revisited

    Energy Technology Data Exchange (ETDEWEB)

    Borodin, Oleg [U.S. Army Research Lab., Adelphi, MD (United States); Han, Sang D. [North Carolina State Univ., Raleigh, NC (United States); Daubert, James S. [North Carolina State Univ., Raleigh, NC (United States); Seo, D. M. [North Carolina State Univ., Raleigh, NC (United States); Yun, Sung-Hyun [Gwangju Inst. of Science and Technology (Korea, Republic of); Henderson, Wesley A. [North Carolina State Univ., Raleigh, NC (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-01-14

    Molecular dynamics (MD) simulations of acetonitrile (AN) mixtures with LiBF4, LiCF3SO3 and LiCF3CO2 provide extensive details about the molecular- and mesoscale-level solution interactions and thus explanations as to why these electrolytes have very different thermal phase behavior and electrochemical/physicochemical properties. The simulation results are in full accord with a previous experimental study of these (AN)n-LiX electrolytes. This computational study reveals how the structure of the anions strongly influences the ionic association tendency of the ions, the manner in which the aggregate solvates assemble in solution and the length of time in which the anions remain coordinated to the Li+ cations in the solvates which result in dramatic variations in the transport properties of the electrolytes.

  18. Dynamical climatology of the NASA Langley Research Center Interactive Modeling Project for Atmospheric Chemistry and Transport (IMPACT) model

    Science.gov (United States)

    Pierce, R. Bradley; Al-Saadi, Jassim A.; Eckman, Richard S.; Fairlie, T. Duncan; Grose, William L.; Kleb, Mary M.; Natarajan, Murali; Olson, Jennifer R.

    2000-12-01

    A comparison of the NASA Langley Research Center (LaRC) Interactive Modeling Project for Atmospheric Chemistry and Transport (IMPACT) model's dynamical characteristics with assimilated data sets and observations is presented to demonstrate the ability of the model to represent the dynamical characteristics of Earth's troposphere and stratosphere. The LaRC IMPACT model is a coupled chemical/dynamical general circulation model (GCM) of the Earth's atmosphere extending from the surface to the lower mesosphere. It has been developed as a tool for assessing the effects of chemical, dynamical, and radiative coupling in the stratosphere on the Earth's climate. The LaRC IMPACT model winds and temperatures are found to be in fairly good agreement with Upper Atmospheric Research Satellite (UARS) United Kingdom Meteorological Office (UKMO) assimilated winds and temperatures in the lower stratosphere. The model upper stratospheric zonal mean temperatures are also in good agreement with the UARS-UKMO climatology except for a cold winter pole which results from the upward extension of the cold vortex temperatures and an elevated winter stratopause in the model. The cold pole bias is consistent with the overprediction of the winter stratospheric jet strength, and is characteristic of stratospheric GCMs in general. The model northern and southern hemisphere stratospheric eddy heat and momentum fluxes are within the expected interannual variability of the UARS-UKMO climatology. The combined effects of water vapor transport, radiative, convective, and planetary boundary layer parameterizations are shown to produce tropospheric winds and circulation statistics that are in good agreement with the UARS-UKMO climatology, although the model tropopause and upper tropospheric temperatures are generally cold relative to the UARS-UKMO temperatures. Comparisons between the model and UARS-UKMO climatology indicate that the model does a reasonable job in reproducing the frequency of observed

  19. Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions

    Czech Academy of Sciences Publication Activity Database

    Kohagen, Miriam; Mason, Philip E.; Jungwirth, Pavel

    2014-01-01

    Roč. 118, č. 28 (2014), s. 7902-7909. ISSN 1520-6106 R&D Projects: GA ČR GBP208/12/G016; GA MŠk LH12001 Institutional support: RVO:61388963 Keywords : calcium chloride * aqueous solution * molecular dynamics * neutron scattering Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.302, year: 2014

  20. Incorporating modeling and simulations in undergraduate biophysical chemistry course to promote understanding of structure-dynamics-function relationships in proteins.

    Science.gov (United States)

    Hati, Sanchita; Bhattacharyya, Sudeep

    2016-03-01

    A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and simulations. In particular, modern computational tools are employed to elucidate the relationship between structure, dynamics, and function in proteins. Computer-based laboratory protocols that we introduced in three modules allow students to visualize the secondary, super-secondary, and tertiary structures of proteins, analyze non-covalent interactions in protein-ligand complexes, develop three-dimensional structural models (homology model) for new protein sequences and evaluate their structural qualities, and study proteins' intrinsic dynamics to understand their functions. In the fourth module, students are assigned to an authentic research problem, where they apply their laboratory skills (acquired in modules 1-3) to answer conceptual biophysical questions. Through this process, students gain in-depth understanding of protein dynamics-the missing link between structure and function. Additionally, the requirement of term papers sharpens students' writing and communication skills. Finally, these projects result in new findings that are communicated in peer-reviewed journals. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:140-159, 2016. PMID:26801683

  1. Comparison of Chain Conformation of Poly(vinyl alcohol) in Solutions and Melts from Quantum Chemistry Based Molecular Dynamics Simulations

    Science.gov (United States)

    Jaffe, Richard; Han, Jie; Matsuda, Tsunetoshi; Yoon, Do; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.

  2. Solvation of solid phosphorus heteropolytungstates by ketones

    International Nuclear Information System (INIS)

    A study was made on the mechanism of ketone vapor absorption by anhydrous 12-tungstophosphates of alkali and transition metals. Methods of 1H NMR and infrared spectroscopy, X-ray phase analysis, thermogravimetry were used to investigate the state of organic reagent molecules in solvates. Formation of R1R2CO...H+...OCR1R2 complex in H3PW12O40X6R1R2CO was established and its mobility at 293 and 80 K was evaluated. Sufficient difference of tungstophosphoric acid and its Li, Na, Co, Ni, Cu salts from tungstophosphates with large K and Rb cation with respect to the character of sorption and binding of carbonyl reagent molecules was shown

  3. Electron solvation and geminate ion recombination in ionic liquids

    International Nuclear Information System (INIS)

    The behavior of radiation-induced active species in ionic liquids attract much attention from view point of radiation induced decomposition and reaction in ionic liquids. The formation process, lifetime, yield and reactivity of solvated electrons were studied in alkyl ammonium ionic liquid by electron beam pulse radiolysis method. As a result, the G-value of the solvated electron is about 1, the lifetime is about 300 ns, the high efficiency reaction between the dry electron and solute were clarified. Most of the ionized electron would recombine with parent radical cation geminately. Pre-solvated electron reaction and geminate ion recombination were investigated using the femtosecond pulse radiolysis system. (author)

  4. Molecular dynamics simulations and quantum chemistry as useful complements to RNA structural bioinformatics

    Czech Academy of Sciences Publication Activity Database

    Šponer, Jiří

    2009-01-01

    Roč. 26, č. 6 (2009), s. 824-825. ISSN 0739-1102. [The 17th Conversation. 16.06.2009-20.06.2009, Albany] Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : molecular dynamics * RNA Subject RIV: BO - Biophysics

  5. Gravitational instabilities in a protosolar-like disc I: dynamics and chemistry

    CERN Document Server

    Evans, M G; Boley, A C; Caselli, P; Durisen, R H; Hartquist, T W; Rawlings, J M C

    2015-01-01

    To date, most simulations of the chemistry in protoplanetary discs have used 1+1D or 2D axisymmetric $\\alpha$-disc models to determine chemical compositions within young systems. This assumption is inappropriate for non-axisymmetric, gravitationally unstable discs, which may be a significant stage in early protoplanetary disc evolution. Using 3D radiative hydrodynamics, we have modelled the physical and chemical evolution of a 0.17 M$_{\\odot}$ self-gravitating disc over a period of 2000 yr. The 0.8 M$_{\\odot}$ central protostar is likely to evolve into a solar-like star, and hence this Class 0 or early Class I young stellar object may be analogous to our early Solar System. Shocks driven by gravitational instabilities enhance the desorption rates, which dominate the changes in gas-phase fractional abundances for most species. We find that at the end of the simulation, a number of species distinctly trace the spiral structure of our relatively low-mass disc, particularly CN. We compare our simulation to that o...

  6. Dynamic Covalent Chemistry-based Sensing: Pyrenyl Derivatives of Phenylboronic Acid for Saccharide and Formaldehyde

    Science.gov (United States)

    Chang, Xingmao; Fan, Jiayun; Wang, Min; Wang, Zhaolong; Peng, Haonan; He, Gang; Fang, Yu

    2016-08-01

    We synthesized two specially designed pyrenyl (Py) derivatives of phenylboronic acid, PSNB1 and PSNB2, of which PSNB2 self-assemble to form dynamic aggregate in methanol-water mixture (1:99, v/v) via intermolecular H-bonding and pi-pi stacking. Interestingly, the dynamic aggregate shows smart response to presence of fructose (F) as evidenced by fluorescence color change from green to blue. More interestingly, the fluorescence emission of the resulted PSNB2-F changes from blue to green with the addition of formaldehyde (FA). The reason behind is formation of a PSNB2-F dimer via FA cross-linking. Based upon the reactions as found, sensitive and fast sensing of F and FA in water was realized, of which the experimental DLs could be significantly lower than 10 μM for both analytes, and the response times are less than 1 min. It is believed that not only the materials as created may have the potential to find real-life applications but also the strategy as developed can be adopted to develop other dynamic materials.

  7. Influence of a Carrington-like event on the atmospheric chemistry, temperature and dynamics: revised

    International Nuclear Information System (INIS)

    This study investigates the influence of a major solar proton event (SPE) similar to the Carrington event of 1–2 September 1859 by means of the 3D chemistry climate model (CCM) SOCOL v2.0. Ionization rates were parameterized according to CRAC:CRII (Cosmic Ray-induced Atmospheric Cascade: Application for Cosmic Ray Induced Ionization), a detailed state-of-the-art model describing the effects of SPEs in the entire altitude range of the CCM from 0 to 80 km. This is the first study of the atmospheric effect of such an extreme event that considers all the effects of energetic particles, including the variability of galactic cosmic rays, in the entire atmosphere. We assumed two scenarios for the event, namely with a hard (as for the SPE of February 1956) and soft (as for the SPE of August 1972) spectrum of solar particles. We have placed such an event in the year 2020 in order to analyze the impact on a near future atmosphere. We find statistically significant effects on NOx, HOx, ozone, temperature and zonal wind. The results show an increase of NOx of up to 80 ppb in the northern polar region and an increase of up to 70 ppb in the southern polar region. HOx shows an increase of up to 4000%. Due to the NOx and HOx enhancements, ozone reduces by up to 60% in the mesosphere and by up to 20% in the stratosphere for several weeks after the event started. Total ozone shows a decrease of more than 20 DU in the northern hemisphere and up to 20 DU in the southern hemisphere. The model also identifies SPE induced statistically significant changes in the surface air temperature, with warming in the eastern part of Europe and Russia of up to 7 K for January. (letter)

  8. Solvation effect on the tunneling rates of proton transfer

    International Nuclear Information System (INIS)

    Solvation effects on the tunneling rates in the case of coupled motion of two protons along the reaction coordinate was semiempirically, CNDO/2, computed. The following molecular transition-state complexes (TSC) were studied: +AH--BH--A, where A was either NH3 or H2O and BH was HF. Solvation was modeled with water molecules attached to each side of the perpendicular axis, through the bridge HF at different distances F/O. FN and FO (on-line) distances were also varied. Lower and narrower barriers were observed with the close positioning of the solvating molecules. This effect is reflected in higher tunneling probabilities. Thus, solvation favors the tunnel phenomenon in proton-transfer processes

  9. Molecular hydrogen solvated in water – A computational study

    International Nuclear Information System (INIS)

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

  10. Ionic strength independence of charge distributions in solvation of biomolecules.

    Science.gov (United States)

    Virtanen, J J; Sosnick, T R; Freed, K F

    2014-12-14

    Electrostatic forces enormously impact the structure, interactions, and function of biomolecules. We perform all-atom molecular dynamics simulations for 5 proteins and 5 RNAs to determine the dependence on ionic strength of the ion and water charge distributions surrounding the biomolecules, as well as the contributions of ions to the electrostatic free energy of interaction between the biomolecule and the surrounding salt solution (for a total of 40 different biomolecule/solvent combinations). Although water provides the dominant contribution to the charge density distribution and to the electrostatic potential even in 1M NaCl solutions, the contributions of water molecules and of ions to the total electrostatic interaction free energy with the solvated biomolecule are comparable. The electrostatic biomolecule/solvent interaction energies and the total charge distribution exhibit a remarkable insensitivity to salt concentrations over a huge range of salt concentrations (20 mM to 1M NaCl). The electrostatic potentials near the biomolecule's surface obtained from the MD simulations differ markedly, as expected, from the potentials predicted by continuum dielectric models, even though the total electrostatic interaction free energies are within 11% of each other. PMID:25494774

  11. Crystallization of Esomeprazole Magnesium Water/Butanol Solvate.

    Science.gov (United States)

    Skieneh, Jenna; Khalili Najafabadi, Bahareh; Horne, Stephen; Rohani, Sohrab

    2016-01-01

    The molecular structure of esomeprazole magnesium derivative in the solid-state is reported for the first time, along with a simplified crystallization pathway. The structure was determined using the single crystal X-ray diffraction technique to reveal the bonding relationships between esomeprazole heteroatoms and magnesium. The esomeprazole crystallization process was carried out in 1-butanol and water was utilized as anti-solvent. The product proved to be esomeprazole magnesium tetrahydrate with two 1-butanol molecules that crystallized in P6₃ space group, in a hexagonal unit cell. Complete characterization of a sample after drying was conducted by the use of powder X-ray diffraction (PXRD), ¹H-nuclear magnetic resonance (NMR), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), infrared spectroscopy (IR), and dynamic vapor sorption (DVS). Investigation by ¹H-NMR and TGA has shown that the solvent content in the dried sample consists of two water molecules and 0.3 butanol molecules per esomeprazole magnesium molecule. This is different from the single crystal X-ray diffraction results and can be attributed to the loss of some water and 1-butanol molecules stabilized by intermolecular interactions. The title compound, after drying, is a true solvate in terms of water; conversely, 1-butanol fills the voids of the crystal lattice in non-stoichiometric amounts. PMID:27120591

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

    Science.gov (United States)

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

    2014-08-12

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

  13. Crystallization of Esomeprazole Magnesium Water/Butanol Solvate

    Directory of Open Access Journals (Sweden)

    Jenna Skieneh

    2016-04-01

    Full Text Available The molecular structure of esomeprazole magnesium derivative in the solid-state is reported for the first time, along with a simplified crystallization pathway. The structure was determined using the single crystal X-ray diffraction technique to reveal the bonding relationships between esomeprazole heteroatoms and magnesium. The esomeprazole crystallization process was carried out in 1-butanol and water was utilized as anti-solvent. The product proved to be esomeprazole magnesium tetrahydrate with two 1-butanol molecules that crystallized in P63 space group, in a hexagonal unit cell. Complete characterization of a sample after drying was conducted by the use of powder X-ray diffraction (PXRD, 1H-nuclear magnetic resonance (NMR, thermogravimetric analysis (TGA, differential scanning calorimetry (DSC, infrared spectroscopy (IR, and dynamic vapor sorption (DVS. Investigation by 1H-NMR and TGA has shown that the solvent content in the dried sample consists of two water molecules and 0.3 butanol molecules per esomeprazole magnesium molecule. This is different from the single crystal X-ray diffraction results and can be attributed to the loss of some water and 1-butanol molecules stabilized by intermolecular interactions. The title compound, after drying, is a true solvate in terms of water; conversely, 1-butanol fills the voids of the crystal lattice in non-stoichiometric amounts.

  14. Molecular hydrogen solvated in water – A computational study

    Energy Technology Data Exchange (ETDEWEB)

    Śmiechowski, Maciej, E-mail: Maciej.Smiechowski@pg.gda.pl [Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk (Poland)

    2015-12-28

    The aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H{sub 2} molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the H{sub 2} molecule without major structural distortions and two-dimensional, radial-angular distribution functions indicate that as opposed to strictly tangential, the orientation of these water molecules is such that the solute is solvated with one of the free electron pairs of H{sub 2}O. The calculated self-diffusion coefficient of H{sub 2}(aq) agrees very well with experimental results and the time dependence of mean square displacement suggests the presence of caging on a time scale corresponding to hydrogen bond network vibrations in liquid water. Orientational correlation function of H{sub 2} experiences an extremely short-scale decay, making the H{sub 2}–H{sub 2}O interaction potential essentially isotropic by virtue of rotational averaging. The inclusion of explicit polarizability in the model allows for the calculation of Raman spectra that agree very well with available experimental data on H{sub 2}(aq) under differing pressure conditions, including accurate reproduction of the experimentally noted trends with solute pressure or concentration.

  15. The Formation of Uranus and Neptune in Solid-Rich Feeding Zones: Connecting Chemistry and Dynamics

    OpenAIRE

    Dodson-Robinson, Sarah E.; Bodenheimer, Peter

    2009-01-01

    The core accretion theory of planet formation has at least two fundamental problems explaining the origins of Uranus and Neptune: (1) dynamical times in the trans-Saturnian solar nebula are so long that core growth can take > 15 Myr, and (2) the onset of runaway gas accretion that begins when cores reach 10 Earth masses necessitates a sudden gas accretion cutoff just as the ice giant cores reach critical mass. Both problems may be resolved by allowing the ice giants to migrate outward after t...

  16. Structure and solvation forces in confined films of alkanes

    OpenAIRE

    Dijkstra, Marjolein

    1998-01-01

    We compute by computer simulations the solvation force of a system of linear and branched alkanes confined in a slab geometry. The solvation force for linear decane oscillates with distance with a periodicity close to the width of the molecules. The branched alkanes, 2- methylundecane and 2-methylheptane, show a similar oscillatory behaviour, however the oscillations are decreased with a factor of about three and show a long-range attractive force. In addition, we show that the critical tempe...

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

    Science.gov (United States)

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

    2015-09-10

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

  18. Thermodynamics of solvation in propylene glycol and methyl cellosolve

    International Nuclear Information System (INIS)

    Highlights: • Experimental values of limiting activity coefficients in propylene glycol and methyl cellosolve are reported. • Gibbs free energy versus enthalpy of solvation plots show the presence of the solvophobic effects in studied solutions. • The solvophobic effect in propylene glycol is as strong as in methanol. • The solvophobic effect in methyl cellosolve is rather weak and can be compared to that in butanol. - Abstract: Limiting activity coefficients of low-polar substances: aliphatic and aromatic hydrocarbons, including alkanes, cycloalkanes, alkylbenzenes, and halobenzenes in two solvents, propylene glycol and methyl cellosolve, were measured at temperature T = 298.15 K using gas chromatographic headspace analysis technique. The Gibbs free energies of solvation were calculated from these data and analyzed together with the enthalpies of solvation for the same systems. It was shown that the Gibbs free energies of solvation in propylene glycol are significantly lower than in its homologue ethylene glycol, and in methyl cellosolve they are lower than in propylene glycol. This difference is mainly due to the solvophobic effect, which strength is decreasing in the same order: ethylene glycol > propylene glycol > methyl cellosolve. The contribution of the solvophobic effect into the Gibbs free energies of solvation can be determined using a Gibbs free energy versus enthalpy of solvation plot. This contribution is shown to grow up linearly with the molecular volume of a solute in propylene glycol and methyl cellosolve, as well as in ethylene glycol and in monohydric alcohols

  19. A method of comparison between a force curve measured on a solvated surface and the solvation structure

    CERN Document Server

    Amano, Ken-ichi

    2012-01-01

    Recent surface force apparatus (SFA) and atomic force microscopy (AFM) can measure force curves between a probe and a sample surface in solvent. The force curve is thought as the solvation structure in some articles, because its shape is generally oscilltive and pitch of the oscillation is about the same as diameter of the solvent. However, it is not the solvation structure. It is just only a mean force between the probe and the sample surface. Therefore, a relation between the mean force and the solvation structure must be elucidated theoretically to deepen understanding of the measured result (the mean force). In this letter, we briefly explain the relation and a method for comparing the measured mean force and the solvation structure (obtained by a simulation or a liquid theory) by using basic statistical mechanics of liquid.

  20. Dynamical Transition of Myoglobin and Cu/Zn Superoxide Dismutase Revealed by Molecular Dynamics Simulation

    Institute of Scientific and Technical Information of China (English)

    张莉莉; 张建华; 周林祥

    2002-01-01

    We have carried out parallel molecular dynamics simulations of solvated and non-solvated myoglobin and solvated Cu/Zn superoxide dismutase at different temperatures. By analysis of several methods, the simulations reproduce the quasielastic neutron scattering experimental results. Below 200 K these two proteins behave as harmonic solids with essentially only vibrational motion, while above this temperature, there is a striking dynamic transition into anharmonic motion. Moreover, the simulations further show that water molecules play an important role for this dynamical transition. There is no such sharp dynamical transition in non-solvated proteins and the higher the solvate density is, the steeper at transition point the curve of mean square displacement versus temperature will be. The simulations also display that the dynamical transition is a general property for globular protein and this transition temperature is a demarcation of enzyme activity.

  1. Fluxes, dynamics and chemistry of suspended particulate matter in a southeast Alaskan fjord

    International Nuclear Information System (INIS)

    The weighted mean fluxes over the June 1982-October 1983 were 290, 519, 812, 1124 g m-2 yr-1, respectively, determined using sediment traps deployed at 40, 120, 300 and 375 m depth in the 380 m water column. The long-term sedimentation rate was estimated at average 589 g m-2 yr-1 from sediment 210Pb profiles. Substantial SPM input to mid-depths (below 100 m) from the side arms was noted. Thus, the flux measured at 120 m depth was designated as the primary flux of the SPM to the basin. The sediment focusing resulting from the V shaped basin does not appear to be important. Using particulate Al as a tracer, resuspension rate was estimated at some 30-80% of the vertical flux below 280 m depth. Based on the SPM dynamics, the non-conservative behavior of particulate biogenic matter, Mn and Fe was investigated using a primary-resuspended-altered flux model

  2. Computing UV/vis spectra using a combined molecular dynamics and quantum chemistry approach: bis-triazin-pyridine (BTP) ligands studied in solution.

    Science.gov (United States)

    Höfener, Sebastian; Trumm, Michael; Koke, Carsten; Heuser, Johannes; Ekström, Ulf; Skerencak-Frech, Andrej; Schimmelpfennig, Bernd; Panak, Petra J

    2016-03-01

    We report a combined computational and experimental study to investigate the UV/vis spectra of 2,6-bis(5,6-dialkyl-1,2,4-triazin-3-yl)pyridine (BTP) ligands in solution. In order to study molecules in solution using theoretical methods, force-field parameters for the ligand-water interaction are adjusted to ab initio quantum chemical calculations. Based on these parameters, molecular dynamics (MD) simulations are carried out from which snapshots are extracted as input to quantum chemical excitation-energy calculations to obtain UV/vis spectra of BTP ligands in solution using time-dependent density functional theory (TDDFT) employing the Tamm-Dancoff approximation (TDA). The range-separated CAM-B3LYP functional is used to avoid large errors for charge-transfer states occurring in the electronic spectra. In order to study environment effects with theoretical methods, the frozen-density embedding scheme is applied. This computational procedure allows to obtain electronic spectra calculated at the (range-separated) DFT level of theory in solution, revealing solvatochromic shifts upon solvation of up to about 0.6 eV. Comparison to experimental data shows a significantly improved agreement compared to vacuum calculations and enables the analysis of relevant excitations for the line shape in solution. PMID:26907588

  3. Final Progress Report for Linking Ion Solvation and Lithium Battery Electrolyte Properties

    Energy Technology Data Exchange (ETDEWEB)

    Henderson, Wesley

    2014-08-29

    The research objective of this proposal was to provide a detailed analysis of how solvent and anion structure govern the solvation state of Li+ cations in solvent-LiX mixtures and how this, in turn, dictates the electrolyte physicochemical and electrochemical properties which govern (in part) battery performance. Lithium battery electrolytes remain a poorly understood and hardly studied topic relative to the research devoted to battery electrodes. This is due to the fact that it is the electrodes which determine the energy (capacity) of the battery. The electrolyte, however, plays a crucial role in the practical energy density, power, low and/or high temperature performance, lifetime, safety, etc. which is achievable. The development within this project of a "looking glass" into the molecular interactions (i.e., solution structure) in bulk electrolytes through a synergistic experimental approach involving three research thrusts complements work by other researchers to optimize multi-solvent electrolytes and efforts to understand/control the electrode-electrolyte interfaces, thereby enabling the rational design of electrolytes for a wide variety of battery chemistries and applications (electrolytes-on-demand). The three research thrusts pursued include: (1) conduction of an in-depth analysis of the thermal phase behavior of diverse solvent-LiX mixtures, (2) exploration of the ionic association/solvate formation behavior of select LiX salts with a wide variety of solvents, and (3) linking structure to properties-determination of electrolyte physicochemical and electrochemical properties for comparison with the ionic association and phase behavior.

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

    Energy Technology Data Exchange (ETDEWEB)

    Queiroz, Thiago B. de, E-mail: thiago.branquinho-de-queiroz@uni-bayreuth.de; Kümmel, Stephan [Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth (Germany)

    2015-07-21

    The description of charge transfer excitations has long been a challenge to time dependent density functional theory. The recently developed concept of “optimally tuned range separated hybrid (OT-RSH) functionals” has proven to describe charge transfer excitations accurately in many cases. However, describing solvated or embedded systems is yet a challenge. This challenge is not only computational but also conceptual, because the tuning requires identifying a specific orbital, typically the highest occupied one of the molecule under study. For solvated molecules, this orbital may be delocalized over the solvent. We here demonstrate that one way of overcoming this problem is to use a locally projected self-consistent field diagonalization on an absolutely localized molecular orbital expansion. We employ this approach to determine ionization energies and the optical gap of solvated oligothiophenes, i.e., paradigm low gap systems that are of relevance in organic electronics. Dioxane solvent molecules are explicitly represented in our calculations, and the ambiguities of straightforward parameter tuning in solution are elucidated. We show that a consistent estimate of the optimal range separated parameter (ω) at the limit of bulk solvation can be obtained by gradually extending the solvated system. In particular, ω is influenced by the solvent beyond the first coordination sphere. For determining ionization energies, a considerable number of solvent molecules on the first solvation shell must be taken into account. We demonstrate that accurately calculating optical gaps of solvated systems using OT-RSH can be done in three steps: (i) including the chemical environment when determining the range-separation parameter, (ii) taking into account the screening due to the solvent, and (iii) using realistic molecular geometries.

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

    International Nuclear Information System (INIS)

    The description of charge transfer excitations has long been a challenge to time dependent density functional theory. The recently developed concept of “optimally tuned range separated hybrid (OT-RSH) functionals” has proven to describe charge transfer excitations accurately in many cases. However, describing solvated or embedded systems is yet a challenge. This challenge is not only computational but also conceptual, because the tuning requires identifying a specific orbital, typically the highest occupied one of the molecule under study. For solvated molecules, this orbital may be delocalized over the solvent. We here demonstrate that one way of overcoming this problem is to use a locally projected self-consistent field diagonalization on an absolutely localized molecular orbital expansion. We employ this approach to determine ionization energies and the optical gap of solvated oligothiophenes, i.e., paradigm low gap systems that are of relevance in organic electronics. Dioxane solvent molecules are explicitly represented in our calculations, and the ambiguities of straightforward parameter tuning in solution are elucidated. We show that a consistent estimate of the optimal range separated parameter (ω) at the limit of bulk solvation can be obtained by gradually extending the solvated system. In particular, ω is influenced by the solvent beyond the first coordination sphere. For determining ionization energies, a considerable number of solvent molecules on the first solvation shell must be taken into account. We demonstrate that accurately calculating optical gaps of solvated systems using OT-RSH can be done in three steps: (i) including the chemical environment when determining the range-separation parameter, (ii) taking into account the screening due to the solvent, and (iii) using realistic molecular geometries

  6. Femtosecond pulse radiolysis study of solvation process of electrons in alcohol

    International Nuclear Information System (INIS)

    The solvation processes of electrons in neat n-alcohols have been studied by using the femtosecond pulse radiolysis. The transient optical absorptions of the solvated electrons and the pre-solvated electrons were observed in the visible region and the infrared region, respectively. The reaction rate constants of a dry electron and a pre-solvated electron were obtained by using electron scavengers. The data suggested a dry electron has much higher reactivity than a pre-solvated electron or a solvated electron. (author)

  7. Pulse radiolysis study of solvated electron formation in glassy alcohols at low temperature

    International Nuclear Information System (INIS)

    Pulse radiolysis study of glass-forming alcohols at low temperature (140K∼RT) was carried out to clarify the primary process of pre-solvated and solvated electron in lower alcohols. The very slow decay of pre-solvated electron and the very slow formation of solvated electron were observed at nanosecond region because of very high viscosity of alcohols near melting and glass transition temperature. The activation energy of solvated electron formation was estimated to be 0.17 eV, and this suggests that the formation process of solvated electron depends on a break of hydrogen bond due to reorientation of OH-groups. (author)

  8. The Chemistry and Flow Dynamics of Molecular Biological Tools Used to Confirm In Situ Bioremediation of Benzene, TBA, and MTBE

    Science.gov (United States)

    North, K. P.; Mackay, D. M.; Scow, K. M.

    2010-12-01

    In situ bioremediation has typically been confirmed by collecting sediment and groundwater samples to directly demonstrate a degradation process in a laboratory microcosm. However, recent advances in molecular biological tools present options for demonstrating degradation processes with field-based tools that are less time-consuming. We have been investigating the capability of some of these molecular biological tools to evaluate in situ biodegradation of tert-butyl alcohol (TBA), methyl tert-butyl ether (MTBE), and benzene at two field sites in California. At both sites, we have deployed Bio-Traps® (“traps”), made of Bio-Sep® beads in slotted PVC pipe, which provide ideal environments for microbial colonization. Stable Isotope Probing can be accomplished by sorbing the13C-labeled organic contaminant of concern onto Bio-Sep® beads (“baiting”); incorporation of 13C into the biomass collected by the trap would indicate that the microbial community was capable of degrading the labeled compound. In addition, we examined the chemistry and flow dynamics of these traps and present those results here. We performed a field experiment and a lab experiment to, in part, define the rate that different baits leached off various traps. At a TBA- and MTBE-contaminated site at Vandenberg AFB, Lompoc, CA, the TBA-dominant plume was effectively treated by recirculation/oxygenation of groundwater, decreasing TBA and MTBE concentrations to detection limits along predicted flowpaths created by two pairs of recirculation wells. We used the generated aerobic treatment zone to deploy traps baited with 13C-labeled MTBE or TBA in a novel, ex situ experimental setup. The groundwater flow extracted from the aerobic treatment zone was split through several chambers, each containing a trap and monitoring of influent and effluent. The chamber effluent was measured throughout a six-week deployment and analyzed for both TBA and MTBE; the majority of mass leached from the baited traps did

  9. Nuclear magnetic resonance studies of the solvation structures of a high-performance nonaqueous redox flow electrolyte

    Science.gov (United States)

    Deng, Xuchu; Hu, Mary; Wei, Xiaoliang; Wang, Wei; Mueller, Karl T.; Chen, Zhong; Hu, Jian Zhi

    2016-03-01

    Understanding the solvation structures of electrolytes is important for developing nonaqueous redox flow batteries that hold considerable potential for future large scale energy storage systems. The utilization of an emerging ionic-derivatived ferrocene compound, ferrocenylmethyl dimethyl ethyl ammonium bis(trifluoromethanesulfonyl)imide (Fc1N112-TFSI), has recently overcome the issue of solubility in the supporting electrolyte. In this work, 13C, 1H and 17O NMR investigations were carried out using electrolyte solutions consisting of Fc1N112-TFSI as the solute and the mixed alkyl carbonate as the solvent. It was observed that the spectra of 13C experience changes of chemical shifts while those of 17O undergo linewidth broadening, indicating interactions between solute and solvent molecules. Quantum chemistry calculations of both molecular structures and chemical shifts (13C, 1H and 17O) are performed for interpreting experimental results and for understanding the detailed solvation structures. The results indicate that Fc1N112-TFSI is dissociated at varying degrees in mixed solvent depending on concentrations. At dilute solute concentrations, most Fc1N112+ and TFSI- are fully disassociated with their own solvation shells formed by solvent molecules. At saturated concentration, Fc1N112+-TFSI- contact ion pairs are formed and the solvent molecules are preferentially interacting with the Fc rings rather than interacting with the ionic pendant arm of Fc1N112-TFSI.

  10. Particulate matter chemistry and dynamics in the Twilight Zone at VERTIGO ALOHA and K2 Sites

    Energy Technology Data Exchange (ETDEWEB)

    Bishop, James K.B.; Wood, T.J.

    2008-03-25

    Understanding particle dynamics in the 'Twilight Zone' is critical to prediction of the ocean's carbon cycle. As part of the VERTIGO (VERtical Transformations In the Global Ocean) project, this rarely sampled regime extending from the base of the euphotic layer to 1000 m, was characterized by double-paired day/night Multiple Unit Large Volume in-situ Filtration System (MULVFS) deployments and by {approx}100 high-frequency CTD/transmissometer/turbidity sensor profiles. VERTIGO studies lasting three weeks, contrasted oligotrophic station ALOHA (22.75{sup o}N 158{sup o}W), sampled in June-July 2004, with a biologically productive location (47{sup o}N 161{sup o}E) near station K2 in the Oyashio, occupied July-August 2005. Profiles of major and minor particulate components (C{sub org}, N, P, Ca, Si, Sr, Ba, Mn) in <1, 1-51, and >51 {micro}m size fractions, in-water optics, neutrally buoyant sediment trap (NBST) fluxes, and zooplankton data were intercompared. MULVFS total C{sub org} and C-Star particle beam attenuation coefficient (C{sub P}) were consistently related at both sites with a 27 {micro}M m{sup -1} conversion factor. 26 At K2, C{sub P} profiles further showed a multitude of transient spikes throughout the water column and spike abundance profiles closely paralleled the double peaked abundance profiles of zooplankton. Also at K2, copepods contributed {approx}40% and 10%, night and day, respectively to >51 {micro}m C{sub org} of MULVFS samples in the mixed layer, but few copepods were collected in deeper waters; however, non-swimming radiolarians were quantitatively sampled. A recent hypothesis regarding POC differences between pumps and bottles is examined in light of these results. Particulate >51 {micro}m C{sub org}, N, and P at both ALOHA and K2 showed strong attenuation with depth at both sites. Notable at ALOHA were unusually high levels of >51 {micro}m Sr (up to 4 nM) in the mixed layer, a reflection of high abundances of SrSO{sub 4

  11. Particulate matter chemistry and dynamics in the twilight zone at VERTIGO ALOHA and K2 sites

    Science.gov (United States)

    Bishop, James K. B.; Wood, T. J.

    2008-12-01

    Understanding particle dynamics in the 'Twilight Zone' is critical to prediction of the ocean's carbon cycle. As part of the VERtical Transport In the Global Ocean (VERTIGO) project, this rarely sampled regime extending from the base of the euphotic layer to 1000 m, was characterized by double-paired day/night Multiple Unit Large Volume in-situ Filtration System (MULVFS) deployments and by ˜100 high-frequency CTD/transmissometer/turbidity sensor profiles. VERTIGO studies lasting 3 weeks, contrasted oligotrophic station ALOHA (22.75°N 158°W), sampled in June-July 2004, with a biologically productive location (47 °N 161°E) near station K2 in the Oyashio, occupied July-August 2005. Profiles of major and minor particulate components (C org, N, P, Ca, Si, Sr, Ba, Mn) in 51 μm size fractions, in-water optics, neutrally buoyant sediment trap (NBST) fluxes, and zooplankton data were intercompared. MULVFS total C org and C-Star particle beam attenuation coefficient ( C P) were consistently related at both sites with a 27 μM m -1 conversion factor. At K2, C P profiles further showed a multitude of transient spikes throughout the water column and spike abundance profiles closely paralleled the double peaked abundance profiles of zooplankton. Also at K2, copepods contributed ˜40% and 10%, night and day, respectively to >51 μm C org of MULVFS samples in the mixed layer, but few copepods were collected in deeper waters; however, non-swimming radiolarians were quantitatively sampled. A recent hypothesis regarding POC differences between pumps and bottles is examined in light of these results. Particulate >51 μm C org, N, and P at both ALOHA and K2 showed strong attenuation with depth at both sites. Notable at ALOHA were unusually high levels of >51 μm Sr (up to 4 nM) in the mixed layer, a reflection of high abundances of SrSO 4 precipitating Acantharia. Notable at K2 were major changes in water column inventories of many particulate components to 700 m over 10 days

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2015-03-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Maoyuan; Besford, Quinn Alexander; Mulvaney, Thomas; Gray-Weale, Angus, E-mail: gusgw@gusgw.net [School of Chemistry, The University of Melbourne, Victoria 3010 (Australia)

    2015-03-21

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

  15. Surface chemistry

    CERN Document Server

    Desai, KR

    2008-01-01

    The surface Chemistry of a material as a whole is crucially dependent upon the Nature and type of surfaces exposed on crystallites. It is therefore vitally important to independently Study different, well - defined surfaces through surface analytical techniques. In addition to composition and structure of surface, the subject also provides information on dynamic light scattering, micro emulsions, colloid Stability control and nanostructures. The present book endeavour to bring before the reader that the understanding and exploitation of Solid state phenomena depended largely on the ability to

  16. In situ/operando soft x-ray spectroscopy characterization of ion solvation and catalysis

    Science.gov (United States)

    Liu, Yi-Sheng; Guo, Jinghua

    Many important systems especially in energy-related regime are based on the complexity of material architecture, chemistry and interactions among constituents within. To understand and thus ultimately control the varying applications calls for in-situ/operando characterization tools. We will present the recent development of the in-situ/operando soft X-ray spectroscopic in the studies of catalytic and alkali ion solvation under bias condition, and reveal how to overcome the challenge that soft X-rays cannot easily peek into the high-pressure catalytic cells or liquid electrochemical cells. Also the different feasible detection approaches can provide surface and bulk sensitivity experimentally from those in-situ cells. The unique design of in-situ/operando soft X-ray spectroscopy instrumentation and fabrication principle with examples in Ca, Na, Mg based solutions at ambient pressure/temperature and high temperature (~250°C) gas catalysis will be shown.

  17. Earle K. Plyler Prize for Molecular Spectroscopy & Dynamics Lecture: Broadband Rotational Spectroscopy for Chemical Kinetics, Molecular Structure, and Analytical Chemistry

    Science.gov (United States)

    Pate, Brooks

    2013-03-01

    Advances in high-speed digital electronics have enabled a new generation of molecular rotational spectroscopy techniques that provide instantaneous broadband spectral coverage. These techniques use a chirped excitation pulse to coherently excite the molecular sample over a spectral bandwidth of 10 GHz or larger through rapid passage. The subsequent time-domain emission is recorded using high-speed digitizers (up to 100 Gigasample/s) and the frequency domain spectrum is produced by fast Fourier transformation. The chirped-pulse Fourier transform (CP-FT) method has been implemented in the microwave frequency range (2-40 GHz) for studies of cold samples in pulsed jet sources and in the mm-wave/terahertz (THz) frequency range for studies of samples at room-temperature. The method has opened new applications for molecular rotational spectroscopy in the area of chemical kinetics where dynamic rotational spectroscopy is used to measure the rates of unimolecular isomerization reactions in highly excited molecules prepared by pulsed infrared laser excitation. In these applications, the isomerization rate is obtained from an analysis of the overall line shapes which are modified by chemical exchange leading to coalescence behavior similar to the effect in NMR spectroscopy. The sensitivity of the method and the ability to extend it to low frequency (2-8 GHz) have significantly increased the size range of molecules and molecular clusters for structure determination using isotopic substitution to build up the 3D molecular structures atom-by-atom. Application to the structure of water clusters with up to 15 water molecules will be presented. When coupled with advances in solid-state mm-wave/THz devices, this method provides a direct digital technique for analytical chemistry of room-temperature gases based on molecular rotational spectroscopy. These high-throughput methods can analyze complex sample mixtures with unmatched chemical selectivity and short analysis times. Work

  18. Streamwater chemistry and flow dynamics along vegetation-soil gradient in a subalpine Abies fabri forest watershed, China.

    Science.gov (United States)

    Shan, Bao-Qing; Wang, Wei-Dong; Yin, Cheng-Qing

    2004-01-01

    Streamwater chemistry and spatial flow dynamics from a subalpine Abies fabri forest in an experimental watershed located in the east slope of Gongga Mountain were analyzed to gain insights into the gradient effect of primary community succession on the stream biogeochemical process. Results showed that high sand content (exceeding 80%) and porosity in the soil(exceeding 20% in A horizon and 35% in B horizon), as well as a thick humus layer on the soil surface, made the water exchange quickly in the Huangbengliu (HBL) watershed. Consequently, no surface runoff was observed, and the stream discharge changed rapidly with the daily precipitation. The flow trends of base ions in the stream water were influenced by the Abies fabri succession gradient. Ca2+ , HCO- and SO4(2-) were the dominant anions in the streamwater in this region. A significant difference of Ca2+, HCO3(-) and SO4(2-) concentration exported between the succession stages in the watershed can be found. But they had the similar temporal change in the stream flow. Ca2+, HCO3(-) and SO4(2-) showed significantly negative correlations with the daily precipitation and the stream discharge. Concentrations of Cl-, Na+, K+, and Mg2+ were low in all streamwaters monitored and we observed no differences along the Abies fabri succession gradient. Low ratios of Na: (Na + Ca) (range from 0.1 to 0.2) implied cations were from bedrock weathering (internal source process in the soil system) in this region. But, a variance analysis showed there were almost no differences between rainwater and streamwaters for Mg2+ , Na+, K+, and Cl- concentrations. This indicated that they might be come from rainfall inputs(external source). The highly mobile capacity, rapid water exchange between precipitation and discharge, and long-term export lead to this observed pattern were suggested. PMID:15559799

  19. Streamwater chemistry and flow dynamics along vegetation-soil gradient in a subalpine Abies fabri forest watershed,China

    Institute of Scientific and Technical Information of China (English)

    SHAN Bao-qing; WANG Wei-dong; YIN Cheng-qing

    2004-01-01

    Streamwater chemistry and spatial flow dynamics from a subalpine Abies fabri forest in an experimental watershed located in the east slope of Gongga Mountain were analyzed to gain insights into the gradient effect of primary community succession on the stream biogeochemical process. Results showed that high sand content(exceeding 80%) and porosity in the soil(exceeding 20% in A horizon and 35% in B horizon), as well as a thick humus layer on the soil surface, made the water exchange quickly in the Huangbengliu(HBL) watershed. Consequently, no surface runoff was observed, and the stream discharge changed rapidly with the daily precipitation. The flow trends of base ions in the stream water were influenced by the Abies fabri succession gradient. Ca2+, HCO3- and SO42- were the dominant anions in the streamwater in this region. A significant difference of Ca2+, HCO3- and SO42- concentration exported between the succession stages in the watershed can be found. But they had the similar temporal change in the stream flow. Ca2+, HCO3- and SO42- showed significantly negative correlations with the daily precipitation and the stream discharge. Concentrations of Cl-, Na+, K+, and Mg2+ were low in all streamwaters monitored and we observed no differences along the Abies fabri succession gradient. Low ratios of Na:(Na+Ca) (range from 0.1 to 0.2) implied cations were from bedrock weathering(internal source process in the soil system) in this region. But, a variance analysis showed there were almost no differences between rainwater and streamwaters for Mg2+, Na+, K+, and Cl- concentrations. This indicated that they might be come from rainfall inputs (external source). We suggest that the highly mobile capacity, rapid water exchange between precipitation and discharge, and long-term export lead to this observed pattern.

  20. Non-Isothermal Desolvation Kinetics of Erythromycin A Acetone Solvate

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The desolvation of erythromycin acetone solvate was investigated under non-isothermal conditions by a thermogravimetric analyzer. This paper emphasized the kinetic analysis of non-isothermal TG-DTA data by Achar method and Coats-Redfern method to fit various solid-state reaction models, and to achieve kinetic parameters of desolvation. The mechanism of thermal desolvation was evaluated using the kinetic compensation effect. The results show that kinetics of desolvation of erythromycin acetone solvate was compatible with the mechanism of a two-dimensional diffusion controlled and was best expressed by Valensi equation. Corresponding to the integral method and the differential method, the activation energy of desolvation of erythromycin acetone solvate was estimated to be 51.26-57.11 kJ/mol, and the pre-exponential factor was 8.077 × 106 s-1-4.326 × 107 s-1,respectively.

  1. SISGR: Linking Ion Solvation and Lithium Battery Electrolyte Properties

    Energy Technology Data Exchange (ETDEWEB)

    Trulove, Paul C. [U.S. Naval Academy, Annapolis, MD (United States); Foley, Matthew P. [U.S. Naval Academy, Annapolis, MD (United States)

    2012-09-30

    The solvation and phase behavior of the model battery electrolyte salt lithium trifluoromethanesulfonate (LiCF3SO3) in commonly used organic solvents; ethylene carbonate (EC), gamma-butyrolactone (GBL), and propylene carbonate (PC) was explored. Data from differential scanning calorimetry (DSC), Raman spectroscopy, and X-ray diffraction were correlated to provide insight into the solvation states present within a sample mixture. Data from DSC analyses allowed the construction of phase diagrams for each solvent system. Raman spectroscopy enabled the determination of specific solvation states present within a solvent-salt mixture, and X-ray diffraction data provided exact information concerning the structure of a solvates that could be isolated Thermal analysis of the various solvent-salt mixtures revealed the phase behavior of the model electrolytes was strongly dependent on solvent symmetry. The point groups of the solvents were (in order from high to low symmetry): C2V for EC, CS for GBL, and C1 for PC(R). The low symmetry solvents exhibited a crystallinity gap that increased as solvent symmetry decreased; no gap was observed for EC-LiTf, while a crystallinity gap was observed spanning 0.15 to 0.3 mole fraction for GBL-LiTf, and 0.1 to 0.33 mole fraction for PC(R)-LiTf mixtures. Raman analysis demonstrated the dominance of aggregated species in almost all solvent compositions. The AGG and CIP solvates represent the majority of the species in solutions for the more concentrated mixtures, and only in very dilute compositions does the SSIP solvate exist in significant amounts. Thus, the poor charge transport characteristics of CIP and AGG account for the low conductivity and transport properties of LiTf and explain why is a poor choice as a source of Li+ ions in a Li-ion battery.

  2. Combustion chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Brown, N.J. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    This research is concerned with the development and use of sensitivity analysis tools to probe the response of dependent variables to model input variables. Sensitivity analysis is important at all levels of combustion modeling. This group`s research continues to be focused on elucidating the interrelationship between features in the underlying potential energy surface (obtained from ab initio quantum chemistry calculations) and their responses in the quantum dynamics, e.g., reactive transition probabilities, cross sections, and thermal rate coefficients. The goals of this research are: (i) to provide feedback information to quantum chemists in their potential surface refinement efforts, and (ii) to gain a better understanding of how various regions in the potential influence the dynamics. These investigations are carried out with the methodology of quantum functional sensitivity analysis (QFSA).

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

    International Nuclear Information System (INIS)

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

  4. Electrodeposition of Lithium from Lithium-Containing Solvate Ionic Liquids

    OpenAIRE

    Vanhoutte, Gijs; Brooks, Neil R.; Schaltin, Stijn; Opperdoes, Bastiaan; Van Meervelt, Luc; Locquet, Jean-Pierre; Vereecken, Philippe M.; Fransaer, Jan; Binnemans, Koen

    2014-01-01

    Lithium-containing solvate ionic liquids [Li(L)n][X], with ligands L = 1,2-dimethoxyethane (G1, monoglyme) or 1-methoxy-2-(2-methoxyethyl)ether (G2, diglyme) (with n = 1, 2 or 3) and with anions X = bis(trifluoromethylsulfonyl)imide (Tf2N–), bromide (Br–) or iodide (I–), were synthesized and used as electrolytes for the electrodeposition of lithium metal. Very high lithium-ion concentrations could be obtained, since the lithium ion is part of the cationic structure of the solvate ionic liquid...

  5. Solvated electrons formed in methanol cluster in ethane

    International Nuclear Information System (INIS)

    The authors have studied the spectral shift of the solvated electron in MeOH/C2H6 mixture using pulse radiolysis. The solvated electrons were formed by ionizing the solution. The spectral shift can be explained in terms of MeOH cluster size formed in the solution. With increasing temperature at constant mole fraction of MeOH, the spectral maximum shifts toward low energy. The width at red side increased with increasing temperature, however, there is no significant changes in the blue side of the spectra with temperature

  6. Solvation force between tethered polyelectrolyte layers. A density functional approach

    Directory of Open Access Journals (Sweden)

    O. Pizio

    2012-10-01

    Full Text Available We use a version of the density functional theory to study the solvation force between two plates modified with a tethered layer of chains. The chains are built of tangentially jointed charged spherical segments. The plates are immersed in an electrolyte solution that involves cations, anions and solvent molecules. The latter molecules are modelled as hard spheres. We study the dependence of the solvation force and the structure of chains and of solute molecules on the grafting density, length of chains, architecture of the chains and on concentration of the solute.

  7. Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein

    International Nuclear Information System (INIS)

    The dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties of solvation water of ice around its two crystallographic planes: basal and prism. Three main conclusions are inferred from our investigations. The first one is that the solvation shell of CfAFP does not seem to be particularly far-ranged, at least not beyond what is usually observed for proteins that do not interact with ice. Therefore, it does not appear to us that the antifreeze activity is enhanced by a long-ranged retardation of water mobility. Also the correlation between the collective mobility of water and the collective mobility of protein atoms highly resembles the one measured for the protein that does not interact with ice. Our second conclusion is that the dynamical properties of solvation water of CfAFP are non-uniform. The dynamics of solvation water of ice-binding plane is, in some respects, different from the dynamics of solvation water of the two remaining planes. The feature that distinguishes the dynamics of solvation water of the three planes is the activation energy of diffusion process. The third conclusion is that—from the three analyzed solvation shells of CfAFP—the dynamical properties of solvation water of the ice-binding plane resemble the most the properties of solvation water of ice; note, however, that these properties still clearly differ from the dynamic properties of solvation water of ice

  8. Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein

    Energy Technology Data Exchange (ETDEWEB)

    Kuffel, Anna; Czapiewski, Dariusz; Zielkiewicz, Jan, E-mail: jaz@chem.pg.gda.pl [Department of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80–233 Gdansk (Poland)

    2015-10-07

    The dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties of solvation water of ice around its two crystallographic planes: basal and prism. Three main conclusions are inferred from our investigations. The first one is that the solvation shell of CfAFP does not seem to be particularly far-ranged, at least not beyond what is usually observed for proteins that do not interact with ice. Therefore, it does not appear to us that the antifreeze activity is enhanced by a long-ranged retardation of water mobility. Also the correlation between the collective mobility of water and the collective mobility of protein atoms highly resembles the one measured for the protein that does not interact with ice. Our second conclusion is that the dynamical properties of solvation water of CfAFP are non-uniform. The dynamics of solvation water of ice-binding plane is, in some respects, different from the dynamics of solvation water of the two remaining planes. The feature that distinguishes the dynamics of solvation water of the three planes is the activation energy of diffusion process. The third conclusion is that—from the three analyzed solvation shells of CfAFP—the dynamical properties of solvation water of the ice-binding plane resemble the most the properties of solvation water of ice; note, however, that these properties still clearly differ from the dynamic properties of solvation water of ice.

  9. Bad chemistry

    OpenAIRE

    Petsko, Gregory A

    2004-01-01

    General chemistry courses haven't changed significantly in forty years. Because most basic chemistry students are premedical students, medical schools have enormous influence and could help us start all over again to create undergraduate chemistry education that works.

  10. Local Aqueous Solvation Structure Around Ca2+ During Ca2+---Cl– Pair Formation

    Energy Technology Data Exchange (ETDEWEB)

    Baer, Marcel D.; Mundy, Christopher J.

    2016-03-03

    The molecular details of single ion solvation around Ca2+ and ion-pairing of Ca2--Cl- are investigated using ab initio molecular dynamics. The use of empirical dispersion corrections to the BLYP functional are investigated by comparison to experimentally available extended X-ray absorption fine structure (EXAFS) measurements, which probes the first solvation shell in great detail. Besides finding differences in the free-energy for both ion-pairing and the coordination number of ion solvation between the quantum and classical descriptions of interaction, there were important differences found between dispersion corrected and uncorrected density functional theory (DFT). Specifically, we show significantly different free-energy landscapes for both coordination number of Ca2+ and its ion-pairing with Cl- depending on the DFT simulation protocol. Our findings produce a self-consistent treatment of short-range solvent response to the ion and the intermediate to long-range collective response of the electrostatics of the ion-ion interaction to produce a detailed picture of ion-pairing that is consistent with experiment. MDB is supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative at Pacific Northwest National Laboratory. It was conducted under the Laboratory Directed Research and Development Program at PNNL, a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy. CJM acknowledges support from US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. This research used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Additional computing resources were generously allocated by PNNL's Institutional Computing program. The authors thank Prof. Tom Beck for discussions

  11. Summer carbonate chemistry dynamics in the Southern Yellow Sea and the East China Sea: Regional variations and controls

    Science.gov (United States)

    Qu, Baoxiao; Song, Jinming; Yuan, Huamao; Li, Xuegang; Li, Ning; Duan, Liqin; Chen, Xin; Lu, Xi

    2015-12-01

    Surface partial pressure of CO2 (pCO2) and pertinent parameters (i.e., pH, total alkalinity, dissolved oxygen, chlorophyll a) were investigated in the southern Yellow Sea (SYS) and the East China Sea (ECS) basing on two surveys conducted in June and August of 2013. The results suggested carbonate chemistry dynamics and related controlling factors were provided with significant temporal and spatial variations in different subregions of these two continental shelf seas. The western of SYS (SYSW) was CO2-undersaturated both in June and August, with the average FCO2 -1.88 mmol m-2 d-1 and -3.72 mmol m-2 d-1, respectively. The phytoplankton initiated CO2-absorption and the suspended sediment induced CO2-emission jointly controlled the air-sea CO2 exchange there. The center of SYS (SYSC) also behaved as an obvious CO2 sink (-1.57 mmol m-2 d-1and -3.99 mmol m-2 d-1 in June and August, respectively), probably due to elevated TA/DIC ratio and the subsequent effects of spring bloom. As for the Yangtze River estuary (YRE), it changed from an obvious CO2 sink (-1.28 mmol m-2 d-1) in June into a very weak CO2 source (0.04 mmol m-2 d-1) in August. This change was probably associated with the rising of seawater temperature and monthly variation of Yangtze River discharge. The inner shelf of ECS (ECSS) experienced obvious air-sea CO2 flux changes during from June (-8.88 mmol m-2 d-1) to August (-0.36 mmol m-2 d-1) as well. Biological DIC consumption in the upper layer and DIC regenerated from respiration in the subsurface jointly controlled this pCO2 variation. As a whole, the SYS and ECS acted as an obvious CO2 sink during summer and could absorb atmospheric CO2 with the average air-sea flux (FCO2) -2.68 mmol m-2 d-1. The summary of air-sea CO2 flux in the ECS and SYS during recent two decades indicated the ECS served as quite a stable CO2 sink, whereas the SYS experienced obvious change. Discharge of Yangtze River and anthropogenic nutrients loading could profoundly affect the

  12. Effect of Solvation Film on the Viscosity of Colloidal Dispersions

    Institute of Scientific and Technical Information of China (English)

    PENG Chang-Sheng; GU Qing-Bao; SONG Shao-Xian

    2005-01-01

    Viscosity is one of the most important properties of colloids in mixing, transportation, stabilization, energy consumption, and so on. According to Einstein's viscosity equation, the viscosity of a colloidal dispersion increases with the increase of particle concentration. And the equation can be applicable to all micro-particle dispersions, because the effect of solvation films coated on particles can be neglectable in that case. But with the decrease of particle size to nano-scale, the formation of solvation films on nano-particles can greatly affect the viscosity of a dispersion, and Einstein's equation may not be applicable to this case. In this work, one kind of micro-size silica particle and two kinds of nano-size silica particles were used to investigate the effect of solvation films on dispersion viscosity, dispersed in water and ethyl alcohol solvents, respectively. The results of theoretical calculation and experimental investigation show that the increase of viscosity is contributed from solvation films by more than 95 percent for nano-particle dispersions, while less than 10 percent for micro-particle dispersions.

  13. Structural Interactions within Lithium Salt Solvates. Acyclic Carbonates and Esters

    Energy Technology Data Exchange (ETDEWEB)

    Afroz, Taliman [North Carolina State Univ., Raleigh, NC (United States); Seo, D. M. [North Carolina State Univ., Raleigh, NC (United States); Han, Sang D. [North Carolina State Univ., Raleigh, NC (United States); Boyle, Paul D. [North Carolina State Univ., Raleigh, NC (United States); Henderson, Wesley A. [North Carolina State Univ., Raleigh, NC (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-03-06

    Solvate crystal structures serve as useful models for the molecular-level interactions within the diverse solvates present in liquid electrolytes. Although acyclic carbonate solvents are widely used for Li-ion battery electrolytes, only three solvate crystal structures with lithium salts are known for these and related solvents. The present work, therefore, reports six lithium salt solvate structures with dimethyl and diethyl carbonate: (DMC)2:LiPF6, (DMC)1:LiCF3SO3, (DMC)1/4:LiBF4, (DEC)2:LiClO4, (DEC)1:LiClO4 and (DEC)1:LiCF3SO3 and four with the structurally related methyl and ethyl acetate: (MA)2:LiClO4, (MA)1:LiBF4, (EA)1:LiClO4 and (EA)1:LiBF4.

  14. The solvation of carbohydrates in dimethylsulfoxide and water

    International Nuclear Information System (INIS)

    The solvation of sucrose and other carbohydrates in DMSO and water is probed by intermolecular NOE measurements. The NOE effects are interpreted in terms of specific binding of the solvent to certain sites of the molecules. It is shown that DMSO attaches to specific sites of the sucrose molecule, whereas for water such a clear differentiation cannot be proven. (author)

  15. Relation between a force curve measured on a solvated surface and the solvation structure: Relational expressions for a binary solvent and a molecular liquid

    OpenAIRE

    Amano, Ken-ichi; Suzuki, Kazuhiro; Fukuma, Takeshi; Onishi, Hiroshi

    2012-01-01

    Recent atomic force microscopy (AFM) can measure force curves between a probe and a sample surface in several solvents. The force curve is thought as the solvation structure in some cases, because its shape is generally oscilltive and pitch of the oscillation is about the same as diameter of the solvent. However, it is not the solvation structure. It is just only a mean force between the probe and sample surface. Since theoretical relation between the mean force and the solvation structure ha...

  16. Atomic hydration potentials using a Monte Carlo Reference State (MCRS for protein solvation modeling

    Directory of Open Access Journals (Sweden)

    Makeev Vsevolod J

    2007-03-01

    Full Text Available Abstract Background Accurate description of protein interaction with aqueous solvent is crucial for modeling of protein folding, protein-protein interaction, and drug design. Efforts to build a working description of solvation, both by continuous models and by molecular dynamics, yield controversial results. Specifically constructed knowledge-based potentials appear to be promising for accounting for the solvation at the molecular level, yet have not been used for this purpose. Results We developed original knowledge-based potentials to study protein hydration at the level of atom contacts. The potentials were obtained using a new Monte Carlo reference state (MCRS, which simulates the expected probability density of atom-atom contacts via exhaustive sampling of structure space with random probes. Using the MCRS allowed us to calculate the expected atom contact densities with high resolution over a broad distance range including very short distances. Knowledge-based potentials for hydration of protein atoms of different types were obtained based on frequencies of their contacts at different distances with protein-bound water molecules, in a non-redundant training data base of 1776 proteins with known 3D structures. Protein hydration sites were predicted in a test set of 12 proteins with experimentally determined water locations. The MCRS greatly improves prediction of water locations over existing methods. In addition, the contribution of the energy of macromolecular solvation into total folding free energy was estimated, and tested in fold recognition experiments. The correct folds were preferred over all the misfolded decoys for the majority of proteins from the improved Rosetta decoy set based on the structure hydration energy alone. Conclusion MCRS atomic hydration potentials provide a detailed distance-dependent description of hydropathies of individual protein atoms. This allows placement of water molecules on the surface of proteins and in

  17. Ion solvation in propylene carbonate and its mixtures with water and methanol

    International Nuclear Information System (INIS)

    Solvodynamic radii and solvation numbers of some ions (including I-) in propylene carbonate as well as their solvodynamic radii in mixtures of propylene carbonate-water and propylene carbonate-methanol were determined. Effect of medium components and solvated ion characteristics on the process of ion solvation was considered. It is shown that small size anions in propylene carbonate are weakly solvated, whereas bulky lightly polarized anions interact strongly with the solvent. Addition of water or methanol to propylene carbonate leads to intensification of ion solvation

  18. Microscopic linear liquid streams in vacuum: Injection of solvated biological samples into X-ray free electron lasers

    International Nuclear Information System (INIS)

    Microscopic linear liquid free-streams offer a means of gently delivering biological samples into a probe beam in vacuum while maintaining the sample species in a fully solvated state. By employing gas dynamic forces to form the microscopic liquid stream (as opposed to a conventional solid-walled convergent nozzle), liquid free-streams down to 300 nm diameter have been generated. Such 'Gas Dynamic Virtual Nozzles' (GDVN) are ideally suited to injecting complex biological species into an X-ray Free Electron Laser (XFEL) to determine the structure of the biological species via Serial Femtosecond Crystallography (SFX). GDVN injector technology developed for this purpose is described.

  19. Complex chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Bong Gon; Kim, Jae Sang; Kim, Jin Eun; Lee, Boo Yeon

    2006-06-15

    This book introduces complex chemistry with ten chapters, which include development of complex chemistry on history coordination theory and Warner's coordination theory and new development of complex chemistry, nomenclature on complex with conception and define, chemical formula on coordination compound, symbol of stereochemistry, stereo structure and isomerism, electron structure and bond theory on complex, structure of complex like NMR and XAFS, balance and reaction on solution, an organo-metallic chemistry, biology inorganic chemistry, material chemistry of complex, design of complex and calculation chemistry.

  20. Complex chemistry

    International Nuclear Information System (INIS)

    This book introduces complex chemistry with ten chapters, which include development of complex chemistry on history coordination theory and Warner's coordination theory and new development of complex chemistry, nomenclature on complex with conception and define, chemical formula on coordination compound, symbol of stereochemistry, stereo structure and isomerism, electron structure and bond theory on complex, structure of complex like NMR and XAFS, balance and reaction on solution, an organo-metallic chemistry, biology inorganic chemistry, material chemistry of complex, design of complex and calculation chemistry.

  1. Ionic force field optimization based on single-ion and ion-pair solvation properties

    CERN Document Server

    Fyta, Maria; Dzubiella, Joachim; Vrbka, Lubos; Netz, Roland R

    2009-01-01

    Molecular dynamics simulations of ionic solutions depend sensitively on the force fields employed for the ions. To resolve the fine differences between ions of the same valence and roughly similar size and in particular to correctly describe ion-specific effects, it is clear that accurate force fields are necessary. In the past, optimization strategies for ionic force fields either considered single-ion properties (such as the solvation free energy at infinite dilution or the ion-water structure) or ion-pair properties (in the form of ion-ion distribution functions). In this paper we investigate strategies to optimize ionic force fields based on single-ion and ion-pair properties simultaneously. To that end, we simulate five different salt solutions, namely CsCl, KCl, NaI, KF, and CsI, at finite ion concentration. The force fields of these ions are systematically varied under the constraint that the single-ion solvation free energy matches the experimental value, which reduces the two-dimensional $\\{\\sigma,\\e...

  2. Use of semantic technologies for the development of a dynamic trajectories generator in a Semantic Chemistry eLearning platform

    OpenAIRE

    Huber, Richard; Hantelmann, Kirsten; Todor, Alexandru; Krebs, Sebastian; Heese, Ralf; Paschke, Adrian

    2010-01-01

    ChemgaPedia is a multimedia, webbased eLearning service platform that currently contains about 18.000 pages organized in 1.700 chapters covering the complete bachelor studies in chemistry and related topics of chemistry, pharmacy, and life sciences. The eLearning encyclopedia contains some 25.000 media objects and the eLearning platform provides services such as virtual and remote labs for experiments. With up to 350.000 users per month the platform is the most frequently used scientific educ...

  3. Mathematical Chemistry

    OpenAIRE

    Trinajstić, Nenad; Gutman, Ivan

    2002-01-01

    A brief description is given of the historical development of mathematics and chemistry. A path leading to the meeting of these two sciences is described. An attempt is made to define mathematical chemistry, and journals containing the term mathematical chemistry in their titles are noted. In conclusion, the statement is made that although chemistry is an experimental science aimed at preparing new compounds and materials, mathematics is very useful in chemistry, among other things, to produc...

  4. Spatially Resolved Artificial Chemistry

    DEFF Research Database (Denmark)

    Fellermann, Harold

    2009-01-01

    made a class of models accessible to the realms of artificial chemistry that represent reacting molecules in a coarse-grained fashion in continuous space. This chapter introduces the mathematical models of Brownian dynamics (BD) and dissipative particle dynamics (DPD) for molecular motion and reaction...

  5. Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. I. Polycyclic aromatic hydrocarbons.

    Science.gov (United States)

    Calvo, F; Yurtsever, E

    2016-06-14

    This work theoretically examines the progressive coating of planar polycyclic aromatic hydrocarbon (PAH) molecules ranging from benzene to circumcoronene (C54H18) by para-hydrogen and ortho-deuterium. The coarse-grained Silvera-Goldman potential has been extended to model the interactions between hydrogen molecules and individual atoms of the PAH and parametrized against quantum chemical calculations for benzene-H2. Path-integral molecular dynamics simulations at 2 K were performed for increasingly large amounts of hydrogen coating the PAH up to the first solvation shell and beyond. From the simulations, various properties were determined such as the size of the first shell and its thickness as well as the solvation energy. The degree of delocalization was notably quantified from an energy landscape perspective, by monitoring the fluctuations among inherent structures sampled by the trajectories. Our results generally demonstrate a high degree of localization owing to relatively strong interactions between hydrogen and the PAH, and qualitatively minor isotopic effects. In the limit of large hydrogen amounts, the shell size and solvation energy both follow approximate linear relations with the numbers of carbon and hydrogen in the PAH. PMID:27306002

  6. Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. I. Polycyclic aromatic hydrocarbons

    Science.gov (United States)

    Calvo, F.; Yurtsever, E.

    2016-06-01

    This work theoretically examines the progressive coating of planar polycyclic aromatic hydrocarbon (PAH) molecules ranging from benzene to circumcoronene (C54H18) by para-hydrogen and ortho-deuterium. The coarse-grained Silvera-Goldman potential has been extended to model the interactions between hydrogen molecules and individual atoms of the PAH and parametrized against quantum chemical calculations for benzene-H2. Path-integral molecular dynamics simulations at 2 K were performed for increasingly large amounts of hydrogen coating the PAH up to the first solvation shell and beyond. From the simulations, various properties were determined such as the size of the first shell and its thickness as well as the solvation energy. The degree of delocalization was notably quantified from an energy landscape perspective, by monitoring the fluctuations among inherent structures sampled by the trajectories. Our results generally demonstrate a high degree of localization owing to relatively strong interactions between hydrogen and the PAH, and qualitatively minor isotopic effects. In the limit of large hydrogen amounts, the shell size and solvation energy both follow approximate linear relations with the numbers of carbon and hydrogen in the PAH.

  7. Molecular dynamics simulations of small halogenated organics at the air-water interface: implications in water treatment and atmospheric chemistry

    Czech Academy of Sciences Publication Activity Database

    Habartová, Alena; Valsaraj, K. T.; Roeselová, Martina

    2013-01-01

    Roč. 117, č. 38 (2013), s. 9205-9215. ISSN 1089-5639 R&D Projects: GA ČR GA13-06181S Institutional support: RVO:61388963 Keywords : aerosol * air bubbles * interfacial concentration Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.775, year: 2013

  8. Incorporating Modeling and Simulations in Undergraduate Biophysical Chemistry Course to Promote Understanding of Structure-Dynamics-Function Relationships in Proteins

    Science.gov (United States)

    Hati, Sanchita; Bhattacharyya, Sudeep

    2016-01-01

    A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and…

  9. Studies in chemical dynamics and radiation chemistry. Technical progress report, 1 July 1974--30 June 1975

    International Nuclear Information System (INIS)

    Research progress in the following areas is reported: low energy electron scattering; photoelectron spectrometry; elementary reactions by photolysis at variable wavelengths; collisions in crossed molecular beams; and, diffusion kinetics in the radiation chemistry of water. Publications related to the work are included. (JGB)

  10. Dissecting ion-specific dielectric spectra of sodium-halide solutions into solvation water and ionic contributions

    Energy Technology Data Exchange (ETDEWEB)

    Rinne, Klaus F.; Netz, Roland R. [Fachbereich Physik, Freie Universität Berlin, 14195 Berlin (Germany); Gekle, Stephan [Physikalisches Institut, Universität Bayreuth, 95440 Bayreuth (Germany)

    2014-12-07

    Using extensive equilibrium molecular dynamics simulations we determine the dielectric spectra of aqueous solutions of NaF, NaCl, NaBr, and NaI. The ion-specific and concentration-dependent shifts of the static dielectric constants and the dielectric relaxation times match experimental results very well, which serves as a validation of the classical and non-polarizable ionic force fields used. The purely ionic contribution to the dielectric response is negligible, but determines the conductivity of the salt solutions. The ion-water cross correlation contribution is negative and reduces the total dielectric response by about 5%-10% for 1 M solutions. The dominating water dielectric response is decomposed into different water solvation shells and ion-pair configurations, by this the spectral blue shift and the dielectric decrement of salt solutions with increasing salt concentration is demonstrated to be primarily caused by first-solvation shell water. With rising salt concentration the simulated spectra show more pronounced deviations from a single-Debye form and can be well described by a Cole-Cole fit, in quantitative agreement with experiments. Our spectral decomposition into ionic and different water solvation shell contributions does not render the individual contributions more Debye-like, this suggests the non-Debye-like character of the dielectric spectra of salt solutions not to be due to the superposition of different elementary relaxation processes with different relaxation times. Rather, the non-Debye-like character is likely to be an inherent spectral signature of solvation water around ions.

  11. Aqueous solvation of methane from first principles

    CERN Document Server

    Rossato, Lorenzo; Silvestrelli, Pier Luigi

    2012-01-01

    Structural, dynamical, bonding, and electronic properties of water molecules around a soluted methane molecule are studied from first principles. The results are compatible with experiments and qualitatively support the conclusions of recent classical Molecular Dynamics simulations concerning the controversial issue on the presence of "immobilized" water molecules around hydrophobic groups: the hydrophobic solute slightly reduces (by a less than 2 factor) the mobility of many surrounding water molecules rather than immobilizing just the few ones which are closest to methane, similarly to what obtained by previous first-principles simulations of soluted methanol. Moreover, the rotational slowing down is compatible with that one predicted on the basis of the excluded volume fraction, which leads to a slower Hydrogen bond-exchange rate. The analysis of simulations performed at different temperatures suggests that the target temperature of the soluted system must be carefully chosen, in order to avoid artificial ...

  12. Gas phase ion chemistry

    CERN Document Server

    Bowers, Michael T

    1979-01-01

    Gas Phase Ion Chemistry, Volume 1 covers papers on the advances of gas phase ion chemistry. The book discusses the advances in flow tubes and the measurement of ion-molecule rate coefficients and product distributions; the ion chemistry of the earth's atmosphere; and the classical ion-molecule collision theory. The text also describes statistical methods in reaction dynamics; the state selection by photoion-photoelectron coincidence; and the effects of temperature and pressure in the kinetics of ion-molecule reactions. The energy distribution in the unimolecular decomposition of ions, as well

  13. Electrostatics of solvated systems in periodic boundary conditions

    OpenAIRE

    Andreussi, Oliviero; Marzari, Nicola

    2014-01-01

    Continuum solvation methods can provide an accurate and inexpensive embedding of quantum simulations in liquid or complex dielectric environments. Notwithstanding a long history and manifold applications to isolated systems in open boundary conditions, their extension to materials simulations --- typically entailing periodic-boundary conditions --- is very recent, and special care is needed to address correctly the electrostatic terms. We discuss here how periodic-boundary corrections develop...

  14. Effect of solvation on the spectroscopy of U4+ ion

    International Nuclear Information System (INIS)

    Complete text of publication follows: The framework of this project is the interpretation of NMRD (Nuclear Magnetic Relaxation Dispersion) experiments performed on solvated U4+, NpO2+ and PuO22+, which all have an f2 configuration. Unexpectedly U4+ has a much lower nuclear relaxation time than the two actinyl ions. This observation raises the question of the nature and ordering of the low-lying electronic states originating from the 5f2 configuration. In this preliminary study we address this problem by investigating the electronic spectrum of U4+. The first step is the determination of the spectrum in gas phase, which can be compared to experimental data. The results on the naked ion show that the electronic transitions are very sensitive to the choice of the correlation method, particularly the transition from the 3H4 ground state to the highest excited 1S0 state of the 5f0 manifold, which appears to be a delicate problem. For the computation of the spectrum of the solvated species, one can either use a reaction field to model the solvent or treat the first coordination sphere around the ion explicitly. Both approaches have been investigated. For the second one, we chose to add eight water molecules rather than nine to keep a high symmetry system even if [U(H2O)9]4+ is considered the most stable hydrate in aqueous solution. We used the two-step SO-CI method EPCISO (Effective and Polarised CI-SO), which treats correlation with multi-reference CI or perturbative CASPT2 approaches in the first step and introduces spin-orbit interaction within an intermediate Hamiltonian scheme in the second step of the calculation. The comparison of the spectra of the solvated and bare U4+ ion reveals the influence of solvation on the 5f0 manifold

  15. Solvation of alkane and alcohol molecules. Energy contributions

    OpenAIRE

    Pais, A. A. C. C.; Sousa, A.; Eusébio, M. E.; Redinha, J. S.

    2001-01-01

    In this work we conduct a systematic ab initio study of the solvation of small alkane, monoalcohol and diol molecules, in polar solvents with different properties. A choice of basis set suitable for the type of compounds under study is presented. The various components of the solvent–solute interaction and the cavitation energy are treated individually and their variation with chain length and introduction of hydroxy groups assessed. The use of solute molecules in which controlled changes are...

  16. Solvation of Oxytetracycline Hydrochloride in Ethanol-Water Mixed Solvents.

    OpenAIRE

    Esam A Gomaa; Elsayed M Abou Elleef; Elsayed T Helmy

    2014-01-01

    The aim of this study was to determine the t hermodynamic functions, Gibbs energy, enthalpy and entropy for the solution processes of oxytetracycline hydrochloride in the mixed solvent (ethanol+water) from solubility val ues obtained at temperatures ranging from 293.15 K to 308.15 K. The respective thermodynamic functions for mixing and solvation processes as well as the activity coefficients for the solute were calculated. The experimental results enable us to estimate th e value of thermody...

  17. Drama in Dynamics: Boom, Splash, and Speed

    Energy Technology Data Exchange (ETDEWEB)

    Heather Marie Netzloff

    2004-12-19

    The full nature of chemistry and physics cannot be captured by static calculations alone. Dynamics calculations allow the simulation of time-dependent phenomena. This facilitates both comparisons with experimental data and the prediction and interpretation of details not easily obtainable from experiments. Simulations thus provide a direct link between theory and experiment, between microscopic details of a system and macroscopic observed properties. Many types of dynamics calculations exist. The most important distinction between the methods and the decision of which method to use can be described in terms of the size and type of molecule/reaction under consideration and the type and level of accuracy required in the final properties of interest. These considerations must be balanced with available computational codes and resources as simulations to mimic ''real-life'' may require many time steps. As indicated in the title, the theme of this thesis is dynamics. The goal is to utilize the best type of dynamics for the system under study while trying to perform dynamics in the most accurate way possible. As a quantum chemist, this involves some level of first principles calculations by default. Very accurate calculations of small molecules and molecular systems are now possible with relatively high-level ab initio quantum chemistry. For example, a quantum chemical potential energy surface (PES) can be developed ''on-the-fly'' with dynamic reaction path (DRP) methods. In this way a classical trajectory is developed without prior knowledge of the PES. In order to treat solvation processes and the condensed phase, large numbers of molecules are required, especially in predicting bulk behavior. The Effective Fragment Potential (EFP) method for solvation decreases the cost of a fully quantum mechanical calculation by dividing a chemical system into an ab initio region that contains the solute and an ''effective fragment

  18. The Effects of Fast Molecular Motions and Solvation on NMR Parameters

    Czech Academy of Sciences Publication Activity Database

    Dračínský, Martin; Bouř, Petr; Exner, T.; Hodgkinson, P.

    Leipzig : European Science Foundation, 2013. s. 69-70. [CPMD - Leipzig 2013. Matter, life , light from ab initio molecular dynamics simulations. 02.09.2013-06.09.2013, Leipzig] Institutional support: RVO:61388963 Keywords : NMR spectroscopy * DFT calculations * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry

  19. Charge-transfer excitations in low-gap systems under the influence of solvation and conformational disorder: Exploring range-separation tuning

    International Nuclear Information System (INIS)

    Charge transfer excitations play a prominent role in the fields of molecular electronics and light harvesting. At the same time they have developed a reputation for being hard to predict with time-dependent density functional theory, which is the otherwise predominant method for calculating molecular structure and excitations. Recently, it has been demonstrated that range-separated hybrid functionals, in particular with an “optimally tuned” range separation parameter, describe charge-transfer excitations reliably for different molecules. Many of these studies focused on molecules in vacuum. Here we investigate the influence of solvation on the electronic excitations of thiophene oligomers, i.e., paradigm low gap systems. We take into account bulk solvation using a continuum solvation model and geometrical distortions from molecular dynamics. From our study, three main findings emerge. First, geometrical distortions increase absorption energies by about 0.5 eV for the longer thiophene oligomers. Second, combining optimal tuning of the range separation parameter with a continuum solvation method is not straightforward and has to be approached with great care. Third, optimally tuned range-separated hybrids without a short-range exchange component tend to inherit undesirable characteristics of semi-local functionals: with increasing system size the range separation parameter takes a smaller value, leading to a functional of effectively more semi-local nature and thus not accurately capturing, e.g., the saturation of the optical gap with increasing system size

  20. Charge-transfer excitations in low-gap systems under the influence of solvation and conformational disorder: Exploring range-separation tuning

    Energy Technology Data Exchange (ETDEWEB)

    Queiroz, Thiago B. de, E-mail: thiago.branquinho-de-queiroz@uni-bayreuth.de; Kümmel, Stephan [Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth (Germany)

    2014-08-28

    Charge transfer excitations play a prominent role in the fields of molecular electronics and light harvesting. At the same time they have developed a reputation for being hard to predict with time-dependent density functional theory, which is the otherwise predominant method for calculating molecular structure and excitations. Recently, it has been demonstrated that range-separated hybrid functionals, in particular with an “optimally tuned” range separation parameter, describe charge-transfer excitations reliably for different molecules. Many of these studies focused on molecules in vacuum. Here we investigate the influence of solvation on the electronic excitations of thiophene oligomers, i.e., paradigm low gap systems. We take into account bulk solvation using a continuum solvation model and geometrical distortions from molecular dynamics. From our study, three main findings emerge. First, geometrical distortions increase absorption energies by about 0.5 eV for the longer thiophene oligomers. Second, combining optimal tuning of the range separation parameter with a continuum solvation method is not straightforward and has to be approached with great care. Third, optimally tuned range-separated hybrids without a short-range exchange component tend to inherit undesirable characteristics of semi-local functionals: with increasing system size the range separation parameter takes a smaller value, leading to a functional of effectively more semi-local nature and thus not accurately capturing, e.g., the saturation of the optical gap with increasing system size.

  1. Charge-transfer excitations in low-gap systems under the influence of solvation and conformational disorder: Exploring range-separation tuning

    Science.gov (United States)

    de Queiroz, Thiago B.; Kümmel, Stephan

    2014-08-01

    Charge transfer excitations play a prominent role in the fields of molecular electronics and light harvesting. At the same time they have developed a reputation for being hard to predict with time-dependent density functional theory, which is the otherwise predominant method for calculating molecular structure and excitations. Recently, it has been demonstrated that range-separated hybrid functionals, in particular with an "optimally tuned" range separation parameter, describe charge-transfer excitations reliably for different molecules. Many of these studies focused on molecules in vacuum. Here we investigate the influence of solvation on the electronic excitations of thiophene oligomers, i.e., paradigm low gap systems. We take into account bulk solvation using a continuum solvation model and geometrical distortions from molecular dynamics. From our study, three main findings emerge. First, geometrical distortions increase absorption energies by about 0.5 eV for the longer thiophene oligomers. Second, combining optimal tuning of the range separation parameter with a continuum solvation method is not straightforward and has to be approached with great care. Third, optimally tuned range-separated hybrids without a short-range exchange component tend to inherit undesirable characteristics of semi-local functionals: with increasing system size the range separation parameter takes a smaller value, leading to a functional of effectively more semi-local nature and thus not accurately capturing, e.g., the saturation of the optical gap with increasing system size.

  2. Combinatorial chemistry

    DEFF Research Database (Denmark)

    Nielsen, John

    1994-01-01

    An overview of combinatorial chemistry is presented. Combinatorial chemistry, sometimes referred to as `irrational drug design,' involves the generation of molecular diversity. The resulting chemical library is then screened for biologically active compounds.......An overview of combinatorial chemistry is presented. Combinatorial chemistry, sometimes referred to as `irrational drug design,' involves the generation of molecular diversity. The resulting chemical library is then screened for biologically active compounds....

  3. Positronium chemistry

    CERN Document Server

    Green, James

    1964-01-01

    Positronium Chemistry focuses on the methodologies, reactions, processes, and transformations involved in positronium chemistry. The publication first offers information on positrons and positronium and experimental methods, including mesonic atoms, angular correlation measurements, annihilation spectra, and statistical errors in delayed coincidence measurements. The text then ponders on positrons in gases and solids. The manuscript takes a look at the theoretical chemistry of positronium and positronium chemistry in gases. Topics include quenching, annihilation spectrum, delayed coincidence

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

    Science.gov (United States)

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

    2013-01-01

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

  5. Modifying Poisson equation for near-solute dielectric polarization and solvation free energy

    Science.gov (United States)

    Yang, Pei-Kun

    2016-06-01

    The dielectric polarization P is important for calculating the stability of protein conformation and the binding affinity of protein-protein/ligand interactions and for exploring the nonthermal effect of an external electric field on biomolecules. P was decomposed into the product of the electric dipole moment per molecule p; bulk solvent density Nbulk; and relative solvent molecular density g. For a molecular solute, 4πr2p(r) oscillates with the distance r to the solute, and g(r) has a large peak in the near-solute region, as observed in molecular dynamics (MD) simulations. Herein, the Poisson equation was modified for computing p based on the modified Gauss's law of Maxwell's equations, and the potential of the mean force was used for computing g. For one or two charged atoms in a water cluster, the solvation free energies of the solutes obtained by these equations were similar to those obtained from MD simulations.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-01-20

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

  7. Spicing up continuum solvation models with SaLSA: the spherically-averaged liquid susceptibility ansatz

    CERN Document Server

    Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Arias, T A

    2014-01-01

    Continuum solvation models enable electronic structure calculations of systems in liquid environments, but because of the large number of empirical parameters, they are limited to the class of systems in their fit set (typically organic molecules). Here, we derive a solvation model with no empirical parameters for the dielectric response by taking the linear response limit of a classical density functional for molecular liquids. This model directly incorporates the nonlocal dielectric response of the liquid using an angular momentum expansion, and with a single fit parameter for dispersion contributions it predicts solvation energies of neutral molecules with an RMS error of 1.3 kcal/mol in water and 0.8 kcal/mol in chloroform and carbon tetrachloride. We show that this model is more accurate for strongly polar and charged systems than previous solvation models because of the parameter-free electric response, and demonstrate its suitability for ab initio solvation, including self-consistent solvation in quant...

  8. Dynamics of seawater carbonate chemistry, production, and calcification of a coral reef flat, central Great Barrier Reef

    Directory of Open Access Journals (Sweden)

    R. Albright

    2013-10-01

    Full Text Available Ocean acidification is projected to shift coral reefs from a state of net accretion to one of net dissolution this century. Presently, our ability to predict global-scale changes to coral reef calcification is limited by insufficient data relating seawater carbonate chemistry parameters to in situ rates of reef calcification. Here, we investigate diel and seasonal trends in carbonate chemistry of the Davies Reef flat in the central Great Barrier Reef and relate these trends to benthic carbon fluxes by quantifying net ecosystem calcification (nec and net community production (ncp. Results show that seawater carbonate chemistry of the Davies Reef flat is highly variable over both diel and seasonal cycles. pH (total scale ranged from 7.92 to 8.17, pCO2 ranged from 272 to 542 μatm, and aragonite saturation state (Ωarag ranged from 2.9 to 4.1. Diel cycles in carbonate chemistry were primarily driven by ncp, and warming explained 35% and 47% of the seasonal shifts in pCO2 and pH, respectively. Daytime ncp averaged 37 ± 19 mmol C m−2 h−1 in summer and 33 ± 13 mmol C m−2 h−1 in winter; nighttime ncp averaged −30 ± 25 and −7 ± 6 mmol C m−2 h−1 in summer and winter, respectively. Daytime nec averaged 11 ± 4 mmol CaCO3 m−2 h−1 in summer and 8 ± 3 mmol CaCO3 m−2 h−1 in winter, whereas nighttime nec averaged 2 ± 4 mmol and −1 ± 3 mmol CaCO3 m−2 h−1 in summer and winter, respectively. Net ecosystem calcification was highly sensitive to changes in Ωarag for both seasons, indicating that relatively small shifts in Ωarag may drive measurable shifts in calcification rates, and hence carbon budgets, of coral reefs throughout the year.

  9. Dynamics of seawater carbonate chemistry, production, and calcification of a coral reef flat, Central Great Barrier Reef

    Directory of Open Access Journals (Sweden)

    R. Albright

    2013-05-01

    Full Text Available Ocean acidification is projected to shift coral reefs from a state of net accretion to one of net dissolution this century. Presently, our ability to predict global-scale changes to coral reef calcification is limited by insufficient data relating seawater carbonate chemistry parameters to in situ rates of reef calcification. Here, we investigate natural trends in carbonate chemistry of the Davies Reef flat in the central Great Barrier Reef on diel and seasonal timescales and relate these trends to benthic carbon fluxes by quantifying net ecosystem calcification (nec and net community production (ncp. Results show that seawater carbonate chemistry of the Davies Reef flat is highly variable over both diel and seasonal timescales. pH (total scale ranged from 7.92 to 8.17, pCO2 ranged from 272 to 542 μatm, and aragonite saturation state (Ωarag ranged from 2.9 to 4.1. Diel cycles in carbonate chemistry were primarily driven by ncp, and warming explained 35% and 47% of the seasonal shifts in pCO2 and pH, respectively. Daytime ncp averaged 36 ± 19 mmol C m−2 h−1 in summer and 33 ± 13 mmol C m−2 h−1 in winter; nighttime ncp averaged −22 ± 20 and −7 ± 6 mmol C m−2 h−1 in summer and winter, respectively. Daytime nec averaged 11 ± 4 mmol CaCO3 m−2 h−1 in summer and 8 ± 3 mmol CaCO3 m−2 h−1 in winter, whereas nighttime nec averaged 2 ± 4 mmol and −1 ± 3 mmol CaCO3 m−2 h−1 in summer and winter, respectively. Net ecosystem calcification was positively correlated with Ωarag for both seasons. Linear correlations of nec and Ωarag indicate that the Davies Reef flat may transition from a state of net calcification to net dissolution at Ωarag values of 3.4 in summer and 3.2 in winter. Diel trends in Ωarag indicate that the reef flat is currently below this calcification threshold 29.6% of the time in summer and 14.1% of the time in winter.

  10. Solid-State Chemistry in France: Structures and Dynamics of a Scientific Community since World War II

    OpenAIRE

    Teissier, Pierre

    2010-01-01

    This paper tells the history of solid-state chemistry in France from 1945 to the present. There, the chemical study of solids was carried out by a national, academic community of solid-state chemists, which experienced three successive organizational regimes. It was first framed by prewar traditions, taking the form of a feudal regime of Parisian "research schools" until the late 1950s. As the first post-World War II generation gained power and influence, research schools tended to drop their...

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

    Science.gov (United States)

    Arias, Tomas

    2015-03-01

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

  12. The coupling between stability and ion pair formation in magnesium electrolytes from first-principles quantum mechanics and classical molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Rajput, Nav Nidhi; Qu, Xiaohuui; Sa, Niya; Burrell, Anthony K.; Persson, Kristin A.

    2015-03-11

    In this work we uncover a novel effect between concentration dependent ion pair formation and anion stability at reducing potentials, e.g., at the metal anode. Through comprehensive calculations using both first-principles as well as well-benchmarked classical molecular dynamics over a matrix of electrolytes, covering solvents and salt anions with a broad range in chemistry, we elucidate systematic correlations between molecular level interactions and composite electrolyte properties, such as electrochemical stability, solvation structure, and dynamics. We find that Mg electrolytes are highly prone to ion pair formation, even at modest concentrations, for a wide range of solvents with different dielectric constants, which have implications for dynamics as well as charge transfer. Specifically, we observe that, at Mg metal potentials, the ion pair undergoes partial reduction at the Mg cation center (Mg2+ -> Mg+), which competes with the charge transfer mechanism and can activate the anion to render it susceptible to decomposition. Specifically, TFSI exhibits a significant bond weakening while paired with the transient, partially reduced Mg+. In contrast, BH4 and BF4 are shown to be chemically stable in a reduced ion pair configuration. Furthermore, we observe that higher order glymes as well as DMSO improve the solubility of Mg salts, but only the longer glyme chains reduce the dynamics of the ions in solution. This information provides critical design metrics for future electrolytes as it elucidates a close connection between bulk solvation and cathodic stability as well as the dynamics of the salt.

  13. Surface layer ozone and nitric oxides in the Arctic: The inuence of boundary layer dynamics, snowpack chemistry, surface exchanges, and seasonality

    Science.gov (United States)

    Van Dam, Brie A.

    The snowpack is a region of active chemistry. Aqueous chemistry in a quasi-liquid layer on snow grains and gas-phase chemical reactions in snow interstitial air can lead to the production or destruction of important trace gases. Physical transport parameters such as wind pumping and diffusion affect the vertical distribution of gases within the snowpack. The resulting emission or uptake of trace gases at the atmosphere-snowpack interface can have significant in uence on the chemistry of the lower atmosphere. In this work the dynamic interactions between the snowpack and atmosphere are examined from multiple perspectives. The primary focus is on ozone (O3) and nitrogen oxides (NOx) in the Arctic, a region undergoing widespread environmental change. To investigate an ice-sheet location with year round snow cover, data from a two-year campaign at Summit, Greenland are implemented. At Summit this study examines (1) the processes contributing to vigorous chemistry in snow interstitial air, and (2) the role of the boundary layer over snow in determining surface layer NOx. Physical and chemical processes are shown to contribute to distinct seasonal and diurnal cycles of O3, NO, and NO2 in the snowpack. Boundary layer depths estimated from sonic anemometer turbulence quantities are used alongside sodar-derived values to show that the depth of the stable to weakly stable boundary layer at Summit was not a primary factor in determining NO x in early summer. Motivated by observations of an increase in the length of the snow-free season in the Arctic in recent decades, data from a one-year experiment at the seasonally-snow covered location of Toolik Lake, AK are also incorporated. This study shows the first observations of springtime ozone depletion events at a location over 200 km from the coast in the Arctic. FLEXPART analysis is used to illustrate that these inland events are linked to transport conditions. Lastly at this location, eddy-covariance O3 uxes were calculated to

  14. Prominent Chemists Team Up to Review Frontiers in Chemistry.

    Science.gov (United States)

    Baum, Rudy M.

    1989-01-01

    Discusses a symposium which focused on the influence of inorganic chemistry on organic synthesis, the impact of organic chemistry on biochemistry and vice versa, chemical reaction dynamics, and advances in inorganic chemistry. Explains the purpose of the symposium was to illustrate the intellectual dynamism of modern chemistry. (MVL)

  15. Social Chemistry

    OpenAIRE

    Lichtfouse, Eric; Schwarzbauer, Jan; Robert, Didier

    2012-01-01

    International audience This article is both an essay to propose social chemistry as a new scientific discipline, and a preface of the book Environmental Chemistry for a Sustainable World. Environmental chemistry is a fast emerging discipline aiming at the understanding the fate of pollutants in ecosystems and at designing novel processes that are safe for ecosystems. Past pollution should be cleaned, future pollution should be predicted and avoided (Lichtfouse et al., 2005a). Such advices ...

  16. Computational chemistry

    OpenAIRE

    Truhlar, Donald G.; McKoy, Vincent

    2000-01-01

    Computational chemistry has come of age. With significant strides in computer hardware and software over the last few decades, computational chemistry has achieved full partnership with theory and experiment as a tool for understanding and predicting the behavior of a broad range of chemical, physical, and biological phenomena. The Nobel Prize award to John Pople and Walter Kohn in 1998 highlighted the importance of these advances in computational chemistry. With massively parallel computers ...

  17. Bioinorganic Chemistry

    OpenAIRE

    Bertini, Ivano; Gray, Harry B.; Lippard, Stephen J.; Valentine, Joan Selverstone

    1994-01-01

    This book covers material that could be included in a one-quarter or one-semester course in bioinorganic chemistry for graduate students and advanced undergraduate students in chemistry or biochemistry. We believe that such a course should provide students with the background required to follow the research literature in the field. The topics were chosen to represent those areas of bioinorganic chemistry that are mature enough for textbook presentation. Although each chapter presents material...

  18. Solvation of a Small Metal-Binding Peptide in Room-Temperature Ionic Liquids

    Energy Technology Data Exchange (ETDEWEB)

    Shim, Youngseon; Jung, Younjoon [Seoul National Univ., Seoul (Korea, Republic of); Kim, Hyung J. [Carnegie Mellon Univ., Pittsburgh (United States)

    2012-11-15

    Structural properties of a small hexapeptide molecule modeled after metal-binding siderochrome immersed in a room-temperature ionic liquid (RTIL) are studied via molecular dynamics simulations. We consider two different RTILs, each of which is made up of the same cationic species, 1-butyl-3-methylimidazolium (BMI{sup +}), but different anions, hexafluorophosphate (PF{sub 6}{sup -}) and chloride (Cl{sup -}). We investigate how anionic properties such as hydrophobicity/hydrophilicity or hydrogen bonding capability affect the stabilization of the peptide in RTILs. To examine the effect of peptide-RTIL electrostatic interactions on solvation, we also consider a hypothetical solvent BMI{sup 0}Cl{sup 0}, a non-ionic counter-part of BMI{sup +}Cl{sup -}. For reference, we investigate solvation structures in common polar solvents, water and dimethylsulfoxide (DMSO). Comparison of BMI{sup +}Cl{sup -} and BMI{sup 0}Cl{sup 0} shows that electrostatic interactions of the peptide and RTIL play a significant role in the conformational fluctuation of the peptide. For example, strong electrostatic interactions between the two favor an extended conformation of the peptide by reducing its structural fluctuations. The hydrophobicity/hydrophilicity of RTIL anions also exerts a notable influence; specifically, structural fluctuations of the peptide become reduced in more hydrophilic BMI{sup +}Cl{sup -}, compared with those in more hydrophobic BMI{sup +}PF{sub 6}{sup -}. This is ascribed to the good hydrogen-bond accepting power of chloride anions, which enables them to bind strongly to hydroxyl groups of the peptide and to stabilize its structure. Transport properties of the peptide are examined briefly. Translations of the peptide significantly slow down in highly viscous RTILs.

  19. Multibody correlations in the hydrophobic solvation of glycine peptides

    International Nuclear Information System (INIS)

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

  20. Multibody correlations in the hydrophobic solvation of glycine peptides

    Science.gov (United States)

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

    2014-12-01

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

  1. Multibody correlations in the hydrophobic solvation of glycine peptides

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Robert C.; Drake, Justin A.; Pettitt, B. Montgomery, E-mail: mpettitt@utmb.edu [Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas 77555-0304 (United States)

    2014-12-14

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

  2. Solvation quantities from a COSMO-RS equation of state

    International Nuclear Information System (INIS)

    Highlights: • Extension of the successful COSMO-RS model to an equation-of-state model. • Two scaling constants, obtained from atom-specific contributions. • Overall estimation of the solvation quantities and contributions. - Abstract: This work focuses on the extension of the successful COSMO-RS model of mixtures into an equation-of-state model of fluids and its application for the estimation of solvation/hydration quantities of a variety of chemical substances. These quantities include free-energies, enthalpies and entropies of hydration as well as the separate contributions to each of them. Emphasis is given on the estimation of contributions from the conformational changes of solutes upon solvation and the associated restructuring of solvent in its immediate neighborhood. COSMO-RS is a quantum-mechanics based group/segment contribution model in which the Quasi-Chemical (QC) approach is used for the description of the non-random distribution of interacting segments in the system. Thus, the equation-of-state development is done through such a QC framework. The new model will not need any adjustable parameters for the strong specific interactions, such as hydrogen bonds, since they will be provided by the quantum-mechanics based cosmo-files – a key feature of COSMO-RS model. It will need, however, one volumetric and one energy parameter per fluid, which are scaling constants or molecular descriptors of the fluid and are obtained from rather easily available data such as densities, boiling points, vapor pressures, heats of vaporization or second virial coefficients. The performance and the potential of the new equation-of-state model to become a fully predictive model are critically discussed

  3. Technetium chemistry

    International Nuclear Information System (INIS)

    Technetium chemistry is a young and developing field. Despite the limited knowledge of its chemistry, technetium is the workhorse for nuclear medicine. Technetium is also a significant environmental concern because it is formed as a byproduct of nuclear weapons production and fission-power generators. Development of new technetium radio-pharmaceuticals and effective environmental control depends strongly upon knowledge of basic technetium chemistry. The authors performed research into the basic coordination and organometallic chemistry of technetium and used this knowledge to address nuclear medicine and environmental applications. This is the final report of a three-year Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL)

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

    CERN Document Server

    Andreussi, Oliviero; Marzari, Nicola

    2011-01-01

    The solvation model proposed by Fattebert and Gygi [Journal of Computational Chemistry 23, 662 (2002)] and Scherlis et al. [Journal of Chemical Physics 124, 074103 (2006)] is reformulated, overcoming some of the numerical limitations encountered and extending its range of applicability. We first recast the problem in terms of induced polarization charges that act as a direct mapping of the self-consistent continuum dielectric; this allows to define a functional form for the dielectric that is well behaved both in the high-density region of the nuclear charges and in the low-density region where the electronic wavefunctions decay into the solvent. Second, we outline an iterative procedure to solve the Poisson equation for the quantum fragment embedded in the solvent that does not require multi-grid algorithms, is trivially parallel, and can be applied to any Bravais crystallographic system. Last, we capture some of the non-electrostatic or cavitation terms via a combined use of the quantum volume and quantum s...

  5. Thermodynamics of DL-alanine solvation in water-dimethylsulfoxide mixtures at 298.15 K

    Science.gov (United States)

    Roy, S.; Mahali, K.; Mondal, S.; Dolui, B. K.

    2015-04-01

    In this study we mainly discuss the transfer Gibbs free energy Δ G {/t 0}( i) and Δ S {/t 0}( i)entropy of DL-alanine at 298.15 K and consequently the involved chemical transfer free energy (Δ G {/t,ch 0}( i)) and entropy ( TΔ S {/t,ch 0}( i)) in aqueous mixtures of dimethylsulfoxide are discussed to clarify the solvation chemistry of DL-alanine. For the evaluation of these energy terms, solubility of this amino acid has been measured by formol titrimetry at five equidistant temperatures i.e., from 288.15 to 308.15 K in different composition of this mixed solvent system. The various solvent parameters as well as thermodynamic parameters like molar volume, density, dipole moment and solvent diameter of this solvent system have also been reported here. The chemical effects of the transfer Gibbs energies (Δ G {/t,ch 0}( i)) and entropies of transfer ( TΔ S {/t,ch 0}( i)) have been obtained after elimination of cavity effect and dipole-dipole interaction effects from the total transfer energies. Here the chemical contribution of transfer energetics of DL-alanine is mainly guided by the composite effects of increased dispersion interaction, basicity effect and decreased acidity, hydrogen bonding effects, hydrophilic hydration and hydrophobic hydration of aqueous DMSO mixtures as compared to that of reference solvent, water.

  6. Solvation of erbium(3) in aqueous dimethylsulfoxide solutions

    International Nuclear Information System (INIS)

    Solvation of Er3+ in aqua-dimethylsulfoxide solutions with concentration of DMSO from 0 to 89 mol.% was studied by electron spectroscopy method. Variation of Er3+ spectral characteristics during increasing DMSO concentration was demonstrated to be due to H2O -> DMSO substitution in first coordination sphere of Er3+, which was followed by strengthening of M-O bond with increasing covalence as well as distortion of coordination polyherdron. Concentration of DMSO in the H2O-DMSO mixture decreases with decline in radius of rare earth ion

  7. Molecular Modeling of Trifluoromethanesulfonic Acid for Solvation Theory

    CERN Document Server

    Paddison, S J; Zawodzinski, T; Reagor, D W; Paddison, Stephen J.; Pratt, Lawrence R.; Zawodzinski, Thomas; Reagor, David W.

    1997-01-01

    Reported here are theoretical calculations on the triflic acid and water, establishing molecular scale information necessary to modeling of the structure, thermodynamics, and ionic transport of Nafion membranes. To characterize side chain flexibility and accessibility of the acid proton, free energies for rotation of both carbon-sulfur and sulfur-oxygen (hydroxyl) bonds are presented. The energetic barrier to rotation of the acid proton away from the sulfonic acid oxygen plane is substantially flattened, with barrier less than one kcal/mol, by electrostatic solvation. The activation free energy for acid-water proton interchange is about 4.7 kcal/mol.

  8. The thermodynamic characteristics of solvation of ions in organic solvents

    International Nuclear Information System (INIS)

    Influence of temperature and nature of solvent on the change in the Gibbs energy, enthalpy and specific heat during solvation of individual ions of alkali metal halides MX (M = Li-Cs; X = Cl-I) was discussed by generalizing the results of investigation of thermodynamic properties of electrolytes solutions in organic solvents. Using continual and ion-dipole approximation the role of different contributions (electrostatic, cavity formation) into the character of ionic characteristics variation, depending on ion size, solvent nature and temperature, was ascertained

  9. Chemistry and isotopic composition of precipitation and surface waters in Khumbu valley (Nepal Himalaya): N dynamics of high elevation basins

    International Nuclear Information System (INIS)

    We monitored the chemical and isotopic compositions of wet depositions, at the Pyramid International Laboratory (5050 m a.s.l.), and surrounding surface waters, in the Khumbu basin, to understand precipitation chemistry and to obtain insights regarding ecosystem responses to atmospheric inputs. The major cations in the precipitation were NH4+ and Ca2+, whereas the main anion was HCO3−, which constituted approximately 69% of the anions, followed by NO3−, SO42− and Cl−. Data analysis suggested that Na+, Cl− and K+ were derived from the long-range transport of marine aerosols. Ca2+, Mg2+ and HCO3− were related to rock and soil dust contributions and the NO3− and SO42− concentrations were derived from anthropogenic sources. Furthermore, NH4+ was derived from gaseous NH3 scavenging. The isotopic composition of weekly precipitation ranged from − 1.9 to − 23.2‰ in δ18O, and from − 0.8 to − 174‰ in δ2H, with depleted values characterizing the central part of the monsoon period. The chemical composition of the stream water was dominated by calcite and/or gypsum dissolution. However, the isotopic composition of the stream water did not fully reflect the composition of the monsoon precipitation, which suggested that other water sources contributed to the stream flow. Precipitation contents for all ions were the lowest ones among those measured in high elevation sites around the world. During the monsoon periods the depositions were not substantially influenced by anthropogenic inputs, while in pre- and post-monsoon seasons the Himalayas could not represent an effective barrier for airborne pollution. In the late monsoon phase, the increase of ionic contents in precipitation could also be due to a change in the moisture source. The calculated atmospheric N load (0.30 kg ha−1 y−1) was considerably lower than the levels that were measured in other high-altitude environments. Nevertheless, the NO3− concentrations in the surface waters (from 2

  10. The Effect of Solvation on the Radiation Damage Rate Constants for Adenine

    DEFF Research Database (Denmark)

    Milhøj, Birgitte Olai; Sauer, Stephan P. A.

    2016-01-01

    It is a well known fact, that water plays an important part in almost all biological systems and that inclusion of solvation effects might therefore be of utmost importance in studies of radiation damage to DNA. In the present investigation we have studied the effect of different solvation models...

  11. Solvated Positron Chemistry. The Reaction of Hydrated Positrons with Chloride Ions

    DEFF Research Database (Denmark)

    Mogensen, O. E.; Shantarovich, V. P.

    1974-01-01

    The reaction of hydrated positrons (caq+ with cloride ions in aqueous solutions has been studied by means of positron annihilation angular correlation measurements. A rate constant of k = (2.5 ± 0.5) × 1010 M−1 s−1 was found. Probably the reacting positrons annihilated from an e+ Cl− bound state ...... resulting in an angular correlation curve 8% narrower than for the hydrated positron. Carbontetrachloride in benzene seems to give similar, but smaller effect....

  12. Solvated Positron Chemistry - Positron Reactions with Pseudo-Halide Ions in Water

    DEFF Research Database (Denmark)

    Mogensen, O. E.; Pedersen, Niels Jørgen; Andersen, Jan Rud

    1982-01-01

    The hydrated positron e+aq reactions with SCN−, OCN−, CN−, S2− were studied by means of the angular correlation technique. The positron forms bound states with SCN−, CN−, and S2− but not with OCN−. Apparently, the e+aq reaction with SH− results in a positron bound state with S2−. It was difficult...... to determine the shapes of the bound-state angular correlation curves. Only in the SCN− case could a very rough estimate of the rate constant be obtained. Estimates of the binding energies relative to those of the corresponding halide ion states could be determined for SCN− and S2−....

  13. Good chemistry

    OpenAIRE

    Petsko, Gregory A

    2004-01-01

    The subject matter in chemistry courses reflects almost nothing of the issues that chemists are interested in. It is important to formulate a set of topics - and a Medical College Admissions Test reflecting them - that would leave chemistry departments no choice but to change their teaching.

  14. Semiconducting single-walled carbon nanotubes sorting with a removable solubilizer based on dynamic supramolecular coordination chemistry

    Science.gov (United States)

    Toshimitsu, Fumiyuki; Nakashima, Naotoshi

    2014-10-01

    Highly pure semiconducting single-walled carbon nanotubes (SWNTs) are essential for the next generation of electronic devices, such as field-effect transistors and photovoltaic applications; however, contamination by metallic SWNTs reduces the efficiency of their associated devices. Here we report a simple and efficient method for the separation of semiconducting- and metallic SWNTs based on supramolecular complex chemistry. We here describe the synthesis of metal-coordination polymers (CP-Ms) composed of a fluorene-bridged bis-phenanthroline ligand and metal ions. On the basis of a difference in the ‘solubility product’ of CP-M-solubilized semiconducting SWNTs and metallic SWNTs, we readily separated semiconducting SWNTs. Furthermore, the CP-M polymers on the SWNTs were simply removed by adding a protic acid and inducing depolymerization to the monomer components. We also describe molecular mechanics calculations to reveal the difference of binding and wrapping mode between CP-M/semiconducting SWNTs and CP-M/metallic SWNTs. This study opens a new stage for the use of such highly pure semiconducting SWNTs in many possible applications.

  15. The Structure and Dynamics of an AGN Torus: CO Line Predictions for ALMA from 3D Hydrodynamical Simulations with X-ray Driven Chemistry

    CERN Document Server

    Perez-Beaupuits, Juan-Pablo; Spaans, Marco

    2011-01-01

    Many efforts have been made to model the mass distribution and dynamical evolution of the circumnuclear gas in active galactic nuclei (AGNs). However, chemical evolution is not included in detail in three-dimensional (3-D) hydrodynamic simulations. The X-ray radiation from the AGN can drive the gas chemistry and affect the thermodynamics, as well as the excitation of the interstellar medium (ISM). Therefore, we estimate the effects (on chemical abundances and excitation) of X-ray irradiation by the AGN, for atomic and molecular gas in a 3-D hydrodynamic model of an AGN torus. We obtain the abundances of various species from an X-ray chemical model. A 3-D radiative transfer code estimates the level populations, which result in line intensity maps. Predictions for the CO J=1-0 to J=9-8 lines indicate that mid-J CO lines are excellent probes of density and dynamics in the central (1000m K) central (1) AGNs. The spatial scales (>0.25 pc) probed with our simulations match the size of the structures that ALMA will ...

  16. Hydration and Solvation of Metal Perchlorates Extracted with Trioctylphosphine Oxide in Hexane

    International Nuclear Information System (INIS)

    Perchlorates of Sc3+, Y3+, La3+, and Eu3+ have each been extracted from 0.1 mol dm-3 aqueous solution of μ=1 with trioctylphosphine oxide (TOPO) in hexane. The hydration number of the extracted salts has been determined by Karl Fischer titration. Sc3+, Y3+, and Eu3+ are extracted as the tetra- and hexa-solvates of TOPO but the assumption of octa-solvate on addition to the tetra-solvate explains the extraction data of La3+ well. The hydration number of tetra-solvates is 2 (Sc3+ and Eu3+), 3 (Y3+) and probably 4 for La3+ ion. That of hexa-and octa- solvates is 4-5. (author). 1 tabs

  17. Non-Equilibrium Chemistry of Dynamically Evolving Prestellar Cores: I. Basic Magnetic and Non-Magnetic Models and Parameter Studies

    CERN Document Server

    Tassis, Konstantinos; Yorke, Harold W; Turner, Neal

    2011-01-01

    We combine dynamical and non-equilibrium chemical modeling of evolving prestellar molecular cloud cores, and explore the evolution of molecular abundances in the contracting core. We model both magnetic cores, with varying degrees of initial magnetic support, and non-magnetic cores, with varying collapse delay times. We explore, through a parameter study, the competing effects of various model parameters in the evolving molecular abundances, including the elemental C/O ratio, the temperature, and the cosmic-ray ionization rate. We find that different models show their largest quantitative differences at the center of the core, whereas the outer layers, which evolve slower, have abundances which are severely degenerate among different dynamical models. There is a large range of possible abundance values for different models at a fixed evolutionary stage (central density), which demonstrates the large potential of chemical differentiation in prestellar cores. However, degeneracies among different models, compou...

  18. On the solvates of vanadyl (4) chlorides with alcohols

    International Nuclear Information System (INIS)

    Methods of IR spectroscopy, chemical and X-ray diffraction analyses were used to study the nature of alcoholysis products of vanadium tetrachloride by methanol, ethanol and isopropanol. Formation of VOCl2 x 3ROH (R = Me, Et) (1) solvates of green colour and VOCl2 · 4(i-PrOH) (2) solvates of blue colour was established. Crystals 2 are monoclinic: a=15.782, b=11.439, c=11.707 A, β=90.92 deg, z=4, sp.gr. C2/c. Compound 2 is of ionic structure, composed of (VOCl(i-PrOH)4)+ octahedral cations and Cl- anions. Lengths of V=O, V-Cl and V-O(ROH) bonds were determined; they equal to 1.800 A; 2.12 A; 2.031, 2151 A respectively; VOC angles are eqaul to 127.2; 131.7 deg for cis and trans positions with respect to vanadyl oxygen atom consequently

  19. Electrostatics of solvated systems in periodic boundary conditions

    Science.gov (United States)

    Andreussi, Oliviero; Marzari, Nicola

    2014-12-01

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

  20. Structural Interactions within Lithium Salt Solvates: Cyclic Carbonates and Esters

    Energy Technology Data Exchange (ETDEWEB)

    Seo, D. M.; Afroz, Taliman; Allen, Joshua L.; Boyle, Paul D.; Trulove, Paul C.; De Long, Hugh C.; Henderson, Wesley A.

    2014-11-13

    Only limited information is available regarding the manner in which cyclic carbonate and ester solvents coordinate Li+ cations in electrolyte solutions for lithium batteries. One approach to gleaning significant insight into these interactions is to examine crystalline solvate structures. To this end, eight new solvate structures are reported with ethylene carbonate, γ-butyrolactone and γ-valerolactone: (EC)3:LiClO4, (EC)2:LiClO4, (EC)2:LiBF4, (GBL)4:LiPF6, (GBL)1:LiClO4, (GVL)1:LiClO4, (GBL)1:LiBF4 and (GBL)1:LiCF3SO3. The crystal structure of (EC)1:LiCF3SO3 is also re-reported for comparison. These structures enable the factors which govern the manner in which the ions are coordinated and the ion/solvent packing—in the solid-state—to be scrutinized in detail.

  1. Benchmarking the multipole shielding polarizability/reaction field approach to solvation against QM/MM: Applications to the shielding constants of N-methylacetamide

    Science.gov (United States)

    Kjær, Hanna; Sauer, Stephan P. A.; Kongsted, Jacob

    2011-01-01

    We present a benchmark study of a combined multipole shielding polarizability/reaction field (MSP/RF) approach to the calculation of both specific and bulk solvation effects on nuclear magnetic shielding constants of solvated molecules. The MSP/RF scheme is defined by an expansion of the shielding constants of the solvated molecule in terms of electric field and field gradient property derivatives derived from single molecule ab initio calculations. The solvent electric field and electric field gradient are calculated based on data derived from molecular dynamics simulations, thereby accounting for solute-solvent dynamical effects. The MSP/RF method is benchmarked against polarizable quantum mechanics/molecular mechanics (QM/MM) calculations. The best agreement between the MSP/RF and QM/MM approaches is found by truncating the electric field expansion in the MSP/RF approach at the linear electric field level which is due to the cancelation of errors. In addition, we investigate the sensitivity of the results due to the choice of one-electron basis set in the ab initio calculations of the property derivatives and find that these derivatives are affected by the basis set in a way similar to the shielding constants themselves.

  2. Chemistry and isotopic composition of precipitation and surface waters in Khumbu valley (Nepal Himalaya): N dynamics of high elevation basins

    Energy Technology Data Exchange (ETDEWEB)

    Balestrini, Raffaella, E-mail: balestrini@irsa.cnr.it [Water Research Institute, National Research Council (IRSA-CNR), Via del Mulino 19, Brugherio, MB (Italy); Polesello, Stefano [Water Research Institute, National Research Council (IRSA-CNR), Via del Mulino 19, Brugherio, MB (Italy); Sacchi, Elisa [Department of Earth and Environmental Sciences, University of Pavia and IGG-CNR, Via Ferrata 1, 27100 Pavia (Italy)

    2014-07-01

    We monitored the chemical and isotopic compositions of wet depositions, at the Pyramid International Laboratory (5050 m a.s.l.), and surrounding surface waters, in the Khumbu basin, to understand precipitation chemistry and to obtain insights regarding ecosystem responses to atmospheric inputs. The major cations in the precipitation were NH{sub 4}{sup +} and Ca{sup 2+}, whereas the main anion was HCO{sub 3}{sup −}, which constituted approximately 69% of the anions, followed by NO{sub 3}{sup −}, SO{sub 4}{sup 2−} and Cl{sup −}. Data analysis suggested that Na{sup +}, Cl{sup −} and K{sup +} were derived from the long-range transport of marine aerosols. Ca{sup 2+}, Mg{sup 2+} and HCO{sub 3}{sup −} were related to rock and soil dust contributions and the NO{sub 3}{sup −} and SO{sub 4}{sup 2−} concentrations were derived from anthropogenic sources. Furthermore, NH{sub 4}{sup +} was derived from gaseous NH{sub 3} scavenging. The isotopic composition of weekly precipitation ranged from − 1.9 to − 23.2‰ in δ{sup 18}O, and from − 0.8 to − 174‰ in δ{sup 2}H, with depleted values characterizing the central part of the monsoon period. The chemical composition of the stream water was dominated by calcite and/or gypsum dissolution. However, the isotopic composition of the stream water did not fully reflect the composition of the monsoon precipitation, which suggested that other water sources contributed to the stream flow. Precipitation contents for all ions were the lowest ones among those measured in high elevation sites around the world. During the monsoon periods the depositions were not substantially influenced by anthropogenic inputs, while in pre- and post-monsoon seasons the Himalayas could not represent an effective barrier for airborne pollution. In the late monsoon phase, the increase of ionic contents in precipitation could also be due to a change in the moisture source. The calculated atmospheric N load (0.30 kg ha{sup −1} y{sup −1

  3. 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

  4. Dynamics and mechanisms of hot chemistry stimulated by recoil methods. Progress report, 1 March 1979-29 February 1980

    International Nuclear Information System (INIS)

    The secondary excitation function for production of cyclobutane-t from the hot hydrogen replacement reaction with cyclobutane was estimated and reported. Using a stepladder model the average stepsizes for cascade deactivation by several bath gases have been determined. Further progress on the interpretation of the dynamics which follow hot chlorine replacement reactions in small ring compounds has also been made. A new silylation reaction with sulfur dixoide was discovered. The process involves the direct attack of hexamethyldisilazane on sulfur dioxide leading eventually to 1,1,1-Trimethyl-N-sulfinyl silanamine

  5. Quantum chemistry

    CERN Document Server

    Lowe, John P

    1993-01-01

    Praised for its appealing writing style and clear pedagogy, Lowe's Quantum Chemistry is now available in its Second Edition as a text for senior undergraduate- and graduate-level chemistry students. The book assumes little mathematical or physical sophistication and emphasizes an understanding of the techniques and results of quantum chemistry, thus enabling students to comprehend much of the current chemical literature in which quantum chemical methods or concepts are used as tools. The book begins with a six-chapter introduction of standard one-dimensional systems, the hydrogen atom,

  6. Modelling non-equilibrium secondary organic aerosol formation and evaporation with the aerosol dynamics, gas- and particle-phase chemistry kinetic multi-layer model ADCHAM

    Directory of Open Access Journals (Sweden)

    P. Roldin

    2014-01-01

    Full Text Available We have developed the novel Aerosol Dynamics, gas- and particle-phase chemistry model for laboratory CHAMber studies (ADCHAM. The model combines the detailed gas phase Master Chemical Mechanism version 3.2, an aerosol dynamics and particle phase chemistry module (which considers acid catalysed oligomerization, heterogeneous oxidation reactions in the particle phase and non-ideal interactions between organic compounds, water and inorganic ions and a kinetic multilayer module for diffusion limited transport of compounds between the gas phase, particle surface and particle bulk phase. In this article we describe and use ADCHAM to study: (1 the mass transfer limited uptake of ammonia (NH3 and formation of organic salts between ammonium (NH4+ and carboxylic acids (RCOOH, (2 the slow and almost particle size independent evaporation of α-pinene secondary organic aerosol (SOA particles, and (3 the influence of chamber wall effects on the observed SOA formation in smog chambers. ADCHAM is able to capture the observed α-pinene SOA mass increase in the presence of NH3(g. Organic salts of ammonium and carboxylic acids predominantly form during the early stage of SOA formation. These salts contribute substantially to the initial growth of the homogeneously nucleated particles. The model simulations of evaporating α-pinene SOA particles support the recent experimental findings that these particles have a semi-solid tar like amorphous phase state. ADCHAM is able to reproduce the main features of the observed slow evaporation rates if low-volatility and viscous oligomerized SOA material accumulates in the particle surface layer upon evaporation. The evaporation rate is mainly governed by the reversible decomposition of oligomers back to monomers. Finally, we demonstrate that the mass transfer limited uptake of condensable organic compounds onto wall deposited particles or directly onto the Teflon chamber walls of smog chambers can have profound influence on

  7. Extending students' practice of metacognitive regulation strategies in the undergraduate chemistry laboratory and investigation of Pb2+ binding to calmodulin with circular dichroism and molecular dynamics modeling

    Science.gov (United States)

    Valencia Navarro, Laura N.

    The following dissertation was composed of two projects in chemistry education and benchwork/computational biochemistry. The chemistry education research explored students' practice of metacognitive strategies while solving open-ended laboratory problems when engaged in an instructional environment, the Science Writing Heuristic (SWH), that was characterized as supporting metacognitive regulation strategy use. Through in-depth interviews with students, results demonstrated that students in the SWH environment, compared to non-SWH students, used metacognitive strategies to a greater degree and to a greater depth when solving open-ended laboratory problems. As students engaged in higher levels of metacognitive regulation, their elective use of peers became a prominent path for supporting the practice of metacognitive strategies. Students claimed that the structure of the SWH weekly laboratory experiments improved their ability to solve open-ended lab problems. This research not only provided a lens into students' descriptions of their regulation strategy practices in the laboratory, but it also supported that the way that a laboratory environment is arranged can affect these regulation strategy practices and their transfer to new situations. In the biochemical study on the binding of Pb2+ to calmodulin (CaM), data was acquired via circular dichroism (CD) and molecular dynamics modeling. CD signal data indicated a unique signal from Pb-CaM and a significantly smaller ratio theta208/theta222 for Pb-CaM than Ca-CaM. An analysis of secondary structure content indicated that alpha-helical structure decreased and random coil structure increased when CaM was saturated with Pb2+ compared to Ca2+ saturated CaM. A molecular dynamics simulation of Pb2+ binding to CaM showed that Pb2+ ions bound to sites outside of the known canonical binding sites including the linker region, and indicated change in secondary structure. These results support the theory of opportunistic binding

  8. Trace Chemistry

    Science.gov (United States)

    Radhakrishnan, Krishnan; Whitefield, Philip

    1999-01-01

    , in addition, of the pressure, temperature, and velocity. A near term goal of the experimental program should be to confirm the nonlinear effects of sulfur speciation, and if present, to provide an explanation for them. It is also desirable to examine if the particulate matter retains any sulfur. The recommendation is to examine the effects on SOx production of variations in fuel-bound sulfur and aromatic content (which may affect the amount of particulates formed). These experiments should help us to understand if there is a coupling between particulate formation and SO, concentration. Similarly, any coupling with NOx can be examined either by introducing NOx into the combustion air or by using fuel-bound nitrogen. Also of immediate urgency is the need to establish and validate a detailed mechanism for sulfur oxidation/aerosol formation, whose chemistry is concluded to be homogeneous, because there is not enough surface area for heterogeneous effects. It is envisaged that this work will involve both experimental and theoretical programs. The experimental work will require, in addition to the measurements described above, fundamental studies in devices such as flow reactors and shock tubes. Complementing this effort should be modeling and theoretical activities. One impediment to the successful modeling of sulfur oxidation is the lack of reliable data for thermodynamic and transport properties for several species, such as aqueous nitric acid, sulfur oxides, and sulfuric acid. Quantum mechanical calculations are recommended as a convenient means of deriving values for these properties. Such calculations would also help establish rate constants for several important reactions for which experimental measurements are inherently fraught with uncertainty. Efforts to implement sufficiently detailed chemistry into computational fluid dynamic codes should be continued. Zero- and one-dimensional flow models are also useful vehicles for elucidating the minimal set of species and

  9. Solvation of electrolytes and nonelectrolytes in aqueous solutions.

    Science.gov (United States)

    Afanas'ev, V N

    2011-05-26

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

  10. Materials Chemistry

    CERN Document Server

    Fahlman, Bradley D

    2011-01-01

    The 2nd edition of Materials Chemistry builds on the strengths that were recognized by a 2008 Textbook Excellence Award from the Text and Academic Authors Association (TAA). Materials Chemistry addresses inorganic-, organic-, and nano-based materials from a structure vs. property treatment, providing a suitable breadth and depth coverage of the rapidly evolving materials field. The 2nd edition continues to offer innovative coverage and practical perspective throughout. After briefly defining materials chemistry and its history, seven chapters discuss solid-state chemistry, metals, semiconducting materials, organic "soft" materials, nanomaterials, and materials characterization. All chapters have been thoroughly updated and expanded with, for example, new sections on ‘soft lithographic’ patterning, ‘click chemistry’ polymerization, nanotoxicity, graphene, as well as many biomaterials applications. The polymer and ‘soft’ materials chapter represents the largest expansion for the 2nd edition. Each ch...

  11. Introductory Chemistry

    OpenAIRE

    Baron, Mark; Gonzalez-Rodriguez, Jose; Stevens, Gary; Gray, Nathan; Atherton, Thomas; Winn, Joss

    2010-01-01

    Teaching and Learning resources for the 1st Year Introductory Chemistry course (Forensic Science). 30 credits. These are Open Educational Resources (OER), made available for re-use under a Creative Commons license.

  12. Time-resolved radiation chemistry: Dynamics of electron attachment to uracil following UV excitation of iodide-uracil complexes

    International Nuclear Information System (INIS)

    Electron attachment to uracil was investigated by applying time-resolved photoelectron imaging to iodide-uracil (I–U) complexes. In these studies, an ultraviolet pump pulse initiated charge transfer from the iodide to the uracil, and the resulting dynamics of the uracil temporary negative ion were probed. Five different excitation energies were used, 4.00 eV, 4.07 eV, 4.14 eV, 4.21 eV, and 4.66 eV. At the four lowest excitation energies, which lie near the vertical detachment energy of the I–U complex (4.11 eV), signatures of both the dipole bound (DB) as well as the valence bound (VB) anion of uracil were observed. In contrast, only the VB anion was observed at 4.66 eV, in agreement with previous experiments in this higher energy range. The early-time dynamics of both states were highly excitation energy dependent. The rise time of the DB anion signal was ∼250 fs at 4.00 eV and 4.07 eV, ∼120 fs at 4.14 eV and cross-correlation limited at 4.21 eV. The VB anion rise time also changed with excitation energy, ranging from 200 to 300 fs for excitation energies 4.00–4.21 eV, to a cross-correlation limited time at 4.66 eV. The results suggest that the DB state acts as a “doorway” state to the VB anion at 4.00–4.21 eV, while direct attachment to the VB anion occurs at 4.66 eV

  13. Analytical chemistry

    International Nuclear Information System (INIS)

    This book is comprised of nineteen chapters, which describes introduction of analytical chemistry, experimental error and statistics, chemistry equilibrium and solubility, gravimetric analysis with mechanism of precipitation, range and calculation of the result, volume analysis on general principle, sedimentation method on types and titration curve, acid base balance, acid base titration curve, complex and firing reaction, introduction of chemical electro analysis, acid-base titration curve, electrode and potentiometry, electrolysis and conductometry, voltammetry and polarographic spectrophotometry, atomic spectrometry, solvent extraction, chromatograph and experiments.

  14. Cluster Chemistry

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    @@ Cansisting of eight scientists from the State Key Laboratory of Physical Chemistry of Solid Surfaces and Xiamen University, this creative research group is devoted to the research of cluster chemistry and creation of nanomaterials.After three-year hard work, the group scored a series of encouraging progresses in synthesis of clusters with special structures, including novel fullerenes, fullerene-like metal cluster compounds as well as other related nanomaterials, and their properties study.

  15. Green Chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Collison, Melanie

    2011-05-15

    Green chemistry is the science of chemistry used in a way that will not use or create hazardous substances. Dr. Rui Resendes is working in this field at GreenCentre Canada, an offshoot of PARTEQ Innovations in Kingston, Ontario. GreenCentre's preliminary findings suggest their licensed product {sup S}witchable Solutions{sup ,} featuring 3 classes of solvents and a surfactant, may be useful in bitumen oil sands extraction.

  16. Diffusion-limited solvated electron reactions in ethanol and water

    International Nuclear Information System (INIS)

    The rate constants for reaction of solvated electrons with Ag+, CuCl+, CdNO3+, NH4+, and I2 have been measured in ethanol solution. The state of ionization and diffusion constants of the ions were established by conductivity measurements. The rare constants for the reactions with positive ions are all equal to the calculated diffusion-limited constant within 10%. The reaction with NH4+ is orders of magnitude larger in ethanol than in either water or liquid ammonia. Rate constants for hydrated electron reactions with I2, I3, Br2, and Br3 have also been measured. The reaction radii for reaction with the halogens are large (9 to 15 A). A reaction probability varying exponentially with the distance between the reactants is incorporated into diffusion theory to explain the results

  17. Solvation of Oxytetracycline Hydrochloride in Ethanol-Water Mixed Solvents.

    Directory of Open Access Journals (Sweden)

    Esam A Gomaa

    2014-06-01

    Full Text Available The aim of this study was to determine the t hermodynamic functions, Gibbs energy, enthalpy and entropy for the solution processes of oxytetracycline hydrochloride in the mixed solvent (ethanol+water from solubility val ues obtained at temperatures ranging from 293.15 K to 308.15 K. The respective thermodynamic functions for mixing and solvation processes as well as the activity coefficients for the solute were calculated. The experimental results enable us to estimate th e value of thermodynamic solubility product, K sp(th , of oxytetracycline hydrochloride in the mixed solvent. In addition, Gibbs energy, enthalpy, entropy for the solution processes and free energies of transfer of oxytetracycline hydrochloride from water t o ethanol solutions.

  18. Layering transitions and solvation forces in an asymmetrically confined fluid.

    Science.gov (United States)

    Stewart, M C; Evans, R

    2014-04-01

    We consider a simple fluid confined between two parallel walls (substrates), separated by a distance L. The walls exert competing surface fields so that one wall is attractive and may be completely wet by liquid (it is solvophilic) while the other is solvophobic. Such asymmetric confinement is sometimes termed a "Janus Interface." The second wall is: (i) purely repulsive and therefore completely dry (contact angle θ = 180°) or (ii) weakly attractive and partially dry (θ is typically in the range 160-170°). At low temperatures, but above the bulk triple point, we find using classical density functional theory (DFT) that the fluid is highly structured in the liquid part of the density profile. In case (i), a sequence of layering transitions occurs: as L is increased at fixed chemical potential μ close to bulk gas-liquid coexistence μco, new layers of liquid-like density develop discontinuously. In contrast to confinement between identical walls, the solvation force is repulsive for all wall separations and jumps discontinuously at each layering transition and the excess grand potential exhibits many metastable minima as a function of the adsorption. For a fixed temperature T = 0.56TC, where TC is the bulk critical temperature, we determine the transition lines in the L, μ plane. In case (ii), we do not find layering transitions and the solvation force oscillates about zero. We discuss how our mean-field DFT results might be altered by including effects of fluctuations and comment on how the phenomenology we have revealed might be relevant for experimental and simulation studies of water confined between hydrophilic and hydrophobic substrates, emphasizing it is important to distinguish between cases (i) and (ii). PMID:24712805

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

    Science.gov (United States)

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

    2013-12-27

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

  20. Solvated electrons in hexamethylphosphorictriamide and mixtures with water

    International Nuclear Information System (INIS)

    γ-Radiolysis of hexamethylphosphorictriamide (HMPA) gives G(H2) = 3.3, reduced by excess N2O to 1.4, and a yield of G(N2) = 4.4 from plots of 1/G(N2) vs 1/[N2O]. This latter yield is in excellent agreement with the published data. From competition studies of N2O with 10 other scavengers (some of which are either good electron or H atom scavengers in other liquids), it is concluded that solvated electrons are evidently the sole radiation-produced precursors of the N2 and of the scavengeable H2 in HMPA. However, two reasons are found for doubting the existence of a direct correspondence between G(N2) and G(e-sub(s)) in this dipolar aprotic solvent. First, in binary mixtures of HMPA and H2O the γ-radiolysis yield of N2 from N2O solutions passed through a maximum, rather than showing a continuous transition with solvent composition. Second, when solvated electrons were produced by reaction of sodium (in the form of dilute sodium amalgams) with the solvent in the presence of N2O, only one N2 was produced for every H2 molecule inhibited by the N2O. Therefore, it is suggested that G(N2) should not be accepted as G(e-sub(S)) in preference to the pulse radiolysis value of 2.3, because of the ambiguous nature of N2O scavenging reactions in HMPA, as in some other aprotic media. (author)

  1. Dynamics and mechanisms of hot chemistry stimulated by recoil methods. Progress report, March 1, 1976--February 28, 1977

    International Nuclear Information System (INIS)

    The results obtained from the nuclear recoil chemical activation of cyclobutane-t reported earlier in this laboratory have indicated that vibration to translation energy transfer is the most important collisional process for all but the most efficient energy transfer agents. Classical and semi-classical dynamical collisional models suggest that the most effective energy transfer interactions are delocalized in nature involving at least one half of the excited cyclobutane molecule. The formalism used to explore the energy transfer process also provides data which in conjunction with energy shadowing analysis is used to interpret the energetics and mechanism of the primary hot tritium reaction with cyclobutane. The hot atom reaction between nuclear recoil produced chlorine atoms and hydrogen is characterized. The steady-state non-Boltzmann theory formalism is applied to the H2 and D2 reaction mixtures to further explore the high energy inverse isotope effect first reported in this laboratory. A detailed study of reactions of recoil chlorine with the scavenger ethylene used in the hydrogen studies is also reported

  2. Dynamics and mechanisms of catalytic processes and hot chemistry. Progress report, March 1, 1982-February 28, 1983

    International Nuclear Information System (INIS)

    The characterization of photo-assistance and photochemical changes in reactions catalyzed with Wilkinson's Catalyst has been extended to include kinetic analysis and a preliminary determination of the main features in the action spectrum. Photo-assistance in olefin hydrogenation and photochemical transformation of the catalyst to promote olefin isomerization occur over distinct spectral regions. Kinetic analysis of the yield data indicates the metastable isomerization catalyst formed is long lived and operates with a substantial turnover number and corresponding high quantum yield. Products from the new reaction between sulfur dioxide and hexamethyldisilazane discovered in this laboratory were further characterized. This reaction represents a facile silylation process in the absence of acidic hydrogen which produces synthetically and analytically useful materials. The new solid product, ammonium trimethylsilyl sulfite, was studied in detail. This ionic compound has an unusually high vapor pressure at 250C, and the gas phase components in equilibrium with the solid were identified by FT-1R methods. A patent filed by DOE in this area is pending. The dynamical model developed in this laboratory to describe recoil processes has been applied to investigations of the moderated nuclear recoil technique for measuring thermal rate constants. The general applicability and constraints of the method have been identified from the results obtained in several model systems. The recoil spectrum for chlorine-36 produced via the (n,γ) process has been calculated from the prompt gamma ray spectrum and compared with that of chlorine-38 previously reported from this laboratory. 3 figures, 4 tables

  3. Effects of dynamic strain on crack tip chemistry. Volume 1. Tests using a segmented artificial crevice. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Parkins, R.N.; Liu, Y.

    1986-06-01

    Work was done on potential, current and solution composition changes along stress corrosion cracks in a NiCrMoV steel in NaOH solutions and in type 304 stainless steel in NaCl solutions. Surfaces of the steels were exposed to the relevant solution in a creviced situation simulating a crack, the dynamically straining tip of which was simulated by a tensile specimen located at the remote end of the crack. With the 304 stainless steel in dilute chloride solutions, large potential gradients can persist along simulated cracks. Depending upon the solution composition and applied potential, large changes in the pH of the enclave solution can occur and these can be enhanced in the vicinity of the straining tensile specimen simulating the crack tip. Pitting, with associated chloride ion concentration changes, can occur on the simulated crack sides, but opening and closing the crack, to displace about 80% of the enclave solution, had little effect upon the potential distribution.

  4. Manipulation of gold colloidal nanoparticles with atomic force microscopy in dynamic mode: influence of particle–substrate chemistry and morphology, and of operating conditions

    Science.gov (United States)

    Darwich, Samer; Rao, Akshata; Gnecco, Enrico; Jayaraman, Shrisudersan; Haidara, Hamidou

    2011-01-01

    Summary One key component in the assembly of nanoparticles is their precise positioning to enable the creation of new complex nano-objects. Controlling the nanoscale interactions is crucial for the prediction and understanding of the behaviour of nanoparticles (NPs) during their assembly. In the present work, we have manipulated bare and functionalized gold nanoparticles on flat and patterned silicon and silicon coated substrates with dynamic atomic force microscopy (AFM). Under ambient conditions, the particles adhere to silicon until a critical drive amplitude is reached by oscillations of the probing tip. Beyond that threshold, the particles start to follow different directions, depending on their geometry, size and adhesion to the substrate. Higher and respectively, lower mobility was observed when the gold particles were coated with methyl (–CH3) and hydroxyl (–OH) terminated thiol groups. This major result suggests that the adhesion of the particles to the substrate is strongly reduced by the presence of hydrophobic interfaces. The influence of critical parameters on the manipulation was investigated and discussed viz. the shape, size and grafting of the NPs, as well as the surface chemistry and the patterning of the substrate, and finally the operating conditions (temperature, humidity and scan velocity). Whereas the operating conditions and substrate structure are shown to have a strong effect on the mobility of the particles, we did not find any differences when manipulating ordered vs random distributed particles. PMID:21977418

  5. Manipulation of gold colloidal nanoparticles with atomic force microscopy in dynamic mode: influence of particle–substrate chemistry and morphology, and of operating conditions

    Directory of Open Access Journals (Sweden)

    Samer Darwich

    2011-02-01

    Full Text Available One key component in the assembly of nanoparticles is their precise positioning to enable the creation of new complex nano-objects. Controlling the nanoscale interactions is crucial for the prediction and understanding of the behaviour of nanoparticles (NPs during their assembly. In the present work, we have manipulated bare and functionalized gold nanoparticles on flat and patterned silicon and silicon coated substrates with dynamic atomic force microscopy (AFM. Under ambient conditions, the particles adhere to silicon until a critical drive amplitude is reached by oscillations of the probing tip. Beyond that threshold, the particles start to follow different directions, depending on their geometry, size and adhesion to the substrate. Higher and respectively, lower mobility was observed when the gold particles were coated with methyl (–CH3 and hydroxyl (–OH terminated thiol groups. This major result suggests that the adhesion of the particles to the substrate is strongly reduced by the presence of hydrophobic interfaces. The influence of critical parameters on the manipulation was investigated and discussed viz. the shape, size and grafting of the NPs, as well as the surface chemistry and the patterning of the substrate, and finally the operating conditions (temperature, humidity and scan velocity. Whereas the operating conditions and substrate structure are shown to have a strong effect on the mobility of the particles, we did not find any differences when manipulating ordered vs random distributed particles.

  6. Manipulation of gold colloidal nanoparticles with atomic force microscopy in dynamic mode: influence of particle-substrate chemistry and morphology, and of operating conditions.

    Science.gov (United States)

    Darwich, Samer; Mougin, Karine; Rao, Akshata; Gnecco, Enrico; Jayaraman, Shrisudersan; Haidara, Hamidou

    2011-01-01

    One key component in the assembly of nanoparticles is their precise positioning to enable the creation of new complex nano-objects. Controlling the nanoscale interactions is crucial for the prediction and understanding of the behaviour of nanoparticles (NPs) during their assembly. In the present work, we have manipulated bare and functionalized gold nanoparticles on flat and patterned silicon and silicon coated substrates with dynamic atomic force microscopy (AFM). Under ambient conditions, the particles adhere to silicon until a critical drive amplitude is reached by oscillations of the probing tip. Beyond that threshold, the particles start to follow different directions, depending on their geometry, size and adhesion to the substrate. Higher and respectively, lower mobility was observed when the gold particles were coated with methyl (-CH(3)) and hydroxyl (-OH) terminated thiol groups. This major result suggests that the adhesion of the particles to the substrate is strongly reduced by the presence of hydrophobic interfaces. The influence of critical parameters on the manipulation was investigated and discussed viz. the shape, size and grafting of the NPs, as well as the surface chemistry and the patterning of the substrate, and finally the operating conditions (temperature, humidity and scan velocity). Whereas the operating conditions and substrate structure are shown to have a strong effect on the mobility of the particles, we did not find any differences when manipulating ordered vs random distributed particles. PMID:21977418

  7. Dynamics and mechanisms of hot chemistry stimulated by recoil methods. Progress report, March 1, 1978--February 28, 1979

    International Nuclear Information System (INIS)

    The nuclear recoil chemical activation process in cyclobutane-t and subsequent inter- and intra-molecular energy transfer in recoil tritium and recoil chlorine hot reaction systems are analyzed. A stepladder model for intermolecular energy transfer from cyclobutane-t on collision shows average quanta of energy transferred range from 0.5 to 10 kcal/collision in He, N2, CO2 and cyclobutane bath gases. The recoil energy spectrum of hot chlorine atoms generated via the 37Cl(n,γ)38Cl reaction is also reported. The average recoil energy is found to be 294 eV and the maximum is 528 eV. Average reaction energy is calculated to be relatively independent of composition over the range from 0 to 99% moderation with noble gases in well scavenged systems of moderate reactivity. Geometrical isomerization accompanying the gas phase chlorine atom replacement reaction in 2,3 dichlorohexafluoro-2-butene as a function of moderation has been further investigated. A thermal or near thermal reaction path having a trans/cis product ratio of 1.3 and a high energy process which preferentially forms trans product from both cis and trans reactant are found. Dynamical features associated with the observed high energy inverse isotope effect in the reaction of chlorine atoms with H2 and D2 have been investigated through a non-Boltzmann rate constant analysis. The origin of this kinetic isotope effect is attributed to the secondary reactive process of collisional dissociation of translationally, vibrationally, and rotationally excited hydrogen chloride product molecules. Investigation of the kinetics and mechanisms of photochemical reactions between sulfur dioxide and aliphatic hydrocarbons has been initiated

  8. Theory of competitive solvation of polymers by two solvents and entropy-enthalpy compensation in the solvation free energy upon dilution with the second solvent

    Science.gov (United States)

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

    2015-06-01

    We develop a statistical mechanical lattice theory for polymer solvation by a pair of relatively low molar mass solvents that compete for binding to the polymer backbone. A theory for the equilibrium mixture of solvated polymer clusters {AiBCj} and free unassociated molecules A, B, and C is formulated in the spirit of Flory-Huggins mean-field approximation. This theoretical framework enables us to derive expressions for the boundaries for phase stability (spinodals) and other basic properties of these polymer solutions: the internal energy U, entropy S, specific heat CV, extent of solvation Φsolv, average degree of solvation , and second osmotic virial coefficient B 2 as functions of temperature and the composition of the mixture. Our theory predicts many new phenomena, but the current paper applies the theory to describe the entropy-enthalpy compensation in the free energy of polymer solvation, a phenomenon observed for many years without theoretical explanation and with significant relevance to liquid chromatography and other polymer separation methods.

  9. Radiation Chemistry

    Science.gov (United States)

    Wojnárovits, L.

    Ionizing radiation causes chemical changes in the molecules of the interacting medium. The initial molecules change to new molecules, resulting in changes of the physical, chemical, and eventually biological properties of the material. For instance, water decomposes to its elements H2 and O2. In polymers, degradation and crosslinking take place. In biopolymers, e.g., DNS strand breaks and other alterations occur. Such changes are to be avoided in some cases (radiation protection), however, in other cases they are used for technological purposes (radiation processing). This chapter introduces radiation chemistry by discussing the sources of ionizing radiation (radionuclide sources, machine sources), absorption of radiation energy, techniques used in radiation chemistry research, and methods of absorbed energy (absorbed dose) measurements. Radiation chemistry of different classes of inorganic (water and aqueous solutions, inorganic solids, ionic liquids (ILs)) and organic substances (hydrocarbons, halogenated compounds, polymers, and biomolecules) is discussed in concise form together with theoretical and experimental backgrounds. An essential part of the chapter is the introduction of radiation processing technologies in the fields of polymer chemistry, food processing, and sterilization. The application of radiation chemistry to nuclear technology and to protection of environment (flue gas treatment, wastewater treatment) is also discussed.

  10. Carbonate chemistry dynamics and biological processes along a river-sea gradient (Gulf of Trieste, northern Adriatic Sea)

    Science.gov (United States)

    Ingrosso, Gianmarco; Giani, Michele; Cibic, Tamara; Karuza, Ana; Kralj, Martina; Del Negro, Paola

    2016-03-01

    In this paper we investigated, for two years and with a bi-monthly frequency, how physical, chemical, and biological processes affect the marine carbonate system in a coastal area characterized by high alkalinity riverine discharge (Gulf of Trieste, northern Adriatic Sea, Mediterranean Sea). By combining synoptic measurements of the carbonate system with in situ determinations of the primary production (14C incorporation technique) and secondary prokaryotic carbon production (3H-leucine incorporation) along a river-sea gradient, we showed that the conservative mixing between river endmember and off-shore waters was the main driver of the dissolved inorganic carbon (DIC) distribution and seasonal variation. However, during spring and summer seasons also the influence of biological uptake and release of DIC was significant. In the surface water of June 2012, the spreading and persistence of nutrient-rich freshwater stimulated the primary production (3.21 μg C L- 1 h- 1) and net biological DIC decrease (- 100 μmol kg- 1), reducing the dissolved CO2 concentration and increasing the pHT. Below the pycnocline of August 2012, instead, an elevated bacterial carbon production rate (0.92 μg C L- 1 h- 1) was related with net DIC increase (92 μmol kg- 1), low dissolved oxygen concentration, and strong pHT reduction, suggesting the predominance of bacterial heterotrophic respiration over primary production. The flux of carbon dioxide estimated at the air-sea interface exerted a low influence on the seasonal variation of the carbonate system. A complex temporal and spatial dynamic of the air-sea CO2 exchange was also detected, due to the combined effects of seawater temperature, river discharge, and water circulation. On annual scale the system was a sink of atmospheric CO2. However, in summer and during elevated riverine discharges, the area close to the river's mouth acted as a source of carbon dioxide. Also the wind speed was crucial in controlling the air-sea CO2

  11. Dynamic Processes in Biology, Chemistry, and Materials Science: Opportunities for UltraFast Transmission Electron Microscopy - Workshop Summary Report

    Energy Technology Data Exchange (ETDEWEB)

    Kabius, Bernd C.; Browning, Nigel D.; Thevuthasan, Suntharampillai; Diehl, Barbara L.; Stach, Eric A.

    2012-07-25

    This report summarizes a 2011 workshop that addressed the potential role of rapid, time-resolved electron microscopy measurements in accelerating the solution of important scientific and technical problems. A series of U.S. Department of Energy (DOE) and National Academy of Science workshops have highlighted the critical role advanced research tools play in addressing scientific challenges relevant to biology, sustainable energy, and technologies that will fuel economic development without degrading our environment. Among the specific capability needs for advancing science and technology are tools that extract more detailed information in realistic environments (in situ or operando) at extreme conditions (pressure and temperature) and as a function of time (dynamic and time-dependent). One of the DOE workshops, Future Science Needs and Opportunities for Electron Scattering: Next Generation Instrumentation and Beyond, specifically addressed the importance of electron-based characterization methods for a wide range of energy-relevant Grand Scientific Challenges. Boosted by the electron optical advancement in the last decade, a diversity of in situ capabilities already is available in many laboratories. The obvious remaining major capability gap in electron microscopy is in the ability to make these direct in situ observations over a broad spectrum of fast (µs) to ultrafast (picosecond [ps] and faster) temporal regimes. In an effort to address current capability gaps, EMSL, the Environmental Molecular Sciences Laboratory, organized an Ultrafast Electron Microscopy Workshop, held June 14-15, 2011, with the primary goal to identify the scientific needs that could be met by creating a facility capable of a strongly improved time resolution with integrated in situ capabilities. The workshop brought together more than 40 leading scientists involved in applying and/or advancing electron microscopy to address important scientific problems of relevance to DOE’s research

  12. Quantum mechanics in chemistry

    CERN Document Server

    Schatz, George C

    2002-01-01

    Intended for graduate and advanced undergraduate students, this text explores quantum mechanical techniques from the viewpoint of chemistry and materials science. Dynamics, symmetry, and formalism are emphasized. An initial review of basic concepts from introductory quantum mechanics is followed by chapters examining symmetry, rotations, and angular momentum addition. Chapter 4 introduces the basic formalism of time-dependent quantum mechanics, emphasizing time-dependent perturbation theory and Fermi's golden rule. Chapter 5 sees this formalism applied to the interaction of radiation and matt

  13. Composition and stability of neodymium solvates in water-propanol solutions

    International Nuclear Information System (INIS)

    The spectrographical method has been used to study the composition and stability of the NdCl3 solvates, formed in the water-propanol solutions. The stability constants of mixed water-propanol solvates as well as the formation reaction equilibrium constants of the mixed solvates are calculated. The coefficients of molar extinction are determined. It is shown that the oversolvation processes in the water-propanol and water-methanol systems are similar and the oversolvation reaction equilibrium constants coincide in the both systems. It is concluded that the composition of the mixed methanol-propanol solvates will be determined by the ratio of methanol: propanol concentrations in the double alcohol methanol-propanol systems

  14. Bayesian Model Averaging for Ensemble-Based Estimates of Solvation Free Energies

    CERN Document Server

    Gosink, Luke J; Reehl, Sarah M; Whitney, Paul D; Mobley, David L; Baker, Nathan A

    2016-01-01

    This paper applies the Bayesian Model Averaging (BMA) statistical ensemble technique to estimate small molecule solvation free energies. There is a wide range methods for predicting solvation free energies, ranging from empirical statistical models to ab initio quantum mechanical approaches. Each of these methods are based on a set of conceptual assumptions that can affect a method's predictive accuracy and transferability. Using an iterative statistical process, we have selected and combined solvation energy estimates using an ensemble of 17 diverse methods from the SAMPL4 blind prediction study to form a single, aggregated solvation energy estimate. The ensemble design process evaluates the statistical information in each individual method as well as the performance of the aggregate estimate obtained from the ensemble as a whole. Methods that possess minimal or redundant information are pruned from the ensemble and the evaluation process repeats until aggregate predictive performance can no longer be improv...

  15. Entropic solvation force between surfaces modified by grafted chains: a density functional approach

    Directory of Open Access Journals (Sweden)

    O. Pizio

    2010-01-01

    Full Text Available The behavior of a hard sphere fluid in slit-like pores with walls modified by grafted chain molecules composed of hard sphere segments is studied using density functional theory. The chains are grafted to opposite walls via terminating segments forming pillars. The effects of confinement and of "chemical" modification of pore walls on the entropic solvation force are investigated in detail. We observe that in the absence of adsorbed fluid the solvation force is strongly repulsive for narrow pores and attractive for wide pores. In the presence of adsorbed fluid both parts of the curve of the solvation force may develop oscillatory behavior dependent on the density of pillars, the number of segments and adsorption conditions. Also, the size ratio between adsorbed fluid species and chain segments is of importance for the development of oscillations. The choice of these parameters is crucial for efficient manipulation of the solvation force as desired for pores of different width.

  16. Unusual solvation through both p-orbital lobes of a carbene carbon

    Energy Technology Data Exchange (ETDEWEB)

    Hadad, C. Z., E-mail: cacier.hadad@udea.edu.co [Grupo de Química-Física Teórica, Instituto de Química, Universidad de Antioquia, A. A. 1226 Medellín (Colombia); Jenkins, Samantha [College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081 (China); Flórez, Elizabeth [Departamento de Ciencias Básicas, Universidad de Medellín, Carrera 87 N° 30-65, Medellín (Colombia)

    2015-03-07

    As a result of a configurational space search done to explain the experimental evidence of transient specific solvation of singlet fluorocarbene amide with tetrahydrofuran, we found that the most stable structures consist in a group in which each oxygen of two tetrahydrofuran molecules act as electron donor to its respective empty p-orbital lobe of the carbene carbon atom, located at each side of the carbene molecular plane. This kind of species, which to our knowledge has not been reported before, explains very well the particular experimental characteristics observed for the transient solvation of this system. We postulate that the simultaneous interaction to both p-orbital lobes seems to confer a special stability to the solvation complexes, because this situation moves away the systems from the proximity of the corresponding transition states for the ylide products. Additionally, we present an analysis of other solvation complexes and a study of the nature of the involved interactions.

  17. Quantum chemistry

    CERN Document Server

    Lowe, John P

    2006-01-01

    Lowe's new edition assumes little mathematical or physical sophistication and emphasizes an understanding of the techniques and results of quantum chemistry. It can serve as a primary text in quantum chemistry courses, and enables students and researchers to comprehend the current literature. This third edition has been thoroughly updated and includes numerous new exercises to facilitate self-study and solutions to selected exercises.* Assumes little initial mathematical or physical sophistication, developing insights and abilities in the context of actual problems* Provides thorough treatment

  18. Polymer Chemistry

    Science.gov (United States)

    Williams, Martha; Roberson, Luke; Caraccio, Anne

    2010-01-01

    This viewgraph presentation describes new technologies in polymer and material chemistry that benefits NASA programs and missions. The topics include: 1) What are Polymers?; 2) History of Polymer Chemistry; 3) Composites/Materials Development at KSC; 4) Why Wiring; 5) Next Generation Wiring Materials; 6) Wire System Materials and Integration; 7) Self-Healing Wire Repair; 8) Smart Wiring Summary; 9) Fire and Polymers; 10) Aerogel Technology; 11) Aerogel Composites; 12) Aerogels for Oil Remediation; 13) KSC's Solution; 14) Chemochromic Hydrogen Sensors; 15) STS-130 and 131 Operations; 16) HyperPigment; 17) Antimicrobial Materials; 18) Conductive Inks Formulations for Multiple Applications; and 19) Testing and Processing Equipment.

  19. Path-integral molecular dynamics simulations of BeO embedded in helium clusters: Formation of the stable HeBeO complex

    International Nuclear Information System (INIS)

    Path-integral molecular dynamics simulations have been performed to understand the quantum helium solvation structures in the HenBeO cluster up to n = 100. Our simulations show that one helium atom is strongly bound to BeO to form HeBeO and that the first solvation shell around the HeBeO complex includes roughly 12-14 helium atoms. The second solvation structure was also observed for n > 20. Both the first and second solvation shells show an anisotropic behavior but the anisotropy for the second solvation shell was found to be much weaker than that for the first solvation shell, as expected. The present simulations suggest that the HeBeO complex may be formed in large helium clusters

  20. Structural and Thermodynamic Properties of the Cm(III) Ion Solvated by Water and Methanol.

    Science.gov (United States)

    Kelley, Morgan P; Yang, Ping; Clark, Sue B; Clark, Aurora E

    2016-05-16

    The geometric and electronic structures of the 9-coordinate Cm(3+) ion solvated with both water and methanol are systematically investigated in the gas phase at each possible solvent-shell composition and configuration using density functional theory and second-order Møller-Plesset perturbation theory. Ab initio molecular dynamics simulations are employed to assess the effects of second and third solvent shells on the gas-phase structure. The ion-solvent dissociation energy for methanol is greater than that of water, potentially because of increased charge donation to the ion made possible by the electron-rich methyl group. Further, the ion-solvent dissociation energy and the ion-solvent distance are shown to be dependent on the solvent-shell composition. This has implications for solvent exchange, which is generally the rate-limiting step in complexation reactions utilized in the separation of curium from complex metal mixtures that derive from the advanced nuclear fuel cycle. PMID:27120717

  1. ARE MODELS OF ANION HYDRATION OVERBOUND ? THE SOLVATION OF THE ELECTRON AND CHLORIDE ANION COMPARED

    OpenAIRE

    Sprik, M.

    1991-01-01

    By means of a fully polarizable model for the chloride ion-water interaction we show that the modelling of anion solvation suffers from a similar inconsistency as the current electron-solvent potentials. Either the bulk hydration enthalpies are correct with the first hydration shell overbound, or the potential is adapted to describe the local environment of the solute at the expense of a major loss of solvation enthalpy. It is argued that boundary effects in the simulation are at least partly...

  2. Crystal solvates of active pharmaceutical ingredients actual for industry of Latvia

    OpenAIRE

    Veldre, Kaspars

    2013-01-01

    Crystal solvates of active pharmaceutical ingredients actual for industry of Latvia ABSTRACT This doctoral thesis project is focused on investigation of active pharmaceutical ingredients (API), which are important for industry of Latvia. Crystal solvate search and screening was performed for compounds described and novel crystalline forms were obtained. Stability in acquisition, production and storage conditions was evaluated. Crystal structure determination was performed for selected A...

  3. Spicing up continuum solvation models with SaLSA: The spherically averaged liquid susceptibility ansatz

    Energy Technology Data Exchange (ETDEWEB)

    Sundararaman, Ravishankar; Schwarz, Kathleen A.; Letchworth-Weaver, Kendra; Arias, T. A. [Department of Physics, Cornell University, Ithaca, New York 14853 (United States)

    2015-02-07

    Continuum solvation models enable electronic structure calculations of systems in liquid environments, but because of the large number of empirical parameters, they are limited to the class of systems in their fit set (typically organic molecules). Here, we derive a solvation model with no empirical parameters for the dielectric response by taking the linear response limit of a classical density functional for molecular liquids. This model directly incorporates the nonlocal dielectric response of the liquid using an angular momentum expansion, and with a single fit parameter for dispersion contributions it predicts solvation energies of neutral molecules with a RMS error of 1.3 kcal/mol in water and 0.8 kcal/mol in chloroform and carbon tetrachloride. We show that this model is more accurate for strongly polar and charged systems than previous solvation models because of the parameter-free electric response, and demonstrate its suitability for ab initio solvation, including self-consistent solvation in quantum Monte Carlo calculations.

  4. Solvatochromism and preferential solvation in mixtures of Methanol with Ethanol, 1-Propanol and 1-Butanol

    Directory of Open Access Journals (Sweden)

    Masoumeh Sayadian

    2014-12-01

    Full Text Available The spectral shift of 4-nitroaniline was determined in pure methanol, ethanol, 1-propanol and 1-butanol and binary mixtures of methanol with other 1-alkanols at 25 ⁰C by UV-vis spectroscopy. The effect of specific and non-specific solute-solvent interactions on the spectral shift was investigated by using the linear solvation energy relationship concept. A multiple linear regression analysis was used to correlate the spectral shift with microscopic Kamlet-Taft parameters (a, b and p* in pure solvents. Results indicate that the spectral shift is highly related with the specific solute-solvent interactions. In binary mixtures, a nonideal behavior of spectral shift was observed respective to the analytical mole fraction of alcohols; indicating preferential solvation. The spectral shifts were fitted to a known preferential solvation model named solvent exchange model to calculate the preferential solvation parameters. The preference of solute to be solvated by one of the solvating species relative to others was explained in terms of solvent-solvent and solute-solvent interactions.

  5. Weighted-density functionals for cavity formation and dispersion energies in continuum solvation models

    Energy Technology Data Exchange (ETDEWEB)

    Sundararaman, Ravishankar; Gunceler, Deniz; Arias, T. A. [Department of Physics, Cornell University, Ithaca, New York 14853 (United States)

    2014-10-07

    Continuum solvation models enable efficient first principles calculations of chemical reactions in solution, but require extensive parametrization and fitting for each solvent and class of solute systems. Here, we examine the assumptions of continuum solvation models in detail and replace empirical terms with physical models in order to construct a minimally-empirical solvation model. Specifically, we derive solvent radii from the nonlocal dielectric response of the solvent from ab initio calculations, construct a closed-form and parameter-free weighted-density approximation for the free energy of the cavity formation, and employ a pair-potential approximation for the dispersion energy. We show that the resulting model with a single solvent-independent parameter: the electron density threshold (n{sub c}), and a single solvent-dependent parameter: the dispersion scale factor (s{sub 6}), reproduces solvation energies of organic molecules in water, chloroform, and carbon tetrachloride with RMS errors of 1.1, 0.6 and 0.5 kcal/mol, respectively. We additionally show that fitting the solvent-dependent s{sub 6} parameter to the solvation energy of a single non-polar molecule does not substantially increase these errors. Parametrization of this model for other solvents, therefore, requires minimal effort and is possible without extensive databases of experimental solvation free energies.

  6. Hiking the valleys of quatum chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Aikens, Christine Marie

    2005-08-01

    This thesis is concerned with both the application and the extension of quantum chemical methods. Each chapter of the thesis represents a paper that has been published in or will be submitted to a scientific journal. The first three chapters of this thesis describe contributions made to chemistry through the use of quantum chemical methods, while the final two chapters illustrate the development of new methods. Chapter 2 and Chapter 3 characterize a study of the electronic structure and magnetic properties of homodinuclear titanium(III) complexes, in order to determine trends related to their potential use as molecular magnets. Chapter 2 focuses on hydride and halide bridging and terminal ligands, while Chapter 3 explores bridging ligands from other groups in the periodic table. Chapter 4 portrays a study of the solvation of glycine. Microsolvation and continuum solvation approaches are investigated in order to study the structures of small glycine-water clusters and determine the energy difference between the zwitterionic and nonionized forms of glycine, the simplest amino acid. Chapters 5 and 6 describe the implementation of analytic gradients, which are required for efficient molecular geometry optimizations, for two open-shell second-order perturbation theory methods. Chapter 5 discusses gradients for unrestricted Moeller-Plesset perturbation theory, and Chapter 6 describes gradients for Z-averaged perturbation theory.

  7. Organic chemistry

    International Nuclear Information System (INIS)

    The activities of the mycotoxin research group are discussed. This includes the isolation and structure determination of mycotoxins, plant products, the biosyntheris of mycotoxins, the synthesis and characteristics of steroids, the synthesis and mechanistic aspects of heterocyclic chemistry and the functionality of steroids over long distances. Nmr spectra and mass spectroscopy are some of the techniques used

  8. Reinventing Chemistry

    OpenAIRE

    Whitesides, George McClelland

    2015-01-01

    Chemistry is in a period of change, from an era focused on molecules and reactions, to one in which manipulations of systems of molecules and reactions will be essential parts of controlling larger systems. This Essay traces paths from the past to possible futures.

  9. Chemistry Notes

    Science.gov (United States)

    School Science Review, 1972

    1972-01-01

    Short articles on the kinetics of the hydrogen peroxide-iodide ion reaction, simulation of fluidization catalysis, the use of Newman projection diagrams to represent steric relationships in organic chemistry, the use of synthetic substrates for proteolytic enzyme reactions, and two simple clock reactions"--hydrolysis of halogenoalkanes and…

  10. Electrolytes and Interphasial Chemistry in Li Ion Devices

    Directory of Open Access Journals (Sweden)

    Kang Xu

    2010-01-01

    Full Text Available Since its appearance in 1991, the Li ion battery has been the major power source driving the rapid digitalization of our daily life; however, much of the processes and mechanisms underpinning this newest battery chemistry remains poorly understood. As in any electrochemical device, the major challenge comes from the electrolyte/electrode interfaces, where the discontinuity in charge distribution and extreme disequality in electric forces induce diversified processes that eventually determine the kinetics of Li+ intercalation chemistry. This article will summarize the most recent efforts on the fundamental understanding of the interphases in Li ion devices. Emphasis will be placed on the formation chemistry of the so-called “SEI” on graphitic anode, the effect of solvation sheath structure of Li+ on the intercalation energy barrier, and the feasibility of tailoring a desired interphase. Biologically inspired approaches to an ideal interphase will also be briefly discussed.

  11. A solution for an inverse problem in liquid AFM: calculation of three-dimensional solvation structure on a sample surface

    CERN Document Server

    Amano, Ken-ich

    2013-01-01

    Recent frequency-modulated atomic force microscopy (FM-AFM) can measure three-dimensional force distribution between a probe and a sample surface in liquid. The force distribution is, in the present circumstances, assumed to be solvation structure on the sample surface, because the force distribution and solvation structure have somewhat similar shape. However, the force distribution is exactly not the solvation structure. If we would like to obtain the solvation structure by using the liquid AFM, a method for transforming the force distribution into the solvation structure is necessary. Therefore, in this letter, we present the transforming method in a brief style. We call this method as a solution for an inverse problem, because the solvation structure is obtained at first and the force distribution is obtained next in general calculation processes. The method is formulated (mainly) by statistical mechanics of liquid.

  12. Zwitterionic phosphorylated quinines as chiral solvating agents for NMR spectroscopy.

    Science.gov (United States)

    Rudzińska-Szostak, Ewa; Górecki, Łukasz; Berlicki, Łukasz; Ślepokura, Katarzyna; Mucha, Artur

    2015-10-01

    Because of their unique 3D arrangement, naturally occurring Cinchona alkaloids and their synthetic derivatives have found wide-ranging applications in chiral recognition. Recently, we determined the enantioselective properties of C-9-phosphate mixed triesters of quinine as versatile chiral solvating agents in nuclear magnetic resonance (NMR) spectroscopy. In the current study, we introduce new zwitterionic members of this class of molecules containing a negatively charged phosphate moiety (i.e., ethyl, n-butyl and phenyl hydrogen quininyl phosphate). An efficient approach for synthesizing these compounds is elaborated, and full characterization, including conformational and autoaggregation phenomena studies, was performed. Therefore, their ability to induce NMR anisochrony of selected enantiomeric substrates (i.e., primarily N-DNB-protected amino acids and their methyl esters) was analyzed compared to uncharged diphenyl quininyl phosphate and its positively charged quaternary ammonium hydrochloride salt. In addition, (1) H and (13) C NMR experiments revealed their enantiodiscrimination potential toward novel analytes, such as secondary amines and nonprotected amino acids. PMID:26415853

  13. Several interfaces between radiation physics and chemistry that could pleasure each other more

    International Nuclear Information System (INIS)

    This paper offers an overview of currently active areas in Radiation Chemistry that may be pertinent to what Radiation Physicists can calculate. It begins with an overlapping topic, the nonhomogeneous kinetics of reactions in spurs followed by electron thermalization distances and thermal electron mobilities in fluids, electron scattering in gases, and finally, a possible new approach to calculating the energies and shapes of the optical absorption bands of solvated electrons. 18 figures, 2 tables

  14. Preferential solvation of xylitol in ethanol + water co-solvent mixtures according to the ikbi and qlqc methods

    OpenAIRE

    Daniel Delgado; Edgar vargas; Fleming Martínez

    2014-01-01

    The preferential solvation parameters, i.e., the differences between the local around the solute and bulk mole fractions of the solvents in solutions of xylitol in ethanol + water binary mixtures are derived from their thermodynamic properties by means of the inverse Kirkwood-Buff integrals (IKBI) and quasi-lattice quasi-chemical (QLQC) methods. According to IKBI method it is found that xylitol is sensitive to solvation effects, so the preferential solvation parameter δxE,S, is slightly posit...

  15. Fine chemistry

    International Nuclear Information System (INIS)

    The 1988 progress report of the Fine Chemistry laboratory (Polytechnic School, France) is presented. The research programs are centered on the renewal of the organic chemistry most important reactions and on the invention of new, highly efficient and highly selective reactions, by applying low cost reagents and solvents. An important research domain concerns the study and fabrication of new catalysts. They are obtained by means of the reactive sputtering of the metals and metal oxydes thin films. The Monte Carlo simulations of the long-range electrostatic interaction in a clay and the obtention of acrylamides from anhydrous or acrylic ester are summarized. Moreover, the results obtained in the field of catalysis are also given. The published papers and the congress communications are included

  16. Organometallic chemistry

    OpenAIRE

    Bashkin, James K.; M.L.H. Green; Dr. M. L. H. Green

    1982-01-01

    Transition metal organometallic chemistry is a rapidly expanding field, which has an important relationship to industrial problems of petrochemical catalysis. This thesis describes studies of fundamental organometallic reaction processes, such as C-H and C-C bond formation and cleavage, and investigations of the structure and bonding of organometallic compounds. A number of techniques were used to pursue these studies, including synthesis, X-ray crystallography, and semi-em...

  17. Disk Chemistry*

    OpenAIRE

    Thi Wing-Fai

    2015-01-01

    The chemical species in protoplanetary disks react with each other. The chemical species control part of the thermal balance in those disks. How the chemistry proceeds in the varied conditions encountered in disks relies on detailed microscopic understanding of the reactions through experiments or theoretical studies. This chapter strives to summarize and explain in simple terms the different types of chemical reactions that can lead to complex species. The first part of the chapter deals wit...

  18. Interstellar chemistry

    OpenAIRE

    Klemperer, William

    2006-01-01

    In the past half century, radioastronomy has changed our perception and understanding of the universe. In this issue of PNAS, the molecular chemistry directly observed within the galaxy is discussed. For the most part, the description of the molecular transformations requires specific kinetic schemes rather than chemical thermodynamics. Ionization of the very abundant molecular hydrogen and atomic helium followed by their secondary reactions is discussed. The rich variety of organic species o...

  19. Analytical chemistry

    International Nuclear Information System (INIS)

    The division for Analytical Chemistry continued to try and develope an accurate method for the separation of trace amounts from mixtures which, contain various other elements. Ion exchange chromatography is of special importance in this regard. New separation techniques were tried on certain trace amounts in South African standard rock materials and special ceramics. Methods were also tested for the separation of carrier-free radioisotopes from irradiated cyclotron discs

  20. Relation between a force curve measured on a solvated surface and the solvation structure: Relational expressions for a binary solvent and a molecular liquid

    CERN Document Server

    Amano, Ken-ichi

    2012-01-01

    Recent atomic force microscopy (AFM) can measure force curves between a probe and a sample surface in several solvents. The force curve is thought as the solvation structure in some cases, because its shape is generally oscilltive and pitch of the oscillation is about the same as diameter of the solvent. However, it is not the solvation structure. It is just only a mean force between the probe and sample surface. Since theoretical relation between the mean force and the solvation structure had not been clearly known, we have recently derived a relational expression within a simple liquid. Although we have derived the relational expression within the simple liquid, the relational expressions for a binary solvent and a molecular liquid have still not known clearly. Hence, we try to obtain the relational expressions in the two types of the solvents. In this letter, we briefly derive the relations and explain a method for comparing the mean force measured by liquid AFM and the solvation structure (obtained by a s...

  1. Computational chemistry

    Science.gov (United States)

    Arnold, J. O.

    1987-01-01

    With the advent of supercomputers, modern computational chemistry algorithms and codes, a powerful tool was created to help fill NASA's continuing need for information on the properties of matter in hostile or unusual environments. Computational resources provided under the National Aerodynamics Simulator (NAS) program were a cornerstone for recent advancements in this field. Properties of gases, materials, and their interactions can be determined from solutions of the governing equations. In the case of gases, for example, radiative transition probabilites per particle, bond-dissociation energies, and rates of simple chemical reactions can be determined computationally as reliably as from experiment. The data are proving to be quite valuable in providing inputs to real-gas flow simulation codes used to compute aerothermodynamic loads on NASA's aeroassist orbital transfer vehicles and a host of problems related to the National Aerospace Plane Program. Although more approximate, similar solutions can be obtained for ensembles of atoms simulating small particles of materials with and without the presence of gases. Computational chemistry has application in studying catalysis, properties of polymers, all of interest to various NASA missions, including those previously mentioned. In addition to discussing these applications of computational chemistry within NASA, the governing equations and the need for supercomputers for their solution is outlined.

  2. Green chemistry

    International Nuclear Information System (INIS)

    A grand challenge facing government, industry, and academia in the relationship of our technological society to the environment is reinventing the use of materials. To address this challenge, collaboration from an interdisciplinary group of stakeholders will be necessary. Traditionally, the approach to risk management of materials and chemicals has been through inerventions intended to reduce exposure to materials that are hazardous to health and the environment. In 1990, the Pollution Prevention Act encouraged a new tact-elimination of hazards at the source. An emerging approach to this grand challenge seeks to embed the diverse set of environmental perspectives and interests in the everyday practice of the people most responsible for using and creating new materials--chemists. The approach, which has come to be known as Green Chemistry, intends to eliminate intrinsic hazard itself, rather than focusing on reducing risk by minimizing exposure. This chapter addresses the representation of downstream environmental stakeholder interests in the upstream everyday practice that is reinventing chemistry and its material inputs, products, and waste as described in the '12 Principles of Green Chemistry'

  3. Green chemistry

    International Nuclear Information System (INIS)

    The depletion of world fossil fuel reserves and the involvement of greenhouse gases in the global warming has led to change the industrial and energy policies of most developed countries. The goal is now to reserve petroleum to the uses where it cannot be substituted, to implement renewable raw materials obtained from plants cultivation, and to consider the biodegradability of molecules and of manufactured objects by integrating the lifetime concept in their expected cycle of use. The green chemistry includes the design, development and elaboration of chemical products and processes with the aim of reducing or eliminating the use and generation of harmful compounds for the health and the environment, by adapting the present day operation modes of the chemical industry to the larger framework of the sustainable development. In addition to biofuels, this book reviews the applications of green chemistry in the different industrial processes in concern. Part 1 presents the diversity of the molecules coming from renewable carbon, in particular lignocellulose and the biotechnological processes. Part 2 is devoted to materials and treats of the overall available technological solutions. Part 3 focusses on functional molecules and chemical intermediates, in particular in sugar- and fats-chemistry. Part 4 treats of biofuels under the aspects of their production and use in today's technologies. The last part deals with the global approaches at the environmental and agricultural levels. (J.S.)

  4. Muons in chemistry

    Science.gov (United States)

    Clayden, N. J.

    2013-12-01

    Positive muons have long been used as extrinsic probes in chemistry, offering unique properties for the investigation of local magnetism, dynamics, transport and radical kinetics. Exciting new developments in muon beam lines offer the opportunity of extending these studies selectively to surfaces permitting, for example, the detection of increased mobility of polymer chains at the surface of a polymer film. So called pump and probe methods, involving external perturbations by laser irradiation to manipulate vibrational and electronic states, can be followed by muon pulses allowing the probing of the properties of these states. Muoniated radical probes are finding greater use in soft matter. Selectivity is achieved in these complex systems through an appropriate target molecule giving the chance to measure partitioning and interfacial transfer in surfactant systems. Improvements in sample environments allow the observation of muons in increasingly extreme combinations of temperature and pressure, such as supercritical water, allowing the characterization of the chemistry in these systems.

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

    Science.gov (United States)

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

    2015-06-30

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

  6. Historical Account And Branching To Rarefied Gas Dynamics Of Atomic and Molecular Beams : A Continuing And Fascinating Odyssey Commemorated By Nobel Prizes Awarded To 23 Laureates In Physics And Chemistry

    Science.gov (United States)

    Campargue, Roger

    2005-05-01

    This Historical Account derived in part from D. R. Herschbach was presented as an opening lecture of the Molecular Beam Session organized at the 24th International Symposium on Rarefied Gas Dynamics held in Bari, Italy, in July 2004. The emphasis is on the impressive results due to the molecular beam techniques in the last century. The first section summarizes the historical beam experiments performed by 14 Nobel Prize laureates having used the thermally effusive sources to establish the basic principles of Modern Physics. The second section is on the branching of Molecular Beams to Rarefied Gas Dynamics having permitted to investigate the physics of supersonic free jets and transform the molecular beam techniques. Finally, the last section relates the spectacular molecular beam experiments in helium free jet ultracooling, molecular spectroscopy, chemical reaction dynamics, clustering and modification of low density matter, and biomolecule mass spectrometry, rewarded by nine Nobel Prizes in Chemistry from 1986 to 2002.

  7. Bulk versus Interfacial Aqueous Solvation of Dicarboxylate Dianions

    Czech Academy of Sciences Publication Activity Database

    Minofar, B.; Mucha, M.; Jungwirth, Pavel; Yang, X.; Fu, Y. J.; Wang, X. B.; Wang, L. S.

    2004-01-01

    Roč. 126, č. 37 (2004), s. 11691-11698. ISSN 0002-7863 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4055905 Keywords : dicarboxylate dianions Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.903, year: 2004

  8. Quantum Simulations of Solvated Biomolecules Using Hybrid Methods

    Science.gov (United States)

    Hodak, Miroslav

    2009-03-01

    One of the most important challenges in quantum simulations on biomolecules is efficient and accurate inclusion of the solvent, because the solvent atoms usually outnumber those in the biomolecule of interest. We have developed a hybrid method that allows for explicit quantum-mechanical treatment of the solvent at low computational cost. In this method, Kohn-Sham (KS) density functional theory (DFT) is combined with an orbital-free (OF) DFT. Kohn-Sham (KS) DFT is used to describe the biomolecule and its first solvation shells, while the orbital-free (OF) DFT is employed for the rest of the solvent. The OF part is fully O(N) and capable of handling 10^5 solvent molecules on current parallel supercomputers, while taking only ˜ 10 % of the total time. The compatibility between the KS and OF DFT methods enables seamless integration between the two. In particular, the flow of solvent molecules across the KS/OF interface is allowed and the total energy is conserved. As the first large-scale applications, the hybrid method has been used to investigate the binding of copper ions to proteins involved in prion (PrP) and Parkinson's diseases. Our results for the PrP, which causes mad cow disease when misfolded, resolve a contradiction found in experiments, in which a stronger binding mode is replaced by a weaker one when concentration of copper ions is increased, and show how it can act as a copper buffer. Furthermore, incorporation of copper stabilizes the structure of the full-length PrP, suggesting its protective role in prion diseases. For alpha-synuclein, a Parkinson's disease (PD) protein, we show that Cu binding modifies the protein structurally, making it more susceptible to misfolding -- an initial step in the onset of PD. In collaboration with W. Lu, F. Rose and J. Bernholc.

  9. Competitive solvation of (bis)(trifluoromethanesulfonyl)imide anion by acetonitrile and water

    DEFF Research Database (Denmark)

    Chaban, Vitaly

    2014-01-01

    Competitive solvation of an ion by two or more solvents is one of the key phenomena determining the identity of our world. Solvation in polar solvents frequently originates from non-additive non-covalent interactions. Pre-parametrized potentials poorly capture these interactions, unless the force...... temperature coupling. Using a competitive solvation of (bis)(trifluoromethanesulfonyl)imide anion in acetonitrile and water, the work demonstrates efficiency and robustness of PM7-MD. (C) 2014 Elsevier B.V. All rights reserved.......Competitive solvation of an ion by two or more solvents is one of the key phenomena determining the identity of our world. Solvation in polar solvents frequently originates from non-additive non-covalent interactions. Pre-parametrized potentials poorly capture these interactions, unless the force...... field derivation is repeated for every new system. Development cost increases drastically as new chemical species are supplied. This work represents an alternative simulation approach, PM7-MD, by coupling the latest semiempirical parametrization, PM7, with equation-of-motion propagation scheme and...

  10. Anion Coordination Interactions in Solvates with the Lithium Salts LiDCTA and LiTDI

    Energy Technology Data Exchange (ETDEWEB)

    McOwen, Dennis W.; Delp, Samuel A.; Paillard, Elie; Herriot, Cristelle; Han, Sang D.; Boyle, Paul D.; Sommer, Roger D.; Henderson, Wesley A.

    2014-04-17

    Lithium 4,5-dicyano-1,2,3-triazolate (LiDCTA) and lithium 2-trifluoromethyl-4,5-dicyanoimidazole (LiTDI) are two salts proposed for lithium battery electrolyte applications, but little is known about the manner in which the DCTA- and TDI- anions coordinate Li+ cations. To explore this in-depth, crystal structures are reported here for two solvates with LiDCTA: (G2)1:LiDCTA and (G1)1:LiDCTA with diglyme and monoglyme, respectively, and seven solvates with LiTDI: (G1)2:LiTDI, (G2)2:LiTDI, (G3)1:LiTDI, (THF)1:LiTDI, (EC)1:LiTDI, (PC)1:LiTDI and (DMC)1/2:LiTDI with monoglyme, diglyme, triglyme, tetrahydrofuran, ethylene carbonate, propylene carbonate and dimethyl carbonate, respectively. These latter solvate structures are compared with the previously reported acetonitrile (AN)2:LiTDI structure. The solvates indicate that the LiTDI salt is much less associated than the LiDCTA salt and that the ions in LiTDI, when aggregated in solvates, have a very similar TDI-...Li+ cation mode of coordination through both the anion ring and cyano nitrogen atoms. Such coordination facilitates the formation of polymeric ion aggregates, instead of dimers. Insight into such ion speciation is instrumental for understanding the electrolyte properties of aprotic solvent mixtures with these salts.

  11. Hypercarbon chemistry

    International Nuclear Information System (INIS)

    This text points out the emerging significance of higher-valent carbon compounds. It describes the compounds of carbon with coordination numbers greater than four and explores the delocalized bonds of π aromatic molecules as a basis for rational description of orbitals; localized multicentered orbitals; the interactions of metallic ions with other atoms and molecules; the skeletal electron counts as a guide for synthesis; and the isolobal concept. Illustrated are the ways in which these subjects bring together structure and reactivity in the great diversity of novel carbon chemistry and its relationship to that of boron, lithium, hydrogen, the metals, and others

  12. Theoretical chemistry periodicities in chemistry and biology

    CERN Document Server

    Eyring, Henry

    1978-01-01

    Theoretical Chemistry: Periodicities in Chemistry and Biology, Volume 4 covers the aspects of theoretical chemistry. The book discusses the stably rotating patterns of reaction and diffusion; the chemistry of inorganic systems exhibiting nonmonotonic behavior; and population cycles. The text also describes the mathematical modeling of excitable media in neurobiology and chemistry; oscillating enzyme reactions; and oscillatory properties and excitability of the heart cell membrane. Selected topics from the theory of physico-chemical instabilities are also encompassed. Chemists, mechanical engin

  13. 2010 Gordon Research Conference On Radiation Chemistry

    International Nuclear Information System (INIS)

    The 2010 Gordon Conference on Radiation Chemistry will present cutting edge research regarding the study of radiation-induced chemical transformations. Radiation Chemistry or 'high energy' chemistry is primarily initiated by ionizing radiation: i.e. photons or particles with energy sufficient to create conduction band electrons and 'holes', excitons, ionic and neutral free radicals, highly excited states, and solvated electrons. These transients often interact or 'react' to form products vastly different than those produced under thermal equilibrium conditions. The non-equilibrium, non-thermal conditions driving radiation chemistry exist in plasmas, star-forming regions, the outer solar system, nuclear reactors, nuclear waste repositories, radiation-based medical/clinical treatment centers and in radiation/materials processing facilities. The 2010 conference has a strong interdisciplinary flavor with focus areas spanning (1) the fundamental physics and chemistry involved in ultrafast (atto/femtosecond) energy deposition events, (2) radiation-induced processes in biology (particularly spatially resolved studies), (3) radiation-induced modification of materials at the nanoscale and cosmic ray/x-ray mediated processes in planetary science/astrochemistry. While the conference concentrates on fundamental science, topical applied areas covered will also include nuclear power, materials/polymer processing, and clinical/radiation treatment in medicine. The Conference will bring together investigators at the forefront of their field, and will provide opportunities for junior scientists and graduate students to present work in poster format or as contributors to the Young Investigator session. The program and format provides excellent avenues to promote cross-disciplinary collaborations.

  14. Colloidal europium nanoparticles via a solvated metal atom dispersion approach and their surface enhanced Raman scattering studies.

    Science.gov (United States)

    Urumese, Ancila; Jenjeti, Ramesh Naidu; Sampath, S; Jagirdar, Balaji R

    2016-08-15

    Chemistry of lanthanide metals in their zerovalent state at the nanoscale remains unexplored due to the high chemical reactivity and difficulty in synthesizing nanoparticles by conventional reduction methods. In the present study, europium(0) nanoparticles, the most reactive of all the rare earth metals have been synthesized by solvated metal atom dispersion (SMAD) method using hexadecyl amine as the capping agent. The as-prepared europium nanoparticles show surface Plasmon resonance (SPR) band in the visible region of the electromagnetic spectrum. This lead to the investigation of its surface enhanced Raman scattering (SERS) using visible light excitation source. The SERS activity of europium nanoparticles has been followed using 4-aminothiophenol and biologically important molecules such as hemoglobin and Cyt-c as the analytes. This is the first example of lanthanide metal nanoparticles as SERS substrate which can possibly be extended to other rare-earth metals. Since hemoglobin absorbs in the visible region, the use of visible light excitation source leads to surface enhanced resonance Raman spectroscopy (SERRS). The interaction of biomolecules with Eu(0) has been followed using FT-IR and UV-visible spectroscopy techniques. The results indicate that there is no major irreversible change in the structure of biomolecules upon interaction with europium nanoparticles. PMID:27214148

  15. Chemistry in space

    CERN Document Server

    Rehder, Dieter

    2010-01-01

    The dynamic field of extraterrestrial chemistry brings together ideas of chemistr, astrophysics, and biology to the study of molecules between stars, around stars, and on plantes. This book serves as an introduction to chemial processes under ?unearthly? and hence usually extreme conditions (temperature, pressure, high or low density, bombardment by cosmic rays), and their impact on the early development of our solar system, as well as providing a deeper understanding of processes in earthly regions where conditions approach those of extraterrestrial areas.A unique and extraordinary perspe

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

    CERN Document Server

    Sundararaman, Ravishankar

    2014-01-01

    Many important applications of electronic structure methods involve molecules or solid surfaces in a solvent medium. Since explicit treatment of the solvent in such methods is usually not practical, calculations often employ continuum solvation models to approximate the effect of the solvent. Previous solvation models either involve a parametrization based on atomic radii, which limits the class of applicable solutes, or based on solute electron density, which is more general but less accurate, especially for charged systems. We develop an accurate and general solvation model that includes a cavity that is a nonlocal functional of both solute electron density and potential, local dielectric response on this nonlocally-determined cavity, and nonlocal approximations to the cavity-formation and dispersion energies. The dependence of the cavity on the solute potential enables an explicit treatment of the solvent charge asymmetry. With only three parameters per solvent, this `CANDLE' model simultaneously reproduce...

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

    Science.gov (United States)

    Chaban, Vitaly

    2015-07-01

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

  18. Pentaglyme-K salt binary mixtures: phase behavior, solvate structures, and physicochemical properties.

    Science.gov (United States)

    Mandai, Toshihiko; Tsuzuki, Seiji; Ueno, Kazuhide; Dokko, Kaoru; Watanabe, Masayoshi

    2015-01-28

    We prepared a series of binary mixtures composed of certain K salts (KX) and pentaglyme (G5) with different salt concentrations and anionic species ([X](-): [(CF3SO2)2N](-) = [TFSA](-), [CF3SO3](-) = [TfO](-), [C4F9SO3](-) = [NfO](-), PF6(-), SCN(-)), and characterized them with respect to their phase diagrams, solvate structures, and physicochemical properties. Their phase diagrams and thermal stability strongly implied the formation of equimolar complexes. Single-crystal X-ray crystallography was performed on certain equimolar complexes, which revealed that G5 molecules coordinate to K(+) cations in a characteristic manner, like 18-crown-6 ether in the crystalline state, irrespective of the paired anions. The solvate structures in the molten state were elucidated by a combination of temperature-dependent Raman spectroscopy and X-ray crystallography. A drastic spectral variation was observed in the [K(G5)1][TfO] Raman spectra, indicating that solvate structures in the crystalline state break apart upon melting. The solvate stability of [K(G5)1]X is closely related to the ion-ion interaction of the parent salts. A stable solvate forms when the ion-dipole interaction between K(+) and G5 overwhelms the ion-ion interaction between K(+) and X(-). Furthermore, the physicochemical properties of certain equimolar mixtures were evaluated. A Walden plot clearly reflects the ionic nature of the molten equimolar complexes. Judging from the structural characteristics and dissociativity, we classified [K(G5)1]X into two groups, good and poor solvate ionic liquids. PMID:25501925

  19. Photostability and solvation: photodynamics of microsolvated zwitterionic glycine

    Czech Academy of Sciences Publication Activity Database

    Ončák, Milan; Lischka, Hans; Slavíček, Petr

    2010-01-01

    Roč. 12, č. 19 (2010), s. 4906-4914. ISSN 1463-9076 R&D Projects: GA ČR GA203/09/0422; GA MŠk LC512 Institutional research plan: CEZ:AV0Z40400503; CEZ:AV0Z40550506 Keywords : zwitterionic glycine * photodynamics * photostability Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.454, year: 2010

  20. Eighteenth annual West Coast theoretical chemistry conference

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-05-01

    Abstracts are presented from the eighteenth annual west coast theoretical chemistry conference. Topics include molecular simulations; quasiclassical simulations of reactions; photodissociation reactions; molecular dynamics;interface studies; electronic structure; and semiclassical methods of reactive systems.

  1. Modelos contínuos do solvente: fundamentos Continuum solvation models: fundamentals

    Directory of Open Access Journals (Sweden)

    Josefredo R. Pliego Jr

    2006-06-01

    Full Text Available Continuum solvation models are nowadays widely used in the modeling of solvent effects and the range of applications goes from the calculation of partition coefficients to chemical reactions in solution. The present work presents a detailed explanation of the physical foundations of continuum models. We discuss the polarization of a dielectric and its representation through the volume and surface polarization charges. The Poisson equation for a dielectric was obtained and we have also derived and discuss the apparent surface charge method and its application for free energy of solvation calculations.

  2. Thermodynamics of the Solvation and phase distributions of ethylenediamine in acetonitrile-dimethylsulfoxide-hexane systems

    Science.gov (United States)

    Semenov, I. M.; Repkin, G. I.; Sharnin, V. A.

    2013-03-01

    The enthalpies of dissolution and solvation of ethylenediamine over the range of compositions of a mixed acetonitrile-dimethylsulfoxide solvent at 298 K are determined calorimetrically. It is found that with an increase in the acetonitrile concentration, the solvation exothermicity of ethylenediamine declines, owing to the resolvation of amino groups. The Gibbs energies of transfer of ethylenediamine from dimethylsulfoxide into its mixtures with acetonitrile are determined from the distribution of a substance between immiscible phases. It is found that increasing the acetonitrile concentration in a binary solvent improves the stability of the ethylenediamine solvatocomplex, owing to a change in the entropy component of the Gibbs energy.

  3. Phase Equilibria and Ionic Solvation in the Lithium Tetrafluoroborate-Dimethylsulfoxide System

    Science.gov (United States)

    Gafurov, M. M.; Kirillov, S. A.; Gorobets, M. I.; Rabadanov, K. Sh.; Ataev, M. B.; Tretyakov, D. O.; Aydemirov, K. M.

    2015-01-01

    The phase diagram and electrical conductivity isotherms for the lithium tetrafluoroborate (LiBF4)-dimethylsulfoxide (DMSO) system and Raman spectra of DMSO and the LiBF4-DMSO solution were studied. Spectroscopic signatures of a H-bond between DMSO and BF4 - ions were found. The bonds of Li+ ions to the solvent were stronger than the bonds in DMSO dimers because formation of the solvate destroyed dimeric DMSO molecules. The τω values for DMSO molecules in the Li+-ion solvate shell of the LiBF4-DMSO system were similar to those for associated solvent molecules.

  4. Angle-Resolved Photoemission of Solvated Electrons in Sodium-Doped Clusters

    CERN Document Server

    West, Adam H C; Luckhaus, David; Saak, Clara-Magdalena; Doppelbauer, Maximilian; Signorell, Ruth

    2015-01-01

    Angle-resolved photoelectron spectroscopy of the unpaired electron in sodium-doped water, methanol, ammonia, and dimethyl ether clusters is presented. The experimental observations and the complementary calculations are consistent with surface electrons for the cluster size range studied. Evidence against internally solvated electrons is provided by the photoelectron angular distribution. The trends in the ionization energies seem mainly determined by the degree of hydrogen bonding in the solvent and the solvation of the ion core. The onset ionization energies of water and methanol clusters do not level off at small cluster sizes, but decrease slightly with increasing cluster size.

  5. Cyclodextrin chemistry

    International Nuclear Information System (INIS)

    The chemistry of cyclodextrins was studied. This study included synthesising some cyclodextrin derivatives, preparing selected inclusion complexes with cyclodextrin and investigating the effects of gamma irradiation on cyclodextrins and certain linear oligosaccharides. This report presents a brief review of the structure and properties of cyclodextrins, the synthesis of cyclodextrin derivatives, their complexation and applications. This is followed by a description of the synthesis of some cyclodextrin derivatives and the preparation of inclusion complexes of cyclodextrin with some organic compounds. Finally, the effects of gamma irradiation on cyclodextrins, some of their derivatives and certain structurally related carbohydrates are discussed. The gamma irradiation studies were carried out for two reasons: to study the effects of gamma irradiation on cyclodextrins and their derivatives; and to investigate selectivity during the gamma irradiation of cyclodextrin derivatives

  6. Dynamics and chemistry of Venus' large and complex cloud system : a science case for an in-situ long-term chemical laboratory

    Science.gov (United States)

    Widemann, Thomas; Määttänen, Anni; Wilquet, Valérie; McGouldrick, Kevin; Jessup, Kandis Lea; Wilson, Colin; Limaye, Sanjay; EuroVenus Consortium, the

    2014-05-01

    combine through meso-scale convection. In situ sampling of these aerosols represents a key measurement for constraining their properties, and identifying their role in the sulfurohydrological cycle by means of microphysical models of steadily increasing complexity. A probe/lander making a single descent will lack the spatial, temporal and local time coverage to address the coupling of compositional variations with radiative and dynamical properties of the atmosphere at cloud level, requiring a long duration flight. Establishing a long-term chemical laboratory in the cloud layer which would measure the detailed composition of both gas and liquid phases, and their latitudinal, diurnal and vertical variability using a combination of mass spectrometry, gas chromatography, tunable laser transmission spectrometry, and polar nephelometry would significantly address all of these objectives. It would allow the determination of the size distribution, shape, and real and imaginary refractive indices of the cloud particles, and the measurement of intensity and polarization phase functions. Our target species would include those known to be associated with cloud formation (e.g. H2SO4, SO3, SO2, H2O), as well as species important in stratospheric chemistry (e.g. CO, ClCOx, Ox, HCl, HF) and surface-atmosphere buffering (e.g. CO, OCS, SOx, Ox, H2S).

  7. Physical chemistry of the interface between oxide and aqueous solution

    International Nuclear Information System (INIS)

    The behavior and properties of small oxide particles in aqueous suspension are dominated by the physico-chemistry of their surface. It is electrostatically charged and strongly solvated. The origin of the surface charge is discussed through the MUSIC model [Hiemstra 1996], allowing to estimate the acid-base behavior of surface oxygen atoms. The stability of aqueous dispersions of particles is analysed following the DLVO model, with a special attention on the hydration layers allowing the peptization of flocs. Different adsorption mechanisms of metal cations are presented in terms of coordination chemistry (outer- and inner-sphere complexes) emphasizing the coordinating ability of the surface towards metal complexes in solution. The anion adsorption is also studied in relation with some interesting consequences on spinel iron oxide nano-particles. (author)

  8. Magnetic ionic liquids in analytical chemistry: A review.

    Science.gov (United States)

    Clark, Kevin D; Nacham, Omprakash; Purslow, Jeffrey A; Pierson, Stephen A; Anderson, Jared L

    2016-08-31

    Magnetic ionic liquids (MILs) have recently generated a cascade of innovative applications in numerous areas of analytical chemistry. By incorporating a paramagnetic component within the cation or anion, MILs exhibit a strong response toward external magnetic fields. Careful design of the MIL structure has yielded magnetoactive compounds with unique physicochemical properties including high magnetic moments, enhanced hydrophobicity, and the ability to solvate a broad range of molecules. The structural tunability and paramagnetic properties of MILs have enabled magnet-based technologies that can easily be added to the analytical method workflow, complement needed extraction requirements, or target specific analytes. This review highlights the application of MILs in analytical chemistry and examines the important structural features of MILs that largely influence their physicochemical and magnetic properties. PMID:27506339

  9. Physical chemistry and the environment

    International Nuclear Information System (INIS)

    From the ozone hole and the greenhouse effect to plastics recycling and hazardous waste disposal, society faces a number of issues, the solutions to which require an unprecedented understanding of the properties of molecules. We are coming to realize that the environment is a coupled set of chemical systems, its dynamics determining the welfare of the biosphere and of humans in particular. These chemical systems are governed by fundamental molecular interactions, and they present chemists with an unparalleled challenge. The application of current concepts of molecular behavior and of up-to-date experimental and computational techniques can provide us with insights into the environment that are needed to mitigate past damage, to anticipate the impact of current human activity, and to avoid future insults to the environment. Environmental chemistry encompasses a number of separate, yet interlocking, areas of research. In all of these areas progress is limited by an inadequate understanding of the underlying chemical processes involved. Participation of all chemical approaches -- experimental, theoretical and computational -- and of all disciplines of chemistry -- organic, inorganic, physical, analytical and biochemistry -- will be required to provide the necessary fundamental understanding. The Symposium on ''Physical Chemistry and the Environment'' was designed to bring the many exciting and challenging physical chemistry problems involved in environmental chemistry to the attention of a larger segment of the physical chemistry community

  10. 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.

  11. Science Update: Inorganic Chemistry

    Science.gov (United States)

    Rawls, Rebecca

    1978-01-01

    This first in a series of articles describing the state of the art of various branches of chemistry reviews inorganic chemistry, including bioinorganic, photochemistry, organometallic, and solid state chemistries. (SL)

  12. Why Teach Environmental Chemistry?

    Science.gov (United States)

    Gardner, Marjorie H.

    1974-01-01

    Discusses the importance of teaching environmental chemistry in secondary school science classes, and outlines five examples of environmental chemistry problems that focus on major concepts of chemistry and have critical implications for human survival and well-being. (JR)

  13. Molecular dynamics studies on the adaptability of an ionic liquid in the extraction of solid nanoparticles.

    Science.gov (United States)

    Frost, Denzil S; Machas, Michael; Dai, Lenore L

    2012-10-01

    Recently, a number of publications have suggested that ionic liquids (ILs) can absorb solid particles. This development may have implications in fields like oil sand processing, oil spill beach cleanup, and water treatment. In this Article, we provide a computational investigation of this phenomenon via molecular dynamics simulations. Two particle surface chemistries were investigated: (1) hydrocarbon-saturated and (2) silanol-saturated, representing hydrophobic and hydrophilic particles, respectively. Employing 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF(6)]) as a model IL, these nanoparticles were allowed to equilibrate at the IL/water and IL/hexane interfaces to observe the interfacial self-assembled structures. At the IL/water interface, the hydrocarbon-based nanoparticles were nearly completely absorbed by the IL, while the silica nanoparticles maintained equal volume in both phases. At the IL/hexane interface, the hydrocarbon nanoparticles maintained minimal interactions with the IL, whereas the silica nanoparticles were nearly completely absorbed by it. Studies of these two types of nanoparticles immersed in the bulk IL indicate that the surface chemistry has a great effect on the corresponding IL liquid structure. These effects include layering of the ions, hydrogen bonding, and irreversible absorption of some ions to the silica nanoparticle surface. We quantify these effects with respect to each nanoparticle. The results suggest that ILs likely exhibit this absorption capability because they can form solvation layers with reduced dynamics around the nanoparticles. PMID:22950605

  14. Public perception of chemistry

    OpenAIRE

    Stražar, Alenka

    2015-01-01

    The thesis deals with the perception of chemistry among the public, which reflects the stereotypes that people have about chemistry. It presents the existing classification of stereotypes about chemistry and their upgrade. An analysis of movies that reflect the existing perception of chemistry in the public is written. Literature on selected aspects of the application of chemistry in movies is collected and analyzed. A qualification of perception of chemistry in the movies is presented based ...

  15. Hydrophobic ampersand hydrophilic: Theoretical models of solvation for molecular biophysics

    International Nuclear Information System (INIS)

    Molecular statistical thermodynamic models of hydration for chemistry and biophysics have advanced abruptly in recent years. With liquid water as solvent, salvation phenomena are classified as either hydrophobic or hydrophilic effects. Recent progress in treatment of hydrophilic effects have been motivated by continuum dielectric models interpreted as a modelistic implementation of second order perturbation theory. New results testing that perturbation theory of hydrophilic effects are presented and discussed. Recent progress in treatment of hydrophobic effects has been achieved by applying information theory to discover models of packing effects in dense liquids. The simplest models to which those ideas lead are presented and discussed

  16. Radiation Chemistry 2008 Gordon Research Conference - July 6-11, 2008

    International Nuclear Information System (INIS)

    Radiation Chemistry is chemistry initiated by ionizing radiation: i.e. photons or particles with energy sufficient to create charge pairs and/or free radicals in a medium. The important transients include conduction band electrons and 'holes', excitons, ionic and neutral free radicals, highly excited states, and solvated electrons. Effects of radiation span timescales from the energy deposition in femtoseconds, through geminate recombination in picoseconds and nanoseconds, to fast radical chemistry in microseconds and milliseconds, and ultimately to processes like cancer occurring decades later. The radiation sources used to study these processes likewise run from femtosecond lasers to nanosecond accelerators to years of gamma irradiation. As a result the conference has a strong interdisciplinary flavor ranging from fundamental physics to clinical biology. While the conference focuses on fundamental science, application areas highlighted in the present conference will include nuclear power, polymer processing, and extraterrestrial chemistry.

  17. Radiation Chemistry 2008 Gordon Research Conference - July 6-11, 2008

    Energy Technology Data Exchange (ETDEWEB)

    David M. Bartels

    2009-05-15

    Radiation Chemistry is chemistry initiated by ionizing radiation: i.e. photons or particles with energy sufficient to create charge pairs and/or free radicals in a medium. The important transients include conduction band electrons and 'holes', excitons, ionic and neutral free radicals, highly excited states, and solvated electrons. Effects of radiation span timescales from the energy deposition in femtoseconds, through geminate recombination in picoseconds and nanoseconds, to fast radical chemistry in microseconds and milliseconds, and ultimately to processes like cancer occurring decades later. The radiation sources used to study these processes likewise run from femtosecond lasers to nanosecond accelerators to years of gamma irradiation. As a result the conference has a strong interdisciplinary flavor ranging from fundamental physics to clinical biology. While the conference focuses on fundamental science, application areas highlighted in the present conference will include nuclear power, polymer processing, and extraterrestrial chemistry.

  18. Science Update: Inorganic Chemistry.

    Science.gov (United States)

    Rawls, Rebecca

    1981-01-01

    Describes areas of inorganic chemistry which have changed dramatically in the past year or two, including photochemistry, electrochemistry, organometallic complexes, inorganic reaction theory, and solid state chemistry. (DS)

  19. Migration chemistry

    International Nuclear Information System (INIS)

    Migration chemistry, the influence of chemical -, biochemical - and physico-chemical reactions on the migration behaviour of pollutants in the environment, is an interplay between the actual natur of the pollutant and the characteristics of the environment, such as pH, redox conditions and organic matter content. The wide selection of possible pollutants in combination with varying geological media, as well as the operation of different chemical -, biochemical - and physico-chemical reactions compleactes the prediction of the influence of these processes on the mobility of pollutants. The report summarizes a wide range of potential pollutants in the terrestrial environment as well as a variety of chemical -, biochemical - and physico-chemical reactions, which can be expected to influence the migration behaviour, comprising diffusion, dispersion, convection, sorption/desorption, precipitation/dissolution, transformations/degradations, biochemical reactions and complex formation. The latter comprises the complexation of metal ions as well as non-polar organics to naturally occurring organic macromolecules. The influence of the single types of processes on the migration process is elucidated based on theoretical studies. The influence of chemical -, biochemical - and physico-chemical reactions on the migration behaviour is unambiguous, as the processes apparently control the transport of pollutants in the terrestrial environment. As the simple, conventional KD concept breaks down, it is suggested that the migration process should be described in terms of the alternative concepts chemical dispersion, average-elution-time and effective retention. (AB) (134 refs.)

  20. The link between physics and chemistry in track modelling

    International Nuclear Information System (INIS)

    The physical structure of a radiation track provides the initial conditions for the modelling of radiation chemistry. These initial conditions are not perfectly understood, because there are important gaps between what is provided by a typical track structure model and what is required to start the chemical model. This paper addresses the links between the physics and chemistry of tracks, with the intention of identifying those problems that need to be solved in order to obtain an accurate picture of the initial conditions for the purposes of modelling chemistry. These problems include the reasons for the increased yield of ionisation relative to homolytic bond breaking in comparison with the gas phase. A second area of great importance is the physical behaviour of low-energy electrons in condensed matter (including thermolisation and solvation). Many of these processes are not well understood, but they can have profound effects on the transient chemistry in the track. Several phenomena are discussed, including the short distance between adjacent energy loss events, the molecular nature of the underlying medium, dissociative attachment resonances and the ability of low-energy electrons to excite optically forbidden molecular states. Each of these phenomena has the potential to modify the transient chemistry substantially and must therefore be properly characterised before the physical model of the track can be considered to be complete. (orig.)

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

    Energy Technology Data Exchange (ETDEWEB)

    Sundararaman, Ravishankar; Goddard, William A. [Joint Center for Artificial Photosynthesis, Pasadena, California 91125 (United States)

    2015-02-14

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

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

    Science.gov (United States)

    Sundararaman, Ravishankar; Goddard, William A

    2015-02-14

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

  3. Ni(salen): a system that forms many solvates with interacting Ni atoms

    NARCIS (Netherlands)

    Siegler, M.A.M.; Lutz, M.

    2009-01-01

    Recrystallization of [N,N’-Ethylene-bis(salicylideneiminato)]-nickel(II) [Ni(salen)] has been carried out from a large selection of solvents. Crystals can be either solvent free or solvates. This study is based on X-ray crystal structure determinations, which include the redetermination of Ni(salen)

  4. Determination of solvation and specific interaction enthalpies of adamantane derivatives in aprotic solvents

    International Nuclear Information System (INIS)

    Solution and solvation enthalpies at infinite dilution of 1-bromoadamantane, 1-adamantanol, and 2-adamantanone are reported at 298.15 K in a set of 14 aprotic solvents. The specific interaction enthalpies of the solid solutes are calculated using a methodology recently published by other authors. 1-Adamantanol's specific interaction enthalpies show a good correlation with the Kamlet-Taft β scale

  5. Solvation phenomena in association theories with applications to oil & gas and chemical industries

    DEFF Research Database (Denmark)

    Kontogeorgis, Georgios; Folas, Georgios; Muro Sunè, Nuria;

    2008-01-01

    Association theories e.g. those belonging to the SAFT family account explicitly for self- and cross-association (solvation) phenomena. Such phenomena are of great practical importance as they affect, often dramatically, the phase behaviour of many mixtures of industrial relevance. From the scient...

  6. Yield and properties of solvated electrons created by hexamethylphosphorictriamide gamma radiolysis

    International Nuclear Information System (INIS)

    Hexamethylphosphorictriamide was irradiated by gamma rays to investigate the reactivity of electrons by using different scavengers. Parabromophenol and nitrous oxide were used to study the yield in solvated electrons. The G values are: H2 1.15+-0.15, N2 or Br- 4.4+-0.4 and CH4 0.18+-0.05

  7. IR SPECTRA BY DFT FOR GLUCOSE AND ITS EPIMERS: A COMPARISON BETWEEN VACUUM AND SOLVATED SPECTRA

    Science.gov (United States)

    Infrared spectra were calculated for the low energy geometry optimized structures of glucose and all of its epimers, at B3LYP/6-311++G** level of theory. Calculations were performed both in vacuo and using the COSMO solvation method. Frequencies, zero point energies, enthalpies, entropies, and rel...

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

    Science.gov (United States)

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

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

  9. Constraints on nebular dynamics and chemistry based on observations of annealed magnesium silicate grains in comets and in disks surrounding Herbig Ae/Be stars

    OpenAIRE

    Hill, Hugh G. M.; Grady, Carol A.; Nuth, Joseph A.; Hallenbeck, Susan L.; Sitko, Michael L.

    2001-01-01

    Understanding dynamic conditions in the Solar Nebula is the key to prediction of the material to be found in comets. We suggest that a dynamic, large-scale circulation pattern brings processed dust and gas from the inner nebula back out into the region of cometesimal formation—extending possibly hundreds of astronomical units (AU) from the sun—and that the composition of comets is determined by a chemical reaction network closely coupled to the dynamic transport of dus...

  10. 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

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Siqin [The HKUST Shenzhen Research Institute, Shenzhen (China); Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); Sheong, Fu Kit [Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); Huang, Xuhui, E-mail: xuhuihuang@ust.hk [The HKUST Shenzhen Research Institute, Shenzhen (China); Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); Division of Biomedical Engineering, Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong)

    2015-08-07

    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.

  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)

    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. Chemistry Division: Annual progress report for period ending March 31, 1987

    Energy Technology Data Exchange (ETDEWEB)

    1987-08-01

    This report is divided into the following sections: coal chemistry; aqueous chemistry at high temperatures and pressures; geochemistry of crustal processes to high temperatures and pressures; chemistry of advanced inorganic materials; structure and dynamics of advanced polymeric materials; chemistry of transuranium elements and compounds; separations chemistry; reactions and catalysis in molten salts; surface science related to heterogeneous catalysis; electron spectroscopy; chemistry related to nuclear waste disposal; computational modeling of security document printing; and special topics. (DLC)

  13. Chemistry Division: Annual progress report for period ending March 31, 1987

    International Nuclear Information System (INIS)

    This report is divided into the following sections: coal chemistry; aqueous chemistry at high temperatures and pressures; geochemistry of crustal processes to high temperatures and pressures; chemistry of advanced inorganic materials; structure and dynamics of advanced polymeric materials; chemistry of transuranium elements and compounds; separations chemistry; reactions and catalysis in molten salts; surface science related to heterogeneous catalysis; electron spectroscopy; chemistry related to nuclear waste disposal; computational modeling of security document printing; and special topics

  14. Industrial Chemistry and School Chemistry: Making Chemistry Studies More Relevant

    Science.gov (United States)

    Hofstein, Avi; Kesner, Miri

    2006-01-01

    In this paper, we present the development and implementation over the period of more than 15 years of learning materials focusing on industrial chemistry as the main theme. The work was conducted in the Department of Science Teaching at the Weizmann Institute of Science, Israel. The project's general goal was to teach chemistry concepts in the…

  15. Protein hydration and dynamics

    International Nuclear Information System (INIS)

    Inelastic neutron scattering can measure the protein thermal fluctuations under the physiological aqueous environment, especially it is powerful to observe the low-energy protein dynamics in THz region, which are revealed theoretically to be coupled with solvations. Neutron enables the selective observation of protein and hydration water by deuteration. The complementary analysis with molecular dynamics simulation is also effective for the study of protein hydration. Some examples of the application toward the understanding of molecular basis of protein functions will be introduced. (author)

  16. Hydrophobic Solvation : A 2D IR Spectroscopic Inquest

    NARCIS (Netherlands)

    Bakulin, Artem A.; Liang, Chungwen; Jansen, Thomas La Cour; Wiersma, Douwe A.; Bakker, Huib J.; Pshenichnikov, Maxim S.

    2009-01-01

    For decades, the enigma of the hydrophobic force has captured the imagination of scientists. in particular, Frank and Evans' idea that the hydrophobic effect was mainly due to some kind of "iceberg" formation around a hydrophobic solute stimulated many experiments and molecular dynamics simulation s

  17. Rapid automated nuclear chemistry

    International Nuclear Information System (INIS)

    Rapid Automated Nuclear Chemistry (RANC) can be thought of as the Z-separation of Neutron-rich Isotopes by Automated Methods. The range of RANC studies of fission and its products is large. In a sense, the studies can be categorized into various energy ranges from the highest where the fission process and particle emission are considered, to low energies where nuclear dynamics are being explored. This paper presents a table which gives examples of current research using RANC on fission and fission products. The remainder of this text is divided into three parts. The first contains a discussion of the chemical methods available for the fission product elements, the second describes the major techniques, and in the last section, examples of recent results are discussed as illustrations of the use of RANC

  18. Rapid automated nuclear chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, R.A.

    1979-05-31

    Rapid Automated Nuclear Chemistry (RANC) can be thought of as the Z-separation of Neutron-rich Isotopes by Automated Methods. The range of RANC studies of fission and its products is large. In a sense, the studies can be categorized into various energy ranges from the highest where the fission process and particle emission are considered, to low energies where nuclear dynamics are being explored. This paper presents a table which gives examples of current research using RANC on fission and fission products. The remainder of this text is divided into three parts. The first contains a discussion of the chemical methods available for the fission product elements, the second describes the major techniques, and in the last section, examples of recent results are discussed as illustrations of the use of RANC.

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

    Science.gov (United States)

    Kar, Parimal; Lipowsky, Reinhard; Knecht, Volker

    2013-05-16

    Both KNI-10033 and KNI-10075 are high affinity preclinical HIV-1 protease (PR) inhibitors with affinities in the picomolar range. In this work, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method has been used to investigate the potency of these two HIV-1 PR inhibitors against the wild-type and mutated proteases assuming that potency correlates with the affinity of the drugs for the target protein. The decomposition of the binding free energy reveals the origin of binding affinities or mutation-induced affinity changes. Our calculations indicate that the mutation I50V causes drug resistance against both inhibitors. On the other hand, we predict that the mutant I84V causes drug resistance against KNI-10075 while KNI-10033 is more potent against the I84V mutant compared to wild-type protease. Drug resistance arises mainly from unfavorable shifts in van der Waals interactions and configurational entropy. The latter indicates that neglecting changes in configurational entropy in the computation of relative binding affinities as often done is not appropriate in general. For the bound complex PR(I50V)-KNI-10075, an increased polar solvation free energy also contributes to the drug resistance. The importance of polar solvation free energies is revealed when interactions governing the binding of KNI-10033 or KNI-10075 to the wild-type protease are compared to the inhibitors darunavir or GRL-06579A. Although the contributions from intermolecular electrostatic and van der Waals interactions as well as the nonpolar component of the solvation free energy are more favorable for PR-KNI-10033 or PR-KNI-10075 compared to PR-DRV or PR-GRL-06579A, both KNI-10033 and KNI-10075 show a similar affinity as darunavir and a lower binding affinity relative to GRL-06579A. This is because of the polar solvation free energy which is less unfavorable for darunavir or GRL-06579A relative to KNI-10033 or KNI-10075. The importance of the polar solvation as revealed here

  20. From Matter to Life:Chemistry?Chemistry!

    Institute of Scientific and Technical Information of China (English)

    Jean-Marie; LEHN

    2007-01-01

    1 Results Animate as well as inanimate matter,living organisms as well as materials,are formed of molecules and of the organized entities resulting from the interaction of molecules with each other.Chemistry provides the bridge between the molecules of inanimate matter and the highly complex molecular architectures and systems which make up living organisms. Synthetic chemistry has developed a very powerful set of methods for constructing ever more complex molecules.Supramolecular chemistry seeks to con...

  1. Green chemistry: A tool in Pharmaceutical Chemistry

    OpenAIRE

    Smita Talaviya; Falguni Majumdar

    2012-01-01

    Green chemistry expresses an area of research developing from scientific discoveries about pollution awareness and it utilizes a set of principles that reduces or eliminates the use or generation of hazardous substances in all steps of particular synthesis or process. Chemists and medicinal scientists can greatly reduce the risk to human health and the environment by following all the valuable principles of green chemistry. The most simple and direct way to apply green chemistry in pharmaceut...

  2. A modification of the generalized Born theory for improved estimates of solvation energies and pK shifts

    Science.gov (United States)

    Jayaram, B.; Liu, Y.; Beveridge, D. L.

    1998-07-01

    We present herein an appraisal on the performance of the generalized Born (GB) model in estimating the solvation energies of small molecules and pKa shifts of dicarboxylic acids. The quality of the solvation energy results obtained with the GB model was exceedingly good as already reported in the literature but the pKa shift estimates fell short of expectations. Analysis of the problem on a simple prototype system revealed that with the GB model, the estimates of the two components, viz. the shielding and the self-energy terms, to be somewhat in error. These errors compensate each other in the calculation of solvation energies but affect the intramolecular interaction energies and hence pK shifts differently. We examine here the feasibility of introducing modifications to the GB model for a simultaneous evaluation of both solvation and intramolecular interaction energies.

  3. Ionic strength independence of charge distributions in solvation of biomolecules

    OpenAIRE

    Virtanen, J. J.; Sosnick, T. R.; Freed, K. F.

    2014-01-01

    Electrostatic forces enormously impact the structure, interactions, and function of biomolecules. We perform all-atom molecular dynamics simulations for 5 proteins and 5 RNAs to determine the dependence on ionic strength of the ion and water charge distributions surrounding the biomolecules, as well as the contributions of ions to the electrostatic free energy of interaction between the biomolecule and the surrounding salt solution (for a total of 40 different biomolecule/solvent combinations...

  4. Ultrafast photoinduced intra- und intermolecular charge transfer and solvation

    OpenAIRE

    Bizjak, Tanja

    2004-01-01

    Intra- and intermolecular charge transfer as well as internal conversion processes are studied in various molecular systems. The dynamics of these fundamental photoinduced processes are investigated by pump-probe femtosecond spectroscopy and steady-state fluorescence. Transient spectra are obtained using white light continuum as probe, while time resolved measurements are performed by probing at specific wavelengths with non dispersive detec-tion. Noncollinearly phase matched optical parametr...

  5. Chemistry Rocks: Redox Chemistry as a Geologic Tool.

    Science.gov (United States)

    Burns, Mary Sue

    2001-01-01

    Applies chemistry to earth science, uses rocks in chemistry laboratories, and teaches about transition metal chemistry, oxidation states, and oxidation-reduction reactions from firsthand experiences. (YDS)

  6. Structural studies of several solvated potassium salts of tenatoprazole crystallizing as conglomerates

    Science.gov (United States)

    Tauvel, G.; Sanselme, M.; Coste-Leconte, S.; Petit, S.; Coquerel, G.

    2009-11-01

    Despite the weak acidic character of tenatoprazole it is possible to crystallize, in strong alkaline media, different solvated salts of this active pharmaceutical ingredient. Among these solid phases, some potassium salts exhibiting non congruent solubilities, form stable conglomerates in equilibrium with their mother liquors without detectable partial solid solutions between the enantiomers. The crystal structures of the ethanol and the ethylene glycol stoichiometric solvates of potassium salts have been determined by single crystal X-ray diffraction, revealing that the solvent molecules play an important role in the crystal cohesion. They participate to the coordination polyhedra of the potassium cations and also contribute to strong periodic bond chains. Moreover, there is no direct link between the tenatoprazole anions and the potassium cations, so the solvent molecules act as electrostatic relays between ions of opposite charges.

  7. Quantitative Prediction of Solvation Free Energy in Octanol of Organic Compounds

    Directory of Open Access Journals (Sweden)

    Eduardo J. Delgado

    2009-03-01

    Full Text Available The free energy of solvation, ΔGS0 , in octanol of organic compunds is quantitatively predicted from the molecular structure. The model, involving only three molecular descriptors, is obtained by multiple linear regression analysis from a data set of 147 compounds containing diverse organic functions, namely, halogenated and non-halogenated alkanes, alkenes, alkynes, aromatics, alcohols, aldehydes, ketones, amines, ethers and esters; covering a ΔGS0 range from about –50 to 0 kJ·mol-1. The model predicts the free energy of solvation with a squared correlation coefficient of 0.93 and a standard deviation, 2.4 kJ·mol-1, just marginally larger than the generally accepted value of experimental uncertainty. The involved molecular descriptors have definite physical meaning corresponding to the different intermolecular interactions occurring in the bulk liquid phase. The model is validated with an external set of 36 compounds not included in the training set.

  8. A Valence-Bond Nonequilibrium Solvation Model for a Twisting Cyanine Dye

    CERN Document Server

    McConnell, Sean; Olsen, Seth

    2014-01-01

    We study a two-state valence-bond electronic Hamiltonian model of non-equilibrium solvation during the excited-state twisting reaction of monomethine cyanines. These dyes are of interest because of the strong environment-dependent enhancement of their fluorescence quantum yield that results from suppression of competing non-radiative decay via twisted internal charge-transfer (TICT) states. For monomethine cyanines, where the ground state is a superposition of structures with different bond and charge localization, there are two twisting pathways with different charge localization in the excited state. The Hamiltonian designed to be as simple as possible consistent with a few well-enumerated assumptions. It is defined by three parameters and is a function of two $\\pi$-bond twisting angle coordinates and a single solvation coordinate. For parameters corresponding to symmetric monomethines, there are two low-energy twisting channels on the excited-state surface that lead to a manifold of twisted intramolecular ...

  9. FPS scientific and supercomputers computers in chemistry

    International Nuclear Information System (INIS)

    FPS Array Processors, scientific computers, and highly parallel supercomputers are used in nearly all aspects of compute-intensive computational chemistry. A survey is made of work utilizing this equipment, both published and current research. The relationship of the computer architecture to computational chemistry is discussed, with specific reference to Molecular Dynamics, Quantum Monte Carlo simulations, and Molecular Graphics applications. Recent installations of the FPS T-Series are highlighted, and examples of Molecular Graphics programs running on the FPS-5000 are shown

  10. Selected new developments in computational chemistry.

    OpenAIRE

    Darden, T A; Bartolotti, L; Pedersen, L G

    1996-01-01

    Molecular dynamics is a general technique for simulating the time-dependent properties of molecules and their environments. Quantum mechanics, as applied to molecules or clusters of molecules, provides a prescription for predicting properties exactly (in principle). It is reasonable to expect that both will have a profound effect on our understanding of environmental chemistry in the future. In this review, we consider several recent advances and applications in computational chemistry. Image...

  11. Convergence of Phase-Field Free Energy and Boundary Force for Molecular Solvation

    OpenAIRE

    Dai, Shibin; Li, Bo; Lu, Jianfeng

    2016-01-01

    We study a phase-field variational model for the solvaiton of charged molecules with an implicit solvent. The solvation free-energy functional of all phase fields consists of the surface energy, solute excluded volume and solute-solvent van der Waals dispersion energy, and electrostatic free energy. The surface energy is defined by the van der Waals--Cahn--Hilliard functional with squared gradient and a double-well potential. The electrostatic part of free energy is defined through the electr...

  12. Relation of physico-chemical properties of electrolytes with electronic structure of solvated alkali metal ions

    International Nuclear Information System (INIS)

    The nature of bonds, their strength and, accordingly, electric mobility of cation and electrolyte viscosity depending on the type of cation (Li+, Na+, K+, Rb+, Cs+) and molecules (H2O, NH3, H2CO, (CH3)2CO, CH3CN) were ascertained by the method of theoretical-group analysis and linear combinations of solvent cation and molecules orbitals. Regularities of solvation effect on electronic UV-, intramolecular vibrational IR and NMR spectra were revealed

  13. Computer analysis of the decay kinetics of solvated electrons in liquid ethanol at low temperature

    International Nuclear Information System (INIS)

    Decay curves of solvated electrons in pulse (0.5 μs) irradiated ethanol in the temperature range 172-225 K were analyzed assuming four different kinetic models. It has been found that the esub(s)sup(-) decay can be described in terms of a kinetic model based on the competition between a nonhomogeneous geminate recombination and a homogeneous first order process (eq. 2). (author)

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

    Science.gov (United States)

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

    2014-03-01

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

  15. Energy functions for protein design I: Efficient and accurate continuum electrostatics and solvation

    OpenAIRE

    Pokala, Navin; Handel, Tracy M.

    2004-01-01

    Electrostatics and solvation energies are important for defining protein stability, structural specificity, and molecular recognition. Because these energies are difficult to compute quickly and accurately, they are often ignored or modeled very crudely in computational protein design. To address this problem, we have developed a simple, fast, and accurate approximation for calculating Born radii in the context of protein design calculations. When these approximate Born radii are used with th...

  16. Solvatation and ion association in calcium nitrate solutions in acetone on sound data

    International Nuclear Information System (INIS)

    Present article is devoted to solvatation and ion association in calcium nitrate solutions in acetone on sound data. The results of measurement of the rate of distribution and peak value of coefficient of adsorption of supersonic waves in the calcium nitrate solutions in acetone were considered. Measurements were carried out on impulse ultrasonic unit in the frequency range 9.7-106.7 MHz and at temperature range 289-313 K.

  17. Crevice chemistry estimation from bulk water chemistry

    International Nuclear Information System (INIS)

    Since the first PWR plant in Japan started commercial operation in 1970, 22 plants are running in Japan as of the end of 1994. The main purpose of secondary water chemistry control is to minimize the corrosion possibility of the secondary system equipment, especially steam generators (SG). To achieve this objective, much effort has been concentrated on improving secondary water chemistry control. As a result of this effort, the recent secondary water chemistry in Japanese plants is well maintained in every stage of operation. However, to ensure and improve the reliability of SG, it is necessary to control crevice environments, which are located at tube/tube support plate intersections and under the sludge pile on the tube sheet. According to recent crevice monitoring examination results, the concentration behavior impurities in SG bulk water at the crevice is different for each species, and SG bulk water and crevice chemical compositions are not always equal. From these results, to control the crevice chemistry, improving bulk water chemistry control methods and a new type of molar ratio control index is needed. This paper introduces a brief summary of a recent crevice chemistry evaluation technique and bulk water chemistry control method, which is employed for crevice chemistry control, based on crevice monitoring examination results

  18. Development of a solvate as an active pharmaceutical ingredient: Developability, crystallisation and isolation challenges

    Science.gov (United States)

    Douillet, Julien; Stevenson, Neil; Lee, Mei; Mallet, Franck; Ward, Richard; Aspin, Peter; Dennehy, Daniel Robert; Camus, Laure

    2012-03-01

    The preclinical development of an active pharmaceutical ingredient (API) begins with the selection of a solid state form. A solvate may be selected for development if it is sufficiently stable and if the solvent quantity administered to the patient is lower than the tolerated potential daily exposure (PDE). The selection and process development of a solvate is presented here. The initial crystallisation process gave poor control over the particle size distribution (PSD) and inclusion of additional crystallisation solvent in the crystal lattice. These two API attributes were controlled using micronised seeds and optimising the crystallisation conditions. After filtration, slurry washing with a second solvent was used to replace the high boiling point crystallisation solvent to improve the drying efficiency. The slurry washing was modelled and studied in the laboratory to control the level of unbound crystallisation solvent in the API. The API desolvation during slurry washing was studied by considering thermodynamics, by construction of the ternary phase diagram, and kinetics aspects. This work provides useful approaches and considerations to assess the risks specific to the controlled production of a solvate that are rarely presented in the literature.

  19. Solvation of lanthanum complexes with alizarin complexone and fluoride-ion by different organic solvents

    International Nuclear Information System (INIS)

    The complexing of lanthanum alizarin complexonate (AK-La), depending on the nature and concentration of organic solvent in mixed aqueous-organic media is studied. It is found that on interaction a 15-30 nm bathochromic shift of absorption bands, a complexing reaction shift towards the pH 3.4-3.8 more acidic area, a hyperchromic effect are observed. The AK-La complex is polynuclear in a wide range of studied conditions, except for aqueous media (before equilibrium). Solution occurs at the AK-La formation stage, having a stepwise character; the calculated solvate numbers of the complex are divisible by 2.5 in most cases. This value correlates with the determined stoichiometric coefficient of the central ion in the composition of fluorine-containing complex AK:La:F = 3:2.5:1. The solvate number of the latter in isobutyl alcohol during extraction equals 8. The equilibrium constants of formation of solvates having different composition with a number of solvents are determined

  20. A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules

    Science.gov (United States)

    Geng, Weihua; Krasny, Robert

    2013-08-01

    We present a treecode-accelerated boundary integral (TABI) solver for electrostatics of solvated biomolecules described by the linear Poisson-Boltzmann equation. The method employs a well-conditioned boundary integral formulation for the electrostatic potential and its normal derivative on the molecular surface. The surface is triangulated and the integral equations are discretized by centroid collocation. The linear system is solved by GMRES iteration and the matrix-vector product is carried out by a Cartesian treecode which reduces the cost from O(N2) to O(NlogN), where N is the number of faces in the triangulation. The TABI solver is applied to compute the electrostatic solvation energy in two cases, the Kirkwood sphere and a solvated protein. We present the error, CPU time, and memory usage, and compare results for the Poisson-Boltzmann and Poisson equations. We show that the treecode approximation error can be made smaller than the discretization error, and we compare two versions of the treecode, one with uniform clusters and one with non-uniform clusters adapted to the molecular surface. For the protein test case, we compare TABI results with those obtained using the grid-based APBS code, and we also present parallel TABI simulations using up to eight processors. We find that the TABI solver exhibits good serial and parallel performance combined with relatively simple implementation, efficient memory usage, and geometric adaptability.