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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.

    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

  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. 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.

  5. Solvation!

    Energy Technology Data Exchange (ETDEWEB)

    Adamovic, Ivana [Iowa State Univ., Ames, IA (United States)

    2004-01-01

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

  6. 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.

  7. Revisiting the Internal Conformational Dynamics and Solvation Properties of Cyclodextrins

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, Cirstina S.; De Moura, Andri F.; Freitas, Luiz C.; Lins, Roberto D.

    2007-08-06

    Molecular dynamics simulations were used to investigate the internal conformational dynamics and solvation properties of the three natural cyclodextrins, α-, β-, and γ-cyclodextrin, in aqueous solution at room temperature. These glucose-derived oligosacharides present a molecular structure that confers them the ability to complex host molecules and change their physico-chemical properties. The structural behavior of cyclodextrins in solution is crucial for their complexation abilities. Analyses of the obtained trajectories show that inter-glucose secondary hydrogen bonds are present in solution, but show a very dynamical character where alternative hydrogen bonds to water molecules can be formed. Despite of the lower hydrophilicity of the cyclodextrins inner-cavities, they were found to be solvated and the number of water molecules inside of the cavity roughly doubles per glucose unit added to the ring. The residence times for water molecules inside of the cavities are inversely proportional to the cavity size.

  8. 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.

  9. 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

  10. 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.

  11. 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...

  12. 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

  13. 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

  14. 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...

  15. Constitutional dynamic chemistry: bridge from supramolecular chemistry to adaptive chemistry.

    Science.gov (United States)

    Lehn, Jean-Marie

    2012-01-01

    Supramolecular chemistry aims at implementing highly complex chemical systems from molecular components held together by non-covalent intermolecular forces and effecting molecular recognition, catalysis and transport processes. A further step consists in the investigation of chemical systems undergoing self-organization, i.e. systems capable of spontaneously generating well-defined functional supramolecular architectures by self-assembly from their components, thus behaving as programmed chemical systems. Supramolecular chemistry is intrinsically a dynamic chemistry in view of the lability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when the molecular entity contains covalent bonds that may form and break reversibility, so as to allow a continuous change in constitution by reorganization and exchange of building blocks. These features define a Constitutional Dynamic Chemistry (CDC) on both the molecular and supramolecular levels.CDC introduces a paradigm shift with respect to constitutionally static chemistry. The latter relies on design for the generation of a target entity, whereas CDC takes advantage of dynamic diversity to allow variation and selection. The implementation of selection in chemistry introduces a fundamental change in outlook. Whereas self-organization by design strives to achieve full control over the output molecular or supramolecular entity by explicit programming, self-organization with selection operates on dynamic constitutional diversity in response to either internal or external factors to achieve adaptation.The merging of the features: -information and programmability, -dynamics and reversibility, -constitution and structural diversity, points to the emergence of adaptive and evolutive chemistry, towards a chemistry of complex matter.

  16. 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

  17. 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

  18. Ultrafast dynamics of solvation and charge transfer in a DNA-based biomaterial.

    Science.gov (United States)

    Choudhury, Susobhan; Batabyal, Subrata; Mondol, Tanumoy; Sao, Dilip; Lemmens, Peter; Pal, Samir Kumar

    2014-05-01

    Charge migration along DNA molecules is a key factor for DNA-based devices in optoelectronics and biotechnology. The association of a significant amount of water molecules in DNA-based materials for the intactness of the DNA structure and their dynamic role in the charge-transfer (CT) dynamics is less documented in contemporary literature. In the present study, we have used a genomic DNA-cetyltrimethyl ammonium chloride (CTMA) complex, a technological important biomaterial, and Hoechest 33258 (H258), a well-known DNA minor groove binder, as fluorogenic probe for the dynamic solvation studies. The CT dynamics of CdSe/ZnS quantum dots (QDs; 5.2 nm) embedded in the as-prepared and swollen biomaterial have also been studied and correlated with that of the timescale of solvation. We have extended our studies on the temperature-dependent CT dynamics of QDs in a nanoenvironment of an anionic, sodium bis(2-ethylhexyl)sulfosuccinate reverse micelle (AOT RMs), whereby the number of water molecules and their dynamics can be tuned in a controlled manner. A direct correlation of the dynamics of solvation and that of the CT in the nanoenvironments clearly suggests that the hydration barrier within the Arrhenius framework essentially dictates the charge-transfer dynamics.

  19. [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

  20. Solvation structures and dynamics of alkaline earth metal halides in supercritical water: A molecular dynamics study

    Science.gov (United States)

    Keshri, Sonanki; Mandal, Ratnamala; Tembe, B. L.

    2016-09-01

    Constrained molecular dynamics simulations of alkaline earth metal halides have been carried out to investigate their structural and dynamical properties in supercritical water. Potentials of mean force (PMFs) for all the alkaline earth metal halides in supercritical water have been computed. Contact ion pairs (CIPs) are found to be more stable than all other configurations of the ion pairs except for MgI2 where solvent shared ion pair (SShIP) is more stable than the CIP. There is hardly any difference in the PMFs between the M2+ (M = Mg, Ca, Sr, Ba) and the X- (X = F, Cl, Br, I) ions whether the second X- ion is present in the first coordination shell of the M2+ ion or not. The solvent molecules in the solvation shells diffuse at a much slower rate compared to the bulk. Orientational distribution functions of solvent molecules are sharper for smaller ions.

  1. Solvation structure and dynamics of Na+ in liquid ammonia studied by ONIOM-XS MD simulations

    Science.gov (United States)

    Sripradite, Jarukorn; Tongraar, Anan; Kerdcharoen, Teerakiat

    2015-12-01

    The molecular dynamics (MD) technique based on the ONIOM-XS method, known as the ONIOM-XS MD, has been applied to investigate the solvation structure and dynamics of Na+ in liquid ammonia. Regarding the ONIOM-XS MD results, it is observed that Na+ is able to order the surrounding ammonia molecules to form its specific first and second solvation shells with the average coordination numbers of 5.1 and 11.2, respectively. The first solvation shell of Na+ is rather well-defined, forming a preferred 5-fold coordinated complex with a distorted square pyramidal geometry. In this respect, the most preferential Na+(NH3)5 species could convert back and forth to the lower probability Na+(NH3)6 and Na+(NH3)4 configurations. The second solvation shell of Na+ is detectable, in which a number of ammonia molecules, ranging from 7 to 14, are involved in this layer and they are arranged according to recognizable influence of the ion.

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

    Science.gov (United States)

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

    2016-08-01

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

  3. 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

  4. 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...

  5. Probing Solvation Dynamics around Aromatic and Biological Molecules at the Single-Molecular Level.

    Science.gov (United States)

    Dopfer, Otto; Fujii, Masaaki

    2016-05-11

    Solvation processes play a crucial role in chemical reactions and biomolecular recognition phenomena. Although solvation dynamics of interfacial or biological water has been studied extensively in aqueous solution, the results are generally averaged over several solvation layers and the motion of individual solvent molecules is difficult to capture. This review describes the development and application of a new experimental approach, namely, picosecond time-resolved pump-probe infrared spectroscopy of size- and isomer-selected aromatic clusters, in which for the first time the dynamics of a single individual solvent molecule can be followed in real time. The intermolecular isomerization reaction is triggered by resonant photoionization (pump), and infrared photodissociation (probe) at variable delay generates the spectroscopic signature of salient properties of the reaction, including rates, yields, pathways, branching ratios of competing reactions, existence of reaction intermediates, occurrence of back reactions, and time scales of energy relaxation processes. It is shown that this relevant information can reliably be decoded from the experimental spectra by sophisticated molecular dynamics simulations. This review covers a description of the experimental strategies and spectroscopic methods along with all applications to date, which range from aromatic clusters with nonpolar solvent molecules to aromatic monohydrated biomolecules. PMID:27054835

  6. 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...

  7. 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.

  8. 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.

  9. 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...

  10. 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

  11. 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

  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. 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

  15. 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

  16. 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.

  17. Physical Chemistry of Reaction Dynamics in Ionic Liquid

    Energy Technology Data Exchange (ETDEWEB)

    Maroncelli, Mark [Pennsylvania State Univ., University Park, PA (United States)

    2016-10-02

    Work completed over the past year mainly involves finishing studies related to solvation dynamics in ionic liquids, amplifying and extending our initial PFG-NMR work on solute diffusion, and learning how to probe rotational dynamics in ionic liquids.

  18. Physical chemistry of reaction dynamics in ionic liquid

    Energy Technology Data Exchange (ETDEWEB)

    Maroncelli, Mark [Pennsylvania State Univ., University Park, PA (United States)

    2016-10-02

    Work completed over the past year mainly involves finishing studies related to solvation dynamics in ionic liquids, amplifying and extending our initial PFG-NMR work on solute diffusion, and learning how to probe rotational dynamics in ionic liquids.

  19. 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

  20. 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...

  1. 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

  2. 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.

  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

    2016-03-01

    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.

  4. 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

  5. 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

  6. 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

  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. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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

  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. 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.

  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. 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...

  17. 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.

  18. Investigation into the Relaxation Dynamics of Polymer-Protein Conjugates Reveals Surprising Role of Polymer Solvation on Inherent Protein Flexibility.

    Science.gov (United States)

    Russo, Daniela; Plazanet, Marie; Teixeira, José; Moulin, Martine; Härtlein, Michael; Wurm, Frederik R; Steinbach, Tobias

    2016-01-11

    Fully biodegradable protein-polymer conjugates, namely, MBP-PMeEP (maltose binding protein-poly methyl-ethylene phosphonate), have been investigated in order to understand the role of polymer solvation on protein flexibility. Using elastic and quasi-elastic incoherent neutron scattering, in combination with partially deuterated conjugate systems, we are able to disentangle the polymer dynamics from the protein dynamics and meaningfully address the coupling between both components. We highlight that, in the dry state, the protein-polymer conjugates lack any dynamical transition in accordance with the generally observed behavior for dry proteins. In addition, we observe a larger flexibility of the conjugated protein, compared to the native protein, as well as a lack of polymer-glass transition. Only upon water hydration does the conjugate recover its dynamical transition, leading to the conclusion that exclusive polymer solvation is insufficient to unfreeze fluctuations on the picosecond-nanosecond time scale in biomolecules. Our results also confirm the established coupling between polymer and protein dynamics in the conjugate.

  19. Probe dependent anomalies in the solvation dynamics of coumarin dyes in dimethyl sulfoxide-glycerol binary solvent: confirming the local environments are different for coumarin dyes.

    Science.gov (United States)

    Koley, Somnath; Kaur, Harveen; Ghosh, Subhadip

    2014-10-28

    The solvation dynamics of coumarin dyes in dimethyl sulfoxide (DMSO)-glycerol (GLY) binary mixtures were studied across the GLY concentrations. Three coumarin dyes with widely different hydrophobicities were used for probing the entire polarity regions of this solvent mixture. Multiple anomalous concentration regions with significantly slow solvation times were detected from all three coumarin dyes. However, their precise positions were found to be probe molecule dependent. The solvation dynamics of the moderately hydrophobic dye coumarin 480 (C480) maintain a plateau region with a similar solvation time (∼550 ps) with the increase in GLY concentration until X(GLY) (the mole fraction of glycerol) reaches 0.5. This plateau region is followed by a sudden slowdown (to ∼975 ps) on the addition of more GLY to the DMSO-GLY mixture, and then this slow region persists from X(GLY)∼ 0.55 to 0.65 (peak at 0.6). On further addition of GLY (X(GLY) > 0.7), the solvation dynamics again become slower to ∼828 ps (at X(GLY)∼ 0.8) from ∼612 ps (at X(GLY)∼ 0.7). For very high GLY-content samples (X(GLY) > 0.85), the solvation times remain similar on further changes of the GLY concentrations. In contrast to C480, the most hydrophobic dye coumarin 153 (C153) shows a linear increase of solvation time in the DMSO-GLY mixture, from 102 ps (at X(GLY)∼ 0.1) to 946 ps (at X(GLY)∼ 0.9) with increase in GLY concentration, except for the concentration region, X(GLY)∼ 0.45-0.55 (peak at 0.5), where a substantial slowdown of the solvation time is observed. The highly hydrophilic probe coumarin 343 (C343) demonstrates multiple concentration regions (X(GLY)∼ 0.05-0.10, 0.25-0.35 and 0.55-0.65) where the solvation dynamics are significantly retarded. The presence of probe dependent anomalies in the DMSO-GLY mixture is a clear indication of there being different locations of probe molecules within this solvent mixture. We assume that the slowing-down of the solvation time could

  20. Controlling Chemistry in Dynamic Nanoscale Systems

    DEFF Research Database (Denmark)

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

    2011-01-01

    of the 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...

  1. Solvation of uranium hexachloro complexes in room-temperature ionic liquids. A molecular dynamics investigation in two liquids.

    Science.gov (United States)

    Schurhammer, Rachel; Wipff, Georges

    2007-05-10

    We report a molecular dynamics study of the solvation of UCl(6)(-), UCl(6)(2-), and UCl(6)(3-) complexes in the [BMI][Tf(2)N] and [MeBu(3)N][Tf(2)N] ionic liquid cations based on the same anion (bis(trifluoromethylsulfonyl)imide (Tf(2)N-)) and the butyl-3-methyl-imidazolium+ (BMI+) or methyl-tri-n-butyl-ammonium (MeBu(3)N+) cation, respectively. The comparison of two electrostatic models of the complexes (ionic model with -1 charged halides versus quantum mechanically derived charges) yields similar solvation features of a given solute. In the two liquids, the first solvation shell of the complexes is positively charged and evolves from purely cationic in the case of UCl(6)(3-) to a mixture of cations and anions in the case of UCl(6)(-). UCl(6)(3-) is exclusively "coordinated" to BMI+ or MeBu(3)N+ solvent cations that mainly interact via their CH aromatic protons or their N-Me group, respectively. Around the less charged UCl(6)(-) complex, the cations interact via the less polar moieties (butyl chains of BMI+ or MeBu(3)N+) and the anions display nonspecific interactions. In no case does the uranium atom further coordinate solvent ions. According to an energy components analysis, UCl(6)(3-) interacts more attractively with the [BMI][Tf(2)N] liquid than with [MeBu(3)N][Tf(2)N], while UCl(6)(-) does not show any preference, suggesting a significant solvation effect of the redox properties of uranium, also supported by free energy perturbation simulations. The effect of ionic liquid (IL) humidity is investigated by simulating the three complexes in 1:8 water/IL mixtures. In contrast to the case of "naked" ions (e.g., lanthanide(3+), UO2(2+), alkali, or halides), water has little influence on the solvation of the UCl(6)(n-) complexes in the two simulated ILs, as indicated by structural and energy analysis. This is in full agreement with the experimental observations (Nikitenko, S. I.; et al. Inorg. Chem. 2005, 44, 9497).

  2. 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".

  3. Preferential solvation and dynamics of Li{sup +} in aqueous ammonia solution: An ONIOM-XS MD simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Kabbalee, Pilailuk [School of Chemistry, Institute of Science, Suranaree University of Technology and NANOTEC-SUT Center of Excellence on Advanced Functional Nanomaterials, Nakhon Ratchasima 30000 (Thailand); Tongraar, Anan, E-mail: anan_tongraar@yahoo.com [School of Chemistry, Institute of Science, Suranaree University of Technology and NANOTEC-SUT Center of Excellence on Advanced Functional Nanomaterials, Nakhon Ratchasima 30000 (Thailand); Kerdcharoen, Teerakiat [Department of Physics and NANOTEC Center of Excellence, Faculty of Science, Mahidol University, Bangkok 10400 (Thailand)

    2015-01-13

    Highlights: • An ONIOM-XS MD simulation of Li{sup +} in aqueous ammonia solution been performed. • Li{sup +} forms a favorable Li{sup +}[(H{sub 2}O){sub 3}NH{sub 3}][(H{sub 2}O){sub 11}(NH{sub 3}){sub 3}] complex. • The first solvation shell of Li{sup +} is somewhat flexible. • The “structure-making” ability of Li{sup +} is not too strong. • The second solvation shell of Li{sup +} is less structured. - Abstract: A more sophisticated quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) technique based on the ONIOM-XS method, called the ONIOM-XS MD, has been applied for studying the characteristics of Li{sup +} in an aqueous ammonia solution. As compared to the conventional QM/MM MD study, which predicts a clear water preference with the arrangement of the Li{sup +}[(H{sub 2}O){sub 4}][(H{sub 2}O){sub 4}] type, the ONIOM-XS MD simulation clearly reveals that this ion can order both water and ammonia molecules to form the preferred Li{sup +}[(H{sub 2}O){sub 3}NH{sub 3}][(H{sub 2}O){sub 11}(NH{sub 3}){sub 3}] complex. Of particular interest, it is observed that the “structure-making” ability of Li{sup +} is not too strong and that the first solvation shell of Li{sup +} is somewhat flexible, in which other different 4-fold coordinated species, such as Li{sup +}(H{sub 2}O){sub 4} and Li{sup +}(H{sub 2}O){sub 2}(NH{sub 3}){sub 2}, can frequently be formed. In addition, it is found that the second solvation shell of Li{sup +} is less structured, implying a small influence of Li{sup +} in ordering the solvent molecules in this shell.

  4. 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

  5. Solvation structure and dynamics of cis- and trans-1,2 dichloroethene isomers in supercritical carbon dioxide. A molecular dynamics simulation study.

    Science.gov (United States)

    Dellis, Dimitris; Skarmoutsos, Ioannis; Samios, Jannis

    2011-10-27

    Molecular dynamics simulation techniques have been employed to investigate the solvation structure and dynamics in dilute mixtures of cis- and trans-1,2-dichloroethene in supercritical carbon dioxide. The calculations were performed for state points along a near-critical isotherm (1.02 T(c)) over a wide range of densities, using new developed optimized potential models for both isomers. The similarities and differences in the solvation structures around each isomer have been presented and discussed. The local density augmentation and enhancement factors of CO(2) around the isomers have been found significantly larger than the corresponding values for pure supercritical CO(2). The dynamic local density reorganization has been investigated and related to previously proposed relaxation mechanisms. The density dependence of the calculated self-diffusion coefficients has revealed the existence of a plateau in the region of 0.7-1.1 ρ(c), where the local density augmentation exhibits the maximum value. The reorientational dynamics of the C═C bond vector have been also studied, exhibiting significant differences between the two isomers in the case of the second-order Legendre time correlation functions.

  6. 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

  7. 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

  8. 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

  9. 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...

  10. 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

  11. 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

    rearrangement of the solute with X-ray emission spectroscopy, thus establishing time zero for the ensuing X-ray diffuse scattering analysis. The simultaneously recorded X-ray diffuse scattering atterns reveal slower subpicosecond dynamics triggered by the intramolecular structural dynamics of the photoexcited......, 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...

  12. 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

  13. 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.

  14. 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

  15. 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...

  16. A Study of the Solvation Structure of L-Leucine in Alcohol-Water Binary Solvents through Molecular Dynamics Simulations and FTIR and NMR Spectroscopy.

    Science.gov (United States)

    Takamuku, Toshiyuki; Hatomoto, Yohei; Tonegawa, Junko; Tsutsumi, Youichi; Umecky, Tatsuya

    2015-10-26

    The solvation structures of l-leucine (Leu) in aliphatic-alcohol-water and fluorinated-alcohol-water solvents are elucidated for various alcohol contents by using molecular dynamics (MD) simulations and IR, and (1) H and (13) C NMR spectroscopy. The aliphatic alcohols included methanol, ethanol, and 2-propanol, whereas the fluorinated alcohols were 2,2,2-trifluoroethanol and 1,1,1,3,3,3-hexafluoro-2-propanol. The MD results show that the hydrophobic alkyl moiety of Leu is surrounded by the alkyl or fluoroalkyl groups of the alcohol molecules. In particular, TFE and HFIP significantly solvate the alkyl group of Leu. IR spectra reveal that the Leu C-H stretching vibration blueshifts in fluorinated alcohol solutions with increasing alcohol content, whereas the vibration redshifts in aliphatic alcohol solutions. When the C-H stretching vibration blueshifts in the fluorinated alcohol solutions, the hydrogen and carbon atoms of the Leu alkyl group are magnetically shielded. Consequently, TFE and HFIP molecules may solvate the Leu alkyl group through the blue-shifting hydrogen bonds.

  17. 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...

  18. Selective host molecules obtained by dynamic adaptive chemistry.

    Science.gov (United States)

    Matache, Mihaela; Bogdan, Elena; Hădade, Niculina D

    2014-02-17

    Up till 20 years ago, in order to endow molecules with function there were two mainstream lines of thought. One was to rationally design the positioning of chemical functionalities within candidate molecules, followed by an iterative synthesis-optimization process. The second was the use of a "brutal force" approach of combinatorial chemistry coupled with advanced screening for function. Although both methods provided important results, "rational design" often resulted in time-consuming efforts of modeling and synthesis only to find that the candidate molecule was not performing the designed job. "Combinatorial chemistry" suffered from a fundamental limitation related to the focusing of the libraries employed, often using lead compounds that limit its scope. Dynamic constitutional chemistry has developed as a combination of the two approaches above. Through the rational use of reversible chemical bonds together with a large plethora of precursor libraries, one is now able to build functional structures, ranging from quite simple molecules up to large polymeric structures. Thus, by introduction of the dynamic component within the molecular recognition processes, a new perspective of deciphering the world of the molecular events has aroused together with a new field of chemistry. Since its birth dynamic constitutional chemistry has continuously gained attention, in particular due to its ability to easily create from scratch outstanding molecular structures as well as the addition of adaptive features. The fundamental concepts defining the dynamic constitutional chemistry have been continuously extended to currently place it at the intersection between the supramolecular chemistry and newly defined adaptive chemistry, a pivotal feature towards evolutive chemistry.

  19. 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.

  20. 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...

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

    Science.gov (United States)

    Yadav, Rajeev; Sengupta, Bhaswati; Sen, Pratik

    2016-04-01

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

  2. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Brennan, J.G.

    1985-12-01

    This thesis considers three aspects of organoactinide chemistry. In chapter one, a bidentate phosphine ligand was used to kinetically stabilize complexes of the type Cp/sub 2/MX/sub 2/. 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 ..pi..-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.

  4. Solvation of sodium chloride in the 1-butyl-3-methyl-imidazolium bis(trifluoromethylsulfonyl)imide ionic liquid: a molecular dynamics study.

    Science.gov (United States)

    Sieffert, Nicolas; Wipff, Georges

    2007-06-28

    We report molecular dynamics studies on the solvation of sodium chloride in the 1-butyl-3-methyl-imidazolium bis(trifluoromethylsulfonyl)imide ionic liquid ([BMI][Tf2N] IL). We first consider the potential of mean force for dissociating a single Na+Cl- ion pair, showing that the latter prefers to be undissociated rather than dissociated (by ca. 9 kcal/mol), with a free energy barrier of ca. 5 kcal/mol (at d approximately 5.2 A) for the association process. The preference for Na+Cl- association is also observed from a 100 ns molecular dynamics simulation of a concentrated solution, where the Na+Cl- ions tend to form oligomers and microcrystals in the IL. Conversely, the simulation of Na13Cl14- and Na14Cl13+ cubic microcrystals (with, respectively, Cl- and Na+ at the vertices) does not lead to dissolution in the IL. Among these, Na14Cl13+ is found to be better solvated than Na13Cl14-, mainly due to the stronger Na+...Tf2N- interactions as compared to the Cl-...BMI+ interactions at the vertices of the cube. We finally consider the solid/liquid interface between the 100 face of NaCl and the IL, revealing that, in spite of its polar nature, the crystal surface is solvated by the less polar IL components (CF3(Tf2N) and butyl(BMI) groups) rather than by the polar ones (O(Tf2N) and imidazolium(BMI) ring). Specific ordering at the interface is described for both Tf2N- anions and BMI+ cations. In the first IL layer, the ions are rather parallel to the surface, whereas in the second "layer" they are more perpendicular. A similar IL structure is found at the surface of the all-neutral Na0Cl0 solid analogue, confirming that the solvation of the crystal is rather "apolar", due to the mismatch between the IL and the crystal ions. Several comparisons with water, methanol, or different BMI+-based ILs as solvents are presented, allowing us to better understand the specificity of the ionic liquid-NaCl interactions.

  5. 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]-.

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

    DEFF Research Database (Denmark)

    Sørensen, Anne

    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...... combinatorial chemistry, namely the reversible diselenide exchange reaction. The first part of the thesis describes the development of a thermally induced OAr → SeAr migration reaction. Here, it was proven possible to rearrange a variety of substituted O-aryl selenocarbamates into the corresponding Se...

  7. 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)

  8. Dispersed dynamics of solvation in G-quadruplex DNA: comparison of dynamic Stokes shifts of probes in parallel and antiparallel quadruplex structures

    Science.gov (United States)

    Kiran Singh, Moirangthem; Shweta, Him; Sen, Sobhan

    2016-09-01

    G-quadruplex DNA (GqDNA) structures play an important role in many specific cellular functions and are promising anti-tumor targets for small molecules (ligands). Here, we measured the dynamic Stokes shift of a ligand (Hoechst) bound to parallel c-Myc (mPu22) GqDNA over five decades of time from 100 fs to 10 ns, and compared it with the previously reported dynamics of DAPI bound to antiparallel human telomeric (hTelo22) GqDNA (Pal et al 2015 J. Phys. Chem. Lett. 6 1754). Stokes shift data from fluorescence up-conversion and time-correlated single photon counting experiments was combined to cover the broad dynamic range. The results show that the solvation dynamics of Hoechst in parallel mPu22 GqDNA follow a power law relaxation, added to fast 2 ps exponential relaxation, from 100 fs to 10 ns, with only a subtle difference of power law exponents in the two ligand-GqDNA systems (0.06 in Hoechst-mPu22 compared to 0.16 in DAPI-hTelo22). We measured steady-state fluorescence spectra and time-resolved anisotropy decays which confirm the tight binding of Hoechst to parallel mPu22 with a binding constant of ~1  ×  105 M-1. The molecular docking of Hoechst in parallel GqDNA followed by a 50 ns molecular dynamics (MD) simulation on a Hoechst-GqDNA complex reveals that Hoechst binds to one of the outer G-tetrads by end-stacking near G13 and G4, which is different from the binding site of DAPI inside a groove of antiparallel hTelo22 GqDNA. Reconciling previous experimental and simulation results, we assign the 2 ps component to the hydration dynamics of only weakly perturbed water near mPu22 and the power law relaxation to the coupled motion of water and DNA (i.e. DNA backbone, unpaired bases and loops connecting G-tetrads) which come near the Hoechst inside parallel GqDNA.

  9. 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 ...

  10. Synthetic receptors for ammonium ions using dynamic combinatorial chemistry

    NARCIS (Netherlands)

    Hamieh, Saleh

    2015-01-01

    The general topic of this dissertation is the development of synthetic receptors for organic ammonium ions in near physiological conditions using disulfide dynamic combinatorial chemistry (DCC). Chapter 1 explains the importance of this development and the associated difficulties when using the conv

  11. 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

  12. 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...

  13. 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

  14. 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.

  15. 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

  16. Dispersion and Solvation Effects on the Structure and Dynamics of N719 Adsorbed to Anatase Titania (101) Surfaces in Room-Temperature Ionic Liquids: An ab Initio Molecular Simulation Study

    KAUST Repository

    Byrne, Aaron

    2015-12-24

    Ab initio, density functional theory (DFT)-based molecular dynamics (MD) has been carried out to investigate the effect of explicit solvation on the dynamical and structural properties of a [bmim][NTf2] room-temperature ionic liquid (RTIL), solvating a N719 sensitizing dye adsorbed onto an anatase titania (101) surface. The effect of explicit dispersion on the properties of this dye-sensitized solar cell (DSC) interface has also been studied. Upon inclusion of dispersion interactions in simulations of the solvated system, the average separation between the cations and anions decreases by 0.6 Å; the mean distance between the cations and the surface decreases by about 0.5 Å; and the layering of the RTIL is significantly altered in the first layer surrounding the dye, with the cation being on average 1.5 Å further from the center of the dye. Inclusion of dispersion effects when a solvent is not explicitly included (to dampen longer-range interactions) can result in unphysical "kinking" of the adsorbed dye\\'s configuration. The inclusion of solvent shifts the HOMO and LUMO levels of the titania surface by +3 eV. At this interface, the interplay between the effects of dispersion and solvation combines in ways that are often subtle, such as enhancement or inhibition of specific vibrational modes. © 2015 American Chemical Society.

  17. 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.

  18. 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

  19. 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

  20. 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...

  1. 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.

  2. 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...

  3. Influence of GTP/GDP and magnesium ion on the solvated structure of the protein FtsZ: a molecular dynamics study.

    Science.gov (United States)

    Jamous, Carla; Basdevant, Nathalie; Ha-Duong, Tap

    2014-01-01

    We present here a structural analysis of ten extensive all-atom molecular dynamics simulations of the monomeric protein FtsZ in various binding states. Since the polymerization and GTPase activities of FtsZ depend on the nature of a bound nucleotide as well as on the presence of a magnesium ion, we studied the structural differences between the average conformations of the following five systems: FtsZ-Apo, FtsZ-GTP, FtsZ-GDP, FtsZ-GTP-Mg, and FtsZ-GDP-Mg. The in silico solvated average structure of FtsZ-Apo significantly differs from the crystallographic structure 1W59 of FtsZ which was crystallized in a dimeric form without nucleotide and magnesium. The simulated Apo form of the protein also clearly differs from the FtsZ structures when it is bound to its ligand, the most important discrepancies being located in the loops surrounding the nucleotide binding pocket. The three average structures of FtsZ-GTP, FtsZ-GDP, and FtsZ-GTP-Mg are overall similar, except for the loop T7 located at the opposite side of the binding pocket and whose conformation in FtsZ-GDP notably differs from the one in FtsZ-GTP and FtsZ-GTP-Mg. The presence of a magnesium ion in the binding pocket has no impact on the FtsZ conformation when it is bound to GTP. In contrast, when the protein is bound to GDP, the divalent cation causes a translation of the nucleotide outwards the pocket, inducing a significant conformational change of the loop H6-H7 and the top of helix H7.

  4. 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)

  5. 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.

  6. 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

  7. 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...

  8. 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.

  9. 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 .

  10. 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

  11. 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…

  12. 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.

  13. 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)

  14. Interfacial solvation thermodynamics

    Science.gov (United States)

    Ben-Amotz, Dor

    2016-10-01

    Previous studies have reached conflicting conclusions regarding the interplay of cavity formation, polarizability, desolvation, and surface capillary waves in driving the interfacial adsorptions of ions and molecules at air-water interfaces. Here we revisit these questions by combining exact potential distribution results with linear response theory and other physically motivated approximations. The results highlight both exact and approximate compensation relations pertaining to direct (solute-solvent) and indirect (solvent-solvent) contributions to adsorption thermodynamics, of relevance to solvation at air-water interfaces, as well as a broader class of processes linked to the mean force potential between ions, molecules, nanoparticles, proteins, and biological assemblies.

  15. 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.

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

    Science.gov (United States)

    Golmohammadi, Hassan; Dashtbozorgi, Zahra

    2016-09-01

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

  17. 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)

  18. 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.

  19. Determination of solvation kinetics in supercritical fluids

    Energy Technology Data Exchange (ETDEWEB)

    Bright, F.V.

    1993-01-01

    Objective was to study solvation processes in pure and entrainer-modified supercritical fluids. Specific topics were: Kinetics for solvation in supercritical media, influence on entrainers on solvation, reversibility of solvation, effects of solvation on intramolecular solute-solute interaction kinetics, and impact of fluid density on these processes. Time-resolved fluorescence spectroscopy was used as the main analytical tool. A summary is given of the 2.5 years' research.

  20. Femtosecond spectroscopic study of the solvation of amphiphilic molecules by water

    NARCIS (Netherlands)

    Y.L.A. Rezus; H.J. Bakker

    2008-01-01

    We use polarization-resolved mid-infrared pump-probe spectroscopy to study the aqueous solvation of proline and N-methylacetamide. These molecules serve as models to study the solvation of proteins. We monitor the orientational dynamics of partly deuterated water molecules (HDO) that are present at

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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…

  6. Chemistry and dynamics of the Arctic winter 2015/2016: Simulations with the Chemistry-Climate Model EMAC

    Science.gov (United States)

    Khosrawi, Farahnaz; Kirner, Ole; Sinnhuber, Bjoern-Martin; Ruhnke, Roland; Hoepfner, Michael; Woiwode, Wolfgang; Oelhaf, Hermann; Santee, Michelle L.; Manney, Gloria L.; Froidevaux, Lucien; Murtagh, Donal; Braesicke, Peter

    2016-04-01

    Model simulations of the Arctic winter 2015/2016 were performed with the atmospheric chemistry-climate model ECHAM5/MESSy Atmospheric Chemistry (EMAC) for the POLSTRACC (Polar Stratosphere in a Changing Climate) project. The POLSTRACC project is a HALO mission (High Altitude and LOng Range Research Aircraft) that aims to investigate the structure, composition and evolution of the Arctic Upper Troposphere Lower Stratosphere (UTLS) in a changing climate. Especially, the chemical and physical processes involved in Arctic stratospheric ozone depletion, transport and mixing processes in the UTLS at high latitudes, polar stratospheric clouds as well as cirrus clouds are investigated. The model simulations were performed with a resolution of T42L90, corresponding to a quadratic Gaussian grid of approximately 2.8°× 2.8° degrees in latitude and longitude, and 90 vertical layers from the surface up to 0.01 hPa (approx. 80 km). A Newtonian relaxation technique of the prognostic variables temperature, vorticity, divergence and surface pressure towards ECMWF data was applied above the boundary layer and below 10 hPa, in order to nudge the model dynamics towards the observed meteorology. During the Arctic winter 2015/2016 a stable vortex formed in early December, with a cold pool where temperatures reached below the Nitric Acid Trihydrate (NAT) existence temperature of 195 K, thus allowing Polar Stratospheric Clouds (PSCs) to form. The early winter has been exceptionally cold and satellite observations indicate that sedimenting PSC particles have lead to denitrification as well as dehydration of stratospheric layers. In this presentation an overview of the chemistry and dynamics of the Arctic winter 2015/2016 as simulated with EMAC will be given and comparisons to satellite observations such as e.g. Aura/MLS and Odin/SMR will be shown.

  7. 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)

  8. Water Evaporation and Conformational Changes from Partially Solvated Ubiquitin

    Directory of Open Access Journals (Sweden)

    Saravana Prakash Thirumuruganandham

    2010-01-01

    Full Text Available Using molecular dynamics simulation, we study the evaporation of water molecules off partially solvated ubiquitin. The evaporation and cooling rates are determined for a molecule at the initial temperature of 300 K. The cooling rate is found to be around 3 K/ns, and decreases with water temperature in the course of the evaporation. The conformation changes are monitored by studying a variety of intermediate partially solvated ubiquitin structures. We find that ubiquitin shrinks with decreasing hydration shell and exposes more of its hydrophilic surface area to the surrounding.

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

    DEFF Research Database (Denmark)

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

    2005-01-01

    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...

  10. 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.

  11. 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

  12. 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.

  13. 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

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

    Science.gov (United States)

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

    2016-10-01

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

  15. 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)

  16. 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.

  17. 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)

  18. 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

  19. 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.

  20. 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.

  1. Accelerated electronic structure-based molecular dynamics simulations of shock-induced chemistry

    Science.gov (United States)

    Cawkwell, Marc

    2015-06-01

    The initiation and progression of shock-induced chemistry in organic materials at moderate temperatures and pressures are slow on the time scales available to regular molecular dynamics simulations. Accessing the requisite time scales is particularly challenging if the interatomic bonding is modeled using accurate yet expensive methods based explicitly on electronic structure. We have combined fast, energy conserving extended Lagrangian Born-Oppenheimer molecular dynamics with the parallel replica accelerated molecular dynamics formalism to study the relatively sluggish shock-induced chemistry of benzene around 13-20 GPa. We model interatomic bonding in hydrocarbons using self-consistent tight binding theory with an accurate and transferable parameterization. Shock compression and its associated transient, non-equilibrium effects are captured explicitly by combining the universal liquid Hugoniot with a simple shrinking-cell boundary condition. A number of novel methods for improving the performance of reactive electronic structure-based molecular dynamics by adapting the self-consistent field procedure on-the-fly will also be discussed. The use of accelerated molecular dynamics has enabled us to follow the initial stages of the nucleation and growth of carbon clusters in benzene under thermodynamic conditions pertinent to experiments.

  2. 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.

  3. 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...

  4. 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...

  5. 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

  6. 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......We have studied the photoinduced low spin (LS) to high spin (HS) conversion of aqueous Fe(bpy)3 with pulse-limited time resolution. In a combined setup permitting simultaneous X-ray diffuse scattering (XDS) and spectroscopic measurements at a MHz repetition rate we have unraveled the interplay...

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

    Directory of Open Access Journals (Sweden)

    R. H. H. Janssen

    2012-04-01

    Full Text Available 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 model for a case study in Hyytiälä, Finland, and find that it is able to well reproduce the observed dynamics and gas-phase chemistry. We show that the exchange of organic aerosol between the free troposphere and the boundary layer (entrainment must be taken into account in order to explain the observed diurnal cycle in organic aerosol (OA concentration. An examination of the budgets of organic aerosol and terpene concentration shows that the former is dominated by entrainment, while the latter is mainly driven by emission and chemical transformation. We systematically examine the role of the land surface, which governs both the surface energy balance partitioning and terpene-emissions, and the large-scale atmospheric process of vertical subsidence. Entrainment is especially important for the dilution of organic aerosol concentrations under conditions of dry soils and low terpene-emissions. Subsidence suppresses boundary layer growth while enhancing entrainment. Therefore it influences the relationship between organic aerosol and terpene-concentrations. Our findings indicate that the diurnal evolution of SOA in the boundary layer is the result of coupled effects of the land surface, dynamics of the atmospheric boundary layer, chemistry, and free troposphere conditions. This has potentially some consequences for the design of both field campaigns and large-scale modeling studies.

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

    Directory of Open Access Journals (Sweden)

    R. H. H. Janssen

    2012-08-01

    Full Text Available 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 model for a case study in Hyytiälä, Finland, and find that it is able to satisfactorily reproduce the observed dynamics and gas-phase chemistry. We show that the exchange of organic aerosol between the free troposphere and the boundary layer (entrainment must be taken into account in order to explain the observed diurnal cycle in organic aerosol (OA concentration. An examination of the budgets of organic aerosol and terpene concentrations show that the former is dominated by entrainment, while the latter is mainly driven by emission and chemical transformation. We systematically investigate the role of the land surface, which governs both the surface energy balance partitioning and terpene emissions, and the large-scale atmospheric process of vertical subsidence. Entrainment is especially important for the dilution of organic aerosol concentrations under conditions of dry soils and low terpene emissions. Subsidence suppresses boundary layer growth while enhancing entrainment. Therefore, it influences the relationship between organic aerosol and terpene concentrations. Our findings indicate that the diurnal evolution of secondary organic aerosols (SOA in the boundary layer is the result of coupled effects of the land surface, dynamics of the atmospheric boundary layer, chemistry, and free troposphere conditions. This has potentially some consequences for the design of both field campaigns and large-scale modeling studies.

  9. Chemistry of stannylene-based Lewis pairs: dynamic tin coordination switching between donor and acceptor character.

    Science.gov (United States)

    Krebs, Kilian M; Freitag, Sarah; Schubert, Hartmut; Gerke, Birgit; Pöttgen, Rainer; Wesemann, Lars

    2015-03-16

    The coordination chemistry of cyclic stannylene-based intramolecular Lewis pairs is presented. The P→Sn adducts were treated with [Ni(COD)2] and [Pd(PCy3)2] (COD = 1,5-cyclooctadiene, PCy3 = tricyclohexylphosphine). In the isolated coordination compounds the stannylene moiety acts either as an acceptor or a donor ligand. Examples of a dynamic switch between these two coordination modes of the P-Sn ligand are illustrated and the structures in the solid state together with heteronuclear NMR spectroscopic findings are discussed. In the case of a Ni(0) complex, (119)Sn Mössbauer spectroscopy of the uncoordinated and coordinated phosphastannirane ligand is presented.

  10. Nonlinear theory of combustion stability in liquid rocket engine based on chemistry dynamics

    Institute of Scientific and Technical Information of China (English)

    黄玉辉; 王振国; 周进

    2002-01-01

    Detailed models of combustion instability based on chemistry dynamics are developed. The results show that large activation energy goes against the combustion stability. The heat transfer coefficient between the wall and the combust gas is an important bifurcation parameter for the combustion instability. The acoustics modes of the chamber are in competition and cooperation with each other for limited vibration energy. Thermodynamics criterion of combustion stability can be deduced from the nonlinear thermodynamics. Correlations of the theoretical results and historical experiments indicate that chemical kinetics play a critical role in the combustion instability.

  11. Updated Abraham solvation parameters for polychlorinated biphenyls

    NARCIS (Netherlands)

    Noort, van P.C.M.; Haftka, J.J.H.; Parsons, J.R.

    2010-01-01

    This study shows that the recently published polychlorinated biphenyl (PCB) Abraham solvation parameters predict PCB air-n-hexadecane and n-octanol-water partition coefficients very poorly, especially for highly ortho-chlorinated congeners. Therefore, an updated set of PCB solvation parameters was d

  12. Updated Abraham solvation parameters for polychlorinated biphenyls

    NARCIS (Netherlands)

    P.C.M. van Noort; J.J.H. Haftka; J.R. Parsons

    2010-01-01

    This study shows that the recently published polychlorinated biphenyl (PCB) Abraham solvation parameters predict PCB air−n-hexadecane and n-octanol−water partition coefficients very poorly, especially for highly ortho-chlorinated congeners. Therefore, an updated set of PCB solvation parameters was d

  13. 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.

  14. 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.

  15. Desvenlafaxinium chloranilate ethyl acetate solvate

    Directory of Open Access Journals (Sweden)

    Manpreet Kaur

    2013-10-01

    Full Text Available In the cation of the title compound, C16H26NO2+·C6HCl2O4−·C4H8O2, the 1-hydroxy-cyclohexyl ring adopts a slightly distorted chair conformation. The dihedral angle between the mean planes of the 1-hydroxycyclohexyl and 4-hydroxyphenyl rings is 84.0 (8°. In the anion, the hydroxyl H atom is twisted slightly out of the ring plane with a C—C—O—H torsion angle of −171.9°. Disorder was modeled for the methyl group of the acetate group in the solvate with an occupancy ratio of 0.583 (15: 0.417 (15. In the crystal, O—H...O hydrogen bonds are observed between cations and between cations and anions, while bifuricated N—H...(O,O cation–anion hydrogen bonds are also present, forming chains along [010] and [100]. In addition weak cation–anion and cation–solvate C—H...O interactions occur.

  16. 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...

  17. Structure of hen egg-white lysozyme solvated in TFE/water: a molecular dynamics simulation study based on NMR data

    Energy Technology Data Exchange (ETDEWEB)

    Eichenberger, Andreas P.; Gunsteren, Wilfred F. van, E-mail: wfvgn@igc.phys.chem.ethz.ch [Swiss Federal Institute of Technology, Laboratory of Physical Chemistry (Switzerland); Smith, Lorna J. [University of Oxford, Department of Chemistry, Inorganic Chemistry Laboratory (United Kingdom)

    2013-04-15

    Various experimental studies of hen egg white lysozyme (HEWL) in water and TFE/water clearly indicate structural differences between the native state and TFE state of HEWL, e.g. the helical content of the protein in the TFE state is much higher than in the native state. However, the available detailed NMR studies were not sufficient to determine fully a structure of HEWL in the TFE state. Different molecular dynamics (MD) simulations, i.e. at room temperature, at increased temperature and using proton-proton distance restraints derived from NMR NOE data, have been used to generate configurational ensembles corresponding to the TFE state of HEWL. The configurational ensemble obtained at room temperature using atom-atom distance restraints measured for HEWL in TFE/water solution satisfies the experimental data and has the lowest protein energy. In this ensemble residues 50-58, which are part of the {beta}-sheet in native HEWL, adopt fluctuating {alpha}-helical secondary structure.

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

    DEFF Research Database (Denmark)

    Larsen, Dennis

    added to these equilibrator-containing libraries, from which ligands for several transition metals (Pd, Ni, and Zn) were identified. In the second part of this thesis, the discovery that thiosemicarbazones catalyse the tetrahydropyranylation of alcohols in dichloromethane at room temperature......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...... is presented. This represents the first use, to the best of the author’s knowledge, of thiosemicarbazones for organocatalysis. Guided by kinetics studies, a range of catalysts were developed and evaluated, and this showed that thiosemicarbazone catalysts are highly tuneable. The best thiosemicarbazone catalyst...

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

    Energy Technology Data Exchange (ETDEWEB)

    Zelazny, Miroslaw, E-mail: miroslaw.zelazny@uj.edu.pl [Jagiellonian University, Institute of Geography and Spatial Management, Department of Hydrology, 7 Gronostajowa Str., 30-387 Cracow (Poland); Astel, Aleksander, E-mail: astel@apsl.edu.pl [Environmental Chemistry Research Unit, Biology and Environmental Protection Institute, Pomeranian Academy, 22a Arciszewskiego Str., Slupsk, 76-200 (Poland); Wolanin, Anna [Jagiellonian University, Institute of Geography and Spatial Management, Department of Hydrology, 7 Gronostajowa Str., 30-387 Cracow (Poland); Malek, Stanislaw, E-mail: rlmalek@cyf-kr.edu.pl [Department of Forest Ecology, Forest Faculty, Agricultural University of Cracow, 46 29 Listopada Ave., Cracow, 31-425 (Poland)

    2011-05-15

    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.

  20. Effects of Aircraft Wake Dynamics on Measured and Simulated NO(x) and HO(x) Wake Chemistry. Appendix B

    Science.gov (United States)

    Lewellen, D. C.; Lewellen, W. S.

    2001-01-01

    High-resolution numerical large-eddy simulations of the near wake of a B757 including simplified NOx and HOx chemistry were performed to explore the effects of dynamics on chemistry in wakes of ages from a few seconds to several minutes. Dilution plays an important basic role in the NOx-O3 chemistry in the wake, while a more interesting interaction between the chemistry and dynamics occurs for the HOx species. These simulation results are compared with published measurements of OH and HO2 within a B757 wake under cruise conditions in the upper troposphere taken during the Subsonic Aircraft Contrail and Cloud Effects Special Study (SUCCESS) mission in May 1996. The simulation provides a much finer grained representation of the chemistry and dynamics of the early wake than is possible from the 1 s data samples taken in situ. The comparison suggests that the previously reported discrepancy of up to a factor of 20 - 50 between the SUCCESS measurements of the [HO2]/[OH] ratio and that predicted by simplified theoretical computations is due to the combined effects of large mixing rates around the wake plume edges and averaging over volumes containing large species fluctuations. The results demonstrate the feasibility of using three-dimensional unsteady large-eddy simulations with coupled chemistry to study such phenomena.

  1. Molecular theory of solvation: Methodology summary and illustrations

    Directory of Open Access Journals (Sweden)

    A. Kovalenko

    2015-09-01

    Full Text Available Integral equation theory of molecular liquids based on statistical mechanics is quite promising as an essential part of multiscale methodology for chemical and biomolecular nanosystems in solution. Beginning with a molecular interaction potential force field, it uses diagrammatic analysis of the solvation free energy to derive integral equations for correlation functions between molecules in solution in the statistical-mechanical ensemble. The infinite chain of coupled integral equations for many-body correlation functions is reduced to a tractable form for 2- or 3-body correlations by applying the so-called closure relations. Solving these equations produces the solvation structure with accuracy comparable to molecular simulations that have converged but has a critical advantage of readily treating the effects and processes spanning over a large space and slow time scales, by far not feasible for explicit solvent molecular simulations. One of the versions of this formalism, the three-dimensional reference interaction site model (3D-RISM integral equation complemented with the Kovalenko-Hirata (KH closure approximation, yields the solvation structure in terms of 3D maps of correlation functions, including density distributions, of solvent interaction sites around a solute (supramolecule with full consistent account for the effects of chemical functionalities of all species in the solution. The solvation free energy and the subsequent thermodynamics are then obtained at once as a simple integral of the 3D correlation functions by performing thermodynamic integration analytically. Analytical form of the free energy functional permits the self-consistent field coupling of 3D-RISM-KH with quantum chemistry methods in multiscale description of electronic structure in solution, the use of 3D maps of potentials of mean force as scoring functions for molecular recognition and protein-ligand binding in docking protocols for fragment based drug design

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. Determination of solvation kinetics in supercritical fluids. Summary report

    Energy Technology Data Exchange (ETDEWEB)

    Bright, F.V.

    1993-01-01

    Objective was to study solvation processes in pure and entrainer-modified supercritical fluids. Specific topics were: Kinetics for solvation in supercritical media, influence on entrainers on solvation, reversibility of solvation, effects of solvation on intramolecular solute-solute interaction kinetics, and impact of fluid density on these processes. Time-resolved fluorescence spectroscopy was used as the main analytical tool. A summary is given of the 2.5 years` research.

  7. Size distribution dynamics reveal particle-phase chemistry in organic aerosol formation.

    Science.gov (United States)

    Shiraiwa, Manabu; Yee, Lindsay D; Schilling, Katherine A; Loza, Christine L; Craven, Jill S; Zuend, Andreas; Ziemann, Paul J; Seinfeld, John H

    2013-07-16

    Organic aerosols are ubiquitous in the atmosphere and play a central role in climate, air quality, and public health. The aerosol size distribution is key in determining its optical properties and cloud condensation nucleus activity. The dominant portion of organic aerosol is formed through gas-phase oxidation of volatile organic compounds, so-called secondary organic aerosols (SOAs). Typical experimental measurements of SOA formation include total SOA mass and atomic oxygen-to-carbon ratio. These measurements, alone, are generally insufficient to reveal the extent to which condensed-phase reactions occur in conjunction with the multigeneration gas-phase photooxidation. Combining laboratory chamber experiments and kinetic gas-particle modeling for the dodecane SOA system, here we show that the presence of particle-phase chemistry is reflected in the evolution of the SOA size distribution as well as its mass concentration. Particle-phase reactions are predicted to occur mainly at the particle surface, and the reaction products contribute more than half of the SOA mass. Chamber photooxidation with a midexperiment aldehyde injection confirms that heterogeneous reaction of aldehydes with organic hydroperoxides forming peroxyhemiacetals can lead to a large increase in SOA mass. Although experiments need to be conducted with other SOA precursor hydrocarbons, current results demonstrate coupling between particle-phase chemistry and size distribution dynamics in the formation of SOAs, thereby opening up an avenue for analysis of the SOA formation process.

  8. Theory of solvation in polar nematics

    CERN Document Server

    Kapko, V; Kapko, Vitaly; Matyushov, Dmitry V.

    2005-01-01

    We develop a linear response theory of solvation of ionic and dipolar solutes in anisotropic, axially symmetric polar solvents. The theory is applied to solvation in polar nematic liquid crystals. The formal theory constructs the solvation response function from projections of the solvent dipolar susceptibility on rotational invariants. These projections are obtained from Monte Carlo simulations of a fluid of dipolar spherocylinders which can exist both in the isotropic and nematic phase. Based on the properties of the solvent susceptibility from simulations and the formal solution, we have obtained a formula for the solvation free energy which incorporates experimentally available properties of nematics and the length of correlation between the dipoles in the liquid crystal. Illustrative calculations are presented for the Stokes shift and Stokes shift correlation function of coumarin-153 in 4-n-pentyl-4'-cyanobiphenyl (5CB) and 4,4-n-heptyl-cyanopiphenyl (7CB) solvents as a function of temperature in both th...

  9. 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

  10. The Role of Disk Volatile Chemistry and Dynamics in Shaping the Compositions of Nascent Planets

    Science.gov (United States)

    Piso, Ana-Maria; Oberg, Karin I.; Birnstiel, Tilman; Murray-Clay, Ruth

    2016-01-01

    The elemental composition of planets define their chemistry, and could potentially be used as beacons for their formation location if the elemental gas and grain ratios of planet birth environments, i.e. protoplanetary disks, are well understood. In disks, the ratios of volatile elements (e.g., C/O) is regulated by the presence of snowlines of major volatiles at different distances from the central star. We explore the effects of dynamical processes, such as radial drift of solids and viscous gas accretion onto the central star, molecular compositions, and the ice morphology of dust grains in disks on the snowline locations of the main C, O and N carriers in a protoplanetary disk, and their consequences for the C/O/N ratio in gas and dust throughout the disk. We find that radial drift and accretion alone can reduce the snow line radii by 40-60% of the main C and O carriers, i.e. H2O, CO2 and CO, compared to static disks, substantially changing the disk regions where C/O is enhanced over the stellar value. A similar effect is seen for the major nitrogen carriers. We note that N/O enhancements in disk gas can be even more extreme than C/O in the outer disk due to the low volatility of N2 compared to all major C and O carriers. I will discuss these results together with the effects of additional dynamical processes, and outline a path toward a coupled drift-desorption-chemistry model that will provide robust quantitative results for volatile snowline locations and C/N/O abundance ratios as the disk evolves in time.

  11. 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…

  12. 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...

  13. Fast Quantum Molecular Dynamics Simulations of Shock-induced Chemistry in Organic Liquids

    Science.gov (United States)

    Cawkwell, Marc

    2014-03-01

    The responses of liquid formic acid and phenylacetylene to shock compression have been investigated via quantum-based molecular dynamics simulations with the self-consistent tight-binding code LATTE. Microcanonical Born-Oppenheimer trajectories with precise conservation of the total energy were computed without relying on an iterative self-consistent field optimization of the electronic degrees of freedom at each time step via the Fast Quantum Mechanical Molecular Dynamics formalism [A. M. N. Niklasson and M. J. Cawkwell, Phys. Rev. B, 86, 174308 (2012)]. The conservation of the total energy in our trajectories was pivotal for the capture of adiabatic shock heating as well as temperature changes arising from endo- or exothermic chemistry. Our self-consistent tight-binding parameterizations yielded very good predictions for the gas-phase geometries of formic acid and phenylacetylene molecules and the principal Hugoniots of the liquids. In accord with recent flyer-plate impact experiments, our simulations revealed i) that formic acid reacts at relatively low impact pressures but with no change in volume between products and reactants, and ii) a two-step polymerization process for phenylacetylene. Furthermore, the evolution of the HOMO-LUMO gap tracked on-the-fly during our simulations could be correlated with changes transient absorption measured during laser-driven shock compression experiments on these liquids.

  14. 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.

  15. 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

  16. Raman and computational study of solvation and chemisorption of thiazole in silver hydrosol.

    Science.gov (United States)

    Muniz-Miranda, Maurizio; Pagliai, Marco; Muniz-Miranda, Francesco; Schettino, Vincenzo

    2011-03-21

    A SERS investigation combined with ab initio computational analysis involving Car-Parrinello molecular dynamics simulations and Density Functional Theory approach allows fundamental information to be obtained on the behaviour of thiazole in silver aqueous suspension where solvation and chemisorption processes competitively occur.

  17. 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.

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

    Science.gov (United States)

    Sedov, I A; Magsumov, T I

    2015-07-16

    Thermodynamic solvation properties of mixtures of water with tetrahydrofuran at 298 K are studied. The Gibbs free energies and enthalpies of solvation of n-octane and toluene are determined experimentally. For molecular dynamics simulations of the binary solvent, we have modified a TraPPE-UA model for tetrahydrofuran and combined it with the SPC/E potential for water. The excess thermodynamic functions of neon, xenon, and hard spheres with two different radii are calculated using the particle insertion method. Simulated and real systems share the same characteristic trends for the thermodynamic functions. A maximum is present on dependencies of the enthalpy of solvation from the composition of solvent at 70-90 mol % water, making it higher than in both of the cosolvents. It is caused by a high enthalpy of cavity formation in the mixtures rich with water due to solvent reorganization around the cavity, which is shown by calculation of the enthalpy of solvation of hard spheres. Addition of relatively small amounts of tetrahydrofuran to water effectively suppresses the hydrophobic effect, leading to a quick increase of both the entropy and enthalpy of cavity formation and solvation of low polar molecules. PMID:26115405

  19. 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...

  20. Redox entropy of plastocyanin: Developing a microscopic view of mesoscopic polar solvation

    Science.gov (United States)

    LeBard, David N.; Matyushov, Dmitry V.

    2008-04-01

    We report applications of analytical formalisms and molecular dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of the theory required to describe polar solvation at the mesoscopic scale. The analytical techniques include a microscopic formalism based on structure factors of the solvent dipolar orientations and density and continuum dielectric theories. The microscopic theory employs the atomistic structure of the protein with force-field atomic charges and solvent structure factors obtained from separate MD simulations of the homogeneous solvent. The MD simulations provide linear response solvation free energies and reorganization energies of electron transfer in the temperature range of 280-310K. We found that continuum models universally underestimate solvation entropies, and a more favorable agreement is reported between the microscopic calculations and MD simulations. The analysis of simulations also suggests that difficulties of extending standard formalisms to protein solvation are related to the inhomogeneous structure of the solvation shell at the protein-water interface combining islands of highly structured water around ionized residues along with partial dewetting of hydrophobic patches. Quantitative theories of electrostatic protein hydration need to incorporate realistic density profile of water at the protein-water interface.

  1. 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

  2. Redox Entropy of Plastocyanin: Developing a Microscopic View of Mesoscopic Polar Solvation

    CERN Document Server

    LeBard, David N

    2007-01-01

    We report applications of analytical formalisms and Molecular Dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of the theory required to describe polar solvation at the mesoscopic scale. The analytical techniques include a microscopic formalism based on structure factors of the solvent dipolar orientations and density and continuum dielectric theories. The microscopic theory employs the atomistic structure of the protein with force-field atomic charges and solvent structure factors obtained from separate MD simulations of the homogeneous solvent. The MD simulations provide linear response solvation free energies and reorganization energies of electron transfer in the temperature range 280--310 K. We found that continuum models universally underestimate solvation entropies, and a more favorable agreement is reported between the microscopic calculations and MD simulations. The analysis o...

  3. 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

  4. 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.

  5. 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...

  6. 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

  7. 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.

  8. 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.

  9. Investigation of coupling between chemistry and discharge dynamics in radio frequency hydrogen plasmas in the Torr regime

    Energy Technology Data Exchange (ETDEWEB)

    Kalache, B [LPICM, UMR 7647 (CNRS), Ecole Polytechnique, 91128 Palaiseau Cedex (France); Novikova, T [LPICM, UMR 7647 (CNRS), Ecole Polytechnique, 91128 Palaiseau Cedex (France); Morral, A Fontcuberta i [LPICM, UMR 7647 (CNRS), Ecole Polytechnique, 91128 Palaiseau Cedex (France); Cabarrocas, P Roca i [LPICM, UMR 7647 (CNRS), Ecole Polytechnique, 91128 Palaiseau Cedex (France); Morscheidt, W [LIMHP, UPR 1311 (CNRS), UPN, Av. J. B. Clement, 93430 Villetaneuse (France); Hassouni, K [LIMHP, UPR 1311 (CNRS), UPN, Av. J. B. Clement, 93430 Villetaneuse (France)

    2004-07-07

    We present the results of a study of a capacitively coupled hydrogen discharge by means of a one-dimensional numerical fluid model and experiments. The model includes a detailed description of the gas-phase chemistry taking into account the production of H{sup -} ions by dissociative attachment of H{sub 2} vibrational levels. The population of these levels is described by a Boltzmann vibrational distribution function characterized by a vibrational temperature T{sub V}. The effect of the dissociative-attachment reaction on the discharge dynamics was investigated by varying the vibrational temperature, which was used as a model input parameter. Increasing the vibrational temperature from 1000 to 6000 K affects both the chemistry and the dynamics of the electrical discharge. Because of dissociative attachment, the H{sup -} ion density increases by seven orders of magnitude and the H{sup -} ion density to electron density ratio varies from 10{sup -7} to 6, while the positive ion density increases slightly. As a consequence, the atomic hydrogen density increases by a factor of three, and the sheath voltage drops from 95 to 75 V. Therefore, clear evidence of a strong coupling between chemistry and electrical dynamics through the production of H{sup -} ions is demonstrated. Moreover, satisfactory agreement between computed and measured values of atomic hydrogen and H{sup -} ion densities gives further support to the requirement of a detailed description of the hydrogen vibrational kinetics for capacitively coupled radio frequency discharge models in the Torr regime.

  10. 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

  11. 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.

  12. 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.

  13. Seasonal dynamics of water and air chemistry in an indoor chlorinated swimming pool.

    Science.gov (United States)

    Zare Afifi, Mehrnaz; Blatchley, Ernest R

    2015-01-01

    Although swimming is known to be beneficial in terms of cardiovascular health, as well as for some forms of rehabilitation, swimming is also known to present risks to human health, largely in the form of exposure to microbial pathogens and disinfection byproducts (DBPs). Relatively little information is available in the literature to characterize the seasonal dynamics of air and water chemistry in indoor chlorinated swimming pools. To address this issue, water samples were collected five days per week from an indoor chlorinated swimming pool facility at a high school during the academic year and once per week during summer over a fourteen-month period. The samples were analyzed for free and combined chlorine, urea, volatile DBPs, pH, temperature and total alkalinity. Membrane Introduction Mass Spectrometry (MIMS) was used to identify and measure the concentrations of eleven aqueous-phase volatile DBPs. Variability in the concentrations of these DBPs was observed. Factors that influenced variability included bather loading and mixing by swimmers. These compounds have the ability to adversely affect water and air quality and human health. A large fraction of the existing literature regarding swimming pool air quality has focused on trichloramine (NCl₃). For this work, gas-phase NCl₃ was analyzed by an air sparging-DPD/KI method. The results showed that gas-phase NCl₃ concentration is influenced by bather loading and liquid-phase NCl₃ concentration. Urea is the dominant organic-N compound in human urine and sweat, and is known to be an important precursor for producing NCl₃ in swimming pools. Results of daily measurements of urea indicated a link between bather load and urea concentration in the pool.

  14. 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

  15. 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

  16. 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...

  17. 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

  18. 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

  19. 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.

  20. Implications of dynamic imine chemistry for the sustainable synthesis of nitrogen heterocycles via transimination followed by intramolecular cyclisation.

    Science.gov (United States)

    Laha, Joydev K; Tummalapalli, K S Satyanarayana; Jethava, Krupal P

    2016-02-28

    An exploration of a tandem approach to the sustainable synthesis of N-heterocycles from readily available N-aryl benzylamines or imines and ortho-substituted anilines is described, which demonstrates, for the first time, an important synthetic application of dynamic imine chemistry. The key features to the successful development of this protocol include the utilisation of N-aryl benzylamines as imine precursors in transimination, the occurrence of transimination in acetonitrile in the absence of any catalysts, an intramolecular nucleophilic addition occurring in the newly formed imine causing irreversible transimination, and the tandem event occurring under green conditions.

  1. 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

  2. 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

  3. 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…

  4. 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…

  5. 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…

  6. 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

  7. Perspectives on Computational Organic Chemistry

    Science.gov (United States)

    Streitwieser, Andrew

    2009-01-01

    The author reviews how his early love for theoretical organic chemistry led to experimental research and the extended search for quantitative correlations between experiment and quantum calculations. The experimental work led to ion pair acidities of alkali-organic compounds and most recently to equilibria and reactions of lithium and cesium enolates in THF. This chemistry is now being modeled by ab initio calculations. An important consideration is the treatment of solvation in which coordination of the alkali cation with the ether solvent plays a major role. PMID:19518150

  8. 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

  9. 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

  10. 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.

  11. Solvent rearrangements during the transition from hydrophilic to hydrophobic solvation

    Energy Technology Data Exchange (ETDEWEB)

    Penfold, T.J. [Ecole Polytechnique Federale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne (Switzerland); Ecole Polytechnique Federale de Lausanne, Laboratoire de Chimie et Biochimie Computationnelles, ISIC, FSB-BSP, CH-1015 Lausanne (Switzerland); SwissFEL, Paul Scherrer Inst., CH-5232 Villigen (Switzerland); Tavernelli, I., E-mail: ivano.tavernelli@epfl.ch [Ecole Polytechnique Federale de Lausanne, Laboratoire de Chimie et Biochimie Computationnelles, ISIC, FSB-BSP, CH-1015 Lausanne (Switzerland); Doemer, M. [Ecole Polytechnique Federale de Lausanne, Laboratoire de Chimie et Biochimie Computationnelles, ISIC, FSB-BSP, CH-1015 Lausanne (Switzerland); Abela, R. [SwissFEL, Paul Scherrer Inst., CH-5232 Villigen (Switzerland); Roethlisberger, U. [Ecole Polytechnique Federale de Lausanne, Laboratoire de Chimie et Biochimie Computationnelles, ISIC, FSB-BSP, CH-1015 Lausanne (Switzerland); Chergui, M., E-mail: majed.chergui@epfl.ch [Ecole Polytechnique Federale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne (Switzerland)

    2013-01-02

    Highlights: Black-Right-Pointing-Pointer Ab inito molecular dynamics to study the early time dynamics following electron removal from aqueous iodide. Black-Right-Pointing-Pointer Ultrafast formation of a 3-electron bond I{sup 0}-OH{sub 2} complex (<100 fs). Black-Right-Pointing-Pointer Oscillation frequency of complexed water reflects influence of nearby water molecules. -- Abstract: We present an ab initio Born-Oppenheimer molecular dynamics study of the early time solvent dynamics after electron abstraction from aqueous iodide. An initial response occurs within {approx}75 fs, corresponding to a water molecule sharing almost one electron with the iodine. This is followed by the formation of a transient I{sup 0} Midline-Horizontal-Ellipsis OH{sub 2} complex within {approx}500 fs. Further insight into the driving forces for this complex are obtained using an energy decomposition analysis and frequency calculations of small clusters. It is shown that the anisotropic solvation shell structure of iodide before electron abstraction is likely to be an important factor in the formation of the complex.

  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. 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].

  14. 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...

  15. 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.

  16. Solvation-driven charge transfer and localization in metal complexes.

    Science.gov (United States)

    Rondi, Ariana; Rodriguez, Yuseff; Feurer, Thomas; Cannizzo, Andrea

    2015-05-19

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

  17. 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 ...

  18. 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.

  19. 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

  20. 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.

  1. Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen-Hydrogen Correlations.

    Science.gov (United States)

    Velez-Vega, Camilo; McKay, Daniel J J; Kurtzman, Tom; Aravamuthan, Vibhas; Pearlstein, Robert A; Duca, José S

    2015-11-10

    A statistical-mechanical framework for estimation of solvation entropies and enthalpies is proposed, which is based on the analysis of water as a mixture of correlated water oxygens and water hydrogens. Entropic contributions of increasing order are cast in terms of a Mutual Information Expansion that is evaluated to pairwise interactions. In turn, the enthalpy is computed directly from a distance-based hydrogen bonding energy algorithm. The resulting expressions are employed for grid-based analyses of Molecular Dynamics simulations. In this first assessment of the methodology, we obtained global estimates of the excess entropy and enthalpy of water that are in good agreement with experiment and examined the method's ability to enable detailed elucidation of solvation thermodynamic structures, which can provide valuable knowledge toward molecular design.

  2. Probing micro-solvation in "numbers": the case of neutral dipeptides in water.

    Science.gov (United States)

    Takis, Panteleimon G; Papavasileiou, Konstantinos D; Peristeras, Loukas D; Melissas, Vasilios S; Troganis, Anastassios N

    2013-05-21

    How many solvent molecules and in what way do they interact directly with biomolecules? This is one of the most challenging questions regarding a deep understanding of biomolecular functionalism and solvation. We herein present a novel NMR spectroscopic study, achieving for the first time the quantification of the directly interacting water molecules with several neutral dipeptides. Our proposed method is supported by both molecular dynamics simulations and density functional theory calculations, advanced analysis of which allowed the identification of the direct interactions between solute-solvent molecules in the zwitterionic L-alanyl-L-alanine dipeptide-water system. Beyond the quantification of dipeptide-water molecule direct interactions, this NMR technique could be useful for the determination and elucidation of small to moderate bio-organic molecular groups' direct interactions with various polar solvent molecules, shedding light on the biomolecular micro-solvation processes and behaviour in various solvents.

  3. Coordination chemistry strategies for dynamic helicates: time-programmable chirality switching with labile and inert metal helicates.

    Science.gov (United States)

    Miyake, Hiroyuki; Tsukube, Hiroshi

    2012-11-01

    'Chirality switching' is one of the most important chemical processes controlling many biological systems. DNAs and proteins often work as time-programmed functional helices, in which specific external stimuli alter the helical direction and tune the time scale of subsequent events. Although a variety of organic foldamers and their hybrids with natural helices have been developed, we highlight coordination chemistry strategies for development of structurally and functionally defined metal helicates. These metal helicates have characteristic coordination geometries, redox reactivities and spectroscopic/magnetic properties as well as complex chiralities. Several kinds of inert metal helicates maintain rigid helical structures and their stereoisomers are separable by optical resolution techniques, while labile metal helicates offer dynamic inversion of their helical structures via non-covalent interactions with external chemical signals. The latter particularly have dynamically ordered helical structures, which are controlled by the combinations of metal centres and chiral ligands. They further function as time-programmable switches of chirality-derived dynamic rotations, translations, stretching and shape flipping, which are useful applications in nanoscience and related technology.

  4. Synthesis of a Two-Dimensional Covalent Organic Monolayer through Dynamic Imine Chemistry at the Air/Water Interface.

    Science.gov (United States)

    Dai, Wenyang; Shao, Feng; Szczerbiński, Jacek; McCaffrey, Ryan; Zenobi, Renato; Jin, Yinghua; Schlüter, A Dieter; Zhang, Wei

    2016-01-01

    A two-dimensional covalent organic monolayer was synthesized from simple aromatic triamine and dialdehyde building blocks by dynamic imine chemistry at the air/water interface (Langmuir-Blodgett method). The obtained monolayer was characterized by optical microscopy, scanning electron microscopy, and atomic force microscopy, which unambiguously confirmed the formation of a large (millimeter range), unimolecularly thin aromatic polyimine sheet. The imine-linked chemical structure of the obtained monolayer was characterized by tip-enhanced Raman spectroscopy, and the peak assignment was supported by spectra simulated by density functional theory. Given the modular nature and broad substrate scope of imine formation, the work reported herein opens up many new possibilities for the synthesis of customizable 2D polymers and systematic studies of their structure-property relationships.

  5. Lithium ion solvation by ethylene carbonates in lithium-ion battery electrolytes, revisited by density functional theory with the hybrid solvation model and free energy correction in solution.

    Science.gov (United States)

    Cui, Wei; Lansac, Yves; Lee, Hochun; Hong, Seung-Tae; Jang, Yun Hee

    2016-09-14

    Complex formation between lithium (Li(+)) ions and electrolyte molecules would affect the ionic conductivity through the electrolyte in lithium-ion batteries (LIBs). We hence revisit the solvation number of Li(+) in the most commonly used ethylene carbonate (EC) electrolyte. The solvation number n of Li(+)(EC)n in the first solvation shell of Li(+) is estimated on the basis of the free energy calculated by the density functional theory combined with a hybrid solvation model where the explicit solvation shell of Li(+) is immersed in a free volume of an implicit bulk solvent. This new hybrid solvation (implicit and explicit) model predicts the most probable solvation number (n = 4) and solvation free energy (-91.3 kcal mol(-1)) of Li(+) in a good agreement with those predicted by calculations employing simpler solvation models (either implicit or explicit). The desolvation (n = 2) of Li(0)(EC)n upon reduction near anodes is also well described with this new hybrid model.

  6. Aqueous solvation of amphiphilic molecules by extended depolarized light scattering: the case of trimethylamine-N-oxide.

    Science.gov (United States)

    Comez, L; Paolantoni, M; Corezzi, S; Lupi, L; Sassi, P; Morresi, A; Fioretto, D

    2016-04-01

    Hydrophilic and hydrophobic interactions strongly affect the solvation dynamics of biomolecules. To understand their role, small model systems are generally employed to simplify the investigations. In this study the amphiphile trimethylamine N-oxide (TMAO) is chosen as an exemplar, and studied by means of extended frequency range depolarized light scattering (EDLS) experiments as a function of solute concentration. This technique proves to be a suitable tool for investigating different aspects of aqueous solvation, being able at the same time to provide information about relaxation processes and vibrational modes of solvent and solute. In the case study of TMAO, we find that the relaxation dynamics of hydration water is moderately retarded compared to the bulk, and the perturbation induced by the solute on surrounding water is confined to the first hydration shell. The results highlight the hydrophobic character of TMAO in its interaction with water. The number of molecules taking part in the solvation process decreases as the solute concentration increases, following a trend consistent with the hydration water-sharing model, and suggesting that aggregation between solute molecules is negligible. Finally, the analysis of the resonant modes in the THz region and the comparison with the corresponding results obtained for the isosteric molecule tert-butyl alcohol (TBA) allow us to provide new insights into the different solvating properties of these two biologically relevant molecules. PMID:26958663

  7. 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)

  8. 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...

  9. The impact of stratospheric dynamics and chemistry on northern hemisphere mid-latitude ozone loss

    Energy Technology Data Exchange (ETDEWEB)

    Grewe, V.; Dameris, M.; Sausen, R.

    1997-07-03

    The importance of stratospheric dynamics for the stratospheric ozone distribution in the Northern Hemisphere is investigated using multi-annual simulations of the coupled dynamic-chemical general circulation model ECHAM3/CHEM. This model includes a parameterization for heterogeneous reactions on polar stratospheric clouds (PSC) and on sulphate aerosols. A warm and a cold stratospheric winter are examined to estimate the range of chemical ozone loss due to heterogeneous reactions on PSCs. Ozone depletion in the model mainly occurs inside the polar vortex. An additional ozone reduction due to heterogeneous reactions on PSCs is found as well outside the polar vortex. Secondary vortex formation and vortex contraction after an elongation lead to a transport of airmasses with chemically reduced ozone values out of the vortex. Except for such events, the edge of the modelled polar vortex acts as a barrier to transport. During the formation of secondary vortices no additional heterogeneous reactions occur therein. Other dynamic events like the elongation of the polar vortex and its displacement to lower latitudes lead to an intense ozone depletion. A modelled minor stratospheric warming causes a total deactivation of chlorine components and prevents further ozone depletion. In midlatitudes, the amplitude of short-term variations of total ozone is amplified by PSC heterogeneous chemical ozone reduction. (orig.) 27 refs.

  10. 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

    2016-01-01

    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. PMID:27498703

  11. 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.

  12. 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)

  13. 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...

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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.

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

    Science.gov (United States)

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

    2011-09-18

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-06-07

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

  1. 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.

  2. Plume and wake dynamics, mixing, and chemistry behind an HSCT aircraft

    Science.gov (United States)

    Miake-Lye, R. C.; Martinez-Sanchez, M.; Brown, R. C.; Kolb, C. E.

    1991-01-01

    The chemical evolution and mixing and vortical motion of a High Speed Civil Transport's engine exhausts must be analyzed in order to track the gas and its speciation as emissions are mixed to atmospheric scales. Attention is presently given to an analytic model of the wake dynamical processes which accounts for the roll-up of the trailing vorticity, its breakup due to the Crow instability, and the subsequent evolution and motion of the reconnected vorticity. The concentrated vorticity is noted to wrap up the buoyant exhaust and suppress its continued mixing and dilution. The species tracked encompass those which could be heterogeneously reactive on the surfaces of the condensed ice particles, and those capable of reacting with exhaust soot particle surfaces to form active contrail and/or cloud condensation nuclei.

  3. Water-enhanced solvation of organics

    Energy Technology Data Exchange (ETDEWEB)

    Lee, J.H.

    1993-07-01

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

  4. Design, synthesis, physicochemical studies, solvation, and DNA damage of quinoline-appended chalcone derivative: comprehensive spectroscopic approach toward drug discovery.

    Science.gov (United States)

    Kumar, Himank; Chattopadhyay, Anjan; Prasath, R; Devaraji, Vinod; Joshi, Ritika; Bhavana, P; Saini, Praveen; Ghosh, Sujit Kumar

    2014-07-01

    The present study epitomizes the design, synthesis, photophysics, solvation, and interaction with calf-thymus DNA of a potential antitumor, anticancer quinoline-appended chalcone derivative, (E)-3-(anthracen-10-yl)-1-(6,8-dibromo-2-methylquinolin-3-yl)prop-2-en-1-one (ADMQ) using steady state absorption and fluorescence spectroscopy, molecular modeling, molecular docking, Fourier-transform infrared spectroscopy (FTIR), molecular dynamics (MD) simulation, and gel electrophoresis studies. ADMQ shows an unusual photophysical behavior in a variety of solvents of different polarity. The dual emission has been observed along with the formation of twisted intramolecular charge transfer (TICT) excited state. The radiationless deactivation of the TICT state is found to be promoted strongly by hydrogen bonding. Quantum mechanical (DFT, TDDFT, and ZINDO-CI) calculations show that the ADMQ is sort of molecular rotor which undergoes intramolecular twist followed by a complete charge transfer in the optimized excited state. FTIR studies reveals that ADMQ undergoes important structural change from its native structure to a β-hydroxy keto form in water at physiological pH. The concentration-dependent DNA cleavage has been identified in agarose gel DNA electrophoresis experiment and has been further supported by MD simulation. ADMQ forms hydrogen bond with the deoxyribose sugar attached with the nucleobase adenine DA-17 (chain A) and result in significant structural changes which potentially cleave DNA double helix. The compound does not exhibit any deleterious effect or toxicity to the E. coli strain in cytotoxicity studies. The consolidated spectroscopic research described herein can provide enormous information to open up new avenues for designing and synthesizing chalcone derivatives with low systematic toxicity for medicinal chemistry research.

  5. 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

    2016-03-21

    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.

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

    Science.gov (United States)

    Chen, Zhan; Wei, Guo-Wei

    2011-11-21

    Solvation is of fundamental importance to biomolecular systems. Implicit solvent models, particularly those based on the Poisson-Boltzmann equation for electrostatic analysis, are established approaches for solvation analysis. However, ad hoc solvent-solute interfaces are commonly used in the implicit solvent theory. Recently, we have introduced differential geometry based solvation models which allow the solvent-solute interface to be determined by the variation of a total free energy functional. Atomic fixed partial charges (point charges) are used in our earlier models, which depends on existing molecular mechanical force field software packages for partial charge assignments. As most force field models are parameterized for a certain class of molecules or materials, the use of partial charges limits the accuracy and applicability of our earlier models. Moreover, fixed partial charges do not account for the charge rearrangement during the solvation process. The present work proposes a differential geometry based multiscale solvation model which makes use of the electron density computed directly from the quantum mechanical principle. To this end, we construct a new multiscale total energy functional which consists of not only polar and nonpolar solvation contributions, but also the electronic kinetic and potential energies. By using the Euler-Lagrange variation, we derive a system of three coupled governing equations, i.e., the generalized Poisson-Boltzmann equation for the electrostatic potential, the generalized Laplace-Beltrami equation for the solvent-solute boundary, and the Kohn-Sham equations for the electronic structure. We develop an iterative procedure to solve three coupled equations and to minimize the solvation free energy. The present multiscale model is numerically validated for its stability, consistency and accuracy, and is applied to a few sets of molecules, including a case which is difficult for existing solvation models. Comparison is made

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

    CERN Document Server

    Dodson-Robinson, Sarah E

    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 their formation in solid-rich feeding zones with planetesimal surface densities well above the minimum-mass solar nebula. We present new simulations of the formation of Uranus and Neptune in the solid-rich disk of Dodson-Robinson et al. (2009) using the initial semimajor axis distribution of the Nice model (Gomes et al. 2005; Morbidelli et al. 2005; Tsiganis et al. 2005), with one ice giant forming at 12 AU and the other at 15 AU. The innermost ice giant reaches its present mass after 3.8-4.0 Myr and the outermost after 5....

  8. 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.

  9. Chemistry and Molecular Dynamics Simulations of Heme b-HemQ and Coproheme-HemQ.

    Science.gov (United States)

    Hofbauer, Stefan; Dalla Sega, Marco; Scheiblbrandner, Stefan; Jandova, Zuzana; Schaffner, Irene; Mlynek, Georg; Djinović-Carugo, Kristina; Battistuzzi, Gianantonio; Furtmüller, Paul G; Oostenbrink, Chris; Obinger, Christian

    2016-09-27

    Recently, a novel pathway for heme b biosynthesis in Gram-positive bacteria has been proposed. The final poorly understood step is catalyzed by an enzyme called HemQ and includes two decarboxylation reactions leading from coproheme to heme b. Coproheme has been suggested to act as both substrate and redox active cofactor in this reaction. In the study presented here, we focus on HemQs from Listeria monocytogenes (LmHemQ) and Staphylococcus aureus (SaHemQ) recombinantly produced as apoproteins in Escherichia coli. We demonstrate the rapid and two-phase uptake of coproheme by both apo forms and the significant differences in thermal stability of the apo forms, coproheme-HemQ and heme b-HemQ. Reduction of ferric high-spin coproheme-HemQ to the ferrous form is shown to be enthalpically favored but entropically disfavored with standard reduction potentials of -205 ± 3 mV for LmHemQ and -207 ± 3 mV for SaHemQ versus the standard hydrogen electrode at pH 7.0. Redox thermodynamics suggests the presence of a pronounced H-bonding network and restricted solvent mobility in the heme cavity. Binding of cyanide to the sixth coproheme position is monophasic but relatively slow (∼1 × 10(4) M(-1) s(-1)). On the basis of the available structures of apo-HemQ and modeling of both loaded forms, molecular dynamics simulation allowed analysis of the interaction of coproheme and heme b with the protein as well as the role of the flexibility at the proximal heme cavity and the substrate access channel for coproheme binding and heme b release. Obtained data are discussed with respect to the proposed function of HemQ in monoderm bacteria.

  10. Chemistry and Molecular Dynamics Simulations of Heme b-HemQ and Coproheme-HemQ

    Science.gov (United States)

    2016-01-01

    Recently, a novel pathway for heme b biosynthesis in Gram-positive bacteria has been proposed. The final poorly understood step is catalyzed by an enzyme called HemQ and includes two decarboxylation reactions leading from coproheme to heme b. Coproheme has been suggested to act as both substrate and redox active cofactor in this reaction. In the study presented here, we focus on HemQs from Listeria monocytogenes (LmHemQ) and Staphylococcus aureus (SaHemQ) recombinantly produced as apoproteins in Escherichia coli. We demonstrate the rapid and two-phase uptake of coproheme by both apo forms and the significant differences in thermal stability of the apo forms, coproheme-HemQ and heme b-HemQ. Reduction of ferric high-spin coproheme-HemQ to the ferrous form is shown to be enthalpically favored but entropically disfavored with standard reduction potentials of −205 ± 3 mV for LmHemQ and −207 ± 3 mV for SaHemQ versus the standard hydrogen electrode at pH 7.0. Redox thermodynamics suggests the presence of a pronounced H-bonding network and restricted solvent mobility in the heme cavity. Binding of cyanide to the sixth coproheme position is monophasic but relatively slow (∼1 × 104 M–1 s–1). On the basis of the available structures of apo-HemQ and modeling of both loaded forms, molecular dynamics simulation allowed analysis of the interaction of coproheme and heme b with the protein as well as the role of the flexibility at the proximal heme cavity and the substrate access channel for coproheme binding and heme b release. Obtained data are discussed with respect to the proposed function of HemQ in monoderm bacteria. PMID:27599156

  11. Modelling non-equilibrium secondary organic aerosol formation and evaporation with the aerosol dynamics, gas- and particle-phase chemistry kinetic multilayer model ADCHAM

    Energy Technology Data Exchange (ETDEWEB)

    Roldin, P.; Eriksson, A. C.; Nordin, E. Z.; Hermansson, E.; Mogensen, Ditte; Rusanen, A.; Boy, Michael; Swietlicki, E.; Svenningsson, Birgitta; Zelenyuk, Alla; Pagels, J.

    2014-08-11

    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.

  12. Preferential solvation of lysozyme in dimethyl sulfoxide/water binary mixture probed by terahertz spectroscopy.

    Science.gov (United States)

    Das, Dipak Kumar; Patra, Animesh; Mitra, Rajib Kumar

    2016-09-01

    We report the changes in the hydration dynamics around a model protein hen egg white lysozyme (HEWL) in water-dimethyl sulfoxide (DMSO) binary mixture using THz time domain spectroscopy (TTDS) technique. DMSO molecules get preferentially solvated at the protein surface, as indicated by circular dichroism (CD) and Fourier transform infrared (FTIR) study in the mid-infrared region, resulting in a conformational change in the protein, which consequently modifies the associated hydration dynamics. As a control we also study the collective hydration dynamics of water-DMSO binary mixture and it is found that it follows a non-ideal behavior owing to the formation of DMSO-water clusters. It is observed that the cooperative dynamics of water at the protein surface does follow the DMSO-mediated conformational modulation of the protein. PMID:27372901

  13. 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.

  14. 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.

  15. 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)

  16. 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)

  17. Biological soil crusts on initial soils: organic carbon dynamics and chemistry under temperate climatic conditions

    Directory of Open Access Journals (Sweden)

    A. Dümig

    2013-01-01

    Full Text Available Numerous studies have been carried out on the community structure and diversity of biological soil crusts (BSCs as well as their important functions on ecosystem processes. However, the amount of BSC-derived organic carbon (OC input into soils and its chemical composition under natural conditions has rarely been investigated. In this study, different development stages of algae- and moss-dominated BSCs were investigated on a~natural (<17 yr old BSCs and experimental sand dune (<4 yr old BSCs in northeastern Germany. We determined the OC accumulation in BSC-layers and the BSC-derived OC input into the underlying substrates for bulk materials and fractions <63 μm. The chemical composition of OC was characterized by applying solid-state 13C NMR spectroscopy and analysis of the carbohydrate-C signature.14C contents were used to assess the origin and dynamic of OC in BSCs and underlying substrates. Our results indicated a rapid BSC establishment and development from algae- to moss-dominated BSCs within only 4 yr under this temperate climate. The distribution of BSC types was presumably controlled by the surface stability according to the position in the slope. We found no evidence that soil properties influenced the BSC distribution on both sand dunes. 14C contents clearly indicated the existence of two OC pools in BSCs and substrates, recent BSC-derived OC and lignite-derived "old" OC (biologically refractory. The input of recent BSC-derived OC strongly decreased the mean residence time of total OC. The downward translocation of OC into the underlying substrates was only found for moss-dominated BSCs at the natural sand dune which may accelerate soil formation at these spots. BSC-derived OC mainly comprised O-alkyl C (carbohydrate-C and to a lesser extent also alkyl C and N-alkyl C in varying compositions. Accumulation of alkyl C was only detected in BSCs at the experimental dune which may induce a~lower water

  18. 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

  19. 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

  20. 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.

  1. 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

  2. Structure and solvation forces in confined films: Linear and branched alkanes

    Energy Technology Data Exchange (ETDEWEB)

    Gao, J.; Luedtke, W.D.; Landman, U. [School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States)

    1997-03-01

    Equilibrium structures, solvation forces, and conformational dynamics of thin confined films of n-hexadecane and squalane are investigated using a new grand canonical ensemble molecular dynamics method for simulations of confined liquids. The method combines constant pressure simulations with a computational cell containing solid surfaces and both bulk and confined liquid regions in equilibrium with each other. Layered density oscillations in the confined films are found for various widths of the confining gap. The solvation force oscillations as a function of the gap width for the straight chain n-hexadecane liquid are more pronounced exhibiting attractive and repulsive regions, while for the branched alkane the solvation forces are mostly repulsive, with the development of shallow local attractive regions for small values of the gap width. Furthermore, the nature of the transitions between well-formed layered configurations is different in the two systems. The n-hexadecane film exhibits solid-like characteristics portrayed by step-like variations in the number of confined segments occurring in response to a small decrease in the gap width, starting from well-layered states of the film; the behavior of the squalane film is liquid-like, exhibiting a monotonic continuous decrease in the number of confined segments as the gap width is decreased. These characteristics are correlated with structural properties of the confined films which, for n-hexadecane, exhibit enhanced layered ordering and in-plane ordered molecular arrangements, as well as with the relatively high tendency for interlayer molecular interdigitation in the squalane films. Reduced conformational (trans-guache) transition rates in the confined films, compared to their bulk values, are found, and their oscillatory dependence on the degree of confinement is analyzed, showing smaller transition rates for the well-formed layered states of the films. {copyright} {ital 1997 American Institute of Physics.}

  3. 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

  4. 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

  5. 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

  6. 2D and 3D Eulerian Simulations of the Dynamics and Gas and Aerosol Chemistry of a Young Biomass Burning Smoke Plume from a Savannah Fire

    Science.gov (United States)

    Alvarado, M. J.; Prinn, R. G.

    2007-12-01

    The growth of aerosol particles and production of ozone in young smoke plumes is the result of a complex interaction between the mean flow in the smoke plume, turbulent diffusion, gas-phase oxidation, coagulation, and mass transfer between phases. Models allow us to separate the effects of these processes and predict their impact on the global environment. We present the results of two and three-dimensional Eulerian simulations of the dynamics and chemistry of the smoke plume formed by the Timbavati savannah fire studied during SAFARI 2000 (Hobbs et al., 2003, JGR, doi:10.1029/2002JD002352). The dynamical model is an extension of an Eulerian cloud-resolving model that has previously been used to study the role of deep convective clouds on tropospheric chemistry (Wang and Prinn, 2000, JGR, 105(D17) 22,269-22,297). The model includes a source of sensible heat, gases, and particles at the surface to simulate the savannah fire. The new gas and aerosol chemistry model includes heterogeneous chemistry, kinetic mass transfer, coagulation and the formation of secondary organic and inorganic aerosol. Photolysis rates are calculated based on the solution of the radiative transfer equation within the plume, including the scattering and absorption of radiation by the smoke aerosols. Our preliminary 2D Eulerian results using standard chemistry and UV fluxes show that the model can simulate the lower but not the higher levels of O3 observed. Also, the simulated 2D O3 field shows a wave-like pattern in the downwind direction, even though the emissions from the fire are held constant. This suggests that plume heterogeneity in the downwind direction may account for some of the observed variability in O3. We will present results of runs incorporating higher resolution calculation of photolysis rates, heterogeneous HONO formation, and gas phase reactions involving the uncharacterized organic compounds observed in the gas phase of the Timbavati plume in order to better simulate these

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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).

  13. 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.

  14. 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.

  15. Spatially Resolved Artificial Chemistry

    DEFF Research Database (Denmark)

    Fellermann, Harold

    2009-01-01

    Although spatial structures can play a crucial role in chemical systems and can drastically alter the outcome of reactions, the traditional framework of artificial chemistry is a well-stirred tank reactor with no spatial representation in mind. Advanced method development in physical chemistry has...... 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...

  16. 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.

  17. Heterogeneous chemistry and reaction dynamics of the atmospheric oxidants, O3, NO3, and OH, on organic surfaces.

    Science.gov (United States)

    Chapleski, Robert C; Zhang, Yafen; Troya, Diego; Morris, John R

    2016-07-01

    Heterogeneous chemistry of the most important atmospheric oxidants, O3, NO3, and OH, plays a central role in regulating atmospheric gas concentrations, processing aerosols, and aging materials. Recent experimental and computational studies have begun to reveal the detailed reaction mechanisms and kinetics for gas-phase O3, NO3, and OH when they impinge on organic surfaces. Through new research approaches that merge the fields of traditional surface science with atmospheric chemistry, researchers are developing an understanding for how surface structure and functionality affect interfacial chemistry with this class of highly oxidizing pollutants. Together with future research initiatives, these studies will provide a more complete description of atmospheric chemistry and help others more accurately predict the properties of aerosols, the environmental impact of interfacial oxidation, and the concentrations of tropospheric gases.

  18. 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...

  19. Solvated electrons formed in methanol cluster in ethane

    Energy Technology Data Exchange (ETDEWEB)

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

    2000-03-09

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

  20. 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

  1. Differential geometry based solvation model II: Lagrangian formulation.

    Science.gov (United States)

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

    2011-12-01

    Solvation is an elementary process in nature and is of paramount importance to more sophisticated chemical, biological and biomolecular processes. The understanding of solvation is an essential prerequisite for the quantitative description and analysis of biomolecular systems. This work presents a Lagrangian formulation of our differential geometry based solvation models. The Lagrangian representation of biomolecular surfaces has a few utilities/advantages. First, it provides an essential basis for biomolecular visualization, surface electrostatic potential map and visual perception of biomolecules. Additionally, it is consistent with the conventional setting of implicit solvent theories and thus, many existing theoretical algorithms and computational software packages can be directly employed. Finally, the Lagrangian representation does not need to resort to artificially enlarged van der Waals radii as often required by the Eulerian representation in solvation analysis. The main goal of the present work is to analyze the connection, similarity and difference between the Eulerian and Lagrangian formalisms of the solvation model. Such analysis is important to the understanding of the differential geometry based solvation model. The present model extends the scaled particle theory of nonpolar solvation model with a solvent-solute interaction potential. The nonpolar solvation model is completed with a Poisson-Boltzmann (PB) theory based polar solvation model. The differential geometry theory of surfaces is employed to provide a natural description of solvent-solute interfaces. The optimization of the total free energy functional, which encompasses the polar and nonpolar contributions, leads to coupled potential driven geometric flow and PB equations. Due to the development of singularities and nonsmooth manifolds in the Lagrangian representation, the resulting potential-driven geometric flow equation is embedded into the Eulerian representation for the purpose of

  2. Air plasma treatment of liquid covered tissue: long timescale chemistry

    Science.gov (United States)

    Lietz, Amanda M.; Kushner, Mark J.

    2016-10-01

    Atmospheric pressure plasmas have shown great promise for the treatment of wounds and cancerous tumors. In these applications, the sample is usually covered by a thin layer of a biological liquid. The reactive oxygen and nitrogen species (RONS) generated by the plasma activate and are processed by the liquid before the plasma produced activation reaches the tissue. The synergy between the plasma and the liquid, including evaporation and the solvation of ions and neutrals, is critical to understanding the outcome of plasma treatment. The atmospheric pressure plasma sources used in these procedures are typically repetitively pulsed. The processes activated by the plasma sources have multiple timescales—from a few ns during the discharge pulse to many minutes for reactions in the liquid. In this paper we discuss results from a computational investigation of plasma-liquid interactions and liquid phase chemistry using a global model with the goal of addressing this large dynamic range in timescales. In modeling air plasmas produced by a dielectric barrier discharge over liquid covered tissue, 5000 voltage pulses were simulated, followed by 5 min of afterglow. Due to the accumulation of long-lived species such as ozone and N x O y , the gas phase dynamics of the 5000th discharge pulse are different from those of the first pulse, particularly with regards to the negative ions. The consequences of applied voltage, gas flow, pulse repetition frequency, and the presence of organic molecules in the liquid on the gas and liquid reactive species are discussed.

  3. Dynamical amplification of the stratospheric solar response simulated with the Chemistry-Climate Model LMDz-Reprobus

    Science.gov (United States)

    Marchand, M.; Keckhut, P.; Lefebvre, S.; Claud, C.; Cugnet, D.; Hauchecorne, A.; Lefèvre, F.; Lefebvre, M.-P.; Jumelet, J.; Lott, F.; Hourdin, F.; Thuillier, G.; Poulain, V.; Bossay, S.; Lemennais, P.; David, C.; Bekki, S.

    2012-02-01

    The impact of the 11-year solar cycle on the stratosphere and, in particular, on the polar regions is investigated using simulations from the Chemistry Climate Model (CCM) LMDz-Reprobus. The annual solar signal clearly shows a stratospheric response largely driven by radiative and photochemical processes, especially in the upper stratosphere. A month-by-months analysis suggests that dynamical feedbacks play an important role in driving the stratospheric response on short timescales. CCM outputs on a 10 days frequency indicate how, in the northern hemisphere, changes in solar heating in the winter polar stratosphere may influence the upward propagation of planetary waves and thus their deposition of momentum, ultimately modifying the strength of the mean stratospheric overtuning circulation at middle and high latitudes. The model results emphasize that the main temperature and wind responses in the northern hemisphere can be explained by a different timing in the occurrence of Sudden Stratospheric Warmings (SSWs) that are caused by small changes in planetary wave propagation depending on solar conditions. The differences between simulations forced by different solar conditions indicate successive positive and negative responses during the course of the winter. The solar minimum simulation generally indicates a slightly stronger polar vortex early in the winter while the solar maximum simulation experiences more early SSWs with a stronger wave-mean flow interaction and reduced zonal wind at mid-latitudes in the upper stratosphere. The opposite response is observed during mid-winter, in February, with more SSWs simulated for solar minimum conditions while solar maximum conditions are associated with a damped planetary wave activity and a reinforced vortex after the initial stratospheric warming period. In late winter, the response is again reversed, as noticed in the temperature differences, with major SSW mostly observed in the solar maximum simulation and less

  4. Biomolecular solvation study of proteins in liquid water by a wide range gigahertz-to-terahertz spectroscopy

    Science.gov (United States)

    Charkhesht, Ali; George, Deepu; Nguyen, Vinh

    Solvent dynamics within biomolecular solvation layers play a major role in enzyme activity, but obtaining an accurate and quantitative picture of solvent activity around proteins is challenging. Due to the strong absorption of water in the gigahertz-to-terahertz frequencies, it is challenging to study properties of the solvent dynamics as well as conformational changes protein in water. We have developed a highly sensitive dielectric gigahertz-to-terahertz frequency-domain spectroscopy system for probing the collective dynamics of proteins and solvent. Using this technique, we investigate the complex dielectric response of bovine serum albumin and lysozyme proteins in aqueous environment on a wide frequency range from 0.1 GHz up to 2 THz. We explore the conformation flexibility of proteins and compare the hydration dynamics around proteins to understand the effects of surface-mediated solvent dynamics, relationships among different measures of interfacial solvent dynamics, and protein-mediated solvent dynamics.

  5. 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.

  6. 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.

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

    Science.gov (United States)

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

    2016-06-01

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

  8. 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...

  9. Lithium ion solvation by ethylene carbonates in lithium-ion battery electrolytes, revisited by density functional theory with the hybrid solvation model and free energy correction in solution.

    Science.gov (United States)

    Cui, Wei; Lansac, Yves; Lee, Hochun; Hong, Seung-Tae; Jang, Yun Hee

    2016-09-14

    Complex formation between lithium (Li(+)) ions and electrolyte molecules would affect the ionic conductivity through the electrolyte in lithium-ion batteries (LIBs). We hence revisit the solvation number of Li(+) in the most commonly used ethylene carbonate (EC) electrolyte. The solvation number n of Li(+)(EC)n in the first solvation shell of Li(+) is estimated on the basis of the free energy calculated by the density functional theory combined with a hybrid solvation model where the explicit solvation shell of Li(+) is immersed in a free volume of an implicit bulk solvent. This new hybrid solvation (implicit and explicit) model predicts the most probable solvation number (n = 4) and solvation free energy (-91.3 kcal mol(-1)) of Li(+) in a good agreement with those predicted by calculations employing simpler solvation models (either implicit or explicit). The desolvation (n = 2) of Li(0)(EC)n upon reduction near anodes is also well described with this new hybrid model. PMID:27506245

  10. 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.

  11. 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...

  12. Effects of solvation shells and cluster size on the reaction of aluminum clusters with water

    Directory of Open Access Journals (Sweden)

    Weiwei Mou

    2011-12-01

    Full Text Available Reaction of aluminum clusters, Aln (n = 16, 17 and 18, with liquid water is investigated using quantum molecular dynamics simulations, which show rapid production of hydrogen molecules assisted by proton transfer along a chain of hydrogen bonds (H-bonds between water molecules, i.e. Grotthuss mechanism. The simulation results provide answers to two unsolved questions: (1 What is the role of a solvation shell formed by non-reacting H-bonds surrounding the H-bond chain; and (2 whether the high size-selectivity observed in gas-phase Aln-water reaction persists in liquid phase? First, the solvation shell is found to play a crucial role in facilitating proton transfer and hence H2 production. Namely, it greatly modifies the energy barrier, generally to much lower values (< 0.1 eV. Second, we find that H2 production by Aln in liquid water does not depend strongly on the cluster size, in contrast to the existence of magic numbers in gas-phase reaction. This paper elucidates atomistic mechanisms underlying these observations.

  13. 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...

  14. 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…

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

    Science.gov (United States)

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

    2013-09-12

    (211)At radionuclide is of considerable interest as a radiotherapeutic agent for targeted alpha therapy in nuclear medicine, but major obstacles remain because the basic chemistry of astatine (At) is not well understood. The AtO(+) cationic form might be currently used for (211)At-labeling protocols in aqueous solution and has proved to readily react with inorganic/organic ligands. But AtO(+) reactivity must be hindered at first glance by spin restriction quantum rules: the ground state of the free cation has a dominant triplet character. Investigating AtO(+) clustered with an increasing number of water molecules and using various flavors of relativistic quantum methods, we found that AtO(+) adopts in solution a Kramers restricted closed-shell configuration resembling a scalar-relativistic singlet. The ground-state change was traced back to strong interactions, namely, attractive electrostatic interactions and charge transfer, with water molecules of the first solvation shell that lift up the degeneracy of the frontier π* molecular orbitals (MOs). This peculiarity brings an alternative explanation to the highly variable reproducibility reported for some astatine reactions: depending on the production protocols (with distillation in gas-phase or "wet chemistry" extraction), (211)At may or may not readily react. PMID:23944251

  16. 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.

  17. 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

  18. In silico insights into the solvation characteristics of the ionic liquid 1-methyltriethoxy-3-ethylimidazolium acetate for cellulosic biomass.

    Science.gov (United States)

    Schutt, Timothy C; Bharadwaj, Vivek S; Hegde, Govind A; Johns, Adam J; Mark Maupin, C

    2016-09-14

    Lignocellulosic biomass is a domestically grown, sustainable, and potentially carbon-neutral feedstock for the production of liquid fuels and other value added chemicals. This underutilized renewable feedstock has the potential to alleviate some of the current socio-economic dependence on foreign petroleum supplies while stimulating rural economies. Unfortunately, the potential of biomass has largely been underdeveloped due to the recalcitrant nature of lignocellulosic materials. Task-specific ionic liquids (ILs) have shown considerable promise as an alternative non-aqueous solvent for solvation and deconstruction of lignocellulose in the presence of metal chloride catalyst or enzymes. Recently it has been hypothesized that adding oxygen atoms to the tail of an imidazolium cation would alleviate some of the negative characteristics of the ILs by increasing mass transport properties, and decreasing IL deactivation of enzymes, while at the same time retaining favorable solvation characteristics for lignocellulose. Reported here are fully atomistic molecular dynamic simulations of 1-methyltriethoxy-3-ethylimidazolium acetate ([Me-(OEt)3-Et-IM(+)] [OAc(-)]) that elucidate promising molecular-level details pertaining to the solvation characteristics of model compounds of cellulose, and IL-induced side-chain and ring puckering conformations. It is found that the anion interactions with the saccharide induce alternate ring puckering conformations from those seen in aqueous environments (i.e.(1)C4), while the cation interactions are found to influence the conformation of the ω dihedral. These perturbations in saccharide structures are discussed in the context of their contribution to the disruption of hydrogen bonding in cellulosic architecture and their role in solvation. PMID:27510272

  19. In silico insights into the solvation characteristics of the ionic liquid 1-methyltriethoxy-3-ethylimidazolium acetate for cellulosic biomass.

    Science.gov (United States)

    Schutt, Timothy C; Bharadwaj, Vivek S; Hegde, Govind A; Johns, Adam J; Mark Maupin, C

    2016-09-14

    Lignocellulosic biomass is a domestically grown, sustainable, and potentially carbon-neutral feedstock for the production of liquid fuels and other value added chemicals. This underutilized renewable feedstock has the potential to alleviate some of the current socio-economic dependence on foreign petroleum supplies while stimulating rural economies. Unfortunately, the potential of biomass has largely been underdeveloped due to the recalcitrant nature of lignocellulosic materials. Task-specific ionic liquids (ILs) have shown considerable promise as an alternative non-aqueous solvent for solvation and deconstruction of lignocellulose in the presence of metal chloride catalyst or enzymes. Recently it has been hypothesized that adding oxygen atoms to the tail of an imidazolium cation would alleviate some of the negative characteristics of the ILs by increasing mass transport properties, and decreasing IL deactivation of enzymes, while at the same time retaining favorable solvation characteristics for lignocellulose. Reported here are fully atomistic molecular dynamic simulations of 1-methyltriethoxy-3-ethylimidazolium acetate ([Me-(OEt)3-Et-IM(+)] [OAc(-)]) that elucidate promising molecular-level details pertaining to the solvation characteristics of model compounds of cellulose, and IL-induced side-chain and ring puckering conformations. It is found that the anion interactions with the saccharide induce alternate ring puckering conformations from those seen in aqueous environments (i.e.(1)C4), while the cation interactions are found to influence the conformation of the ω dihedral. These perturbations in saccharide structures are discussed in the context of their contribution to the disruption of hydrogen bonding in cellulosic architecture and their role in solvation.

  20. 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.

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

    Science.gov (United States)

    Rinne, Klaus F.; Gekle, Stephan; Netz, Roland R.

    2014-12-01

    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.

  2. 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

  3. 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

  4. Chemistry Notes

    Science.gov (United States)

    School Science Review, 1976

    1976-01-01

    Described are eight chemistry experiments and demonstrations applicable to introductory chemistry courses. Activities include: measure of lattice enthalpy, Le Chatelier's principle, decarboxylation of soap, use of pocket calculators in pH measurement, and making nylon. (SL)

  5. Colour Chemistry

    Science.gov (United States)

    Griffiths, J.; Rattee, I. D.

    1973-01-01

    Discusses the course offerings in pure color chemistry at two universities and the three main aspects of study: dyestuff chemistry, color measurement, and color application. Indicates that there exists a constant challenge to ingenuity in the subject discipline. (CC)

  6. 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 ...

  7. 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

  8. 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....

  9. Crystal Growth, Structure and Morphology of Rifapentine Methanol Solvate

    Institute of Scientific and Technical Information of China (English)

    周堃; 李军; 罗建洪; 金央

    2012-01-01

    Rifapentine, an important antibiotic, was crystallized from methanol solvent in the form of its methanol solvate. The crystal structure of rifapentine methanol solvate belongs to monoclinic, space group P21, with the unit cell parameters of a = 1.2278(3) nm, b = 1.9768(4) rim, c = 1.2473(3) nm, Z= 2, and β = 112.35(3). The parallelepiped.morphology was also predicted by Materials Studio simulation program.. The influence of intermolecular in-teraction was taken into account in the attachment energy model. The crystal shape fits the calculated morphology well, which was performed on the potential energy minimized model using a generic DREIDING 2.21 force fieldand developed minimization protocol with derived'partial charges.

  10. Solvation of complex surfaces via molecular density functional theory

    CERN Document Server

    Levesque, Maximilien; Rotenberg, Benjamin; Jeanmairet, Guillaume; Vuilleumier, Rodolphe; Borgis, Daniel

    2012-01-01

    We show that classical molecular density functional theory (MDFT), here in the homogeneous reference fluid approximation in which the functional is inferred from the properties of the bulk solvent, is a powerful new tool to study, at a fully molecular level, the solvation of complex surfaces and interfaces by polar solvents. This implicit solvent method allows for the determination of structural, orientational and energetic solvation properties that are on a par with all-atom molecular simulations performed for the same system, while reducing the computer time by two orders of magnitude. This is illustrated by the study of an atomistically-resolved clay surface composed of over a thousand atoms wetted by a molecular dipolar solvent. The high numerical efficiency of the method is exploited to carry a systematic analysis of the electrostatic and non-electrostatic components of the surface-solvent interaction within the popular CLAYFF force field. Solvent energetics and structure are found to depend weakly upon ...

  11. Reactivity of aldehydes at the air-water interface. Insights from molecular dynamics simulations and ab initio calculations.

    Science.gov (United States)

    Martins-Costa, Marilia T C; García-Prieto, Francisco F; Ruiz-López, Manuel F

    2015-02-14

    Understanding the influence of solute-solvent interactions on chemical reactivity has been a subject of intense research in the last few decades. Theoretical studies have focused on bulk solvation phenomena and a variety of models and methods have been developed that are now widely used by both theoreticians and experimentalists. Much less attention has been paid, however, to processes that occur at liquid interfaces despite the important role such interfaces play in chemistry and biology. In this study, we have carried out sequential molecular dynamics simulations and quantum mechanical calculations to analyse the influence of the air-water interface on the reactivity of formaldehyde, acetaldehyde and benzaldehyde, three simple aldehydes of atmospheric interest. The calculated free-energy profiles exhibit a minimum at the interface, where the average reactivity indices may display large solvation effects. The study emphasizes the role of solvation dynamics, which are responsible for large fluctuations of some molecular properties. We also show that the photolysis rate constant of benzaldehyde in the range 290-308 nm increases by one order of magnitude at the surface of a water droplet, from 2.7 × 10(-5) s(-1) in the gas phase to 2.8 × 10(-4) s(-1) at the air-water interface, and we discuss the potential impact of this result on the chemistry of the troposphere. Experimental data in this domain are still scarce and computer simulations like those presented in this work may provide some insights that can be useful to design new experiments.

  12. 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.

  13. 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

  14. 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

    2014-08-28

    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.

  15. 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...

  16. 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...

  17. Solvated crystalline forms of nevirapine: thermoanalytical and spectroscopic studies.

    Science.gov (United States)

    Chadha, Renu; Arora, Poonam; Saini, Anupam; Jain, Dharamvir Singh

    2010-09-01

    The study is aimed at exploring the utility of thermoanalytical methods in the solid-state characterization of various crystalline forms of nevirapine. The different forms obtained by recrystallization of nevirapine from various solvents were identified using differential scanning calorimetry and thermogravimetric analysis (TGA). The appearance of desolvation peak accompanied by weight loss in TGA indicated the formation of solvates: hemi-ethanolate (Form I), hemi-acetonitrilate (Form II), hemi-chloroformate (Form III), hemi-THF solvate (Form IV), mixed hemi-ethanolate hemi-hydrate (Form V), and hemi-toluenate (Form VI). The higher desolvation temperatures of all the solvates except toluenate than their respective boiling point indicate tighter binding of solvent. Emphasis has been laid on the determination of heat capacity and heat of solution utilizing microreaction calorimeter to further distinguish the various forms. The enthalpy of solution (ΔH(sol)), an indirect measure of the lattice energy of a solid, was well correlated with the crystallinity of all the solid forms obtained. The magnitude of ΔH(sol) was found to be -14.14 kJ/mol for Form I and -2.83 kJ/mol for Form V in phosphate buffer of pH 2, exhibiting maximum ease of molecular release from the lattice in Form I. The heat capacity for solvation (ΔC(p)) was found to be positive, providing information about the state of solvent molecules in the host lattice. The solubility and dissolution rate of the forms were also found to be in agreement with their enthalpy of solution. Form (I), being the most exothermic, was found to be the most soluble of all the forms.

  18. 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...

  19. 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.

  20. 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...

  1. 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.

  2. 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.

  3. π-Hydrogen Bonding of Aromatics on the Surface of Aerosols: Insights from Ab Initio and Molecular Dynamics Simulation.

    Science.gov (United States)

    Feng, Ya-Juan; Huang, Teng; Wang, Chao; Liu, Yi-Rong; Jiang, Shuai; Miao, Shou-Kui; Chen, Jiao; Huang, Wei

    2016-07-14

    Molecular level insight into the interaction between volatile organic compounds (VOCs) and aerosols is crucial for improvement of atmospheric chemistry models. In this paper, the interaction between adsorbed toluene, one of the most significant VOCs in the urban atmosphere, and the aqueous surface of aerosols was studied by means of combined molecular dynamics simulations and ab initio quantum chemistry calculations. It is revealed that toluene can be stably adsorbed on the surface of aqueous droplets via hydroxyl-π hydrogen bonding between the H atoms of the water molecules and the C atoms in the aromatic ring. Further, significant modifications on the electrostatic potential map and frontier molecular orbital are induced by the solvation effect of surface water molecules, which would affect the reactivity and pathway of the atmospheric photooxidation of toluene. This study demonstrates that the surface interactions should be taken into consideration in the atmospheric chemical models on oxidation of aromatics.

  4. 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...... and 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....

  5. 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)

  6. 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).

  7. 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.

  8. 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

  9. 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...

  10. Organic chemistry

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2003-08-15

    This book with sixteen chapter explains organic chemistry on linkage isomerism such as alkane, cycloalkane, alkene, aromatic compounds, stereo selective isomerization, aromatic compounds, stereo selective isomerization, organic compounds, stereo selective isomerization, organic halogen compound, alcohol, ether, aldehyde and ketone, carboxylic acid, dicarboxylic acid, fat and detergent, amino, carbohydrate, amino acid and protein, nucleotide and nucleic acid and spectroscopy, a polymer and medical chemistry. Each chapter has introduction structure and characteristic and using of organic chemistry.

  11. 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 ...

  12. 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 ...

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

    Directory of Open Access Journals (Sweden)

    Chadha Renu

    2012-10-01

    Full Text Available Abstract Background Atorvastatin calcium (ATC, an anti-lipid biopharmaceutical class II drug, is widely prescribed as a cholesterol-lowering agent and is presently the world’s best-selling medicine. A large number of crystalline forms of ATC have been published in patents. A variety of solid forms may give rise to different physical properties. Therefore, the discovery of new forms of this unusual molecule, ATC, may still provide an opportunity for further improvement of advantageous properties. Results In the present work, eight new solvates (Solvate I-VIII have been discovered by recrystallization method. Thermal behaviour of ATC and its solvates studied by DSC and TGA indicate similar pattern suggesting similar mode of entrapment of solvent molecules. The type of solvent present in the crystal lattice of the solvates is identified by GC-MS analysis and the stoichiometric ratio of the solvents is confirmed by 1HNMR. The high positive value of binding energy determined from thermochemical parameters indicates deep inclusion of the solvent molecules into the host cavity. The XRPD patterns point towards the differences in their crystallanity, however, after desolvation solvate II, III, IV, V and VIII transform to isostructral amorphous desolvated solvates. The order of crystallinity was confirmed by solution calorimetric technique as the enthalpy of solution is an indirect measure of lattice energy. All the solvates behaved endothermically following the order solvate-VIII (1-butanol solvate 13CP/MAS NMR spectral changes. Conclusions Aqueous solubility of solvate-VIII was found to be maximum, however, solvate-I and VIII showed better reduction in total cholesterol and triglyceride levels as compared to atorvastatin against triton-induced dyslipidemia.

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

    Science.gov (United States)

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

    2010-11-01

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

  15. 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

  16. Nucleation, solvation and boiling of helium excimer clusters

    CERN Document Server

    Luna, Luis G Mendoza; Watkins, Mark J; Bonifaci, Nelly; Aitken, Frederic; von Haeften, Klaus

    2015-01-01

    Helium excimers generated by a corona discharge were investigated in the gas and normal liquid phases of helium as a function of temperature and pressure between 3.8 and 5.0 K and 0.2 and 5.6 bar. Intense fluorescence in the visible region showed the rotationally resolved $d^3\\Sigma_u^+ \\rightarrow b^3\\Pi_g$ transition of He$_2^*$. With increasing pressure, the rotational lines merged into single features. The observed pressure dependence of linewidths, shapes and lineshifts established phases of coexistence and separation of excimer-helium mixtures, providing detailed insight into nucleation, solvation and boiling of He$_2^*$-He$_n$ clusters.

  17. 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

  18. 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.

  19. 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 ...

  20. 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...

  1. 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.

  2. 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...

  3. 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−....

  4. 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...

  5. 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

  6. 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

  7. 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

  8. Temperature-dependent solvation modulates the dimensions of disordered proteins.

    Science.gov (United States)

    Wuttke, René; Hofmann, Hagen; Nettels, Daniel; Borgia, Madeleine B; Mittal, Jeetain; Best, Robert B; Schuler, Benjamin

    2014-04-01

    For disordered proteins, the dimensions of the chain are an important property that is sensitive to environmental conditions. We have used single-molecule Förster resonance energy transfer to probe the temperature-induced chain collapse of five unfolded or intrinsically disordered proteins. Because this behavior is sensitive to the details of intrachain and chain-solvent interactions, the collapse allows us to probe the physical interactions governing the dimensions of disordered proteins. We find that each of the proteins undergoes a collapse with increasing temperature, with the most hydrophobic one, λ-repressor, undergoing a reexpansion at the highest temperatures. Although such a collapse might be expected due to the temperature dependence of the classical "hydrophobic effect," remarkably we find that the largest collapse occurs for the most hydrophilic, charged sequences. Using a combination of theory and simulation, we show that this result can be rationalized in terms of the temperature-dependent solvation free energies of the constituent amino acids, with the solvation properties of the most hydrophilic residues playing a large part in determining the collapse.

  9. 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.

  10. 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

  11. 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

  12. Making Crystals from Crystals: A Solid-State Route to the Engineering of Crystalline Materials, Polymorphs, Solvates and Co-Crystals; Considerations on the Future of Crystal Engineering

    Science.gov (United States)

    Braga, Dario; Curzi, Marco; Dichiarante, Elena; Giaffreda, Stefano Luca; Grepioni, Fabrizia; Maini, Lucia; Palladino, Giuseppe; Pettersen, Anna; Polito, Marco

    Making crystals by design is the paradigm of crystal engineering. The main goal is that of obtaining and controlling the collective properties of a crystalline material from the convolution of the physical and chemical properties of the individual building blocks (whether molecules, ions, or metal atoms and ligands) with crystal periodicity and symmetry. Crystal engineering encompasses nowadays all traditional sectors of chemistry from organic to inorganic, organometallic, biological and pharmaceutical chemistry and nanotechnology. The investigation and characterization of the products of a crystal engineering experiment require the utilization of solid state techniques, including theoretical and advanced crystallography methods. Moreover, reactions between crystalline solids and/or between a crystalline solid and a vapour can be used to obtain crystalline materials, including new crystal forms, solvates and co-crystals. Indeed, crystal polymorphism, resulting from different packing arrangements of the same molecular or supramolecular entity in the crystal structure, represents a challenge to crystal makers.

  13. 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,

  14. 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

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

    Science.gov (United States)

    Balestrini, Raffaella; Polesello, Stefano; Sacchi, Elisa

    2014-07-01

    We monitored the chemical and isotopic compositions of wet depositions, at the Pyramid International Laboratory (5050 ma.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 Ca(2+), whereas the main anion was HCO3(-), which constituted approximately 69% of the anions, followed by NO3(-), SO4(2-) and Cl(-). Data analysis suggested that Na(+), Cl(-) and K(+) were derived from the long-range transport of marine aerosols. Ca(2+), Mg(2+) and HCO3(-) were related to rock and soil dust contributions and the NO3(-) and SO4(2-) 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 δ(18)O, and from -0.8 to -174‰ in δ(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(-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

  16. 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

  17. 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...

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models.

    Science.gov (United States)

    Martínez-Fernández, L; Pepino, A J; Segarra-Martí, J; Banyasz, A; Garavelli, M; Improta, R

    2016-09-13

    The optical spectra of 5-methylcytidine in three different solvents (tetrahydrofuran, acetonitrile, and water) is measured, showing that both the absorption and the emission maximum in water are significantly blue-shifted (0.08 eV). The absorption spectra are simulated based on CAM-B3LYP/TD-DFT calculations but including solvent effects with three different approaches: (i) a hybrid implicit/explicit full quantum mechanical approach, (ii) a mixed QM/MM static approach, and (iii) a QM/MM method exploiting the structures issuing from molecular dynamics classical simulations. Ab-initio Molecular dynamics simulations based on CAM-B3LYP functionals have also been performed. The adopted approaches all reproduce the main features of the experimental spectra, giving insights on the chemical-physical effects responsible for the solvent shifts in the spectra of 5-methylcytidine and providing the basis for discussing advantages and limitations of the adopted solvation models. PMID:27529792

  3. 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.

  4. Mechanisms of ultrafast fluorescence depletion spectroscopy and applications to measure slovation dynamics of coummarin 153 in methanol

    Energy Technology Data Exchange (ETDEWEB)

    Yang Songqiu, E-mail: sqyang@dicp.ac.cn [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China); Graduate School of the Chinese Academy of Sciences, Beijing 100039 (China); Liu Jianyong, E-mail: beam@dicp.ac.cn [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China); Zhou Panwang, E-mail: pwzhou@dicp.ac.cn [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China); Chen Junsheng, E-mail: junshengchen@dicp.ac.cn [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China); Graduate School of the Chinese Academy of Sciences, Beijing 100039 (China); Han Keli, E-mail: klhan@dicp.ac.cn [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China); He Guozhong, E-mail: gzhe@dicp.ac.cn [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China)

    2012-09-15

    Subpicosecond fluorescence depletion spectroscopy (FDS) was used to measure the solvation dynamics of coumarin 153 (C153) in methanol. The FDS mechanisms were discussed. A quasi-continuous model was used to describe the solvational relaxation of excited states. The perturbations of the probe pulse on the excited sample system, including up-conversion and stimulated emission, were sufficiently discussed. For a probe molecule used in the FDS experiment, ensuring that the up-conversion perturbation can be negligible is important. FDS was found to be a good technique for measuring the solvation dynamics of C153 in methanol. - Highlights: Black-Right-Pointing-Pointer Mechanisms of subpicosecond fluorescence depletion spectroscopy. Black-Right-Pointing-Pointer Quasi-continuous model was used to describe the solvational relaxation. Black-Right-Pointing-Pointer The solvation dynamics of coumarin 153 in methanol has been measured.

  5. 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

  6. 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.

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

    Science.gov (United States)

    Montgomery Pettitt, B.

    2008-03-01

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

  8. Improved Dielectric Solvation Model for Electronic Structure Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Chipman, Daniel M. [Univ. of Notre Dame, IN (United States)

    2015-12-16

    This project was originally funded for the three year period from 09/01/2009 to 08/31/2012. Subsequently a No-Cost Extension was approved for a revised end date of 11/30/2013. The primary goals of the project were to develop continuum solvation models for nondielectric short-range interactions between solvent and solute that arise from dispersion, exchange, and hydrogen bonding. These goals were accomplished and are reported in the five peer-reviewed journal publications listed in the bibliography below. The secondary goals of the project included derivation of analytic gradients for the models, improvement of the cavity integration scheme, application of the models to the core-level spectroscopy of water, and several other miscellaneous items. These goals were not accomplished because they depended on completion of the primary goals, after which there was a lack of time for any additional effort.

  9. 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

  10. Size and surface chemistry of nanoparticles lead to a variant behavior in the unfolding dynamics of human carbonic anhydrase

    Science.gov (United States)

    Nasir, Irem; Lundqvist, Martin; Cabaleiro-Lago, Celia

    2015-10-01

    The adsorption induced conformational changes of human carbonic anhydrase I (HCAi) and pseudo wild type human carbonic anhydrase II truncated at the 17th residue at the N-terminus (trHCAii) were studied in presence of nanoparticles of different sizes and polarities. Isothermal titration calorimetry (ITC) studies showed that the binding to apolar surfaces is affected by the nanoparticle size in combination with the inherent protein stability. 8-Anilino-1-naphthalenesulfonic acid (ANS) fluorescence revealed that HCAs adsorb to both hydrophilic and hydrophobic surfaces, however the dynamics of the unfolding at the nanoparticle surfaces drastically vary with the polarity. The size of the nanoparticles has opposite effects depending on the polarity of the nanoparticle surface. The apolar nanoparticles induce seconds timescale structural rearrangements whereas polar nanoparticles induce hours timescale structural rearrangements on the same charged HCA variant. Here, a simple model is proposed where the difference in the timescales of adsorption is correlated with the energy barriers for initial docking and structural rearrangements which are firmly regulated by the surface polarity. Near-UV circular dichorism (CD) further supports that both protein variants undergo structural rearrangements at the nanoparticle surfaces regardless of being ``hard'' or ``soft''. However, the conformational changes induced by the apolar surfaces differ for each HCA isoform and diverge from the previously reported effect of silica nanoparticles.The adsorption induced conformational changes of human carbonic anhydrase I (HCAi) and pseudo wild type human carbonic anhydrase II truncated at the 17th residue at the N-terminus (trHCAii) were studied in presence of nanoparticles of different sizes and polarities. Isothermal titration calorimetry (ITC) studies showed that the binding to apolar surfaces is affected by the nanoparticle size in combination with the inherent protein stability. 8-Anilino

  11. 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

  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. 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.

  14. 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.

  15. 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

  16. Supramolecular chemistry-general principles and selected examples from anion recognition and metallosupramolecular chemistry.

    Science.gov (United States)

    Albrecht, Markus

    2007-12-01

    This review gives an introduction into supramolecular chemistry describing in the first part general principles, focusing on terms like noncovalent interaction, molecular recognition, self-assembly, and supramolecular function. In the second part those will be illustrated by simple examples from our laboratories. Supramolecular chemistry is the science that bridges the gap between the world of molecules and nanotechnology. In supramolecular chemistry noncovalent interactions occur between molecular building blocks, which by molecular recognition and self-assembly form (functional) supramolecular entities. It is also termed the "chemistry of the noncovalent bond." Molecular recognition is based on geometrical complementarity based on the "key-and-lock" principle with nonshape-dependent effects, e.g., solvatization, being also highly influential. Self-assembly leads to the formation of well-defined aggregates. Hereby the overall structure of the target ensemble is controlled by the symmetry features of the certain building blocks. Finally, the aggregates can possess special properties or supramolecular functions, which are only found in the ensemble but not in the participating molecules. This review gives an introduction on supramolecular chemistry and illustrates the fundamental principles by recent examples from our group.

  17. 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.

  18. 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

  19. Electrolytes and interphasial chemistry in Li ion devices

    Energy Technology Data Exchange (ETDEWEB)

    Xu, K. [Electrochemistry Branch, Sensors and Electron Devices Directorate, U. S. Army Research Laboratory, Adelphi, Maryland, 20783-1197 (United States)

    2010-07-01

    Since its appearance in 1991, the Li ion battery has been the major power source driving the rapid digitalisation 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{sup +} 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{sup +} 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. (author)

  20. 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.

  1. Dynamics and reactivity of trapped electrons on supported ice crystallites.

    Science.gov (United States)

    Stähler, Julia; Gahl, Cornelius; Wolf, Martin

    2012-01-17

    The solvation dynamics and reactivity of localized excess electrons in aqueous environments have attracted great attention in many areas of physics, chemistry, and biology. This manifold attraction results from the importance of water as a solvent in nature as well as from the key role of low-energy electrons in many chemical reactions. One prominent example is the electron-induced dissociation of chlorofluorocarbons (CFCs). Low-energy electrons are also critical in the radiation chemistry that occurs in nuclear reactors. Excess electrons in an aqueous environment are localized and stabilized by the local rearrangement of the surrounding water dipoles. Such solvated or hydrated electrons are known to play an important role in systems such as biochemical reactions and atmospheric chemistry. Despite numerous studies over many years, little is known about the microscopic details of these electron-induced chemical processes, and interest in the fundamental processes involved in the reactivity of trapped electrons continues. In this Account, we present a surface science study of the dynamics and reactivity of such localized low-energy electrons at D(2)O crystallites that are supported by a Ru(001) single crystal metal surface. This approach enables us to investigate the generation and relaxation dynamics as well as dissociative electron attachment (DEA) reaction of excess electrons under well-defined conditions. They are generated by photoexcitation in the metal template and transferred to trapping sites at the vacuum interface of crystalline D(2)O islands. In these traps, the electrons are effectively decoupled from the electronic states of the metal template, leading to extraordinarily long excited state lifetimes on the order of minutes. Using these long-lived, low-energy electrons, we study the DEA to CFCl(3) that is coadsorbed at very low concentrations (∼10(12) cm(-2)). Using rate equations and direct measurement of the change of surface dipole moment, we

  2. 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

  3. 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.

  4. Controlled Formation and Vibrational Characterization of Large Solvated Ionic Clusters in Cryogenic Ion Traps

    Science.gov (United States)

    Garand, Etienne; Marsh, Brett; Voss, Jonathan; Duffy, Erin M.

    2016-06-01

    An experimental approach for the formation of solvated ionic clusters and their vibrational spectroscopy will be presented. This recently developed apparatus combines an electrospray ionization source, two temperature controlled cryogenic ion traps and a time-of-flight infrared photofragmentation spectrometer, to allow for a universal and controlled formation and characterization of solvent clusters around ionic core as well as product of ion-molecule reaction. Recent results on the spectroscopy of such solvated ions, will be presented and discussed. In particular, this talk will present the structural evolution of glycylglycine as a function of stepwise solvation, and show how the presence of just a few water can modify the geometry of this model peptide. I will also present results solvation of ion that do not form hydrogen bond or strongly interactions with the solvent.

  5. 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.

  6. 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...

  7. Hiking the valleys of quatum chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Aikens, Christine Marie [Iowa State Univ., Ames, IA (United States)

    2005-01-01

    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.

  8. Pressure-induced conformation transition of o-phenylene solvated in bulk hydrocarbons.

    Science.gov (United States)

    Riello, Massimo; Doni, Giovanni; Filip, Sorin V; Gold, Martin; De Vita, Alessandro

    2014-11-26

    The conformational behavior of o-phenylene 8-mers and 10-mers solvated in a series of linear alkane solvents by means of classical molecular dynamics and first-principles calculations was studied. Irrespective of the solvent used, we find that at ambient pressure the molecule sits in the well-defined close-helical arrangement previously observed in light polar solvents. However, for pressures greater than 50 atm, and for tetradecane or larger solvent molecules, our simulations predict that o-phenylene undergoes a conformational transition to an uncoiled, extended geometry with a 35% longer head-to-tail distance and a much larger overlap between its lateral aromatic ring groups. The free energy barrier for the transition was studied as a function of pressure and temperature for both solute molecules in butane and hexadecane. Gas-phase density functional theory-based nudged elastic band calculations on 8-mer and 10-mer o-phenylene were used to estimate how the pressure-induced transition energy barrier changes with solute length. Our results indicate that a sufficiently large solvent molecule size is the key factor enabling a configuration transition upon pressure changes and that longer solute molecules associate with higher conformation transition energy barriers. This suggests the possibility of designing systems in which a solute molecule can be selectively "activated" by a controlled conformation transition achieved at a predefined set of pressure and temperature conditions.

  9. 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...

  10. Kinetics study of the solvated electron decay in THF using laser-synchronised picosecond electron pulse

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Picosecond pulse radiolysis of neat tetrahydrofuran (THF) shows a fast decay of the solvated electron within 2.5ns. The decay of the solvated electron observed at 790nm is because of spur reaction. A numerical simulation using time dependent Smoluchowski equation containing a sink term with a distance dependent reaction rate is used to fit the pulse-probe data and shows that the geminate reaction can proceed at long distance in this low polar solvent.

  11. Extended Debye-Hückel theory for studying the electrostatic solvation energy.

    Science.gov (United States)

    Xiao, Tiejun

    2015-03-16

    The electrostatic part of the solvation energy has been studied by using extended Debye-Hückel (DH) theories. Specifically, our molecular Debye-Hückel theory [J. Chem. Phys. 2011, 135, 104104] and its simplified version, an energy-scaled Debye-Hückel theory, were applied to electrolytes with strong electrostatic coupling. Our theories provide a practical methodology for calculating the electrostatic solvation free energies, and the accuracy was verified for atomic and diatomic charged solutes. PMID:25640184

  12. Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review

    OpenAIRE

    Wei, Guo Wei; Baker, Nathan A.

    2014-01-01

    This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, el...

  13. 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...

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. The Evaluation of the Spanish Air Quality Modelling System: CALIOPE. Dynamics and Chemistry over Europe and Iberian Peninsula for 2004 at high horizontal resolution

    Science.gov (United States)

    Piot, M.; Pay, M.; Jorba, O.; Lopez, E.; Pirez, C.; Gasso, S.; Baldasano, J. M.

    2009-12-01

    In Europe, human exposure to air pollution often exceeds standards set by the EU commission (Directives 1996/62/EC, 2002/3/EC, 2008/50/EC) and the World Health Organization (WHO). Urban/suburban areas are predominantly impacted upon, although exceedances of particulate matter (PM10 and PM2.5) and Ozone (O3) also take place in rural areas. Within the CALIOPE project, a high-resolution air quality forecasting system, namely WRF-ARW/HERMES04/CMAQ/BSC-DREAM, has been developed and applied to the European domain (12x12 sq. km, 1hr) as well as the Spanish domain (4x4 sq. km, 1hr). The simulation of such high-resolution model system has been made possible by its implementation on the MareNostrum supercomputer. This contribution describes a thorough quantitative evaluation study performed for the reference year 2004. The WRF-ARW meteorological model contains 38 vertical layers reaching up to 50 hPa. The vertical resolution of the CMAQ chemistry-transport model for gas-phase and aerosols has been increased from 8 to 15 layers in order to simulate vertical exchanges more accurately. Gas phase boundary conditions are provided by the LMDz-INCA2 global climate-chemistry model. For the European simulation, emissions are disaggregated from the EMEP emission inventory for 2004 to the utilized resolution using the criteria implemented in the HERMES04 emission model. The HERMES04 model system, running through a bottom-up approach, is used to estimate emissions for Spain at a 1x1 sq. km horizontal resolution, every hour. In order to evaluate the performances of the CALIOPE system, the model simulation for Europe was compared with ground-based measurements from the EMEP and the Spanish air quality networks (total of 60 stations for O3, 43 for NO2, 31 for SO2, 25 for PM10 and 16 for PM2.5). The model simulation for Europe satisfactorily reproduces O3 concentrations throughout the year (annual correlation: 0.66) with relatively small errors: MNGE values range from 13% to 26%, and MNBE

  1. 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...

  2. 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...

  3. 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...

  4. 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.

  5. 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...

  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. 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

  8. 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.

  9. 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

  10. 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.

  11. 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.

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

    Science.gov (United States)

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

    2016-03-01

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

  13. Determination of the solvation film thickness of dispersed particles with the method of Einstein viscosity equation

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The dispersion of a solid particle in a liquid may lead to the formation of solvation film onthe particle surface, which can strongly increase the repulsive force between particles and thus strongly affect the stability of dispersions. The solvation film thickness, which varies with the variation of the property of suspension particles and solutions, is one of the most important parameters of the solvation film, and is also one of the most difficult parameters that can be measured accurately. In this paper, a method, based on the Einstein viscosity equation of dispersions, for determining the solvation film thickness of particles is developed. This method was tested on two kinds of silica spherical powders (namely M1 and M2) dispersed in ethyl alcohol, in water, and in a water-ethyl alcohol mixture (1:1 by volume) through measuring the relative viscosity of dispersions of the particles as a function of the volume fraction of the dry particles in the dispersion, and of the specific surface area and the density of the particles. The calculated solvation film thicknesses on M1 are 7.48, 18.65 and 23.74 nm in alcohol, water and the water-ethyl alcohol mixture, 12.41, 12.71 and 13.13 nm on M2 in alcohol, water and the water-ethyl alcohol mixture, respectively.

  14. 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

  15. 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

  16. 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.

  17. Solvation of decane and benzene in mixtures of 1-octanol and N, N-dimethylformamide

    Science.gov (United States)

    Kustov, A. V.; Smirnova, N. L.

    2016-09-01

    The heats of dissolution of decane and benzene in a model system of octanol-1 (OctOH) and N, N-dimethylformamide (DMF) at 308 K are measured using a variable temperature calorimeter equipped with an isothermal shell. Standard enthalpies are determined and standard heat capacities of dissolution in the temperature range of 298-318 K are calculated using data obtained in [1, 2]. The state of hydrocarbon molecules in a binary mixture is studied in terms of the enhanced coordination model (ECM). Benzene is shown to be preferentially solvated by DMF over the range of physiological temperatures. The solvation shell of decane is found to be strongly enriched with 1-octanol. It is obvious that although both hydrocarbons are nonpolar, the presence of the aromatic π-system in benzene leads to drastic differences in their solvation in a lipid-protein medium.

  18. Synthesis and Structure of Solvated Protons Incorporating Weakly Coordinating Anions. Precursors of Superacids

    Institute of Scientific and Technical Information of China (English)

    TSANG,Chi-Wing(曾志荣); YANG,Qing-Chuan(杨清传); MAK,Thomas C.W.(麦松威); XIE,Zuo-Wei(谢作伟)

    2002-01-01

    Six new solvated proton salts of highly halogenated carborane anions, [H(solvent)n] [carborane] (carborane = 1-R-CB11-Y5X-6 (R= H, Me; X, Y= Cl, Br, I), 1-H-CB9Br-9 ) were preparrf from the salt metathesis reaction of Ag(carborane)and HCl in high yields. Single-crystal X-ray analyses show that they are all discrete molecules in the solid-state. Tne mumher of the solvated molecules surrounding H+ ion can not be determined with the knowledge of the size and substituents of the carborane anions. Thnese salts provide convenient weighable sources of Brφnsted acid reagents having a wide range of acidities and good thermal stabilities. TGA results ubducate that the solvated molecules (water or organic molecules) in the catiobs [H(solvent)n]+ can be renoved under high temperature and high vacuum conditions to give superacidic mterials H(carborane) which can protonate olefin.

  19. 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

  20. Ermod: fast and versatile computation software for solvation free energy with approximate theory of solutions.

    Science.gov (United States)

    Sakuraba, Shun; Matubayasi, Nobuyuki

    2014-08-01

    ERmod is a software package to efficiently and approximately compute the solvation free energy using the method of energy representation. Molecular simulation is to be conducted at two condensed-phase systems of the solution of interest and the reference solvent with test-particle insertion of the solute. The subprogram ermod in ERmod then provides a set of energy distribution functions from the simulation trajectories, and another subprogram slvfe determines the solvation free energy from the distribution functions through an approximate functional. This article describes the design and implementation of ERmod, and illustrates its performance in solvent water for two organic solutes and two protein solutes. Actually, the free-energy computation with ERmod is not restricted to the solvation in homogeneous medium such as fluid and polymer and can treat the binding into weakly ordered system with nano-inhomogeneity such as micelle and lipid membrane. ERmod is available on web at http://sourceforge.net/projects/ermod.

  1. 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...

  2. Dynamics of ozone and nitrogen oxides at Summit, Greenland. II. Simulating snowpack chemistry during a spring high ozone event with a 1-D process-scale model

    NARCIS (Netherlands)

    Murray, K.A.; Kramer, L.J.; Doskey, P.V.; Ganzeveld, L.N.; Seok, B.; Dam, van B.; Helmig, D.

    2015-01-01

    Observed depth profiles of nitric oxide (NO), nitrogen dioxide (NO2), and ozone (O3) in snowpack interstitial air at Summit, Greenland were best replicated by a 1-D process-scale model, which included (1) geometrical representation of snow grains as spheres, (2) aqueous-phase chemistry confined to a

  3. Element-specific characterization of transient electronic structure of solvated Fe(II) complexes with time-resolved soft X-ray absorption spectroscopy.

    Science.gov (United States)

    Hong, Kiryong; Cho, Hana; Schoenlein, Robert W; Kim, Tae Kyu; Huse, Nils

    2015-11-17

    the important information contained in transient metal L-edge spectroscopy on changes in the 3d orbitals including oxidation states, orbital symmetries, and covalency, which largely define the chemistry of these complexes. In addition, ligand K-edge spectroscopy reveals the "ligand view" of the valence charge density by probing 1s-2p core-level transitions at the K-edge of light elements such as nitrogen, carbon, and oxygen. In the case of Fe(II) spin-conversion complexes, additional details of the metal-ligand interactions can be obtained by this type of X-ray spectroscopy. With new initiatives in and construction of X-ray free-electron laser sources, we expect time-resolved soft X-ray spectroscopy to pave a new way to study electronic and molecular dynamics of functional materials, thereby answering many interesting scientific questions in inorganic chemistry and material science.

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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

    with two non self-associating compounds may exhibit solvation specifically due to hydrogen bonding or more generally due to Lewis acid-Lewis base interactions. As examples can be mentioned mixtures with polar compounds (water, glycols...) and aromatic hydrocarbons and aqueous ether or ester solutions...... the scientific point of view, solvation phenomena are also very significant because they are present in different types of mixtures and not just those containing two self-associating compounds e.g. water with alcohols or glycols. Mixtures with only one self-associating compound and in some cases even mixtures...

  12. 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).

  13. 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.

  14. 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.

  15. 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 ...

  16. 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.)

  17. 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)

  18. 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.

  19. 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

  20. 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)

  1. 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.)

  2. Structure and photoabsorption properties of cationic alkali dimers solvated in neon clusters.

    Science.gov (United States)

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

    2010-11-01

    We present a theoretical investigation of the structure and optical absorption of M(2)(+) alkali dimers (M=Li,Na,K) solvated in Ne(n) clusters for n=1 to a few tens Ne atoms. For all these alkali, the lowest-energy isomers are obtained by aggregation of the first Ne atoms at the extremity of the alkali molecule. This particular geometry, common to other M(2)(+)-rare gas clusters, is intimately related to the shape of the electronic density of the X  (2)Σ(g)(+) ground state of the bare M(2)(+) molecules. The structure of the first solvation shell presents equilateral Ne(3) and capped pentagonal Ne(6) motifs, which are characteristic of pure rare gas clusters. The size and geometry of the complete solvation shell depend on the alkali and were obtained at n=22 with a D(4h) symmetry for Li and at n=27 with a D(5h) symmetry for Na. For K, our study suggests that the closure of the first solvation shell occurs well beyond n=36. We show that the atomic arrangement of these clusters has a profound influence on their optical absorption spectrum. In particular, the XΣ transition from the X  (2)Σ(g)(+) ground state to the first excited (2)Σ(u)(+) state is strongly blueshifted in the Frank-Condon area.

  3. Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics.

    Science.gov (United States)

    Jia, Xiangyu; Wang, Meiting; Shao, Yihan; König, Gerhard; Brooks, Bernard R; Zhang, John Z H; Mei, Ye

    2016-02-01

    In this work, the solvation free energies of 20 organic molecules from the 4th Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL4) have been calculated. The sampling of phase space is carried out at a molecular mechanical level, and the associated free energy changes are estimated using the Bennett Acceptance Ratio (BAR). Then the quantum mechanical (QM) corrections are computed through the indirect Non-Boltzmann Bennett's acceptance ratio (NBB) or the thermodynamics perturbation (TP) method. We show that BAR+TP gives a minimum analytic variance for the calculated solvation free energy at the Gaussian limit and performs slightly better than NBB in practice. Furthermore, the expense of the QM calculations in TP is only half of that in NBB. We also show that defining the biasing potential as the difference of the solute-solvent interaction energy, instead of the total energy, can converge the calculated solvation free energies much faster but possibly to different values. Based on the experimental solvation free energies which have been published before, it is discovered in this study that BLYP yields better results than MP2 and some other later functionals such as B3LYP, M06-2X, and ωB97X-D.

  4. 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.

  5. Influence of confinement on solvation of ethanol in water studied by Raman spectroscopy

    NARCIS (Netherlands)

    Ratajska-Gadomska, B.; Gadomski, W.

    2010-01-01

    Herewith we present the results of our studies on the effect of confinement on the solvation of ethyl alcohol in aqueous solutions using Raman spectroscopy of the O-H stretching band. Based on Gaussian-Lorentzian deconvolution of the O-H band Raman spectra we investigate the local structures created

  6. 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)

  7. 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.

  8. 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

  9. Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics.

    Science.gov (United States)

    Jia, Xiangyu; Wang, Meiting; Shao, Yihan; König, Gerhard; Brooks, Bernard R; Zhang, John Z H; Mei, Ye

    2016-02-01

    In this work, the solvation free energies of 20 organic molecules from the 4th Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL4) have been calculated. The sampling of phase space is carried out at a molecular mechanical level, and the associated free energy changes are estimated using the Bennett Acceptance Ratio (BAR). Then the quantum mechanical (QM) corrections are computed through the indirect Non-Boltzmann Bennett's acceptance ratio (NBB) or the thermodynamics perturbation (TP) method. We show that BAR+TP gives a minimum analytic variance for the calculated solvation free energy at the Gaussian limit and performs slightly better than NBB in practice. Furthermore, the expense of the QM calculations in TP is only half of that in NBB. We also show that defining the biasing potential as the difference of the solute-solvent interaction energy, instead of the total energy, can converge the calculated solvation free energies much faster but possibly to different values. Based on the experimental solvation free energies which have been published before, it is discovered in this study that BLYP yields better results than MP2 and some other later functionals such as B3LYP, M06-2X, and ωB97X-D. PMID:26731197

  10. Solvation and Acid Strength Effects on Catalysis by Faujasite Zeolites

    Energy Technology Data Exchange (ETDEWEB)

    Gounder, Rajamani P.; Jones, Andrew J.; Carr, Robert T.; Iglesia, Enrique

    2012-02-01

    Kinetic, spectroscopic, and chemical titration data indicate that differences in monomolecular isobutane cracking and dehydrogenation and methanol dehydration turnover rates (per H+) among FAU zeolites treated thermally with steam (H-USY) and then chemically with ammonium hexafluorosilicate (CDHUSY) predominantly reflect differences in the size and solvating properties of their supercage voids rather than differences in acid strength. The number of protons on a given sample was measured consistently by titrations with Na+, with CH3 groups via reactions of dimethyl ether, and with 2,6-di-tert-butylpyridine during methanol dehydration catalysis; these titration values were also supported by commensurate changes in acidic OH infrared band areas upon exposure to titrant molecules. The number of protons, taken as the average of the three titration methods, was significantly smaller than the number of framework Al atoms (Alf) obtained from X-ray diffraction and 27Al magic angle spinning nuclear magnetic resonance spectroscopy on H-USY (0.35 H+/Alf) and CD-HUSY (0.69 H+/Alf). These data demonstrate that the ubiquitous use of Alf sites as structural proxies for active H+ sites in zeolites can be imprecise, apparently because distorted Al structures that are not associated with acidic protons are sometimes detected as Alf sites. Monomolecular isobutane cracking and dehydrogenation rate constants, normalized non-rigorously by the number of Alf species, decreased with increasing Na+ content on both H-USY and CD-HUSY samples and became undetectable at sub-stoichiometric exchange levels (0.32 and 0.72 Na+/Alf ratios, respectively), an unexpected finding attributed incorrectly in previous studies to the presence of minority ‘‘super-acidic’’ sites. These rate constants, when normalized rigorously by the number of residual H+ sites were independent of Na+ content on both H-USY and CD-HUSY samples, reflecting the stoichiometric replacement of protons that are uniform in

  11. 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...

  12. Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions.

    Science.gov (United States)

    Reif, Maria M; Hünenberger, Philippe H

    2011-04-14

    The raw single-ion solvation free energies computed from atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions (finite or periodic system, system or box size) and treatment of electrostatic interactions (Coulombic, lattice-sum, or cutoff-based) used during these simulations. However, as shown by Kastenholz and Hünenberger [J. Chem. Phys. 124, 224501 (2006)], correction terms can be derived for the effects of: (A) an incorrect solvent polarization around the ion and an incomplete or/and inexact interaction of the ion with the polarized solvent due to the use of an approximate (not strictly Coulombic) electrostatic scheme; (B) the finite-size or artificial periodicity of the simulated system; (C) an improper summation scheme to evaluate the potential at the ion site, and the possible presence of a polarized air-liquid interface or of a constraint of vanishing average electrostatic potential in the simulated system; and (D) an inaccurate dielectric permittivity of the employed solvent model. Comparison with standard experimental data also requires the inclusion of appropriate cavity-formation and standard-state correction terms. In the present study, this correction scheme is extended by: (i) providing simple approximate analytical expressions (empirically-fitted) for the correction terms that were evaluated numerically in the above scheme (continuum-electrostatics calculations); (ii) providing correction terms for derivative thermodynamic single-ion solvation properties (and corresponding partial molar variables in solution), namely, the enthalpy, entropy, isobaric heat capacity, volume, isothermal compressibility, and isobaric expansivity (including appropriate standard-state correction terms). The ability of the correction scheme to produce methodology-independent single-ion solvation free energies based on atomistic simulations is tested in the case of Na(+) hydration, and the nature and magnitude of the correction terms for

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

    Science.gov (United States)

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

    2006-11-30

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

  14. 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.

  15. Unified Electrostatic Understanding on the Solvation-Induced Changes in the CN Stretching Frequency and the NMR Chemical Shifts of a Nitrile.

    Science.gov (United States)

    Torii, Hajime

    2016-09-15

    Understanding on the spectroscopic properties of a functional group is essential to use it to detect changes in the structural and/or dynamical properties through the situations of intermolecular interactions. The present study is devoted to elucidating the factors that control the solvation-induced changes in the C≡N stretching frequency and the (13)C and (15)N NMR chemical shifts of the nitrile group. It is shown that the nonelectrostatic contribution of the hydration-induced changes in the C≡N stretching frequency as previously thought, as well as the specific effect of hydrogen bonding on the (13)C and (15)N chemical shifts, actually originate from the spatially inhomogeneous nature of the electrostatic situation generated by the hydrogen-bond donating water molecule, especially by the OH bond dipole. On this basis, a unified electrostatic interaction model that encompasses the cases of both hydration and dipolar solvation is constructed. The responses of electrons in these two cases are also discussed. PMID:27547990

  16. 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

  17. Thermodynamic study of the binding of calcium and magnesium ions with myelin basic protein using the extended solvation theory

    Institute of Scientific and Technical Information of China (English)

    G. Rezaei Behbehani; A.A. Saboury; A. Divsalar

    2008-01-01

    The interaction of myelin basic protein (MBP) from the bovine central nervous system with Ca2+ and Mg2+ ions, named as M2+, was studied by isothermal titration calorimetry at 27℃ in aqueous solution. The extended solvation model was used to reproduce the enthaipies of MBP+M2+ interactions.The solvation parameters recovered from the extended solvation model were attributed to the structural change of MBP due to the metal ion interaction. It was found that there is a set of two identical and noninteracting binding sites for Ca2+ and Mg2+ ions.

  18. HMX/DMF溶剂化物结构和分子间相互作用的理论研究%Theoretical Investigation on Structure and Intermolecular Interaction for HMX/ DMF Solvate

    Institute of Scientific and Technical Information of China (English)

    段晓惠; 于海利; 陈杰; 李洪珍

    2012-01-01

    采用量子化学计算和分子动力学(MD)模拟,研究了溶剂化物环四亚甲基四硝胺(HMX)/N,N-二甲基甲酰胺(DMF)的结构和分子间相互作用.对浸渍在DMF溶剂中的β-HMX分子的MD模拟表明,HMX的分子构象已经从β转变为α相.在MP2/6-31G*水平上的理论计算也说明,在DMF溶剂中,α-HMX比β-HMX更稳定.这解释了在HMX/DMF溶剂化物的多晶型中,所有的HMX分子均呈α构象的原因.采用MP2/6-31 G*方法,对α-HMX和DMF分子间可能的同型和异型二聚体进行结构优化.结果表明,组分间存在C—H…O氢键相互作用,并且α-HMX/DMF的稳定化能非常接近α-HMX/αα-HMX,并远远大于DMF二聚体的.这意味着异型分子间力可和同型分子间力竞争.从热力学的观点来看,共结晶过程可能发生.对α-HMX在DMF中的过饱和溶液的MD模拟表明,分子间相互作用对共结晶有利.这些理论研究对理解在HMX的DMF溶液中为什么发生的是共结晶而不是重结晶提供了有价值的信息.%The structures and intermolecular interactions for octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)/N,N-dimethylformamide (DMF) solvate have been investigated through quantum chemistry calculations and molecular dynamics (MD) simulations.MD simulation for a β-HMX molecule immersed in DMF solvent shows that β conformation has been transformed into α form.Theoretical calculations at the MP2/6-31G* level also indicate that the α HMX is more stable thanβ-HMX in DMF solution.This explains why all HMX molecules present α-form in the polymorphic forms of HMX/DMF solvate.Geometrical optimizations at-the level of MP2/6-31G* are performed for all the possible homodimers and heterodimers between α-HMX and DMF. Results reveal that C—H…O hydrogen bond interactions exist between components. Moreover,the stabilization energy of α-HMX/DMF is very close to that of α-HMX/α-HMX and much larger than that of DMF dimer.This means that the heteromeric

  19. 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)

  20. 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…

  1. 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.

  2. 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

  3. 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...

  4. 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...

  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. 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

  7. 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

  8. Sensitivity of Solvation Environment to Oxidation State and Position in the Early Actinide Period.

    Science.gov (United States)

    Clark, Aurora E; Samuels, Alex; Wisuri, Katy; Landstrom, Sarah; Saul, Tessa

    2015-07-01

    The aqueous solvation of U-Pu in the III-VI oxidation states has been examined using density functional theory and hydrated cluster models of the form An(H2O)30(4+/3+) and AnO2(H2O)30(2+/+) embedded within a polarizable continuum model to approximate the effect of bulk water. The structural features are compared to available data from extended X-ray absorption fine structure. Then, using a multiple-scattering approach, the X-ray absorption near-edge spectra (XANES) have been simulated and compared to experiment. These structural data are complemented by a detailed thermodynamic analysis using a recently benchmarked protocol. The structural, spectroscopic, and thermodynamic information has been used to assign the primary solvation environments in water, with an emphasis upon understanding how oxidation state and position in the period modifies the hydration number and equilibrium between different solvation shell environments. Tetravalent U is proposed to exist in equilibrium between the 8- and 9-coordinate species. Moving to the right of the period, Np(IV) and Pu(IV) exist solely as the octa-aquo species. Reduction to the trivalent ions leads to thermodynamic favorability for this solvation environment, whose features reproduce the XANES spectra. The actinyl dications (AnO2(2+)) of U and Np have a preferred environment in the equatorial plane consisting of 5 solvating waters; however, changes to the ionic radius and electronic structure at Pu leads to an equilibrium between the 4- and 5-coordinate species for PuO2(2+). Reduction of the dications to form the monocations generally leads to a preference for the 4-coordinate primary solvation shell, with an equilibrium existing for uranyl, while the neptunyl and plutonyl species exist solely as AnO2(H2O)4(+). These data provide accurate thermodynamic information for several rare species and the combined thermodynamic, structural, and spectroscopic approach reveals trends in hydration behavior across actinide oxidation

  9. Vibrational Spectroscopic Study on Ion Solvation and Association of Lithium Perchlorate in 4-Methoxymethyl-ethylene Carbonate

    Institute of Scientific and Technical Information of China (English)

    QIAO,Hong-Wei; LUAN,He-Lin; ZHOU,Zhi-Ming; YAO,Wen

    2007-01-01

    Solvation interaction and ion association in solutions of lithium perchlorate/4-methoxymethyl-ethylene carbonate(MEC)have been studied by using Infrared and Raman spectra as a function of concentration of lithium perchlorate.The splitting of ring deformation band and ring ether asymmetric stretching band,and the change of Carbonyl stretching band suggest that there should be a strong interaction between Li+ and the solvent molecules,and the site of solvation should be the oxygen atom of carbonyl group.The apparent solvation number of Li+ was calculated by using band fitting technique.The solvation number was decreased from 3.3 to 1.1 with increasing the concentration of LiClO4/MEC solutions.On the other hand,the band fitting for the ClO ̄4 band revealed the presence of contact ion pair,and free ClO ̄4 anion in the concentrated solutions.

  10. Hybrid Quantum Mechanics/Molecular Mechanics Solvation Scheme for Computing Free Energies of Reactions at Metal-Water Interfaces.

    Science.gov (United States)

    Faheem, Muhammad; Heyden, Andreas

    2014-08-12

    We report the development of a quantum mechanics/molecular mechanics free energy perturbation (QM/MM-FEP) method for modeling chemical reactions at metal-water interfaces. This novel solvation scheme combines planewave density function theory (DFT), periodic electrostatic embedded cluster method (PEECM) calculations using Gaussian-type orbitals, and classical molecular dynamics (MD) simulations to obtain a free energy description of a complex metal-water system. We derive a potential of mean force (PMF) of the reaction system within the QM/MM framework. A fixed-size, finite ensemble of MM conformations is used to permit precise evaluation of the PMF of QM coordinates and its gradient defined within this ensemble. Local conformations of adsorbed reaction moieties are optimized using sequential MD-sampling and QM-optimization steps. An approximate reaction coordinate is constructed using a number of interpolated states and the free energy difference between adjacent states is calculated using the QM/MM-FEP method. By avoiding on-the-fly QM calculations and by circumventing the challenges associated with statistical averaging during MD sampling, a computational speedup of multiple orders of magnitude is realized. The method is systematically validated against the results of ab initio QM calculations and demonstrated for C-C cleavage in double-dehydrogenated ethylene glycol on a Pt (111) model surface.

  11. 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...

  12. 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...

  13. 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.

  14. CPMD simulation of Cu2+ -- phenylalanine complex under micro-solvated environment

    CERN Document Server

    Ganesan, Aravindhan; Wang, Feng; Akola, Jaakko; Larrucea, Julen

    2013-01-01

    The study combines DFT calculations and CPMD simulations to investigate the structures of phenylalanine-copper (II) ([Phe-Cu]2+) complexes and the micro-solvation processes. ....It is found that the phenylalanine moiety appears to be in the neutral form in isolated and mono-hydrated complexes, but in the zwitterionic form in other hydrated complexes (with n no less than 2). .... The present CPMD simulations reveal that the maximum coordination of Cu2+ in the presence of the Phe ligand does not exceed four: the oxygen atoms from three water molecules and one carboxyl oxygen atom of Phe. Any excess water molecules will migrate to the second solvation shell. Moreover a unique structural motif is present in the lowest energy complexes, which is recognized to be significant in stabilizing the structures of the complexes. .....

  15. Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy

    Science.gov (United States)

    Zhang, Bo; Peng, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai; Lu, Benzhuo

    2015-05-01

    We present PAFMPB, an updated and parallel version of the AFMPB software package for fast calculation of molecular solvation-free energy. The new version has the following new features: (1) The adaptive fast multipole method and the boundary element methods are parallelized; (2) A tool is embedded for automatic molecular VDW/SAS surface mesh generation, leaving the requirement for a mesh file at input optional; (3) The package provides fast calculation of the total solvation-free energy, including the PB electrostatic and nonpolar interaction contributions. PAFMPB is implemented in C and Fortran programming languages, with the Cilk Plus extension to harness the computing power of both multicore and vector processing. Computational experiments demonstrate the successful application of PAFMPB to the calculation of the PB potential on a dengue virus system with more than one million atoms and a mesh with approximately 20 million triangles.

  16. 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.

  17. 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 ...

  18. Thermodynamic study of CN~- ion inhibition of Jack bean urease using the extended solvation theory

    Institute of Scientific and Technical Information of China (English)

    G. Rezaei Behbehani; A.A. Saboury; M. Mohebbian; S. Tahmasbi Sarvestani; M. Poorheravi

    2009-01-01

    Cyanide ion was studied as an inhibitor of Jack bean urease at 300 K in 30 mmol/L tris buffer, Ph 7. The inhibition was investigated by isothermal titration calorimetry (ITC). The extended solvation model was used for CN~- + JBU interaction over the whole range of CN~- concentrations. The binding parameters recovered from the solvation model were attributed to the cyanide ion interaction. It was found that cyanide ion acted as a non-cooperative inhibitor of urease, and there is a set of 12 ± 0.12 identical and independent binding sites for CN~- ions. The dissociation equilibrium constant is 749.99 μmol/L. The molar enthalpy of binding is △H=-13.60 KJ mol~(-1).

  19. Green chemistry: A tool in Pharmaceutical Chemistry

    Directory of Open Access Journals (Sweden)

    Smita Talaviya

    2012-07-01

    Full Text Available 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 pharmaceuticals is to utilize eco-friendly, non-hazardous, reproducible and efficient solvents and catalysts in synthesis of drug molecules, drug intermediates and in researches involving synthetic chemistry. Microwave synthesis is also an important tool of green chemistry by being an energy efficient process.

  20. Environmental chemistry: Volume A

    Energy Technology Data Exchange (ETDEWEB)

    Yen, T.F.

    1999-08-01

    This is an extensive introduction to environmental chemistry for engineering and chemical professionals. The contents of Volume A include a brief review of basic chemistry prior to coverage of litho, atmo, hydro, pedo, and biospheres.

  1. CHINESE JOURNAL OF CHEMISTRY

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    @@Chinese Journal of Chemistry is an international journal published in English by the Chinese Chemical Society with its editorial office hosted by Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences.

  2. Solvated electrons at the atmospheric pressure plasma-water anodic interface

    Science.gov (United States)

    Gopalakrishnan, R.; Kawamura, E.; Lichtenberg, A. J.; Lieberman, M. A.; Graves, D. B.

    2016-07-01

    We present results from a particle-in-cell/Monte Carlo model of a dc discharge in argon at atmospheric pressure coupled with a fluid model of an aqueous electrolyte acting as anode to the plasma. The coupled models reveal the structure of the plasma-electrolyte interface and near-surface region, with a special emphasis on solvated or hydrated electrons. Results from the coupled models are in generally good agreement with the experimental results of Rumbach et al (2016 Nat. Commun. 6 7248). Electrons injected from the plasma into the water are solvated, then lost by reaction with water within about 10-20 nm from the surface. The major reaction products are OH- and H2. The solvated electron density profile is controlled by the injected electron current density and subsequent reactions with water, and is relatively independent of the external plasma electric field and the salt concentration in the aqueous electrolyte. Simulations of the effects of added scavenger compounds (H2O2, \\text{NO}2- , \\text{NO}2- and H+) on near-surface solvated electron density generally match the experimental results. The generation of near-surface OH- following electron-water decomposition in the presence of bulk acid creates a highly basic region (pH ~ 11) very near the surface. In the presence of bulk solution acidity, pH can vary from a very acidic pH 2 away from the surface to a very basic pH 11 over a distance of ~200 nm. High near-surface gradients in aqueous solution properties could strongly affect plasma-liquid applications and challenge theoretical understanding of this complex region.

  3. 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...

  4. 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...

  5. Solvation Effects on Hole Mobility in the Poly G/Poly C Duplex

    CERN Document Server

    Lakhno, V D

    2013-01-01

    Theoretical calculations of solvation contribution to hole energy in a polynucleotide chain give very low hole mobility values at zero temperature, \\mu < 10^{-3} cm^2/(V s). We calculated hole mobility at physiological temperature for the Poly G/Poly C DNA duplex, which gave substantially larger mobility values. Mobility over the temperature range 20-400 K was calculated. Taking stacking interaction into account substantially increased hole mobility.

  6. 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.

  7. Organic chemistry experiment

    Energy Technology Data Exchange (ETDEWEB)

    Mun, Seok Sik

    2005-02-15

    This book deals with organic chemistry experiments, it is divided five chapters, which have introduction, the way to write the experiment report and safety in the laboratory, basic experiment technic like recrystallization and extraction, a lot of organic chemistry experiments such as fischer esterification, ester hydrolysis, electrophilic aromatic substitution, aldol reaction, benzoin condensation, wittig reaction grignard reaction, epoxidation reaction and selective reduction. The last chapter introduces chemistry site on the internet and way to find out reference on chemistry.

  8. Frontiers in Gold Chemistry

    OpenAIRE

    Mohamed, Ahmed A.

    2015-01-01

    Basic chemistry of gold tells us that it can bond to sulfur, phosphorous, nitrogen, and oxygen donor ligands. The Frontiers in Gold Chemistry Special Issue covers gold complexes bonded to the different donors and their fascinating applications. This issue covers both basic chemistry studies of gold complexes and their contemporary applications in medicine, materials chemistry, and optical sensors. There is a strong belief that aurophilicity plays a major role in the unending applications of g...

  9. 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.

  10. Thermodynamics for nonequilibrium solvation and numerical evaluation of solvent reorganization energy

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    This work presents a thermodynamic method for treating nonequilibrium solvation. By imposing an extra electric field onto the nonequilibrium solvation system, a virtual constrained equilibrium state is prepared. In this way, the free energy difference between the real nonequilibrium state and the con-strained equilibrium one is simply the potential energy of the nonequilibrium polarization in the extra electronic field, according to thermodynamics. Further, new expressions of nonequilibrium solvation energy and solvent reorganization energy have been formulated. Analysis shows that the present formulations will give a value of reorganization energy about one half of the traditional Marcus theory in polar solvents, thus the explanation on why the traditional theory tends to overestimate this quantity has been found out. For the purpose of numerical determination of solvent reorganization energy, we have modified Gamess program on the basis of dielectric polarizable continuum model. Applying the procedure to the well-investigated intramolecular electron transfer in biphenyl-androstane-naphthyl and biphenyl-androstane-phenanthryl systems, the numerical results of solvent reorganization energy have been found to be in good agreement with the experimental fittings.

  11. How Many Methanol Molecules Can Solvate a Glycine: a PBE1PBE Approach

    Institute of Scientific and Technical Information of China (English)

    WANG Hong-Lei; ZOU Hao; HU Yong-Jun

    2011-01-01

    Microsolvation of glycine in methanol clusters is explored by the use of DFT calculation method. The lowest energy conformations within 16.72 kJ·mol^-1 of the glycine clustering with one to six methanol molecules, which are obtained at the B3LYP/6-31+G(d) level of theory, are reoptimized at PBE1PBE/6-311+G(d,p). The calculated results agree with our previous results with B3LYP (Chin. J. Chem. Phys. 22 (2009) 577) that the clusters of two forms (Z- and N-form) tend to be isoenergetic when the number of the solvate molecules reaches six. Furthermore, this result is in good agreement with the experiment of the tryptophan-methanol clusters, implying that the present treatments are reasonable and reliable. The results also indicate that nine methanol molecules are not enough to fully solvate a glycine molecule, and a tentative estimation is obtained that ten methanol molecules may fully solvate a glycine molecule, which consists with the experiment results.

  12. Solvation of benzophenone anion radical in ethanol and ethanol/2-methyltetrahydrofuran mixture

    International Nuclear Information System (INIS)

    The electron spin-echo modulations and the absoprtion spectra of benzophenone anion radicals generated by γ-irradiation in the glassy matrices of ethanol and ethanol2-methyltetrahydrofuran mixtures have been measured for elucidating the mechanism of spectral shift observed during the solvation of the anion radicals in alcohols. The anion radical generated at 4.2 K in the ethanol matrix maintains the same solvation structure as that of neutral benzophenone. At 77 K ethanol molecules solvate the anion radical by orienting the O-H dipoles toward the anion radical. The anion radical is hydrogen-bonded by two ethanol molecules through the p/sub z/ orbital on the benzophenone oxygen which composes the π orbitals of anion radical. Three kinds of anion radicals are observed in the mixed matrix at 77 K. Two of them are essentially the same as those observed in the ethanol matrix at 4.2 and 77 K. The third has the absorption maximum at 700 nm and is attributed to the anion radical hydrogen-bonded by one ethanol molecule through the p/sub z/ orbital. It is concluded that the spectral shift observed in alcohols is caused by the stabilization of a SOMO π* orbital induced by the hydrogen bonding with the (RO)H--O--H(OR) angle perpendicular to the molecular plane of the anion radical

  13. Structure of Protonated Threonine Dimers in the Gas Phase: Salt-Bridged or Charge-Solvated?

    Science.gov (United States)

    Yin, Hong; Kong, Xianglei

    2015-09-01

    For homodimers of amino acids, their salt-bridged structures are gradually stabilized as the proton affinity of the component amino acid increases. Threonine has a proton affinity value located in the middle of the list of 20 natural amino acids. Thus, identifying whether the most stable isomer of protonated threonine dimer (Thr2H+) has a charge-solvated or salt-bridged structure is important and helpful for understanding the structures of other homodimers. By combining infrared photodissociation (IRPD) spectroscopy and theoretical calculations, the structures of Thr2H+ were investigated. Based on calculations at the M062X/6-311++G(d,p)//M062X/6-311++G(d,p) level, the most stable isomer of Thr2H+ was computed to be a charge-solvated structure, with an energy 3.87 kcal/mol lower than the most stable salt-bridged isomer. The predicted infrared spectrum is in good agreement with the experimental spectrum. To evaluate the temperature effect on the distribution of different isomers, the relative concentrations of the six isomers of Thr2H+ were calculated at different temperatures, according to their partition functions and enthalpies. The results show that the isomers are dominated by charge-solvated structures at a temperature of 300 K.

  14. Interaction Mechanism Insights on the Solvation of Fullerene B(80)with Choline-based Ionic Liquids.

    Science.gov (United States)

    García, Gregorio; Atilhan, Mert; Aparicio, Santiago

    2015-09-24

    Beyond carbon allotropes, other nanostructures such as fullerene B80 are attracting a growing interest due to their potential applications. The use of new materials based on fullerene B80 is still in a premature stage; however many of these applications would require the use of B80 in solution. This paper reports an unprecedented density functional theory (DFT) analysis on the interaction mechanism between B80 and two choline-based ionic liquids as a first insight for the fullerene B80 solvation by ionic liquids. The analysis of properties such as binding energies, charge distributions or intermolecular interactions shed light on the main features, which should govern interaction between ionic liquids and fullerene B80. In addition, the optimization of systems composed by six ionic pairs around a fullerene B80 has supplied some information about the first solvation shell at the molecular level. As a summary, this paper provides the first insights in the rational design of ionic liquids with suitable properties for the solvation of B80.

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

    Science.gov (United States)

    Maggi, Norbert; Arrigo, Patrizio; Ruggiero, Carmelina

    2011-01-01

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

  16. Green Chemistry and Education.

    Science.gov (United States)

    Hjeresen, Dennis L.; Schutt, David L.; Boese, Janet M.

    2000-01-01

    Many students today are profoundly interested in the sustainability of their world. Introduces Green Chemistry and its principles with teaching materials. Green Chemistry is the use of chemistry for pollution prevention and the design of chemical products and processes that are environmentally benign. (ASK)

  17. Dynamics

    CERN Document Server

    Goodman, Lawrence E

    2001-01-01

    Beginning text presents complete theoretical treatment of mechanical model systems and deals with technological applications. Topics include introduction to calculus of vectors, particle motion, dynamics of particle systems and plane rigid bodies, technical applications in plane motions, theory of mechanical vibrations, and more. Exercises and answers appear in each chapter.

  18. Special Feature: Constraints on nebular dynamics and chemistry based on observations of annealed magnesium silicate grains in comets and in disks surrounding Herbig Ae/Be stars

    Science.gov (United States)

    Hill, Hugh G. M.; Grady, Carol A.; Nuth, Joseph A., III; Hallenbeck, Susan L.; Sitko, Michael L.

    2001-02-01

    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 formationextending possibly hundreds of astronomical units (AU) from the sunand that the composition of comets is determined by a chemical reaction network closely coupled to the dynamic transport of dust and gas in the system. This scenario is supported by laboratory studies of Mg silicates and the astronomical data for comets and for protoplanetary disks associated with young stars, which demonstrate that annealing of nebular silicates must occur in conjunction with a large-scale circulation. Mass recycling of dust should have a significant effect on the chemical kinetics of the outer nebula by introducing reduced, gas-phase species produced in the higher temperature and pressure environment of the inner nebula, along with freshly processed grains with "clean" catalytic surfaces to the region of cometesimal formation. Because comets probably form throughout the lifetime of the Solar Nebula and processed (crystalline) grains are not immediately available for incorporation into the first generation of comets, an increasing fraction of dust incorporated into a growing comet should be crystalline olivine and this fraction can serve as a crude chronometer of the relative ages of comets. The formation and evolution of key organic and biogenic molecules in comets are potentially of great consequence to astrobiology.

  19. Constraints on nebular dynamics and chemistry based on observations of annealed magnesium silicate grains in comets and in disks surrounding Herbig Ae/Be stars.

    Science.gov (United States)

    Hill, H G; Grady, C A; Nuth, J A; Hallenbeck, S L; Sitko, M L

    2001-02-27

    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 dust and gas in the system. This scenario is supported by laboratory studies of Mg silicates and the astronomical data for comets and for protoplanetary disks associated with young stars, which demonstrate that annealing of nebular silicates must occur in conjunction with a large-scale circulation. Mass recycling of dust should have a significant effect on the chemical kinetics of the outer nebula by introducing reduced, gas-phase species produced in the higher temperature and pressure environment of the inner nebula, along with freshly processed grains with "clean" catalytic surfaces to the region of cometesimal formation. Because comets probably form throughout the lifetime of the Solar Nebula and processed (crystalline) grains are not immediately available for incorporation into the first generation of comets, an increasing fraction of dust incorporated into a growing comet should be crystalline olivine and this fraction can serve as a crude chronometer of the relative ages of comets. The formation and evolution of key organic and biogenic molecules in comets are potentially of great consequence to astrobiology. PMID:11226213

  20. Mechanistic Insights into Radical-Mediated Oxidation of Tryptophan from ab Initio Quantum Chemistry Calculations and QM/MM Molecular Dynamics Simulations.

    Science.gov (United States)

    Wood, Geoffrey P F; Sreedhara, Alavattam; Moore, Jamie M; Wang, John; Trout, Bernhardt L

    2016-05-12

    An assessment of the mechanisms of (•)OH and (•)OOH radical-mediated oxidation of tryptophan was performed using density functional theory calculations and ab initio plane-wave Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics simulations. For the (•)OH reactions, addition to the pyrrole ring at position 2 is the most favored site with a barrierless reaction in the gas phase. The subsequent degradation of this adduct through a H atom transfer to water was intermittently observed in aqueous-phase molecular dynamics simulations. For the (•)OOH reactions, addition to the pyrrole ring at position 2 is the most favored pathway, in contrast to the situation in the model system ethylene, where concerted addition to the double bond is preferred. From the (•)OOH position 2 adduct QM/MM simulations show that formation of oxy-3-indolanaline occurs readily in an aqueous environment. The observed transformation starts from an initial rupture of the O-O bond followed by a H atom transfer with the accompanying loss of an (•)OH radical to solution. Finally, classical molecular dynamics simulations were performed to equate observed differential oxidation rates of various tryptophan residues in monoclonal antibody fragments. It was found that simple parameters derived from simulation correlate well with the experimental data. PMID:27082439