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Sample records for chemistry solvation dynamics

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

    Energy Technology Data Exchange (ETDEWEB)

    Wishart, J.F.

    2011-06-12

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

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

    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

  3. 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.

  4. 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.

  5. 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.

  6. 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...

  7. Competitive Lithium Solvation of Linear and Cyclic Carbonates from Quantum Chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Borodin, Oleg; Olguin, Marco; Ganesh, P.; Kent, Paul; Allen, Joshua S.; Henderson, Wesley A.

    2015-11-17

    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 with ethylene carbonate:dimethyl carbonate (EC:DMC)-LiPF6 as a model system. A slight 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 (EC:DMC)LiPF6 mixed solvent electrolyte was studied using the BOMD simulations.

  8. 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

  9. 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...

  10. Computational solvation dynamics of oxyquinolinium betaine linked to trehalose

    Science.gov (United States)

    Heid, Esther; Schröder, Christian

    2016-10-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Omelyan, Igor, E-mail: omelyan@ualberta.ca, E-mail: omelyan@icmp.lviv.ua [National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9 (Canada); Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta T6G 2G8 (Canada); Institute for Condensed Matter Physics, National Academy of Sciences of Ukraine, 1 Svientsitskii Street, Lviv 79011 (Ukraine); Kovalenko, Andriy, E-mail: andriy.kovalenko@nrc-cnrc.gc.ca [National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9 (Canada); Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta T6G 2G8 (Canada)

    2013-12-28

    We develop efficient handling of solvation forces in the multiscale method of multiple time step molecular dynamics (MTS-MD) of a biomolecule steered by the solvation free energy (effective solvation forces) obtained from the 3D-RISM-KH molecular theory of solvation (three-dimensional reference interaction site model complemented with the Kovalenko-Hirata closure approximation). To reduce the computational expenses, we calculate the effective solvation forces acting on the biomolecule by using advanced solvation force extrapolation (ASFE) at inner time steps while converging the 3D-RISM-KH integral equations only at large outer time steps. The idea of ASFE consists in developing a discrete non-Eckart rotational transformation of atomic coordinates that minimizes the distances between the atomic positions of the biomolecule at different time moments. The effective solvation forces for the biomolecule in a current conformation at an inner time step are then extrapolated in the transformed subspace of those at outer time steps by using a modified least square fit approach applied to a relatively small number of the best force-coordinate pairs. The latter are selected from an extended set collecting the effective solvation forces obtained from 3D-RISM-KH at outer time steps over a broad time interval. The MTS-MD integration with effective solvation forces obtained by converging 3D-RISM-KH at outer time steps and applying ASFE at inner time steps is stabilized by employing the optimized isokinetic Nosé-Hoover chain (OIN) ensemble. Compared to the previous extrapolation schemes used in combination with the Langevin thermostat, the ASFE approach substantially improves the accuracy of evaluation of effective solvation forces and in combination with the OIN thermostat enables a dramatic increase of outer time steps. We demonstrate on a fully flexible model of alanine dipeptide in aqueous solution that the MTS-MD/OIN/ASFE/3D-RISM-KH multiscale method of molecular dynamics

  12. Atomistic characterization of the active-site solvation dynamics of a model photocatalyst

    Science.gov (United States)

    van Driel, Tim B.; Kjær, Kasper S.; Hartsock, Robert W.; Dohn, Asmus O.; Harlang, Tobias; Chollet, Matthieu; Christensen, Morten; Gawelda, Wojciech; Henriksen, Niels E.; Kim, Jong Goo; Haldrup, Kristoffer; Kim, Kyung Hwan; Ihee, Hyotcherl; Kim, Jeongho; Lemke, Henrik; Sun, Zheng; Sundström, Villy; Zhang, Wenkai; Zhu, Diling; Møller, Klaus B.; Nielsen, Martin M.; Gaffney, Kelly J.

    2016-11-01

    The interactions between the reactive excited state of molecular photocatalysts and surrounding solvent dictate reaction mechanisms and pathways, but are not readily accessible to conventional optical spectroscopic techniques. Here we report an investigation of the structural and solvation dynamics following excitation of a model photocatalytic molecular system [Ir2(dimen)4]2+, where dimen is para-diisocyanomenthane. The time-dependent structural changes in this model photocatalyst, as well as the changes in the solvation shell structure, have been measured with ultrafast diffuse X-ray scattering and simulated with Born-Oppenheimer Molecular Dynamics. Both methods provide direct access to the solute-solvent pair distribution function, enabling the solvation dynamics around the catalytically active iridium sites to be robustly characterized. Our results provide evidence for the coordination of the iridium atoms by the acetonitrile solvent and demonstrate the viability of using diffuse X-ray scattering at free-electron laser sources for studying the dynamics of photocatalysis.

  13. 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.

  14. Dynamic solvation shell and solubility of C60 in organic solvents.

    Science.gov (United States)

    Wang, Chun I; Hua, Chi C; Chen, Show A

    2014-08-21

    The notion of (static) solvation shells has recently proved fruitful in revealing key molecular factors that dictate the solubility and aggregation properties of fullerene species in polar or ionic solvent media. Using molecular dynamics schemes with carefully evaluated force fields, we have scrutinized both the static and the dynamic features of the solvation shells of single C60 particle for three nonpolar organic solvents (i.e., chloroform, toluene, and chlorobenzene) and a range of system temperatures (i.e., T = 250-330 K). The central findings have been that, while the static structures of the solvation shell remain, in general, insensitive to the effects of changing solvent type or system temperature, the dynamic behavior of solvent molecules within the shell exhibits prominent dependence on both factors. Detailed analyses led us to propose the notion of dynamically stable solvation shell, effectiveness of which can be characterized by a new physical parameter defined as the ratio of two fundamental time constants representing, respectively, the solvent relaxation (or residence) time within the first solvation shell and the characteristic time required for the fullerene particle to diffuse a distance comparable to the shell thickness. We show that, for the five (two from the literature) different solvent media and the range of system temperatures examined herein, this parameter bears a value around unity and, in particular, correlates intimately with known trends of solubility for C60 solutions. We also provide evidence revealing that, in addition to fullerene-solvent interactions, solvent-solvent interactions play an important role, too, in shaping the dynamic solvation shell, as implied by recent experimental trends.

  15. Understanding Lithium Solvation and Diffusion through Topological Analysis of First-Principles Molecular Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Bhatia, Harsh [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gyulassy, Attila [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Ong, Mitchell [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Lordi, Vincenzo [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Draeger, Erik [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pask, John [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pascucci, Valerio [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Bremer, Peer -Timo [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-09-27

    The performance of lithium-ion batteries is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact, both, the solvation and diffusivity of Li ions. In this work, we present our application of the topological techniques to extract and predict such behavior in the data generated by the first-principles molecular dynamics simulation of Li ions in an important organic solvent -ethylene carbonate. More specifically, we use the scalar topology of the electron charge density field to analyze the evolution of the solvation structures. This allows us to derive a parameter-free bond definition for lithium-oxygen bonds, to provide a quantitative measure for bond strength, and to understand the regions of influence of each atom in the simulation. This has provided new insights into how and under what conditions certain bonds may form and break. As a result, we can identify and, more importantly, predict, unstable configurations in solvation structures. This can be very useful in understanding when small changes to the atoms' movements can cause significantly different bond structures to evolve. Ultimately, this promises to allow scientists to explore lithium ion solvation and diffusion more systematically, with the aim of new insights and potentially accelerating the calculations themselves.

  16. Solvation dynamics of DCM in a polypeptide-surfactant aggregate: gelatin-sodium dodecyl sulfate.

    Science.gov (United States)

    Halder, Arnab; Sen, Pratik; Burman, Anupam Das; Bhattacharyya, Kankan

    2004-02-03

    Solvation dynamics of 4-(dicyanomethylidene)-2-[p-(dimethylamino)styryl]-6-methyl-4H-pyran (DCM) is studied in a polypeptide-surfactant aggregate consisting of gelatin and sodium dodecyl sulfate (SDS) in potassium dihydrogen phosphate (KP) buffer. The average solvation time (tauS) in gelatin-SDS aggregate at 45 degrees C is found to be 1780 ps, which is about 13 times slower than that in 15 mM SDS in KP buffer at the same temperature. The fluorescence anisotropy decay in gelatin-SDS aggregate is also different from that in SDS micelles in KP buffer. DCM displays negligible emission in the presence of gelatin in aqueous solution. Thus the solvation dynamics in the presence of gelatin and SDS is exclusively due to the probe (DCM) molecules at the gelatin-micelle interface. The slow solvation dynamics is ascribed to the restrictions imposed on the water molecules trapped between the polypeptide chain and micellar aggregates. The critical association concentration (cac) of SDS for gelatin is determined to be 0.5 +/- 0.1 mM.

  17. 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.

  18. 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.

  19. Excited-state solvation and proton transfer dynamics of DAPI in biomimetics and genomic DNA.

    Science.gov (United States)

    Banerjee, Debapriya; Pal, Samir Kumar

    2008-08-14

    The fluorescent probe DAPI (4',6-diamidino-2-phenylindole) is an efficient DNA binder. Studies on the DAPI-DNA complexes show that the probe exhibits a wide variety of interactions of different strengths and specificities with DNA. Recently the probe has been used to report the environmental dynamics of a DNA minor groove. However, the use of the probe as a solvation reporter in restricted environments is not straightforward. This is due to the presence of two competing relaxation processes (intramolecular proton transfer and solvation stabilization) in the excited state, which can lead to erroneous interpretation of the observed excited-state dynamics. In this study, the possibility of using DAPI to unambiguously report the environmental dynamics in restricted environments including DNA is explored. The dynamics of the probe is studied in bulk solvents, biomimetics like micelles and reverse micelles, and genomic DNA using steady-state and picosecond-resolved fluorescence spectroscopies.

  20. Solvation of lithium salts in protic ionic liquids: a molecular dynamics study.

    Science.gov (United States)

    Méndez-Morales, Trinidad; Carrete, Jesús; Cabeza, Óscar; Russina, Olga; Triolo, Alessandro; Gallego, Luis J; Varela, Luis M

    2014-01-23

    The structure of solutions of lithium nitrate in a protic ionic liquid with a common anion, ethylammonium nitrate, at room temperature is investigated by means of molecular dynamics simulations. Several structural properties, such as density, radial distribution functions, hydrogen bonds, spatial distribution functions, and coordination numbers, are analyzed in order to get a picture of the solvation of lithium cations in this hydrogen-bonded, amphiphilically nanostructured environment. The results reveal that the ionic liquid mainly retains its structure upon salt addition, the interaction between the ammonium group of the cation and the nitrate anion being only slightly perturbed by the addition of the salt. Lithium cations are solvated by embedding them in the polar nanodomains of the solution formed by the anions, where they coordinate with the latter in a solid-like fashion reminiscent of a pseudolattice structure. Furthermore, it is shown that the average coordination number of [Li](+) with the anions is 4, nitrate coordinating [Li](+) in both monodentate and bidentate ways, and that in the second coordination layer both ethylammonium cations and other lithiums are also found. Additionally, the rattling motion of lithium ions inside the cages formed by their neighboring anions, indicative of the so-called caging effect, is confirmed by the analysis of the [Li](+) velocity autocorrelation functions. The overall picture indicates that the solvation of [Li](+) cations in this amphiphilically nanostructured environment takes place by means of a sort of inhomogeneous nanostructural solvation, which we could refer to as nanostructured solvation, and which could be a universal solvation mechanism in ionic liquids.

  1. Investigation Solvation Dynamics and Isomerization of Dye IR-140 Using pump supercontinuum-probing Technique

    CERN Document Server

    Wang, D; Wu, S; Yang, H; Xiang, Q G J; Xu, G; Wang, Danling; Jiang, Hongbing; Wu, Songjiang; Yang, Hong; Xiang, Qihuang Gong Junfeng; Xu, Guangzhi

    2001-01-01

    The solvation dynamics and isomerization process of an organic dye, IR-140, in polar solvents and nonpolar solvents have been investigated using pump supercontinuum-probing (PSCP) technique. In all solvents, the dynamics exhibits solvent-dependent. Solvent induced spectral shifts of the absorption and emission spectra of IR-140 have also been studied in a variety of solvents. At the same time, the photoisomerization process has been examined. The approximate energy-band structure of IR-140 was also supposed firstly.

  2. 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.

  3. 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.

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

    Science.gov (United States)

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

    2015-05-21

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

  5. 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...

  6. Architecture and dynamics of proteins and aqueous solvation complexes

    NARCIS (Netherlands)

    Lotze, S.M.

    2015-01-01

    For this thesis, the molecular dynamics of water and biological (model) systems have been studied with advanced nonlinear optical techniques. In chapters 4-5, the technique of femtosecond mid-infrared pump probe spectroscopy has been used to study the energy transfer and the reorientational dynamics

  7. Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery

    Science.gov (United States)

    Lee, Kyung-Koo; Park, Kwanghee; Lee, Hochan; Noh, Yohan; Kossowska, Dorota; Kwak, Kyungwon; Cho, Minhaeng

    2017-01-01

    Lithium cation is the charge carrier in lithium-ion battery. Electrolyte solution in lithium-ion battery is usually based on mixed solvents consisting of polar carbonates with different aliphatic chains. Despite various experimental evidences indicating that lithium ion forms a rigid and stable solvation sheath through electrostatic interactions with polar carbonates, both the lithium solvation structure and more importantly fluctuation dynamics and functional role of carbonate solvent molecules have not been fully elucidated yet with femtosecond vibrational spectroscopic methods. Here we investigate the ultrafast carbonate solvent exchange dynamics around lithium ions in electrolyte solutions with coherent two-dimensional infrared spectroscopy and find that the time constants of the formation and dissociation of lithium-ion···carbonate complex in solvation sheaths are on a picosecond timescale. We anticipate that such ultrafast microscopic fluxional processes in lithium-solvent complexes could provide an important clue to understanding macroscopic mobility of lithium cation in lithium-ion battery on a molecular level. PMID:28272396

  8. 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...

  9. 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.

  10. 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.

  11. 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.

  12. 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...

  13. Temperature-dependent solvation dynamics of water in sodium bis(2-ethylhexyl)sulfosuccinate/isooctane reverse micelles.

    Science.gov (United States)

    Mitra, Rajib Kumar; Sinha, Sudarson Sekhar; Pal, Samir Kumar

    2008-01-01

    In this paper, for the first time, we report a detailed study of the temperature-dependent solvation dynamics of a probe fluorophore, coumarin-500, in AOT/isooctane reverse micelles (RMs) with varying degrees of hydration (w0) of 5, 10, and 20 at four different temperatures, 293, 313, 328, and 343 K. The average solvation time constant becomes faster with the increase in w0 values at a particular temperature. The solvation dynamics of a RM with a fixed w0 value also becomes faster with the increase in temperature. The observed temperature-induced faster solvation dynamics is associated with a transition of bound- to free-type water molecules, and the corresponding activation energy value for the w0 = 5 system has been found to be 3.4 kcal mol-1, whereas for the latter two systems, it is approximately 5 kcal mol-1. Dynamic light scattering measurements indicate an insignificant change in size with temperature for RMs with w0 = 5 and 10, whereas for a w0 = 20 system, the hydrodynamic diameter increases with temperature. Time-resolved fluorescence anisotropy studies reveal a decrease in the rotational restriction on the probe with increasing temperature for all systems. Wobbling-in-cone analysis of the anisotropy data also supports this finding.

  14. Dielectric relaxation and solvation dynamics in a prototypical ionic liquid + dipolar protic liquid mixture: 1-butyl-3-methylimidazolium tetrafluoroborate + water.

    Science.gov (United States)

    Zhang, Xin-Xing; Liang, Min; Hunger, Johannes; Buchner, Richard; Maroncelli, Mark

    2013-12-12

    Dielectric and solvation data on mixtures of 1-butyl-3-methylimidazilium tetrafluoroborate ([Im41][BF4]) + water are reported and used to examine the utility of dielectric solvation models. Dielectric permittivity and loss spectra (25 °C) were recorded over the frequency range 200 MHz to 89 GHz at 17 compositions and fit to a 4-Debye form. Dynamic Stokes shift measurements on the solute coumarin 153 (C153), made by combining fluorescence upconversion (80 fs resolution) and time-correlated single photon counting data (20 ns range), were used to determine the solvation response at 7 compositions (20.5 °C). All properties measured here were found to depend upon mixture composition in a simple continuous manner, especially when viewed in terms of volume fraction. Solvation response functions predicted by a simple dielectric continuum model are similar to but ∼7-fold faster than the spectral response functions measured with C153. The solvation data are in better agreement with the recently published predictions of a semimolecular model of Biswas and co-workers [J. Phys. Chem. B 2011, 115, 4011], but these latter predictions are systematically slow by a factor of ∼3.

  15. Conformational Solvation Studies of LIGNOLs with Molecular Dynamics and Conductor-Like Screening Model

    Directory of Open Access Journals (Sweden)

    Thomas Sandberg

    2012-08-01

    Full Text Available Molecular dynamics (MD simulations were performed on sterically hindered -conidendrin-based chiral 1,4-diols (LIGNOLs from the naturally occurring lignan hydroxymatairesinol (HMR using the GROMACS software. The aim of this study was to explore the conformational behaviour of the LIGNOLs in aqueous solution adopting the TIP4P model. The topologies of the LIGNOLs were constructed manually and they were modeled with the OPLS-AA force field implemented in GROMACS. The four most relevant torsional angles in the LIGNOLs were properly analyzed during the simulations. The determining property for the conformation preferred in aqueous solution was found to be the lowest energy in gas phase. The solvation effects on the LIGNOLs were also studied by quantum chemical calculations applying the COnductor-like Screening MOdel (COSMO. The hydration studies of the MD simulations showed that several of these LIGNOLs, produced from a renewable source, have a great potential of acting as chiral catalysts.

  16. Dynamics of water-alcohol mixtures: Insights from nuclear magnetic resonance, broadband dielectric spectroscopy, and triplet solvation dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Sauer, D.; Schuster, B.; Rosenstihl, M.; Schneider, S.; Blochowicz, T.; Stühn, B.; Vogel, M. [Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstraße 6, 64289 Darmstadt (Germany); Talluto, V.; Walther, T. [Institut für Angewandte Physik, Technische Universität Darmstadt, Schlossgartenstraße 7, 64289 Darmstadt (Germany)

    2014-03-21

    We combine {sup 2}H nuclear magnetic resonance (NMR), broadband dielectric spectroscopy (BDS), and triplet solvation dynamics (TSD) to investigate molecular dynamics in glass-forming mixtures of water and propylene glycol in very broad time and temperature ranges. All methods yield consistent results for the α process of the studied mixtures, which hardly depends on the composition and shows Vogel-Fulcher temperature dependence as well as Cole-Davidson spectral shape. The good agreement between BDS and TDS data reveals that preferential solvation of dye molecules in microheterogeneous mixtures does not play an important role. Below the glass transition temperature T{sub g}, NMR and BDS studies reveal that the β process of the mixtures shows correlation times, which depend on the water concentration, but exhibit a common temperature dependence, obeying an Arrhenius law with an activation energy of E{sub a} = 0.54  eV, as previously reported for mixtures of water with various molecular species. Detailed comparison of NMR and BDS correlation functions for the β process unravels that the former decay faster and more stretched than the latter. Moreover, the present NMR data imply that propylene glycol participates in the β process and, hence, it is not a pure water process, and that the mechanism for molecular dynamics underlying the β process differs in mixtures of water with small and large molecules.

  17. Excitation-energy dependence of solvation dynamics in room-temperature ionic liquids

    Science.gov (United States)

    Kim, Daekeon; Park, Sang-Won; Shim, Youngseon; Kim, Hyung J.; Jung, YounJoon

    2016-07-01

    Influence of the excitation energy of a probe solute molecule on its solvation dynamics and emission spectrum in 1-ethyl-3-methylimidazolium hexafluorophosphate (EMI+PF6-) is studied via molecular dynamics simulations using a coarse-grained model description. By exciting the probe at different energies, each with an extremely narrow distribution, ensuing solvent relaxation and its dynamic variance are monitored using the isoconfigurational ensemble method. Resulting Stokes shift function, S(t), indicates that long-time solvent relaxation becomes slower with the decreasing excitation energy and approaches the equilibrium correlation function, C(t), of solvent fluctuations. This suggests that the system excited at the red-edge of the spectrum observes linear response better than that at the blue-edge. A detailed analysis of nonequilibrium trajectories shows that the effect of initial configurations on variance of relaxation dynamics is mainly confined to short times; it reaches a maximum around 0.1 ≲ t ≲ 1 ps and diminishes as time further increases. The influence of the initial velocity distribution, on the other hand, tends to grow with time and dominates the long-time variations of dynamics. The emission spectrum shows the red-edge effect in accord with previous studies.

  18. 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

  19. First principles pKa calculations on carboxylic acids using the SMD solvation model: effect of thermodynamic cycle, model chemistry, and explicit solvent molecules.

    Science.gov (United States)

    Sutton, Catherine C R; Franks, George V; da Silva, Gabriel

    2012-10-04

    Aqueous pK(a) values are calculated from first principles for a set of carboxylic acids using the SMD solvation model with various model chemistries, thermodynamic cycles, and treatments of explicit solvation. In all, 108 unique theoretical protocols are examined. The direct (D) and water proton exchange (PX) cycles are trialled along with a new approach, termed the semidirect (SD) cycle. The SD thermodynamic cycle offers some improvements over the D and PX schemes, as it bypasses the gas-phase heterolytic bond dissociation calculation required in the conventional D approach while also avoiding an aqueous OH(-) calculation required by the PX method when using water as the reference acid. With all three cycles, the recommended model chemistry employs M05-2X/cc-pVTZ Gibbs energies of solvation with a single discrete water molecule and a high-level composite method for the gas-phase reaction energies. With the SD cycle, these calculations result in a mean unsigned error of less than 1 pK(a) units, with respective mean signed error and maximum unsigned error of less than 0.5 and 2 pK(a) units. Similar results are obtained with the D and PX cycles, and further improvement is required in both the gas and aqueous phase ab initio energy calculations before we can truly discriminate between the thermodynamic cycles investigated here.

  20. 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

    In liquid phase chemistry dynamic solute solvent interactions often govern the path, ultimate outcome, and efficiency of chemical reactions. These steps involve many-body movements on subpicosecond time scales and thus ultrafast structural tools capable of capturing both intramolecular electronic...

  1. 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.

  2. Solvation dynamics of coumarin 153 embedded in AOT + phenol organogels studied by time-resolved fluorescence spectroscopy

    Science.gov (United States)

    Nishiyama, Katsura; Takata, Kei; Watanabe, Keiichi; Shigematsu, Hirotake

    2012-03-01

    We investigate solvation dynamics of organogel utilizing ps-ns fluorescence spectroscopy. The organogel studied in this Letter comprises bis(2-ethylhexyl) sulfosuccinate (AOT) and p-chlorophenol in the m-xylene solvent, that produce an organogel architecture with self-assembly. Within the organogel, an emitting probe, coumarin 153 (C153), is embedded. We then obtain dynamic response functions of solvation derived from the time-resolved fluorescence spectra of C153. We propose that total energy of the C153-organogel system relaxes with a relaxation time of 3.9 ns, whereas the entire rearrangement of the organogel structure around C153 is achieved with that of 6.1 ns, respectively.

  3. Thermochemistry and Dynamics of Reactive Species: Nitrogen-rich Compounds, Metals and SiC Clusters in Free and Solvated Environment

    Science.gov (United States)

    2005-10-31

    of Reactive Species : Nitrogen-rich F49620-02-1-0371 Compounds, Metals and SiC clusters in Free and Solvated Environments Sb. GRANT NUMBER 5c. PROGRAM...F49620-02-1-0371 Thermochemistry and Dynamics of Reactive Species : Nitrogen-rich Compounds, Metals, and SiC clusters in Free and Solvated Environments...research program remain the same as before: obtaining fundamental thermochemical and dynamical data on reactive species Status of Effort This report

  4. 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...

  5. Atomistic characterization of the active-site solvation dynamics of a model photocatalyst

    DEFF Research Database (Denmark)

    Brandt van Driel, Tim; Kjær, Kasper Skov; Hartsock, Robert W.

    2016-01-01

    The interactions between the reactive excited state of molecular photocatalysts and surrounding solvent dictate reaction mechanisms and pathways, but are not readily accessible to conventional optical spectroscopic techniques. Here we report an investigation of the structural and solvation dynami...

  6. Adsorption and solvation of ethanol at the water liquid-vapor interface: a molecular dynamics study

    Science.gov (United States)

    Wilson, M. A.; Pohorille, A.

    1997-01-01

    The free energy profiles of methanol and ethanol at the water liquid-vapor interface at 310K were calculated using molecular dynamics computer simulations. Both alcohols exhibit a pronounced free energy minimum at the interface and, therefore, have positive adsorption at this interface. The surface excess was computed from the Gibbs adsorption isotherm and was found to be in good agreement with experimental results. Neither compound exhibits a free energy barrier between the bulk and the surface adsorbed state. Scattering calculations of ethanol molecules from a gas phase thermal distribution indicate that the mass accommodation coefficient is 0.98, and the molecules become thermalized within 10 ps of striking the interface. It was determined that the formation of the solvation structure around the ethanol molecule at the interface is not the rate-determining step in its uptake into water droplets. The motion of an ethanol molecule in a water lamella was followed for 30 ns. The time evolution of the probability distribution of finding an ethanol molecule that was initially located at the interface is very well described by the diffusion equation on the free energy surface.

  7. Nonadiabatic dynamics of photoinduced proton-coupled electron transfer in a solvated phenol-amine complex.

    Science.gov (United States)

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

    2015-02-12

    Photoinduced concerted electron-proton transfer (EPT), denoted photo-EPT, is important for a wide range of energy conversion processes. Transient absorption and Raman spectroscopy experiments on the hydrogen-bonded p-nitrophenylphenol-t-butylamine complex, solvated in 1,2-dichloroethane, suggested that this complex may undergo photo-EPT. The experiments probed two excited electronic states that were interpreted as an intramolecular charge transfer (ICT) state and an EPT state. Herein mixed quantum mechanical/molecular mechanical nonadiabatic surface hopping dynamics is used to investigate the relaxation pathways following photoexcitation. The potential energy surface is generated on the fly with a semiempirical floating occupation molecular orbital complete active space configuration interaction method for the solute molecule and a molecular mechanical force field for the explicit solvent molecules. The free energy curves along the proton transfer coordinate illustrate that proton transfer is thermodynamically and kinetically favorable on the lower-energy excited state but not on the higher-energy excited state, supporting the characterization of these states as EPT and ICT, respectively. The nonadiabatic dynamics simulations indicate that the population decays from the ICT state to the EPT state in ∼100 fs and from the EPT state to the ground state on the slower time scale of ∼1 ps, qualitatively consistent with the experimental measurements. For ∼54% of the trajectories, the proton transfers from the phenol to the amine in ∼400 fs on the EPT state and then transfers back to the phenol rapidly upon decay to the ground state. Thus, these calculations augment the original interpretation of the experimental data by providing evidence of proton transfer on the EPT state prior to decay to the ground state. The fundamental insights obtained from these simulations are also relevant to other photo-EPT processes.

  8. 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...

  9. 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.

  10. Solvation simplified

    Directory of Open Access Journals (Sweden)

    Omar A. El Seoud

    2010-01-01

    Full Text Available The effects of solvents on chemical phenomena is complex because there are various solute-solvent interaction mechanisms. Solvatochromism refers to the effects of solvents on the spectra of probes. The study of this phenomenon sheds light on the relative importance of the solvation mechanisms. Solvation in pure solvents is quantitatively analyzed in terms of a multi-parameter equation. In binary solvent mixtures, solvation is analyzed by considering the organic solvent, S, water, W, and a 1:1 hydrogen bonded species (S-W. The applications of solvatochromism to understand distinct chemical phenomena, reactivity and swelling of cellulose, is briefly discussed.

  11. 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

  12. 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).

  13. 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".

  14. Molecular dynamics for irradiation driven chemistry

    DEFF Research Database (Denmark)

    Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

    2016-01-01

    that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... capable to operate with a large library of classical potentials, many-body force fields and their combinations. IDMD opens a broad range of possibilities for modelling of irradiation driven modifications and chemistry of complex molecular systems ranging from radiotherapy cancer treatments to the modern...... technologies such as focused electron beam deposition (FEBID). As an example, the new methodology is applied for studying the irradiation driven chemistry caused by FEBID of tungsten hexacarbonyl W(CO)6 precursor molecules on a hydroxylated SiO2 surface. It is demonstrated that knowing the interaction...

  15. Nonequilibrium versus equilibrium molecular dynamics studies of solvation dynamics after photoexcitation of OCIO.

    Science.gov (United States)

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

    2007-10-28

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

  16. Controlling Chemistry in Dynamic Nanoscale Systems

    DEFF Research Database (Denmark)

    Jesorka, Aldo; Lizana, Ludvig; Konkoli, Zoran

    2011-01-01

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

  17. 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.

  18. 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

  19. Understanding solvation

    OpenAIRE

    SEOUD, Omar A. El

    2009-01-01

    The effects of solvents on different chemical phenomena, including reactivity, spectroscopic data, and swelling of biopolymers can be rationalized by use of solvatochromic probes, substances whose UV-vis spectra, absorption, or emission are sensitive to the properties of the medium. Thermo-solvatochromism refers to the effect of temperature on solvatochromism. The study of both phenomena sheds light on the relative importance of the factors that contribute to solvation, namely, properties of ...

  20. Density dependence of the entropy and the solvation shell structure in supercritical water via molecular dynamics simulation.

    Science.gov (United States)

    Ma, Haibo

    2012-06-07

    We perform molecular dynamics simulations of supercritical water (SCW) with a wide range of densities along a near critical isotherm using the simple point charge extended (SPC/E) pair potential in order to study the entropy and the solvation shell structure around a central water molecule. It is shown that both the translational and orientational two-particle correlation entropy terms can serve as the metrics of the translational-orientational structural orders in water and it is revealed that the translational structural order is very sensitive to the density variation in the gas-like and liquid-like region, while the orientational structural order is much more dependent upon compression in the medium-density SCW region. The comparison of the magnitudes of the full thermodynamic excess entropy and two-particle correlation entropy confirms the recent findings that the many-body terms other than two-body ones also present significant and non-neglectable contributions to the full excess entropy for the highly anomalous fluids like water. The analysis of entropy terms as a function of intermolecular distance and the orientational distribution functions as well as the three-dimensional spatial distribution functions indicate that the structural order occurs only in a much more diffused first solvation shell due to the elongated hydrogen bonds under supercritical conditions. It is revealed that no obvious second or higher neighbor shells occur in SCW, in contrast with the feature of normal liquid water that the anomalous decrease of translational order upon compression occurs mainly in the second shell.

  1. 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

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

    NARCIS (Netherlands)

    Noort, van P.C.M.

    2012-01-01

    braham solvation equations find widespread use in environmental chemistry. Until now, the intercept in these equations was determined by fitting experimental data. To simplify the determination of the coefficients in Abraham solvation equations, this study derives theoretical expressions for the val

  3. Evidence of coexistence of change of caged dynamics at T(g) and the dynamic transition at T(d) in solvated proteins.

    Science.gov (United States)

    Capaccioli, S; Ngai, K L; Ancherbak, S; Paciaroni, A

    2012-02-16

    Mössbauer spectroscopy and neutron scattering measurements on proteins embedded in solvents including water and aqueous mixtures have emphasized the observation of the distinctive temperature dependence of the atomic mean square displacements, , commonly referred to as the dynamic transition at some temperature T(d). At low temperatures, increases slowly, but it assumes stronger temperature dependence after crossing T(d), which depends on the time/frequency resolution of the spectrometer. Various authors have made connection of the dynamics of solvated proteins, including the dynamic transition to that of glass-forming substances. Notwithstanding, no connection is made to the similar change of temperature dependence of obtained by quasielastic neutron scattering when crossing the glass transition temperature T(g), generally observed in inorganic, organic, and polymeric glass-formers. Evidences are presented here to show that such a change of the temperature dependence of from neutron scattering at T(g) is present in hydrated or solvated proteins, as well as in the solvent used, unsurprisingly since the latter is just another organic glass-former. If unaware of the existence of such a crossover of at T(g), and if present, it can be mistaken as the dynamic transition at T(d) with the ill consequences of underestimating T(d) by the lower value T(g) and confusing the identification of the origin of the dynamic transition. The obtained by neutron scattering at not so low temperatures has contributions from the dissipation of molecules while caged by the anharmonic intermolecular potential at times before dissolution of cages by the onset of the Johari-Goldstein β-relaxation or of the merged α-β relaxation. The universal change of at T(g) of glass-formers, independent of the spectrometer resolution, had been rationalized by sensitivity to change in volume and entropy of the dissipation of the caged molecules and its contribution to . The same rationalization applies

  4. 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

  5. Solvation Dynamics of CO₂(g) by Monoethanolamine at the Gas-Liquid Interface: A Molecular Mechanics Approach.

    Science.gov (United States)

    Huang, I-Shou; Li, Jia-Jen; Tsai, Ming-Kang

    2016-12-23

    A classical force field approach was used to characterize the solvation dynamics of high-density CO₂(g) by monoethanolamine (MEA) at the air-liquid interface. Intra- and intermolecular CO₂ and MEA potentials were parameterized according to the energetics calculated at the MP2 and BLYP-D2 levels of theory. The thermodynamic properties of CO₂ and MEA, such as heat capacity and melting point, were consistently predicted using this classical potential. An approximate interfacial simulation for CO₂(g)/MEA(l) was performed to monitor the depletion of the CO₂(g) phase, which was influenced by amino and hydroxyl groups of MEA. There are more intramolecular hydrogen bond interactions notably identified in the interfacial simulation than the case of bulk MEA(l) simulation. The hydroxyl group of MEA was found to more actively approach CO₂ and overpower the amino group to interact with CO₂ at the air-liquid interface. With artificially reducing the dipole moment of the hydroxyl group, CO₂-amino group interaction was enhanced and suppressed CO₂(g) depletion. The hydroxyl group of MEA was concluded to play dual but contradictory roles for CO₂ capture.

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

    Science.gov (United States)

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

  7. 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.

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

    Science.gov (United States)

    Reif, Maria M; Hünenberger, Philippe H

    2016-08-25

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

  9. Perturbation of hydration layer in solvated proteins by external electric and electromagnetic fields: Insights from non-equilibrium molecular dynamics

    Science.gov (United States)

    Nandi, Prithwish K.; Futera, Zdenek; English, Niall J.

    2016-11-01

    Given the fundamental role of water in governing the biochemistry of enzymes, and in regulating their wider biological activity (e.g., by local water concentration surrounding biomolecules), the influence of extraneous electric and electromagnetic (e/m) fields thereon is of central relevance to biophysics and, more widely, biology. With the increase in levels of local and atmospheric microwave-frequency radiation present in modern life, as well as other electric-field exposure, the impact upon hydration-water layers surrounding proteins, and biomolecules generally, becomes a particularly pertinent issue. Here, we present a (non-equilibrium) molecular-dynamics-simulation study on a model protein (hen egg-white lysozyme) hydrated in water, in which we determine, inter alia, translational self-diffusivities for both hen egg-white lysozyme and its hydration layer together with relaxation dynamics of the hydrogen-bond network between the protein and its hydration-layer water molecules on a residue-per-residue basis. Crucially, we perform this analysis both above and below the dynamical-transition temperature (at ˜220 K), at 300 and 200 K, respectively, and we compare the effects of external static-electric and e/m fields with linear-response-régime (r.m.s.) intensities of 0.02 V/Å. It was found that the translational self-diffusivity of hen egg-white lysozyme and its hydration-water layer are increased substantially in static fields, primarily due to the induced electrophoretic motion, whilst the water-protein hydrogen-bond-network-rearrangement kinetics can also undergo rather striking accelerations, primarily due to the enhancement of a larger-amplitude local translational and rotational motion by charged and dipolar residues, which serves to promote hydrogen-bond breakage and re-formation kinetics. These external-field effects are particularly evident at 200 K, where they serve to induce the protein- and solvation-layer-response effects redolent of dynamical

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-10-31

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

  11. 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.

  12. 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...

  13. 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.

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

    Science.gov (United States)

    Takayanagi, Toshiyuki; Shiga, Motoyuki

    2002-08-01

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

  15. 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.

  16. Studies on the solvation dynamics of coumarin 153 in 1-ethyl-3-methylimidazolium alkylsulfate ionic liquids: dependence on alkyl chain length.

    Science.gov (United States)

    Das, Sudhir Kumar; Sarkar, Moloy

    2012-08-06

    Steady-state and time-resolved fluorescence behavior of coumarin 153 (C153) is investigated in a series of 1-ethyl-3-methylimidazolium alkylsulfate ([C(2)mim][C(n)OSO(3)]) ionic liquids differing only in the length of the linear alkyl chain (n = 4, 6, and 8) in the anion. The aim of the present study is to understand the role of alkyl chain length in solute rotation and solvation dynamics of C153 in these ionic liquids. The blueshift observed in the steady-state absorption and emission maxima of C153 on going from the C(4)OSO(3) to the C(8)OSO(3) system indicates increasing nonpolar character of the microenvironment of the solute with increasing length of the alkyl side chain of the anion of the ionic liquids. The average solvation time is also found to increase on changing the substituent from butyl to octyl, and this is attributed to the increase in the bulk viscosity of the ILs. A steady blueshift of the time-zero maximum of the fluorescence spectrum with increasing alkyl chain length also indicates that the probe molecule experiences a less polar environment in the early part of the dynamics. Rotational dynamics of C153 are also analyzed by using the Stokes-Einstein-Debye (SED), Gierer-Wirtz (GW), and Dote-Kivelson-Schwartz (DKS) theories. Analyses of the results seem to suggest decoupling of the rotational motion of the probe from solvent viscosity.

  17. Dynamics and Chemistry of Planet Construction

    Science.gov (United States)

    Taylor, G. J.

    2010-03-01

    Sophisticated calculations of how planetesimals assembled into the terrestrial planets can be tested by using models of the chemistry of the solar nebula. Jade Bond (previously at University of Arizona and now at the Planetary Science Institute, Tucson, AZ), Dante Lauretta (University of Arizona) and Dave O'Brien (Planetary Sciences Institute) combined planetary accretion simulations done by O'Brien, Alessandro Morbidelli (Observatoire de Nice, France), and Hal Levison (Southwest Research Institute, Boulder) with calculations of the solar nebula chemistry as a function of time and distance from the Sun to determine the overall chemical composition of the planets formed in the simulations. They then compared the simulated planets with the compositions of Earth and Mars. The simulated planets have chemical compositions similar to real planets, indicating that the accretion calculations are reasonable. Questions remain about the accretion of water and other highly volatile compounds, including C and N, which are essential for life.

  18. Aqueous solvation of Hg(OH)2: energetic and dynamical density functional theory studies of the Hg(OH)2-(H2O)n (n = 1-24) structures.

    Science.gov (United States)

    Amaro-Estrada, J I; Maron, L; Ramírez-Solís, A

    2013-09-19

    A systematic study of the hydration of Hg(OH)2 by the stepwise solvation approach is reported. The optimized structures, solvation energies, and incremental free energies of 1-24 water molecules interacting with the solute have been computed at the B3PW91 level using 6-31G(d,p) basis sets for the O and H atoms. The mercury atom was treated with the Stuttgart-Köln relativistic core potential in combination with an extended optimized valence basis set. One to three direct Hg-water interactions appear along the solvation process. The first solvation shell is fully formed with 24 water molecules. A stable pentacoordinated Hg trigonal bipyramid structure appears for n > 15. Density functional theory (DFT) Born-Oppenheimer molecular dynamics simulations showed the thermal stability of the Hg(OH)2-(H2O)24 structure at room temperature and the persistence of the trigonal bipyramid coordination around Hg. The Gibbs free energy for the first solvation shell is significantly larger for the fully solvated Hg(OH)2 than the one previously obtained for the HgCl2 case, due to σ-acceptor and π-donor properties involving the hydroxyl groups of the solute. This suggests that the transmembrane passage of Hg(OH)2 into the cell via simple diffusion is less favorable compared to the case when the metal is coordinated with two Cl groups.

  19. 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.

  20. 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.

  1. 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]-.

  2. 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.

  3. Supramolecular Chirality in Dynamic Coordination Chemistry

    Directory of Open Access Journals (Sweden)

    Hiroyuki Miyake

    2014-10-01

    Full Text Available Labile metal complexes have a useful coordination bond; which is weaker than a covalent C–C bond and is reversibly and dynamically formed and dissociated. Such labile metal complexes also can be used to construct chiral shapes and offer dynamic conversion of chiral molecular shapes in response to external stimuli. This review provides recent examples of chirality induction and describes the dynamic conversion systems produced by chiral metal complexes including labile metal centers, most of which respond to external stimuli by exhibiting sophisticated conversion phenomena.

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

    DEFF Research Database (Denmark)

    Sørensen, Anne

    experimentally and theoretically and found to be unique in organoselenium chemistry by proceeding through a four-membered cyclic transition state following first-order kinetics. Subsequently, this thesis illustrates how an aliphatic diselenide could be used to catalyse the formation of a disulfide based dynamic......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...... 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...

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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

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

    Directory of Open Access Journals (Sweden)

    J. G. Anet

    2013-06-01

    conclude that especially UV and volcanic eruptions dominate the changes in the ozone, temperature and dynamics while the NOx field is dominated by the EPP. Visible radiation changes have only very minor effects on both stratospheric dynamics and chemistry.

  11. Thermodynamic, dynamic and solvational properties of PDEδ binding to farnesylated cystein: a model study for uncovering the molecular mechanism of PDEδ interaction with prenylated proteins.

    Science.gov (United States)

    Suladze, S; Ismail, S; Winter, R

    2014-01-30

    The protein PDEδ is an important solubilizing factor for several prenylated proteins including the Ras subfamily members. The binding occurs mainly through the farnesyl anchor of Ras proteins, which is recognized by a hydrophobic pocket of PDEδ. In this study, we carried out a detailed study of the thermodynamic and solvational properties of PDEδ binding to farnesyl-cystein, which serves as a model for PDEδ association to prenylated proteins. Using various biophysical approaches in conjunction with theoretical considerations, we show here that binding of the largely hydrophobic ligand surprisingly has enthalpy-driven signature, and the entropy change is largely controlled by the fine balance between the hydrational and conformational terms. Moreover, binding of PDEδ to farnesyl-cystein is accompanied by an increase in thermal stability, the release of about 150 water molecules from the interacting species, a decrease in solvent accessible surface area, and a marked decrease of the volume fluctuations and hence dynamics of the protein. Altogether, our results shed more light on the molecular mechanism of PDEδ interaction with prenylated Ras proteins, which is also prerequisite for an optimization of the structure-based molecular design of drugs against Ras related diseases and for understanding the multitude of biological functions of PDEδ.

  12. Biomolecular electrostatics and solvation: a computational perspective.

    Science.gov (United States)

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

    2012-11-01

    An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

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

    Science.gov (United States)

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

  14. 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.

  15. Dynamics and Chemistry of Marine Stratocumulus (DYCOMS) Experiment.

    Science.gov (United States)

    Lenschow, D. H.; Paluch, I. R.; Bandy, A. R.; Pearson, R., Jr.; Kawa, S. R.; Weaver, C. J.; Huebert, B. J.; Kay, J. G.; Thornton, D. C.; Driedger, A. R., III

    1988-09-01

    A combined atmospheric chemistry-meteorology experiment, the Dynamics and Chemistry of the Marine Stratocumulus (DYCOMS), was carried out during the summer of 1985 over the eastern Pacific Ocean using the NCAR Electra aircraft. The objectives were to 1) study the budgets of several trace reactive species in a relatively pristine, steady-state, horizontally homogeneous, well-mixed boundary layer capped by a strong inversion and 2) study the formation. maintenance and dissipation of marine stratocumulus that persists off the California coast (as well as similar regions elsewhere) in summer. We obtained both mean and turbulence measurements of meteorological variables within and above the cloud-capped boundary layer that is typical of this region. Ozone was used successfully as a tracer for estimating entrainment rate. We found, however, that horizontal variability was large enough for ozone that a correction needs to be included in the ozone budget for the horizontal displacement due to turns even though the airplane was allowed to drift with the wind. The time rate-of-change term was significant in both the ozone and radon budgets; as a result, a considerably longer time interval than the two hours used between sets of flight legs would be desirable to improve the measurement accuracy of this tern.

  16. 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 photoexcitat......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...

  17. 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.

  18. 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.

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

    Science.gov (United States)

    Habershon, Scott

    2014-05-21

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

  20. Future Arctic ozone recovery: the importance of chemistry and dynamics

    Science.gov (United States)

    Bednarz, Ewa M.; Maycock, Amanda C.; Abraham, N. Luke; Braesicke, Peter; Dessens, Olivier; Pyle, John A.

    2016-09-01

    Future trends in Arctic springtime total column ozone, and its chemical and dynamical drivers, are assessed using a seven-member ensemble from the Met Office Unified Model with United Kingdom Chemistry and Aerosols (UM-UKCA) simulating the period 1960-2100. The Arctic mean March total column ozone increases throughout the 21st century at a rate of ˜ 11.5 DU decade-1, and is projected to return to the 1980 level in the late 2030s. However, the integrations show that even past 2060 springtime Arctic ozone can episodically drop by ˜ 50-100 DU below the corresponding long-term ensemble mean for that period, reaching values characteristic of the near-present-day average level. Consistent with the global decline in inorganic chlorine (Cly) over the century, the estimated mean halogen-induced chemical ozone loss in the Arctic lower atmosphere in spring decreases by around a factor of 2 between the periods 2001-2020 and 2061-2080. However, in the presence of a cold and strong polar vortex, elevated halogen-induced ozone losses well above the corresponding long-term mean continue to occur in the simulations into the second part of the century. The ensemble shows a significant cooling trend in the Arctic winter mid- and upper stratosphere, but there is less confidence in the projected temperature trends in the lower stratosphere (100-50 hPa). This is partly due to an increase in downwelling over the Arctic polar cap in winter, which increases transport of ozone into the polar region as well as drives adiabatic warming that partly offsets the radiatively driven stratospheric cooling. However, individual winters characterised by significantly suppressed downwelling, reduced transport and anomalously low temperatures continue to occur in the future. We conclude that, despite the projected long-term recovery of Arctic ozone, the large interannual dynamical variability is expected to continue in the future, thereby facilitating episodic reductions in springtime ozone columns

  1. 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…

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

    Science.gov (United States)

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

    2016-07-01

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

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

    Science.gov (United States)

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

    2016-07-01

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

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

    CERN Document Server

    Hazra, Milan

    2016-01-01

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

  5. 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.

  6. Femtosecond Soft X-ray Spectroscopy of Solvated Transition-Metal Complexes: Deciphering the Interplay of Electronic and Structural Dynamics

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-04-21

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

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

    CERN Document Server

    Chaban, Vitaly

    2014-01-01

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

  8. Crossing the Boundaries within Computational Chemistry: From Molecular Dynamics to Cheminformatics and back.

    Science.gov (United States)

    Riniker, Sereina

    2014-09-01

    The research in the group for computational chemistry at the ETH Zurich focuses on the development of methods and software for classical molecular dynamics simulations and cheminformatics, and their application to biological and chemical questions. Here, important advances and challenges in these subfields of computational chemistry are reviewed and potential opportunities for cross-fertilization are outlined.

  9. 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.

  10. 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.

  11. Structures and Time-Evolution Dynamics of Solvated Electron in Ionic Liquids%离子液中溶剂化电子的结构及其演化动力学

    Institute of Scientific and Technical Information of China (English)

    步宇翔

    2012-01-01

    本文综述了离子型液体介质中过剩电子的结构、存在状态及其时间演化动力学特征。基于从头算分子动力学模拟及计算结果,重点阐述了咪唑型、吡啶型、碱金属离子型熔盐氯化物离子液中与过剩电子溶剂化密切相关的溶剂化能量学、结构特征、可能的存在状态以及态-态转化稳态动力学机制,分析了此类离子型介质中电子高效传导的内在本质及离子液组成离子的重要作用。阳离子的最低未占轨道组成的导带结构是离子液中过剩电子的溶剂化态及其稳定性的决定因素,任何能影响或改变其导带结构的因素均能显著影响过剩电子溶剂化。但快速的态-态转化及电子迁移并不明显取决于其组成离子扩散动力学,而是敏感地受离子液涨落所控制。这种基于溶剂化电子的迁移模式构成了此类离子型介质甚至其他液态介质中电子转移的新途径。%Structures,states and time-evolution dynamics of excess electron in ionic liquid media are surveyed.On the basis of the ab initio calculations and molecular dynamics simulations,we discussed the solvation energetics,structural characters,possible existing states and state-to-state conversion mechanisms associated with solvation of excess electron in the imidazolium-type,the pyridinium-type,and the quaternary ammonium-type chloride room temperature ionic liquids,and a representative alkali-metal halide molten salt,and analyzed the nature of efficient conduction of electrons in such media and the important role of constituent ions of the ionic liquids.The conduction band structure consisted of the lowest unoccupied molecular orbitals of the cations is a decisive factor in determining the solvated states and stability of the excess electron in ionic liquids,and any factors which affect or change the conduction band structure do considerably affect solvation of excess electron in ionic liquids.However,the rapid state

  12. 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.

  13. Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics.

    Science.gov (United States)

    Ufimtsev, Ivan S; Martinez, Todd J

    2009-10-13

    We demonstrate that a video gaming machine containing two consumer graphical cards can outpace a state-of-the-art quad-core processor workstation by a factor of more than 180× in Hartree-Fock energy + gradient calculations. Such performance makes it possible to run large scale Hartree-Fock and Density Functional Theory calculations, which typically require hundreds of traditional processor cores, on a single workstation. Benchmark Born-Oppenheimer molecular dynamics simulations are performed on two molecular systems using the 3-21G basis set - a hydronium ion solvated by 30 waters (94 atoms, 405 basis functions) and an aspartic acid molecule solvated by 147 waters (457 atoms, 2014 basis functions). Our GPU implementation can perform 27 ps/day and 0.7 ps/day of ab initio molecular dynamics simulation on a single desktop computer for these systems.

  14. Cluster-continuum quasichemical theory calculation of the lithium ion solvation in water, acetonitrile and dimethyl sulfoxide: an absolute single-ion solvation free energy scale.

    Science.gov (United States)

    Carvalho, Nathalia F; Pliego, Josefredo R

    2015-10-28

    Absolute single-ion solvation free energy is a very useful property for understanding solution phase chemistry. The real solvation free energy of an ion depends on its interaction with the solvent molecules and on the net potential inside the solute cavity. The tetraphenyl arsonium-tetraphenyl borate (TATB) assumption as well as the cluster-continuum quasichemical theory (CC-QCT) approach for Li(+) solvation allows access to a solvation scale excluding the net potential. We have determined this free energy scale investigating the solvation of the lithium ion in water (H2O), acetonitrile (CH3CN) and dimethyl sulfoxide (DMSO) solvents via the CC-QCT approach. Our calculations at the MP2 and MP4 levels with basis sets up to the QZVPP+diff quality, and including solvation of the clusters and solvent molecules by the dielectric continuum SMD method, predict the solvation free energy of Li(+) as -116.1, -120.6 and -123.6 kcal mol(-1) in H2O, CH3CN and DMSO solvents, respectively (1 mol L(-1) standard state). These values are compatible with the solvation free energy of the proton of -253.4, -253.2 and -261.1 kcal mol(-1) in H2O, CH3CN and DMSO solvents, respectively. Deviations from the experimental TATB scale are only 1.3 kcal mol(-1) in H2O and 1.8 kcal mol(-1) in DMSO solvents. However, in the case of CH3CN, the deviation reaches a value of 9.2 kcal mol(-1). The present study suggests that the experimental TATB scale is inconsistent for CH3CN. A total of 125 values of the solvation free energy of ions in these three solvents were obtained. These new data should be useful for the development of theoretical solvation models.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. Dynamics of the Chemistry of Electronically Excited Atoms in Defined Quantum States.

    Science.gov (United States)

    1978-05-01

    laser development . In essence, this research concerns itself with the elucidation of the role of electronic energy in affecting the chemistry or photochemistry of excited halogen atoms and molecules. While much is known about the dynamics of chemical and physical processes which are carried out on the lowest potential energy hypersurface correlating with reactants and products in their electronic ground state, relatively little is known about the dynamics of such phenomena as energy transfer and chemical reactivity on higher-lying potential

  3. 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.

  4. 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 are p...

  5. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Schurhammer, R

    2001-12-15

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

  7. 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.

  8. Structure, solvation, and dynamics of Mg{sup 2+}, Ca{sup 2+}, Sr{sup 2+}, and Ba{sup 2+} complexes with 3-hydroxyflavone and perchlorate anion in acetonitrile medium: A molecular dynamics simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Agieienko, Vira N.; Kolesnik, Yaroslav V.; Kalugin, Oleg N., E-mail: onkalugin@gmail.com [Department of Inorganic Chemistry, V. N. Karazin Kharkiv National University, Kharkiv 61022 (Ukraine)

    2014-05-21

    Molecular dynamics simulations of complexes of Mg{sup 2+}, Ca{sup 2+}, Sr{sup 2+}, and Ba{sup 2+} with 3-hydroxyflavone (flavonol, 3HF) and ClO {sub 4}{sup −} in acetonitrile were performed. The united atoms force field model was proposed for the 3HF molecule using the results of DFT quantum chemical calculations. 3HF was interpreted as a rigid molecule with two internal degrees of freedom, i.e., rotation of the phenyl ring and of the OH group with respect to the chromone moiety. The interatomic radial distribution functions showed that interaction of the cations with flavonol occurs via the carbonyl group of 3HF and it is accompanied with substitution of one of the acetonitrile molecules in the cations’ first solvation shells. Formation of the cation–3HF complexes does not have significant impact on the rotation of the phenyl ring with respect to the chromone moiety. However, the orientation of the flavonol's OH-group is more sensitive to the interaction with doubly charged cations. When complex with Mg{sup 2+} is formed, the OH-group turns out of the plane of the chromone moiety that leads to rupture of intramolecular H-bond in the ligand molecule. Complexation of Ca{sup 2+}, Sr{sup 2+}, and BaClO {sub 4}{sup +} with 3HF produces two structures with different OH-positions, as in the free flavonol with the intramolecular H-bond and as in the complex with Mg{sup 2+} with disrupted H-bonding. It was shown that additional stabilization of the [MgClO{sub 4}(3HF)]{sup +} and [BaClO{sub 4}(3HF)]{sup +} complexes is determined by strong affinity of perchlorate anion to interact with flavonol via intracomplex hydrogen bond between an oxygen atom of the anion and the hydrogen atom of the 3-hydroxyl group. Noticeable difference in the values of the self-diffusion coefficients for Kt{sup 2+} from one side and ClO {sub 4}{sup −}, 3HF, and AN in the cations’ coordination shell from another side implies quite weak interaction between cation, anion, and ligands in

  9. Dynamical mean-field theory for quantum chemistry.

    Science.gov (United States)

    Lin, Nan; Marianetti, C A; Millis, Andrew J; Reichman, David R

    2011-03-04

    The dynamical mean-field concept of approximating an unsolvable many-body problem in terms of the solution of an auxiliary quantum impurity problem, introduced to study bulk materials with a continuous energy spectrum, is here extended to molecules, i.e., finite systems with a discrete energy spectrum. The application to small clusters of hydrogen atoms yields ground state energies which are competitive with leading quantum chemical approaches at intermediate and large interatomic distances as well as good approximations to the excitation spectrum.

  10. JACOB: a dynamic database for computational chemistry benchmarking.

    Science.gov (United States)

    Yang, Jack; Waller, Mark P

    2012-12-21

    JACOB (just a collection of benchmarks) is a database that contains four diverse benchmark studies, which in-turn included 72 data sets, with a total of 122,356 individual results. The database is constructed upon a dynamic web framework that allows users to retrieve data from the database via predefined categories. Additional flexibility is made available via user-defined text-based queries. Requested sets of results are then automatically presented as bar graphs, with parameters of the graphs being controllable via the URL. JACOB is currently available at www.wallerlab.org/jacob.

  11. A dynamic model reduction algorithm for atmospheric chemistry models

    Science.gov (United States)

    Santillana, Mauricio; Le Sager, Philippe; Jacob, Daniel J.; Brenner, Michael

    2010-05-01

    Understanding the dynamics of the chemical composition of our atmosphere is essential to address a wide range of environmental issues from air quality to climate change. Current models solve a very large and stiff system of nonlinear advection-reaction coupled partial differential equations in order to calculate the time evolution of the concentration of over a hundred chemical species. The numerical solution of this system of equations is difficult and the development of efficient and accurate techniques to achieve this has inspired research for the past four decades. In this work, we propose an adaptive method that dynamically adjusts the chemical mechanism to be solved to the local environment and we show that the use of our approach leads to accurate results and considerable computational savings. Our strategy consists of partitioning the computational domain in active and inactive regions for each chemical species at every time step. In a given grid-box, the concentration of active species is calculated using an accurate numerical scheme, whereas the concentration of inactive species is calculated using a simple and computationally inexpensive formula. We demonstrate the performance of the method by application to the GEOS-Chem global chemical transport model.

  12. Biophysical chemistry.

    Science.gov (United States)

    Häussinger, Daniel; Pfohl, Thomas

    2010-01-01

    Biophysical chemistry at the Department of Chemistry, University of Basel, covers the NMR analysis of protein-protein interaction using paramagnetic tags and sophisticated microscopy techniques investigating the dynamics of biological matter.

  13. Seasonal changes in Titan's middle-atmosphere chemistry and dynamics

    Science.gov (United States)

    Teanby, N. A.; Irwin, P. G. J.; Nixon, C. A.; de Kok, R.; Vinatier, S.; Coustenis, A.; Sefton-Nash, E.; Calcutt, S. B.; Flasar, F. M.

    2013-09-01

    Titan is the largest satellite of Saturn and is the only moon in our solar system with a significant atmo- sphere. Titan's middle-atmosphere (stratosphere and mesosphere) circulation usually comprises a single hemisphere to hemisphere meridional circulation cell, with upwelling air in the summer hemisphere and sub- siding air at the winter pole with an associated winter polar vortex. Titan has an axial tilt (obliquity) of 26.7°, so during its 29.5 Earth year annual cycle pronounced seasonal effects are encountered as the relative solar insolation in each hemisphere changes. The most dramatic of these changes is the reversal in global meridional circulation as the peak solar heating switches hemispheres after an equinox. Titan's northern spring equinox occurred in August 2009, and since then many middle-atmosphere changes have been observed by Cassini that were previously impossible to study (1,2,3,4). Here we present a detailed analysis of the post equinox changes in middle-atmosphere temperature and composition measured with Cassini's Composite InfraRed Spectrometer (CIRS), use these to infer changes in atmospheric circulation, and explore implications for atmospheric photochemical and dynamical processes. Our results show that the meridional circulation has now reversed (1).

  14. Redefining solubility parameters: the partial solvation parameters.

    Science.gov (United States)

    Panayiotou, Costas

    2012-03-21

    The present work reconsiders a classical and universally accepted concept of physical chemistry, the solubility parameter. Based on the insight derived from modern quantum chemical calculations, a new definition of solubility parameter is proposed, which overcomes some of the inherent restrictions of the original definition and expands its range of applications. The original single solubility parameter is replaced by four partial solvation parameters reflecting the dispersion, the polar, the acidic and the basic character of the chemical compounds as expressed either in their pure state or in mixtures. Simple rules are adopted for the definition and calculation of these four parameters and their values are tabulated for a variety of common substances. In contrast, however, to the well known Hansen solubility parameters, their design and evaluation does not rely exclusively on the basic rule of "similarity matching" for solubility but it makes also use of the other basic rule of compatibility, namely, the rule of "complementarity matching". This complementarity matching becomes particularly operational with the sound definition of the acidic and basic components of the solvation parameter based on the third σ-moments of the screening charge distributions of the quantum mechanics-based COSMO-RS theory. The new definitions are made in a simple and straightforward manner, thus, preserving the strength and appeal of solubility parameter stemming from its simplicity. The new predictive method has been applied to a variety of solubility data for systems of pharmaceuticals and polymers. The results from quantum mechanics calculations are critically compared with the results from Abraham's acid/base descriptors.

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

    Science.gov (United States)

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

    1995-01-01

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

  16. 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.

  17. Domain decomposition for implicit solvation models.

    Science.gov (United States)

    Cancès, Eric; Maday, Yvon; Stamm, Benjamin

    2013-08-07

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

  18. 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...

  19. Proton Solvation and Transport in Aqueous and Biomolecular Systems: Insights from Computer Simulations

    OpenAIRE

    Swanson, Jessica M. J.; Maupin, C. Mark; Chen, Hanning; Petersen, Matt K.; Xu, Jiancong; Wu, Yujie; Voth, Gregory A.

    2007-01-01

    The excess proton in aqueous media plays a pivotal role in many fundamental chemical (e.g., acid-base chemistry) and biological (e.g., bioenergetics and enzyme catalysis) processes. Understanding the hydrated proton is, therefore, crucial for chemistry, biology, and materials sciences. Although well studied for over 200 years, excess proton solvation and transport remains to this day mysterious, surprising, and perhaps even misunderstood. In this feature article various efforts to address thi...

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

    Science.gov (United States)

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

  1. INFLUENCE OF SOLVENT ON INTRAMOLECULAR PROTON-TRANSFER IN HYDROGEN MALONATE - MOLECULAR-DYNAMICS SIMULATION STUDY OF TUNNELING BY DENSITY-MATRIX EVOLUTION AND NONEQUILIBRIUM SOLVATION

    NARCIS (Netherlands)

    MAVRI, J; BERENDSEN, HJC; VANGUNSTEREN, WF

    1993-01-01

    A density matrix evolution (DME) method (Berendsen, H. J. C.; Mavri, J. J. Phys. Chem. the preceding paper in this issue) in combination with classical molecular dynamics simulation was applied to calculate the rate of proton tunneling in the intramolecular double-well hydrogen bond of hydrogen malo

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

    Science.gov (United States)

    In the current paper we address the effect of solvation on the landscape of alpha-linked glucose residues. The solvent is introduced via the implicit solvation models COSMO and PCM. Geometry optimizations, at the B3LYP/6-311++G** level of theory with and without implicit solvation were carried out...

  3. On the solvation of L-aspartic acid

    Science.gov (United States)

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

    2004-01-01

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

  4. Trends in Mesospheric Dynamics and Chemistry: Simulations With a Model of the Entire Atmosphere

    Science.gov (United States)

    Brasseur, G. P.

    2005-05-01

    The cooling resulting from infrared CO2 radiative transfer is a major contribution to the energy budget of the middle atmosphere and thermosphere. The rapid increase of the atmospheric CO2 concentration resulting from anthropogenic emissions is therefore expected to lead, in general, to a substantial cooling in this height range. This can potentially be counteracted by heating due to absorption of near infrared radiation by CO2. Changes in ozone as a consequence of increasing methane and water vapor may also have an impact on the energy budget as dynamical changes caused by increased tropospheric temperatures. By means of numerical simulations with a general circulation and chemistry model of the entire atmosphere we will address the following questions: 1.) Can state-of-the-art atmospheric modeling explain the mesospheric temperature trends observed during the last decades? 2.)Which part of the temperature changes resulting from an increase of atmospheric CO2 is caused by local changes in the radiative budget and which part is influenced by remote dynamical effects? The model used is the newly developed Hamburg Model of the Neutral and Ionized Atmosphere (HAMMONIA) that resolves the atmosphere from the Earth's surface up to about 250 km altitude, and is based on the 3-D dynamics from the ECHAM5 general circulation model and the chemistry scheme from MOZART-3. Results from different time slice experiment representative of years 1970 and 2000, and for a doubling of CO2 will be presented.

  5. Dynamic covalent chemistry of bisimines at the solid/liquid interface monitored by scanning tunnelling microscopy

    Science.gov (United States)

    Ciesielski, Artur; El Garah, Mohamed; Haar, Sébastien; Kovaříček, Petr; Lehn, Jean-Marie; Samorì, Paolo

    2014-11-01

    Dynamic covalent chemistry relies on the formation of reversible covalent bonds under thermodynamic control to generate dynamic combinatorial libraries. It provides access to numerous types of complex functional architectures, and thereby targets several technologically relevant applications, such as in drug discovery, (bio)sensing and dynamic materials. In liquid media it was proved that by taking advantage of the reversible nature of the bond formation it is possible to combine the error-correction capacity of supramolecular chemistry with the robustness of covalent bonding to generate adaptive systems. Here we show that double imine formation between 4-(hexadecyloxy)benzaldehyde and different α,ω-diamines as well as reversible bistransimination reactions can be achieved at the solid/liquid interface, as monitored on the submolecular scale by in situ scanning tunnelling microscopy imaging. Our modular approach enables the structurally controlled reversible incorporation of various molecular components to form sophisticated covalent architectures, which opens up perspectives towards responsive multicomponent two-dimensional materials and devices.

  6. 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.

  7. 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.

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

    Science.gov (United States)

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

    2017-01-01

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

  9. An Analysis of the Thermodynamics of Hydrophobic Solvation Based on Scaled Particle Theory

    CERN Document Server

    Qian, H

    2001-01-01

    A comprehensive, semi-quantitative model for the thermodynamics of hydrophobic solvation is presented. The model is based on a very simple premise suggested by the scaled particle theory and treats both solute and solvent molecules as hard spheres. A connection between the peculiarly large heat-capacity change for hydrophobic solvation and the large temperature dependence of the thermal expansivity of water is found. Analysis reveals a possible physical origin for the converging behavior of solvation entropies for a series of homologous hydrophobic compounds. The model suggests that the low solubility and the large heat-capacity change of hydrophobic solvation stem from two distinct aspects of water molecules: the static geometry of the molecule and the dynamic hydrogen bonding network, respectively.

  10. Updated Abraham solvation parameters for polychlorinated biphenyls

    NARCIS (Netherlands)

    van Noort, 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

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

    Directory of Open Access Journals (Sweden)

    Kyung Hwan Kim

    2014-01-01

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

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

    DEFF Research Database (Denmark)

    Larsen, Dennis

    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......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...... gave a 50-fold higher second-order rate constant than the best thiourea catalyst reported for this transformation. A dual Hammett plot analysis and interaction studies by NMR spectroscopy lends support to a reaction mechanism proceeding via an asynchronous [2+2] cycloaddition. The third and final part...

  13. Molecular dynamics for irradiation driven chemistry: application to the FEBID process*

    Science.gov (United States)

    Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

    2016-10-01

    A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package capable to operate with a large library of classical potentials, many-body force fields and their combinations. IDMD opens a broad range of possibilities for modelling of irradiation driven modifications and chemistry of complex molecular systems ranging from radiotherapy cancer treatments to the modern technologies such as focused electron beam deposition (FEBID). As an example, the new methodology is applied for studying the irradiation driven chemistry caused by FEBID of tungsten hexacarbonyl W(CO)6 precursor molecules on a hydroxylated SiO2 surface. It is demonstrated that knowing the interaction parameters for the fragments of the molecular system arising in the course of irradiation one can reproduce reasonably well experimental observations and make predictions about the morphology and molecular composition of nanostructures that emerge on the surface during the FEBID process.

  14. 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.

  15. 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.

  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. Using nonlocal electrostatics for solvation free energy computations ions and small molecules

    CERN Document Server

    Hildebrandt, A; Blossey, R; Lenhof, H P

    2002-01-01

    Solvation free energy is an important quantity in Computational Chemistry with a variety of applications, especially in drug discovery and design. The accurate prediction of solvation free energies of small molecules in water is still a largely unsolved problem, which is mainly due to the complex nature of the water-solute interactions. In this letter we develop a scheme for the determination of the electrostatic contribution to the solvation free energy of charged molecules based on nonlocal electrostatics involving a minimal parameter set which in particular allows to introduce atomic radii in a consistent way. We test our approach on simple ions and small molecules for which both experimental results and other theoretical descriptions are available for quantitative comparison. We conclude that our approach is both physically transparent and quantitatively reliable.

  18. 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

    2016-07-05

    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.

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

    Science.gov (United States)

    Sedlmeier, Felix; Netz, Roland R

    2013-03-21

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

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

    Directory of Open Access Journals (Sweden)

    P. Roldin

    2010-08-01

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

  1. 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.

  2. Making the Earth: Combining Dynamics and Chemistry in the Solar System

    CERN Document Server

    Bond, Jade C; O'Brien, David P

    2009-01-01

    No terrestrial planet formation simulation completed to date has considered the detailed chemical composition of the planets produced. While many have considered possible water contents and late veneer compositions, none have examined the bulk elemental abundances of the planets produced as an important check of formation models. Here we report on the first study of this type. Bulk elemental abundances based on disk equilibrium studies have been determined for the simulated terrestrial planets of O'Brien et al. (2006). These abundances are in excellent agreement with observed planetary values, indicating that the models of O'Brien et al. (2006) are successfully producing planets comparable to those of the Solar System in terms of both their dynamical and chemical properties. Significant amounts of water are accreted in the present simulations, implying that the terrestrial planets form "wet" and do not need significant water delivery from other sources. Under the assumption of equilibrium controlled chemistry...

  3. Partial Overhaul and Initial Parallel Optimization of KINETICS, a Coupled Dynamics and Chemistry Atmosphere Model

    Science.gov (United States)

    Nguyen, Howard; Willacy, Karen; Allen, Mark

    2012-01-01

    KINETICS is a coupled dynamics and chemistry atmosphere model that is data intensive and computationally demanding. The potential performance gain from using a supercomputer motivates the adaptation from a serial version to a parallelized one. Although the initial parallelization had been done, bottlenecks caused by an abundance of communication calls between processors led to an unfavorable drop in performance. Before starting on the parallel optimization process, a partial overhaul was required because a large emphasis was placed on streamlining the code for user convenience and revising the program to accommodate the new supercomputers at Caltech and JPL. After the first round of optimizations, the partial runtime was reduced by a factor of 23; however, performance gains are dependent on the size of the data, the number of processors requested, and the computer used.

  4. 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.

  5. Solvation dynamics in liquids and glasses

    NARCIS (Netherlands)

    Lazonder, Kees; Wiersma, D. A.

    2006-01-01

    Glas maken is één van die technologieën waar de mensheid al lang gebruikt van maakt. Al zo’n vijf duizend jaar om precies te zijn. Dus je zou denken dat we inmiddels wel bijna alles weten wat er over glazen te weten valt. Nou, dat valt tegen. Zeker wanneer je de kennis die we hebben van de fysica va

  6. 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...

  7. Sparingly Solvating Electrolytes for High Energy Density Lithium-Sulfur Batteries

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Lei; Curtiss, Larry A.; Zavadil, Kevin R.; Gewirth, Andrew A.; Shao, Yuyan; Gallagher, Kevin

    2016-07-11

    Moving to lighter and less expensive battery chemistries compared to lithium-ion requires the control of energy storage mechanisms based on chemical transformations rather than intercalation. Lithium sulfur (Li/S) has tremendous theoretical specific energy, but contemporary approaches to control this solution-mediated, precipitation-dissolution chemistry requires using large excesses of electrolyte to fully solubilize the polysulfide intermediate. Achieving reversible electrochemistry under lean electrolyte operation is the only path for Li/S to move beyond niche applications to potentially transformational performance. An emerging topic for Li/S research is the use of sparingly solvating electrolytes and the creation of design rules for discovering new electrolyte systems that fundamentally decouple electrolyte volume from reaction mechanism. This perspective presents an outlook for sparingly solvating electrolytes as the key path forward for longer-lived, high-energy density Li/S batteries including an overview of this promising new concept and some strategies for accomplishing it.

  8. 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.

  9. Room temperature ionic liquid in confined media: a temperature dependence solvation study in [bmim][BF4]/BHDC/benzene reverse micelles.

    Science.gov (United States)

    Pramanik, Rajib; Ghatak, Chiranjib; Rao, Vishal Govind; Sarkar, Souravi; Sarkar, Nilmoni

    2011-05-19

    In this work, we reported a detailed study of the solvation dynamics of coumarin-480 in [bmim][BF(4)]/BHDC/benzene reverse micelles (RMs) with varying [bmim][BF(4)]/BHDC molar ratio (R) 1.00, 1.25, 1.50, and also study the solvation dynamics at five different temperatures from 15 to 35 °C RMs at [bmim][BF(4)]/BHDC molar ratio 1.25 for the first time. The average solvation time constant becomes slightly faster with the increase in R values at a temperature 25 °C. The solvation dynamics of the RMs with R value 1.25 becomes faster with the increase in temperature. We have also investigated temperature-dependent solvation dynamics in neat [bmim][BF(4)]. The solvation dynamics in neat [bmim][BF(4)] has a substantial temperature effect but for the [bmim][BF(4)]/BHDC/benzene RMs the temperature effect on the solvation dynamics is not that significant. Time-resolved fluorescence anisotropy studies reveal a decrease in the rotational restriction on the probe with increasing temperature. Wobbling-in-cone analysis of the anisotropy data also supports this finding.

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

    Science.gov (United States)

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

    2014-12-19

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

  11. 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.

  12. SPECTROSCOPIC STUDIES OF STRUCTURE, DYNAMICS AND REACTIVITY IN IONIC LIQUIDS.

    Energy Technology Data Exchange (ETDEWEB)

    WISHART,J.F.

    2007-11-30

    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

  13. Effect of water chemistry upsets on the dynamics of corrective reagent dosing systems at thermal power stations

    Science.gov (United States)

    Voronov, V. N.; Yegoshina, O. V.; Bolshakova, N. A.; Yarovoi, V. O.; Latt, Aie Min

    2016-12-01

    Typical disturbances in the dynamics of a corrective reagent dosing system under unsteady-state conditions during the unsatisfactory operation of a chemical control system with some water chemistry upsets at thermal and nuclear power stations are considered. An experimental setup representing a physical model for the water chemistry control system is described. The two disturbances, which are most frequently encountered in water chemistry control practice, such as a breakdown or shutdown of temperature compensation during pH measurement and an increase in the heat-transfer fluid flow rate, have been modeled in the process of study. The study of the effect produced by the response characteristics of chemical control analyzers on the operation of a reagent dosing system under unsteady-state conditions is important for the operative control of a water chemistry regime state. The effect of temperature compensation during pH measurement on the dynamics of an ammonia-dosing system in the manual and automatic cycle chemistry control modes has been studied. It has been demonstrated that the reading settling time of a pH meter in the manual ammonia- dosing mode grows with a breakdown in temperature compensation and a simultaneous increase in the temperature of a heat-transfer fluid sample. To improve the efficiency of water chemistry control, some systems for the quality control of a heat-transfer fluid by a chemical parameter with the obligatory compensation of a disturbance in its flow rate have been proposed for use. Experimental results will possibly differ from industrial data due to a great length of sampling lines. For this reason, corrective reagent dosing systems must be adapted to the conditions of a certain power-generating unit in the process of their implementation.

  14. 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.

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

    Science.gov (United States)

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

  16. 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...

  17. 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.

  18. A continuum model of solvation energies including electrostatic, dispersion, and cavity contributions.

    Science.gov (United States)

    Duignan, Timothy T; Parsons, Drew F; Ninham, Barry W

    2013-08-15

    Physically accurate continuum solvent models that can calculate solvation energies are crucial to explain and predict the behavior of solute particles in water. Here, we present such a model applied to small spherical ions and neutral atoms. It improves upon a basic Born electrostatic model by including a standard cavity energy and adding a dispersion component, consistent with the Born electrostatic energy and using the same cavity size parameter. We show that the well-known, puzzling differences between the solvation energies of ions of the same size is attributable to the neglected dispersion contribution. This depends on dynamic polarizability as well as size. Generally, a large cancellation exists between the cavity and dispersion contributions. This explains the surprising success of the Born model. The model accurately reproduces the solvation energies of the alkali halide ions, as well as the silver(I) and copper(I) ions with an error of 12 kJ mol(-1) (±3%). The solvation energy of the noble gases is also reproduced with an error of 2.6 kJ mol(-1) (±30%). No arbitrary fitting parameters are needed to achieve this. This model significantly improves our understanding of ionic solvation and forms a solid basis for the investigation of other ion-specific effects using a continuum solvent model.

  19. Predicting hydrophobic solvation by molecular simulation: 1. Testing united-atom alkane models.

    Science.gov (United States)

    Jorge, Miguel; Garrido, Nuno M; Simões, Carlos J V; Silva, Cândida G; Brito, Rui M M

    2017-03-05

    We present a systematic test of the performance of three popular united-atom force fields-OPLS-UA, GROMOS and TraPPE-at predicting hydrophobic solvation, more precisely at describing the solvation of alkanes in alkanes. Gibbs free energies of solvation were calculated for 52 solute/solvent pairs from Molecular Dynamics simulations and thermodynamic integration making use of the IBERCIVIS volunteer computing platform. Our results show that all force fields yield good predictions when both solute and solvent are small linear or branched alkanes (up to pentane). However, as the size of the alkanes increases, all models tend to increasingly deviate from experimental data in a systematic fashion. Furthermore, our results confirm that specific interaction parameters for cyclic alkanes in the united-atom representation are required to account for the additional excluded volume within the ring. Overall, the TraPPE model performs best for all alkanes, but systematically underpredicts the magnitude of solvation free energies by about 6% (RMSD of 1.2 kJ/mol). Conversely, both GROMOS and OPLS-UA systematically overpredict solvation free energies (by ∼13% and 15%, respectively). The systematic trends suggest that all models can be improved by a slight adjustment of their Lennard-Jones parameters. © 2016 Wiley Periodicals, Inc.

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

    CERN Document Server

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

    2003-01-01

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

  1. Protein-Directed Dynamic Combinatorial Chemistry: A Guide to Protein Ligand and Inhibitor Discovery

    Directory of Open Access Journals (Sweden)

    Renjie Huang

    2016-07-01

    Full Text Available Protein-directed dynamic combinatorial chemistry is an emerging technique for efficient discovery of novel chemical structures for binding to a target protein. Typically, this method relies on a library of small molecules that react reversibly with each other to generate a combinatorial library. The components in the combinatorial library are at equilibrium with each other under thermodynamic control. When a protein is added to the equilibrium mixture, and if the protein interacts with any components of the combinatorial library, the position of the equilibrium will shift and those components that interact with the protein will be amplified, which can then be identified by a suitable biophysical technique. Such information is useful as a starting point to guide further organic synthesis of novel protein ligands and enzyme inhibitors. This review uses literature examples to discuss the practicalities of applying this method to inhibitor discovery, in particular, the set-up of the combinatorial library, the reversible reactions that may be employed, and the choice of detection methods to screen protein ligands from a mixture of reversibly forming molecules.

  2. Active Upper-atmosphere Chemistry and Dynamics from Polar Circulation Reversal on Titan

    Science.gov (United States)

    Teanby, Nicholas A.; Irwin, Patrick Gerard Joseph; Nixon, Conor A.; DeKok, Remco; Vinatier, Sandrine; Coustenis, Athena; Sefton-Nash, Elliot; Calcutt, Simon B.; Flasar, Michael F.

    2012-01-01

    Saturn's moon Titan has a nitrogen atmosphere comparable to Earth's, with a surface pressure of 1.4 bar. Numerical models reproduce the tropospheric conditions very well but have trouble explaining the observed middle-atmosphere temperatures, composition and winds. The top of the middle-atmosphere circulation has been thought to lie at an altitude of 450 to 500 kilometres, where there is a layer of haze that appears to be separated from the main haze deck. This 'detached' haze was previously explained as being due to the colocation of peak haze production and the limit of dynamical transport by the circulation's upper branch. Herewe report a build-up of trace gases over the south pole approximately two years after observing the 2009 post-equinox circulation reversal, from which we conclude that middle-atmosphere circulation must extend to an altitude of at least 600 kilometres. The primary drivers of this circulation are summer-hemisphere heating of haze by absorption of solar radiation and winter-hemisphere cooling due to infrared emission by haze and trace gases; our results therefore imply that these effects are important well into the thermosphere (altitudes higher than 500 kilometres). This requires both active upper-atmosphere chemistry, consistent with the detection of high-complexity molecules and ions at altitudes greater than 950 kilometres, and an alternative explanation for the detached haze, such as a transition in haze particle growth from monomers to fractal structures.

  3. Smart macrocyclic molecules: induced fit and ultrafast self-sorting inclusion behavior through dynamic covalent chemistry.

    Science.gov (United States)

    Han, Ji-Min; Pan, Jin-Long; Lei, Ting; Liu, Chenjiang; Pei, Jian

    2010-12-10

    A family of macrocycles with oligo(ethylene glycol) chains, 4O, 5O, and 6O, was developed to construct a series of new incorporated macrocycles through dynamic covalent chemistry. These flexible macrocycles exhibited excellent "self-sorting" abilities with diamine compounds, which depended on the "induced-fit" rule. For instance, the host macrocycles underwent conformational modulation to accommodate the diamine guests, affording [1+1] intramolecular addition compounds regardless of the flexibility of the diamine. These macrocycles folded themselves to fit various diamines with different chain length through modulation of the flexible polyether chain, and afforded intramolecular condensation products. However, if the chain of the diamine was too long and rigid, oligomers or polymers were obtained from the mixture of the macromolecule and the diamine. All results demonstrated that inclusion compounds involving conformationally suitable aromatic diamines were thermodynamically favorable candidates in the mixture due to the restriction of the macrocycle size. Furthermore, kinetic and thermodynamic studies of self-sorting behaviors of both mixed 4O-5O and 4O-6O systems were investigated in detail. Finally, theoretical calculations were also employed to further understand such self-sorting behavior, and indicated that the large enthalpy change of H(2)NArArNH(2)@4O is the driving force for the sorting behavior. Our system may provide a model to further understand the principle of biomolecules with high specificity due only to their conformational self-adjusting ability.

  4. Making the Earth: Combining dynamics and chemistry in the Solar System

    Science.gov (United States)

    Bond, Jade C.; Lauretta, Dante S.; O'Brien, David P.

    2010-02-01

    No terrestrial planet formation simulation completed to date has considered the detailed chemical composition of the planets produced. While many have considered possible water contents and late veneer compositions, none have examined the bulk elemental abundances of the planets produced as an important check of formation models. Here we report on the first study of this type. Bulk elemental abundances based on disk equilibrium studies have been determined for the simulated terrestrial planets of O'Brien et al. [O'Brien, D.P., Morbidelli, A., Levison, H.F., 2006. Icarus 184, 39-58]. These abundances are in excellent agreement with observed planetary values, indicating that the models of O'Brien et al. [O'Brien, D.P., Morbidelli, A., Levison, H.F., 2006. Icarus 184, 39-58] are successfully producing planets comparable to those of the Solar System in terms of both their dynamical and chemical properties. Significant amounts of water are accreted in the present simulations, implying that the terrestrial planets form "wet" and do not need significant water delivery from other sources. Under the assumption of equilibrium controlled chemistry, the biogenic species N and C still need to be delivered to the Earth as they are not accreted in significant proportions during the formation process. Negligible solar photospheric pollution is produced by the planetary formation process. Assuming similar levels of pollution in other planetary systems, this in turn implies that the high metallicity trend observed in extrasolar planetary systems is in fact primordial.

  5. 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...

  6. 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.

  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. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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...

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

    Science.gov (United States)

    Dorai, Rajesh; Kushner, Mark J.

    2003-05-01

    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.

  14. 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.

  15. Applications of dynamic nuclear polarization to the study of reactions and reagents in organic and biomolecular chemistry.

    Science.gov (United States)

    Hilty, Christian; Bowen, Sean

    2010-08-07

    Nuclear Magnetic Resonance (NMR) is an important spectroscopic tool for the identification and structural characterization of molecules in chemistry and biochemistry. The most significant limitation of NMR compared to other spectroscopies is its relatively low sensitivity, which thus often requires long measurement times or large amounts of sample. A way of increasing sensitivity of single scan NMR spectra by several orders of magnitude is through hyperpolarization of nuclear spins. Dynamic nuclear polarization allows hyperpolarization of most spins in small molecules encountered in chemistry and biochemistry. NMR spectra of small amounts of samples from natural source, or from chemical synthesis can readily be acquired. Perhaps more interestingly, the availability of the entire hyperpolarized NMR signal in one single scan allows the measurement of transient processes in real time, if applied together with a stopped-flow technique. Through observation of chemical shift, different reactant and product species can be distinguished, and kinetics and mechanisms, for example in enzyme catalyzed reactions, can be elucidated. Real-time hyperpolarization-enhanced NMR is uniquely amenable to correlating atomic positions not only through space, but also over time between reactant and product species. Such correlations carry mechanistic information about a reaction, and can prove reaction pathways. Applications of this technique are emerging in different areas of chemistry concerned with rapid reactions, including not only enzymatic processes, but also chemical catalysis and protein folding.

  16. Tris(3-aminophenylphosphine oxide ethanol solvate

    Directory of Open Access Journals (Sweden)

    Jun Han

    2009-04-01

    Full Text Available The title compound crystallized as an ethanol solvate, C18H18N3OP·C2H6O. It is the reduction product of tris(3-nitrophenylphosphine oxide. In the crystal, there are intermolecular N—H...O hydrogen bonds between neighbouring tris(3-aminophenylphosphine oxide molecules and O—H...O hydrogen bonds involving the ethanol solvent molecule.

  17. Temperature and concentration effects on the solvophobic solvation of methane in aqueous salt solutions.

    Science.gov (United States)

    Holzmann, Jörg; Ludwig, Ralf; Geiger, Alfons; Paschek, Dietmar

    2008-12-22

    We perform molecular dynamics (MD) simulations of aqueous salt (NaCl) solutions using the TIP4P-Ew water model (Horn et al., J. Chem. Phys. 2004, 120, 9665) covering broad temperature and concentration ranges extending deeply into the supercooled region. In particular we study the effect of temperature and salt concentration on the solvation of methane at infinite dilution. The salt effect on methane's solvation free energy, solvation enthalpy and entropy, as well as their temperature dependence is found to be semi-quantitatively in accordance with the data of Ben-Naim and Yaacobi (J. Phys. Chem. 1974, 78, 170). To distinguish the influence of local (in close proximity to ions) and global effects, we partition the salt solutions into ion influenced hydration shell regions and bulk water. The chemical potential of methane is systematically affected by the presence of salt in both sub volumes, emphasizing the importance of the global volume contraction due to electrostriction effects. This observation is correlated with systematic structural alterations similar to water under pressure. The observed electrostriction effects are found to become increasingly pronounced under cold (supercooled) conditions. We find that the influence of temperature and salt induced global density changes on the solvation properties of methane is well recovered by simple scaling relation based on predictions of the information theory model of Garde et al. (Phys. Rev. Let. 1999, 77, 4966).

  18. Preferential Solvation of an Asymmetric Redox Molecule

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-12-15

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

  19. 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…

  20. 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…

  1. 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

  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. Automated quantum chemistry based molecular dynamics simulations of electron ionization induced fragmentations of the nucleobases Uracil, Thymine, Cytosine, and Guanine.

    Science.gov (United States)

    Grimme, Stefan; Bauer, Christopher Alexander

    2015-01-01

    The gas-phase decomposition pathways of electron ionization (EI)-induced radical cations of the nucleobases uracil, thymine, cytosine, and guanine are investigated by means of mixed quantum-classical molecular dynamics. No preconceived fragmentation channels are used in the calculations. The results compare well to a plethora of experimental and theoretical data for these important biomolecules. With our combined stochastic and dynamic approach, one can access in an unbiased way the energetically available decomposition mechanisms. Additionally, we are able to separate the EI mass spectra of different tautomers of cytosine and guanine. Our method (previously termed quantum chemistry electron ionization mass spectra) reproduces free nucleobase experimental mass spectra well and provides detailed mechanistic in-sight into high-energy unimolecular decomposition processes.

  4. 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

  5. Proton enhanced dynamic battery chemistry for aprotic lithium-oxygen batteries

    Science.gov (United States)

    Zhu, Yun Guang; Liu, Qi; Rong, Yangchun; Chen, Haomin; Yang, Jing; Jia, Chuankun; Yu, Li-Juan; Karton, Amir; Ren, Yang; Xu, Xiaoxiong; Adams, Stefan; Wang, Qing

    2017-02-01

    Water contamination is generally considered to be detrimental to the performance of aprotic lithium-air batteries, whereas this view is challenged by recent contrasting observations. This has provoked a range of discussions on the role of water and its impact on batteries. In this work, a distinct battery chemistry that prevails in water-contaminated aprotic lithium-oxygen batteries is revealed. Both lithium ions and protons are found to be involved in the oxygen reduction and evolution reactions, and lithium hydroperoxide and lithium hydroxide are identified as predominant discharge products. The crystallographic and spectroscopic characteristics of lithium hydroperoxide monohydrate are scrutinized both experimentally and theoretically. Intriguingly, the reaction of lithium hydroperoxide with triiodide exhibits a faster kinetics, which enables a considerably lower overpotential during the charging process. The battery chemistry unveiled in this mechanistic study could provide important insights into the understanding of nominally aprotic lithium-oxygen batteries and help to tackle the critical issues confronted.

  6. Proton enhanced dynamic battery chemistry for aprotic lithium–oxygen batteries

    Science.gov (United States)

    Zhu, Yun Guang; Liu, Qi; Rong, Yangchun; Chen, Haomin; Yang, Jing; Jia, Chuankun; Yu, Li-Juan; Karton, Amir; Ren, Yang; Xu, Xiaoxiong; Adams, Stefan; Wang, Qing

    2017-01-01

    Water contamination is generally considered to be detrimental to the performance of aprotic lithium–air batteries, whereas this view is challenged by recent contrasting observations. This has provoked a range of discussions on the role of water and its impact on batteries. In this work, a distinct battery chemistry that prevails in water-contaminated aprotic lithium–oxygen batteries is revealed. Both lithium ions and protons are found to be involved in the oxygen reduction and evolution reactions, and lithium hydroperoxide and lithium hydroxide are identified as predominant discharge products. The crystallographic and spectroscopic characteristics of lithium hydroperoxide monohydrate are scrutinized both experimentally and theoretically. Intriguingly, the reaction of lithium hydroperoxide with triiodide exhibits a faster kinetics, which enables a considerably lower overpotential during the charging process. The battery chemistry unveiled in this mechanistic study could provide important insights into the understanding of nominally aprotic lithium–oxygen batteries and help to tackle the critical issues confronted. PMID:28165008

  7. 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.

  8. 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.

  9. 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

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

    Science.gov (United States)

    Huang, WenJuan; Blinov, Nikolay; Kovalenko, Andriy

    2015-04-30

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

  11. 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].

  12. 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.

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

    Science.gov (United States)

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

    1997-01-01

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

  14. 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.

  15. 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.

  16. Distant-ion dragging of polarizable nanodroplets and solvated DNA on nanotubes

    Science.gov (United States)

    Wang, Boyang; Kral, Petr

    2008-03-01

    Long distance Coulombic coupling allows efficient molecular dragging at the nanoscale by moving electrons, ions and molecules [1]. We use molecular dynamics simulations to show that ions intercalated inside semiconducting single-wall carbon nanotubes (SWNT) can be solvated in polarizable nanodroplets adsorbed on the SWNTs, and the coupled systems can be dragged by electric fields [2]. We also demonstrate that solvated single-strand DNA molecules adsorbed on SWNTs can be driven by ionic solutions flowing inside the tubes. These phenomena could be applied in molecular delivery, separation, desalination and be integrated in modern lab-on-a-chip technologies. [1] Boyang Wang and Petr Kral, JACS 128, 15984 (2006). [2] Boyang Wang and Petr Kral, submitted.

  17. The Interaction Between Dynamics and Chemistry of Ozone in the Set-up Phase of the Northern Hemisphere Polar Vortex

    Science.gov (United States)

    Kawa, S. R.; Bevilacqua, R.; Margitan, J. J.; Douglass, A. R.; Schoeberl, M. R.; Hoppel, K.; Sen, B.; Bhartia, P. K. (Technical Monitor)

    2001-01-01

    The morphology and evolution of the stratospheric ozone (O3) distribution at high latitudes in the Northern Hemisphere (NH) are examined for the late summer and fall seasons of 1999. This time period sets the O3 initial condition for the SOLVE/THESEO field mission performed during winter 1999-2000. In situ and satellite data are used along with a three-dimensional model of chemistry and transport (CTM) to determine the key processes that control the distribution of O3 in the lower-to-middle stratosphere. O3 in the vortex at the beginning of the winter season is found to be nearly constant from 500 to above 800 K with a value at 3 ppmv +/- approx. 10%. Values outside the vortex are up to a factor of 2 higher and increase significantly with potential temperature. The seasonal time series of data from POAM shows that relatively low O3 mixing ratios, which characterize the vortex in late fall, are already present at high latitudes at the end of summer before the vortex circulation sets up. Analysis of the CTM output shows that the minimum O3 and increase in variance in late summer are the result of: 1) stirring of polar concentric O3 gradients by nascent wave-driven transport, and 2) an acceleration of net photochemical loss with decreasing solar illumination. The segregation of low O3 mixing ratios into the vortex as the circulation strengthens through the fall suggests a possible feedback role between O3 chemistry and the vortex formation dynamics. Trajectory calculations from O3 sample points early in the fall, however, show only a weak correlation between initial O3 mixing ratio and potential vorticity later in the season consistent with order-of-magnitude calculations for the relative importance of O3 in the fall radiative balance at high latitudes. The possible connection between O3 chemistry and the dynamics of vortex formation does suggest that these feedbacks and sensitivities need to be better understood in order to make confident predictions of the recovery

  18. Molecular dynamics for irradiation driven chemistry: application to the FEBID process

    DEFF Research Database (Denmark)

    Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

    2016-01-01

    involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields...... technologies such as focused electron beam deposition (FEBID). As an example, the new methodology is applied for studying the irradiation driven chemistry caused by FEBID of tungsten hexacarbonyl W(CO)6 precursor molecules on a hydroxylated SiO2 surface. It is demonstrated that knowing the interaction...... parameters for the fragments of the molecular system arising in the course of irradiation one can reproduce reasonably well experimental observations and make predictions about the morphology and molecular composition of nanostructures that emerge on the surface during the FEBID process....

  19. 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.

  20. 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...

  1. Carbonate Chemistry Dynamics in an Area of Active Gas Seepage: the Hudson Canyon, US Atlantic Margin

    Science.gov (United States)

    Garcia-Tigreros Kodovska, F.; Kessler, J. D.; Leonte, M.; Chepigin, A.; Kellermann, M. Y.; Arrington, E. C.; Valentine, D. L.

    2015-12-01

    The fate of oceanic methane and its impact on the global climate has been of particular interest to the global community. The potential for vast amounts of methane to be emitted from the seafloor into the atmosphere due to gas hydrate decomposition has been under scientific evaluation. However, despite the great extent of these geological reservoirs, much of the methane released from the seafloor in deep ocean environments does not reach the atmosphere. Once dissolved in ocean water, the emitted methane can be microbially converted to either carbon dioxide or assimilated to biomass. Here, we will present results from a research cruise to the Hudson Canyon, northern US Atlantic Margin, where we investigated changes in ocean water carbonate chemistry induced by the oxidation of methane released from gas seeps. We will be presenting high precision pH data as well as methane and DIC concentrations, natural stable isotopes, and methane oxidation rates collected inside and adjacent to the Hudson Canyon in the summer of 2014.

  2. 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

  3. 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.

  4. Shock induced chemistry in liquids studied with ultrafast dynamic ellipsometry and visible transient absorption spectroscopy.

    Science.gov (United States)

    Dang, N C; Bolme, C A; Moore, D S; McGrane, S D

    2012-10-25

    The response to ultrafast laser shock loading of nine liquids was monitored in an effort to reveal evidence of chemical changes occurring during the first 350 ps following the shock front. In an effort to compare molecular structures possessing a variety of common bonding patterns, data were acquired for the liquids: cyclohexane, cyclohexene, 1,3-cyclohexadiene, benzene, water, acetonitrile, acrylonitrile, tert-butylacetylene, and phenylacetylene. Transient absorption spectra were measured in the spectral region from 440 to 780 nm over shock stress states from 7 to 20 GPa. Ultrafast dynamic ellipsometry was used to measure the shock and particle velocity as well as the shocked refractive index. Significant transient absorption attributed to chemical reaction was observed for shocked phenylacetylene and acrylonitrile. Evidence of volume decreasing chemical reactions was also observed in the ultrafast dynamic ellipsometry data for phenylacetylene and acrylonitrile. The liquid 1,3-cyclohexadiene exhibited volume decreasing reaction in the ultrafast dynamic ellipsometry data but did not exhibit an increase in the transient absorption spectra. There was no evidence of chemical reaction in cyclohexane, cyclohexene, benzene, water, acetonitrile, or tert-butylacetylene in the first 350 ps, despite the application of shock stress that was in many cases well above the reaction threshold observed at microsecond time scales.

  5. Concentrated Electrolyte for the Sodium-Oxygen Battery: Solvation Structure and Improved Cycle Life.

    Science.gov (United States)

    He, Mingfu; Lau, Kah Chun; Ren, Xiaodi; Xiao, Neng; McCulloch, William D; Curtiss, Larry A; Wu, Yiying

    2016-12-05

    Alkali metal-oxygen batteries are of great interests for energy storage because of their unparalleled theoretical energy densities. Particularly attractive is the emerging Na-O2 battery because of the formation of superoxide as the discharge product. Dimethyl sulfoxide (DMSO) is a promising solvent for this battery but its instability towards Na makes it impractical in the Na-O2 battery. Herein we report the enhanced stability of Na in DMSO solutions containing concentrated sodium trifluoromethanesulfonimide (NaTFSI) salts (>3 mol kg(-1) ). Raman spectra of NaTFSI/DMSO electrolytes and ab initio molecular dynamics simulation reveal the Na(+) solvation number in DMSO and the formation of Na(DMSO)3 (TFSI)-like solvation structure. The majority of DMSO molecules solvating Na(+) in concentrated solutions reduces the available free DMSO molecules that can react with Na and renders the TFSI anion decomposition, which protects Na from reacting with the electrolyte. Using these concentrated electrolytes, Na-O2 batteries can be cycled forming sodium superoxide (NaO2 ) as the sole discharge product with improved long cycle life, highlighting the beneficial role of concentrated electrolytes for Na-based batteries.

  6. Extended solvent-contact model for protein solvation: test cases for dipeptides.

    Science.gov (United States)

    Choi, Hwanho; Kang, Hongsuk; Park, Hwangseo

    2013-05-01

    Solvation effects are critically important in the structural stabilization and functional optimization of proteins. Here, we propose a new solvation free energy function for proteins, and test its applicability in predicting the solvation free energies of dipeptides. The present solvation model involves the improvement of the previous solvent-contact model assuming that the molecular solvation free energy could be given by the sum over the individual atomic contributions. In addition to the existing solvent-contact term, the modified solvation free energy function includes the self-solvation term that reflects the effects of intramolecular interactions in the solute molecule on solute-solvent interactions. Four kinds of atomic parameters should be determined in this solvation model: atomic fragmental volume, maximum atomic occupancy, atomic solvation, and atomic self-solvation parameters. All of these parameters for 16 atom types are optimized with a standard genetic algorithm in such a way to minimize the difference between the solvation free energies of dipeptides obtained from high-level quantum chemical calculations and those predicted by the solvation free energy function. The solvation free energies of dipeptides estimated from the new solvation model are in good agreement with the quantum chemical results. Therefore, the optimized solvation free energy function is expected to be useful for examining the structural and energetic features of proteins in aqueous solution.

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

    Energy Technology Data Exchange (ETDEWEB)

    Virtanen, J. J. [Department of Chemistry, University of Chicago, Chicago, Illinois 60637 (United States); James Franck Institute, University of Chicago, Chicago, Illinois 60637 (United States); Sosnick, T. R. [Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637 (United States); Computation Institute, University of Chicago, Chicago, Illinois 60637 (United States); Freed, K. F. [Department of Chemistry, University of Chicago, Chicago, Illinois 60637 (United States); James Franck Institute, University of Chicago, Chicago, Illinois 60637 (United States); Computation Institute, University of Chicago, Chicago, Illinois 60637 (United States)

    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.

  8. 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.

  9. Potential changes in arctic seasonality and plant communities may impact tundra soil chemistry and carbon dynamics

    Science.gov (United States)

    Crow, S.; Cooper, E.; Beilman, D.; Filley, T.; Reimer, P.

    2009-04-01

    On the Svalbard archipelago, as in other high Arctic regions, tundra soil organic matter (SOM) is primarily plant detritus that is largely stabilized by cold, moist conditions and low nitrogen availability. However, the resistance of SOM to decomposition is also influenced by the quality of organic matter inputs to soil. Different plant communities are likely to give different qualities to SOM, especially where lignin-rich woody species encroach into otherwise graminoid and bryophyte-dominated regions. Arctic woody plant species are particularly sensitive to changes in temperature, snow cover, and growing season length. In a changing environment, litter chemistry may emerge as an important control on tundra SOM stabilization. In summer 2007, we collected plant material and soil from the highly-organic upper horizon (appx. 0-5 cm) and the mineral-dominated lower horizon (appx. 5-10cm) from four locations in the southwest facing valleys of Svalbard, Norway. The central goal of the ongoing experiment is to determine whether a greater abundance of woody plants could provide a negative feedback to warming impacts on the carbon (C) balance of Arctic soils. Towards this, we used a combination of plant biopolymer analyses (cupric oxide oxidation and quantification of lignin-derived phenols and cutin/suberin-derived aliphatics) and radiocarbon-based estimates of C longevity and mean residence time (MRT) to characterize potential links between plant type and soil C pools. We found that graminoid species regenerate above- and belowground tissue each year, whereas woody species (Cassiope tetragona and Dryas octopetala) regenerated only leaves yearly. In contrast, C within live branches and roots persisted for 15-18 yr on average. Leaves from woody species remained nearly intact in surface litter for up to 20 yr without being incorporated into the upper soil horizon. Leaves from both graminoid and woody species were concentrated in lignin-derived phenols relative to roots, but

  10. 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.

  11. 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.

  12. Code interoperability and standard data formats in quantum chemistry and quantum dynamics: The Q5/D5Cost data model.

    Science.gov (United States)

    Rossi, Elda; Evangelisti, Stefano; Laganà, Antonio; Monari, Antonio; Rampino, Sergio; Verdicchio, Marco; Baldridge, Kim K; Bendazzoli, Gian Luigi; Borini, Stefano; Cimiraglia, Renzo; Angeli, Celestino; Kallay, Peter; Lüthi, Hans P; Ruud, Kenneth; Sanchez-Marin, José; Scemama, Anthony; Szalay, Peter G; Tajti, Attila

    2014-03-30

    Code interoperability and the search for domain-specific standard data formats represent critical issues in many areas of computational science. The advent of novel computing infrastructures such as computational grids and clouds make these issues even more urgent. The design and implementation of a common data format for quantum chemistry (QC) and quantum dynamics (QD) computer programs is discussed with reference to the research performed in the course of two Collaboration in Science and Technology Actions. The specific data models adopted, Q5Cost and D5Cost, are shown to work for a number of interoperating codes, regardless of the type and amount of information (small or large datasets) to be exchanged. The codes are either interfaced directly, or transfer data by means of wrappers; both types of data exchange are supported by the Q5/D5Cost library. Further, the exchange of data between QC and QD codes is addressed. As a proof of concept, the H + H2 reaction is discussed. The proposed scheme is shown to provide an excellent basis for cooperative code development, even across domain boundaries. Moreover, the scheme presented is found to be useful also as a production tool in the grid distributed computing environment.

  13. Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study.

    Science.gov (United States)

    Ghobadi, Ahmadreza F; Jayaraman, Arthi

    2016-02-28

    In this paper we study how varying oligonucleic acid backbone chemistry affects the hybridization/melting thermodynamics of oligonucleic acids. We first describe the coarse-grained (CG) model with tunable parameters that we developed to enable the study of both naturally occurring oligonucleic acids, such as DNA, and their chemically-modified analogues, such as peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). The DNA melting curves obtained using such a CG model and molecular dynamics simulations in an implicit solvent and with explicit ions match with the melting curves obtained using the empirical nearest-neighbor models. We use these CG simulations to then elucidate the effect of backbone flexibility, charge, and nucleobase spacing along the backbone on the melting curves, potential energy and conformational entropy change upon hybridization and base-pair hydrogen bond residence time. We find that increasing backbone flexibility decreases duplex thermal stability and melting temperature mainly due to increased conformational entropy loss upon hybridization. Removing charges from the backbone enhances duplex thermal stability due to the elimination of electrostatic repulsion and as a result a larger energetic gain upon hybridization. Lastly, increasing nucleobase spacing decreases duplex thermal stability due to decreasing stacking interactions that are important for duplex stability.

  14. 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.

  15. 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.

  16. The formation of Uranus and Neptune in solid-rich feeding zones: Connecting chemistry and dynamics

    Science.gov (United States)

    Dodson-Robinson, Sarah E.; Bodenheimer, Peter

    2010-05-01

    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 M⊕ necessitates a sudden gas accretion cutoff just as Uranus and Neptune's 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. (Dodson-Robinson, S.E., Willacy, K., Bodenheimer, P., Turner, N.J., Beichman, C.A. [2009]. Icarus 200, 672-693) using the initial semimajor axis distribution of the Nice model (Gomes, R., Levison, H.F., Tsiganis, K., Morbidelli, A. [2005]. Nature 435, 466-469; Morbidelli, A., Levison, H.F., Tsiganis, K., Gomes, R. [2005]. Nature 435, 462-465; Tsiganis, K., Gomes, R., Morbidelli, A., Levison, H.F. [2005]. Nature 435, 459-461), 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 5.3-6 Myr, a considerable time decrease from previous one-dimensional simulations (e.g. Pollack, J.B., Hubickyj, O., Bodenheimer, P., Lissauer, J.J., Podolak, M., Greenzweig, Y. [1996]. Icarus 124, 62-85). The core masses stay subcritical, eliminating the need for a sudden gas accretion cutoff. Our calculated carbon mass fractions of 22% are in excellent agreement with the ice giant interior models of Podolak et al. (Podolak, M., Weizman, A., Marley, M. [1995]. Planet. Space Sci. 43, 1517-1522) and Marley et al. (Marley, M.S., Gómez, P., Podolak, M. [1995]. J. Geophys. Res. 100, 23349-23354). Based on the requirement that the ice giant-forming planetesimals contain >10% mass

  17. 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.

  18. 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....

  19. Quality management science in clinical chemistry: a dynamic framework for continuous improvement of quality.

    Science.gov (United States)

    Westgard, J O; Burnett, R W; Bowers, G N

    1990-10-01

    Current quality assurance approaches will not be adequate to satisfy the needs for quality in the next decade. Quality management science (QMS), as evolving in industry today, provides the dynamic framework necessary to provide continuous improvement of quality. QMS emphasizes the importance of defining quality goals based on the needs and expectations (implied needs) of customers. The laboratory can develop customer-friendly goals and measures of quality by recognizing that customers' experiences are represented by a totality of results. Quality goals and measures are best communicated as "total performance" by specifying a limit and percentile of the distribution, rather than a mean and standard deviation. Application of quality goals within the laboratory will usually require partitioning the total performance goal into components and translating those components into specifications to guide the operation and management of production processes. QMS also extends beyond technical processes to people processes and provides guidance for improving the quality of worklife and caring for the laboratory's most essential resource--our people.

  20. 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.

  1. 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.

  2. Final progress report for linking ion solvation and lithium battery electrolyte properties

    Energy Technology Data Exchange (ETDEWEB)

    Henderson, Wesley [North Carolina State Univ., Raleigh, NC (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Henderson, Wesley

    2014-08-29

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

  4. 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.

  5. 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

  6. Structure of large nitrate-water clusters at ambient temperatures: simulations with effective fragment potentials and force fields with implications for atmospheric chemistry.

    Science.gov (United States)

    Miller, Yifat; Thomas, Jennie L; Kemp, Daniel D; Finlayson-Pitts, Barbara J; Gordon, Mark S; Tobias, Douglas J; Gerber, R Benny

    2009-11-19

    Structural properties of large NO(3)(-).(H(2)O)(n) (n = 15-500) clusters are studied by Monte Carlo simulations using effective fragment potentials (EFPs) and by classical molecular dynamics simulations using a polarizable empirical force field. The simulation results are analyzed with a focus on the description of hydrogen bonding and solvation in the clusters. In addition, a comparison between the electronic structure based EFP and the classical force field description of the 32 water cluster system is presented. The EFP simulations, which focused on the cases of n = 15 and 32, show an internal, fully solvated structure and a "surface adsorbed" structure for the 32 water cluster at 300 K, with the latter configuration being more probable. The internal solvated structure and the "surface adsorbed" structure differ considerably in their hydrogen bonding coordination numbers. The force field based simulations agree qualitatively with these results, and the local geometry of NO(3)(-) and solvation at the surface-adsorbed site in the force field simulations are similar to those predicted using EFPs. Differences and similarities between the description of hydrogen bonding of the anion in the two approaches are discussed. Extensive classical force field based simulations at 250 K predict that long time scale stability of "internal" NO(3)(-), which is characteristic of extended bulk aqueous interfaces, emerges only for n > 300. Ab initio Møller-Plesset perturbation theory is used to test the geometries of selected surface and interior anions for n = 32, and the results are compared to the EFP and MD simulations. Qualitatively, all approaches agree that surface structures are preferred over the interior structures for clusters of this size. The relatively large aqueous clusters of NO(3)(-) studied here are of comparable size to clusters that lead to new particle formation in air. Nitrate ions on the surface of such clusters may have significantly different photochemistry

  7. 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

  8. 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

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

    Science.gov (United States)

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

    2016-03-01

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

  10. 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

  11. Solvation of polymers as mutual association. I. General theory

    Science.gov (United States)

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

    2013-04-01

    A Flory-Huggins (FH) type lattice theory of self-assembly is generalized to describe the equilibrium solvation of long polymer chains B by small solvent molecules A. Solvation is modeled as a thermally reversible mutual association between the polymer and a relatively low molar mass solvent. The FH Helmholtz free energy F is derived for a mixture composed of the A and B species and the various possible mutual association complexes AiB, and F is then used to generate expressions for basic thermodynamic properties of solvated polymer solutions, including the size distribution of the solvated clusters, the fraction of solvent molecules contained in solvated states (an order parameter for solvation), the specific heat (which exhibits a maximum at the solvation transition), the second and the third osmotic virial coefficients, and the boundaries for phase stability of the mixture. Special attention is devoted to the analysis of the "entropic" contribution χs to the FH interaction parameter χ of polymer solutions, both with and without associative interactions. The entropic χs parameter arises from correlations associated with polymer chain connectivity and disparities in molecular structure between the components of the mixture. Our analysis provides the first explanation of the longstanding enigma of why χs for polymer solutions significantly exceeds χs for binary polymer blends. Our calculations also reveal that χs becomes temperature dependent when interactions are strong, in sharp contrast to models currently being used for fitting thermodynamic data of associating polymer-solvent mixtures, where χs is simply assumed to be an adjustable constant based on experience with solutions of homopolymers in nonassociating solvents.

  12. 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

  13. 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.

  14. 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

  15. 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.}

  16. 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

  17. 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...

  18. 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).

  19. 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.

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

    OpenAIRE

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

    2015-01-01

    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, research...

  1. Communication: Barium ions and helium nanodroplets: solvation and desolvation.

    Science.gov (United States)

    Zhang, Xiaohang; Drabbels, Marcel

    2012-08-07

    The solvation of Ba(+) ions created by the photoionization of barium atoms located on the surface of helium nanodroplets has been investigated. The excitation spectra corresponding to the 6p (2)P(1/2) ← 6s (2)S(1/2) and 6p (2)P(3/2) ← 6s (2)S(1/2) transitions of Ba(+) are found to be identical to those recorded in bulk He II [H. J. Reyher, H. Bauer, C. Huber, R. Mayer, A. Schafer, and A. Winnacker, Phys. Lett. A 115, 238 (1986)], indicating that the ions formed at the surface of the helium droplets become fully solvated by the helium. Time-of-flight mass spectra suggest that following the excitation of the solvated Ba(+) ions, these are being ejected from the helium droplets either as bare Ba(+) ions or as small Ba(+)He(n) (n < 20) complexes.

  2. Contribution of Solvation Energy in Protein-Peptide Recognition Systems

    Institute of Scientific and Technical Information of China (English)

    LI,Fei; LI,Wei; SHEN,Jia-Cong

    2001-01-01

    The contribution of solvation energy to guding molecualr recognition for six rigid protein-peptide systems had been eval uated by the variation in the number of the identified native like configurations and in the driving force of specific interac tion resulting from the addition of the explicit solvation term in the force field function. The AMBER force field energy and the total energy including the force field energy and the WZS solvation energy were calculated for sampled configurations. The results obtained by the calculations of both force field and total energies were compared with each other. It suggests that specific recognition of the systems in which the ligands possess larger hydrophobic or aromatic residues while the protein re ceptors provide the active surfaces with hydrophobic property.

  3. 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.

  4. Quantum-chemistry based calibration of the alkali metal cation series (Li(+)-Cs(+)) for large-scale polarizable molecular mechanics/dynamics simulations.

    Science.gov (United States)

    Dudev, Todor; Devereux, Mike; Meuwly, Markus; Lim, Carmay; Piquemal, Jean-Philip; Gresh, Nohad

    2015-02-15

    The alkali metal cations in the series Li(+)-Cs(+) act as major partners in a diversity of biological processes and in bioinorganic chemistry. In this article, we present the results of their calibration in the context of the SIBFA polarizable molecular mechanics/dynamics procedure. It relies on quantum-chemistry (QC) energy-decomposition analyses of their monoligated complexes with representative O-, N-, S-, and Se- ligands, performed with the aug-cc-pVTZ(-f) basis set at the Hartree-Fock level. Close agreement with QC is obtained for each individual contribution, even though the calibration involves only a limited set of cation-specific parameters. This agreement is preserved in tests on polyligated complexes with four and six O- ligands, water and formamide, indicating the transferability of the procedure. Preliminary extensions to density functional theory calculations are reported.

  5. 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.

  6. Large eddy simulation of reactive pollutants in a deep urban street canyon: Coupling dynamics with O3-NOx-VOC chemistry.

    Science.gov (United States)

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

    2017-02-12

    A large eddy simulation (LES) model coupled with O3-NOx-VOC chemistry is implemented to simulate the coupled effects of emissions, mixing and chemical pre-processing within an idealised deep (aspect ratio = 2) urban street canyon under a weak wind condition. Reactive pollutants exhibit significant spatial variations in the presence of two vertically aligned unsteady vortices formed in the canyon. Comparison of the LES results from two chemical schemes (simple NOx-O3 chemistry and a more comprehensive Reduced Chemical Scheme (RCS) chemical mechanism) shows that the concentrations of NO2 and Ox inside the street canyon are enhanced by approximately 30-40% via OH/HO2 chemistry. NO, NOx, O3, OH and HO2 are chemically consumed, while NO2 and Ox (total oxidant) are chemically produced within the canyon environment. Within-canyon pre-processing increases oxidant fluxes from the canyon to the overlying boundary layer, and this effect is greater for deeper street canyons (as found in many traditional European urban centres) than shallower (lower aspect ratio) streets. There is clear evidence of distinct behaviours for emitted chemical species and entrained chemical species, and positive (or negative) values of intensities of segregations are found between pairs of species with similar (or opposite) behaviour. The simplified two-box model underestimated NO and O3 levels, but overestimated NO2 levels for both the lower and upper canyon compared with the more realistic LES-chemistry model. This suggests that the segregation effect due to incomplete mixing reduces the chemical conversion rate of NO to NO2. This study reveals the impacts of nonlinear O3-NOx-VOC photochemical processes in the incomplete mixing environment and provides a better understanding of the pre-processing of emissions within canyons, prior to their release to the urban boundary layer, through the coupling of street canyon dynamics and chemistry.

  7. Intramolecular Charge Transfer and Solvation of Photoactive Molecules with Conjugated Push-Pull Structures.

    Science.gov (United States)

    Zhu, Huaning; Wang, Xian; Ma, Renjun; Kuang, Zhuoran; Guo, Qianjin; Xia, Andong

    2016-10-18

    A comparative investigation on the photophysical properties and solvation-related ICT dynamics of three push-pull compounds containing different donors including carbazole, triphenylamine and phenothiazine, was performed. The steady-state spectra and theoretical calculations show the charge transfers from the central donors to the acceptors at each side. The characterization of the extent of charge transfer was determined by various means, including estimation of the dipole moment, the electron density distribution of HOMO and LUMO, CDD and change in Gibb's free energy, which show the charge transfer strength to be in the order PDHP > BDHT > PDHC. This suggests that the electron-donating ability of the donor groups plays a crucial role in the charge transfer in these compounds. The TA data show the excited-state relaxation dynamics follow a sequential model: FC→ICT→ICT'→S0 , and are affected by the solvent polarity. The results presented here demonstrate that the compound with a higher degree of ICT characteristic interacts more strongly with stronger polar solvent molecules, which can accelerate the solvation and spectral evolution to lower energy levels. The A-π-D-π-A architectures with prominent ICT characteristics based on carbazole, triphenylamine and phenothiazine might be potential scaffolds for light-harvesting and photovoltaic devices. These results are of value for understanding structure-property relationships and the rational design of functional materials for photoelectric applications.

  8. Carbonate chemistry dynamics over a Caribbean shelf reef (Cayo Enrique) at the Atlantic Ocean Acidification Test-bed, La Parguera, Puerto Rico

    Science.gov (United States)

    Gledhill, D. K.; Corredor, J. E.; Langdon, C.; Manzello, D.; Sabine, C. L.; Hensley, V.; Brocco, B.; Musielewicz, S.; Lawrence-Slavas, N.; Capella, J. E.

    2010-12-01

    Changes in surface ocean chemistry in direct response to rising atmospheric carbon dioxide (CO2) concentration may pose challenges to a range of marine ecosystems in coming decades. Monitoring this ocean acidification (OA) at regional and local-scales is an important requirement towards improving our understanding of the potential long-term consequences. Coral reef ecosystems are of particular concern given the potential effects OA may have on net community calcification and ultimately reef accretion rates. While the dynamics and trends in oceanic carbonate chemistry are reasonably well constrained, how OA is manifested within the shallow coastal waters where coral reef ecosystems reside is less understood. Community-scale metabolic processes impart an important control on near-reef carbonate chemistry. Constraining the near-reef variability in carbonate chemistry across diel, seasonal, and annual scales is a critical requirement towards assigning potential biogeochemical thresholds of OA. The Atlantic OA Test-bed in the La Parguera Marine Reserve, Puerto Rico was established in 2009 to provide sustained high temporal resolution monitoring of carbonate chemistry within an Atlantic tropical coral reef ecosystem. Presented here are the results of over a year’s worth of sustained monitoring at the Cayo Enrique forereef characterizing the temporal dynamics in carbonate chemistry. The Cayo Enrique reef is a source of CO2 to the atmosphere (1.7 mmol CO2 m-2 d-1, SE = 0.1) with both calcification and respiration serving to consistently elevate pCO2,sw relative to oceanic waters. Once pCO2,sw increase by a further 100 µatm in response to rising atmospheric CO2, these waters will likely reach undersaturation with respect to 13 mol % MgCO3 phases during winter months. While high-Mg calcites are prominent mineral phases of shallow tropical carbonate marine sediments, their relative importance as cementing agents of modern coral reef frameworks demands further investigation

  9. 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.

  10. Predicting Solvation Free Energies and Thermodynamics in Polar Solvents and Mixtures Using a Solvation-Layer Interface Condition

    CERN Document Server

    Tabrizi, Amirhossein Molavi; Rahimi, Ali Mehdizadeh; Knepley, Matthew G; Bardhan, Jaydeep P

    2016-01-01

    We demonstrate that with two small modifications, the popular dielectric continuum model is capable of predicting, with high accuracy, ion solvation thermodynamics in numerous polar solvents, and ion solvation free energies in water--co-solvent mixtures. The first modification involves perturbing the macroscopic dielectric-flux interface condition at the solute--solvent interface with a nonlinear function of the local electric field, giving what we have called a solvation-layer interface condition (SLIC). The second modification is a simple treatment of the microscopic interface potential (static potential). We show that the resulting model exhibits high accuracy without the need for fitting solute atom radii in a state-dependent fashion. Compared to experimental results in nine water--co-solvent mixtures, SLIC predicts transfer free energies to within 2.5 kJ/mol. The co-solvents include both protic and aprotic species, as well as biologically relevant denaturants such as urea and dimethylformamide. Furthermo...

  11. 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.

  12. 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

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

    Science.gov (United States)

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

  14. 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

  15. 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

  16. Oxide/Water Interfaces: How the Surface Chemistry Modifies the Electronic Energy Alignment

    Science.gov (United States)

    Sprik, Michiel

    2014-03-01

    The minimum of the d-electron conduction band of an aqueous transition metal oxide electrode is typically no more than a few 100 mV away from the standard hydrogen electrode (SHE). Because of this favourable alignment of the electronic energy levels (near) metallic transition metal oxides with partly filled d bands can be used as electrocatalysts while the compounds with finite electronic gap can be used as photocatalysts. However, because of their ionic character, transition metal-oxide surfaces also show amphiphilic acid-base activity. At low pH the basic sites are protonated and at high pH the acidic sites deprotonated creating an electrical double layer with corresponding surface potential. The alignment of the electronic energy levels, and by implication their redox activity, is therefore pH dependent. In fact, even in absence of protonic surface charge, the coordination with water molecules is already capable of shifting the electronic energy levels of the oxide by 1 eV or more. Computation of the electronic energies in transition metal oxide electrodes requires therefore a detailed modeling of their aqueous surface chemistry. The solvation energy of the proton is the common energy reference for both redox potentials on the SHE scale and acidity constants (pKa). Computation of the H+ solvation energy is therefore a key component in a unified treatment of redox and acid-base chemistry. In this talk we outline the Density Functional Theory based Molecular Dynamics (DFTMD) method we have developed for this purpose. The central tool of our approach is a method for reversible insertion of protons in the aqueous part of the DFTMD model system. As an illustration we discuss the application to the rutile TiO2/water and MnO2/water interface.

  17. A continuum solvent model of the multipolar dispersion solvation energy.

    Science.gov (United States)

    Duignan, Timothy T; Parsons, Drew F; Ninham, Barry W

    2013-08-15

    The dispersion energy is an important contribution to the total solvation energies of ions and neutral molecules. Here, we present a new continuum model calculation of these energies, based on macroscopic quantum electrodynamics. The model uses the frequency dependent multipole polarizabilities of molecules in order to accurately calculate the dispersion interaction of a solute particle with surrounding water molecules. It includes the dipole, quadrupole, and octupole moment contributions. The water is modeled via a bulk dielectric susceptibility with a spherical cavity occupied by the solute. The model invokes damping functions to account for solute-solvent wave function overlap. The assumptions made are very similar to those used in the Born model. This provides consistency and additivity of electrostatic and dispersion (quantum mechanical) interactions. The energy increases in magnitude with cation size, but decreases slightly with size for the highly polarizable anions. The higher order multipole moments are essential, making up more than 50% of the dispersion solvation energy of the fluoride ion. This method provides an accurate and simple way of calculating the notoriously problematic dispersion contribution to the solvation energy. The result establishes the importance of using accurate calculations of the dispersion energy for the modeling of solvation.

  18. 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.

  19. 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

  20. A multistate empirical valence bond model for solvation and transport simulations of OH- in aqueous solutions.

    Science.gov (United States)

    Ufimtsev, Ivan S; Kalinichev, Andrey G; Martinez, Todd J; Kirkpatrick, R James

    2009-11-07

    We describe a new multistate empirical valence bond (MS-EVB) model of OH(-) in aqueous solutions. This model is based on the recently proposed "charged ring" parameterization for the intermolecular interaction of hydroxyl ion with water [Ufimtsev, et al., Chem. Phys. Lett., 2007, 442, 128] and is suitable for classical molecular simulations of OH(-) solvation and transport. The model reproduces the hydration structure of OH(-)(aq) in good agreement with experimental data and the results of ab initio molecular dynamics simulations. It also accurately captures the major structural, energetic, and dynamic aspects of the proton transfer processes involving OH(-) (aq). The model predicts an approximately two-fold increase of the OH(-) mobility due to proton exchange reactions.

  1. 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…

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

    Science.gov (United States)

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

    2016-11-01

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

  4. Specifics of solvation of sulfonated polyelectrolytes in water, dimethylmethylphosphonate, and their mixture: A molecular simulation study

    Science.gov (United States)

    Vishnyakov, Aleksey; Neimark, Alexander V.

    2008-04-01

    Sulfonated polyelectrolyte membranes (PEMs), such as Nafion and styrene-olefin block copolymers, are explored as permselective membranes for fuel cells as well as suitable barrier materials against chemical agents. The permselective properties of PEM are determined by their microphase segregation into hydrophilic and hydrophobic domains. We performed classical molecular dynamics simulations of solvation of the hydrophilic fragments of PEM exemplified on sulfonated polystyrene (sPS) with potassium, calcium, and aluminum as counterions, in water, phosphor-organic nerve agent simulant dimethylmethylphosphonate (DMMP), and their binary mixture. The force field for the sulfonate group has been developed by optimizing the potential parameters to fit the benzenesulfonate conformations obtained from the density functional theory. For a comparison, we considered perfluorosulfonate oligomers representing fragments of Nafion polymer. We found a noticeable difference between the geometries of the polymer backbone in different solvents. The polymer backbone is stiffer in DMMP for both sPS and Nafion. An anisotropic structuring of the solvent around the phenylsulfonate group is substantially stronger than around the Nafion sidechain due to the rigidity and the anisotropy of the phenylsulfonate group. The counterion significantly affects the conformations of solvated sPS: the rigidity of the backbone increases when potassium or calcium ions are replaced by trivalent aluminum ions.

  5. Multiscale Modeling of Chemistry in Water: Are We There Yet?

    Science.gov (United States)

    Bulo, Rosa E; Michel, Carine; Fleurat-Lessard, Paul; Sautet, Philippe

    2013-12-10

    This paper critically evaluates the state of the art in combined quantum mechanical/molecular mechanical (QM/MM) approaches to the computational description of chemistry in water and supplies guidelines for the setup of customized multiscale simulations of aqueous processes. We differentiate between structural and dynamic performance, since some tasks, e.g., the reproduction of NMR or UV-vis spectra, require only structural accuracy, while others, i.e., reaction mechanisms, require accurate dynamic data as well. As a model system for aqueous solutions in general, the approaches were tested on a QM water cluster in an environment of MM water molecules. The key difficulty is the description of the possible diffusion of QM molecules into the MM region and vice versa. The flexible inner region ensemble separator (FIRES) approach constrains QM solvent molecules within an active (QM) region. Sorted adaptive partitioning (SAP), difference-based adaptive solvation (DAS), and buffered-force (BF) are all adaptive approaches that use a buffer zone in which solvent molecules gradually adapt from QM to MM (or vice versa). The costs of SAP and DAS are relatively high, while BF is fast but sacrifices conservation of both energy and momentum. Simulations in the limit of an infinitely small buffer zone, where DAS and SAP become equivalent, are discussed as well and referred to as ABRUPT. The best structural accuracy is obtained with DAS, BF, and ABRUPT, all three of similar quality. FIRES performs very well for dynamic properties localized deep within the QM region. By means of elimination DAS emerges as the best overall compromise between structural and dynamic performance. Eliminating the buffer zone (ABRUPT) improves efficiency and still leads to surprisingly good results. While none of the many new flavors are perfect, all together this new field already allows accurate description of a wide range of structural and dynamic properties of aqueous solutions.

  6. The vapor-liquid interface potential of (multi)polar fluids and its influence on ion solvation.

    Science.gov (United States)

    Horváth, Lorand; Beu, Titus; Manghi, Manoel; Palmeri, John

    2013-04-21

    The interface between the vapor and liquid phase of quadrupolar-dipolar fluids is the seat of an electric interfacial potential whose influence on ion solvation and distribution is not yet fully understood. To obtain further microscopic insight into water specificity we first present extensive classical molecular dynamics simulations of a series of model liquids with variable molecular quadrupole moments that interpolates between SPC/E water and a purely dipolar liquid. We then pinpoint the essential role played by the competing multipolar contributions to the vapor-liquid and the solute-liquid interface potentials in determining an important ion-specific direct electrostatic contribution to the ionic solvation free energy for SPC/E water-dominated by the quadrupolar and dipolar parts-beyond the dominant polarization one. Our results show that the influence of the vapor-liquid interfacial potential on ion solvation is strongly reduced due to the strong partial cancellation brought about by the competing solute-liquid interface potential.

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

    Energy Technology Data Exchange (ETDEWEB)

    Netzloff, Heather Marie [Iowa State Univ., Ames, IA (United States)

    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

  8. 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)

  9. Chemistry Dashboard

    Science.gov (United States)

    The Chemistry Dashboard is part of a suite of dashboards developed by EPA to help evaluate the safety of chemicals. The Chemistry Dashboard provides access to a variety of information on over 700,000 chemicals currently in use.

  10. 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)

  11. Heterocyclic chemistry

    OpenAIRE

    Hemming, Karl

    2011-01-01

    Recent progress in the synthesis of heterocyclic compounds is presented\\ud 2010 offered highlights in pericyclic chemistry, particularly 1,3-dipolar cycloaddition chemistry, asymmetric synthesis, gold catalysis, organocatalysis, hydroamination, C–H activation and multicomponent reactions.

  12. 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.

  13. 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.

  14. 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.

  15. 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....

  16. 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

  17. 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 ...

  18. Forensic chemistry.

    Science.gov (United States)

    Bell, Suzanne

    2009-01-01

    Forensic chemistry is unique among chemical sciences in that its research, practice, and presentation must meet the needs of both the scientific and the legal communities. As such, forensic chemistry research is applied and derivative by nature and design, and it emphasizes metrology (the science of measurement) and validation. Forensic chemistry has moved away from its analytical roots and is incorporating a broader spectrum of chemical sciences. Existing forensic practices are being revisited as the purview of forensic chemistry extends outward from drug analysis and toxicology into such diverse areas as combustion chemistry, materials science, and pattern evidence.

  19. 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.

  20. 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 ...

  1. 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.

  2. Molecular Biodynamers : Dynamic Covalent Analogues of Biopolymers

    NARCIS (Netherlands)

    Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H

    2017-01-01

    Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and

  3. Studies of Negative Ion Reactions: Solvated Ions and Strong Acids,

    Science.gov (United States)

    1986-03-07

    both simple and solvated negative tons, Including association of HS04 "(H2 504 )m(HNO3)n with HCI and of NO3- with HNO3 , together with several reactions...of its high vapor pressure. We have measured rate coefficients [91 for the association of HC with HS04 (H2SO4)m(lN03)n for m-0 to 3 and n-O, 1. At the

  4. Tris[2-(deuteriomethylsulfanylphenyl]phosphine deuteriochloroform 0.125-solvate

    Directory of Open Access Journals (Sweden)

    Seik Weng Ng

    2008-05-01

    Full Text Available The title deuterated tripodal phosphine, C21H12D9PS3·0.125CDCl3, crystallizes as two independent molecules, one of which lies on a general position and the other about a threefold rotation axis, and as a deuteriochloroform solvate. The solvent molecule is disordered about a site of symmetry 3, so that the ratio of phosphine to solvent is 8:1. The P atom adopts a pyramidal coordination geometry.

  5. 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.

  6. 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.

  7. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-08-28

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

  9. Accurate estimation of solvation free energy using polynomial fitting techniques.

    Science.gov (United States)

    Shyu, Conrad; Ytreberg, F Marty

    2011-01-15

    This report details an approach to improve the accuracy of free energy difference estimates using thermodynamic integration data (slope of the free energy with respect to the switching variable λ) and its application to calculating solvation free energy. The central idea is to utilize polynomial fitting schemes to approximate the thermodynamic integration data to improve the accuracy of the free energy difference estimates. Previously, we introduced the use of polynomial regression technique to fit thermodynamic integration data (Shyu and Ytreberg, J Comput Chem, 2009, 30, 2297). In this report we introduce polynomial and spline interpolation techniques. Two systems with analytically solvable relative free energies are used to test the accuracy of the interpolation approach. We also use both interpolation and regression methods to determine a small molecule solvation free energy. Our simulations show that, using such polynomial techniques and nonequidistant λ values, the solvation free energy can be estimated with high accuracy without using soft-core scaling and separate simulations for Lennard-Jones and partial charges. The results from our study suggest that these polynomial techniques, especially with use of nonequidistant λ values, improve the accuracy for ΔF estimates without demanding additional simulations. We also provide general guidelines for use of polynomial fitting to estimate free energy. To allow researchers to immediately utilize these methods, free software and documentation is provided via http://www.phys.uidaho.edu/ytreberg/software.

  10. 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.

  11. 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.

  12. 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.

  13. Biodegradable Polycaprolactone as Ion Solvating Polymer for Solution-Processed Light-Emitting Electrochemical Cells

    Science.gov (United States)

    Jürgensen, Nils; Zimmermann, Johannes; Morfa, Anthony John; Hernandez-Sosa, Gerardo

    2016-11-01

    In this work, we demonstrate the use of the biodegradable polymer polycaprolactone (PCL) as the ion solvating polymer in solution-processed light-emitting electrochemical cells (LEC). We show that the inclusion of PCL in the active layer yields higher ionic conductivities and thus contributes to a rapid formation of the dynamic p-i-n junction and reduction of operating voltages. PCL shows no phase separation with the emitter polymer and reduces film roughness. The devices show light-emission at voltages as low as 3.2 V and lifetimes on the order of 30 h operating above 150 cd m‑2 with turn-on times <20 s and current and luminous efficacies of 3.2 Cd A‑1 and 1.5 lm W‑1 respectively.

  14. 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.

  15. Thermodynamic properties of water solvating biomolecular surfaces

    Science.gov (United States)

    Heyden, Matthias

    Changes in the potential energy and entropy of water molecules hydrating biomolecular interfaces play a significant role for biomolecular solubility and association. Free energy perturbation and thermodynamic integration methods allow calculations of free energy differences between two states from simulations. However, these methods are computationally demanding and do not provide insights into individual thermodynamic contributions, i.e. changes in the solvent energy or entropy. Here, we employ methods to spatially resolve distributions of hydration water thermodynamic properties in the vicinity of biomolecular surfaces. This allows direct insights into thermodynamic signatures of the hydration of hydrophobic and hydrophilic solvent accessible sites of proteins and small molecules and comparisons to ideal model surfaces. We correlate dynamic properties of hydration water molecules, i.e. translational and rotational mobility, to their thermodynamics. The latter can be used as a guide to extract thermodynamic information from experimental measurements of site-resolved water dynamics. Further, we study energy-entropy compensations of water at different hydration sites of biomolecular surfaces. This work is supported by the Cluster of Excellence RESOLV (EXC 1069) funded by the Deutsche Forschungsgemeinschaft.

  16. 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...

  17. Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.

    Science.gov (United States)

    Riniker, Sereina; Christ, Clara D; Hansen, Halvor S; Hünenberger, Philippe H; Oostenbrink, Chris; Steiner, Denise; van Gunsteren, Wilfred F

    2011-11-24

    The calculation of the relative free energies of ligand-protein binding, of solvation for different compounds, and of different conformational states of a polypeptide is of considerable interest in the design or selection of potential enzyme inhibitors. Since such processes in aqueous solution generally comprise energetic and entropic contributions from many molecular configurations, adequate sampling of the relevant parts of configurational space is required and can be achieved through molecular dynamics simulations. Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given.

  18. Differences in physical chemistry and dissolution rate of solid particle aerosols from solution pressurised inhalers.

    Science.gov (United States)

    Buttini, Francesca; Miozzi, Michele; Balducci, Anna Giulia; Royall, Paul G; Brambilla, Gaetano; Colombo, Paolo; Bettini, Ruggero; Forbes, Ben

    2014-04-25

    Solution composition alters the dynamics of beclomethasone diproprionate (BDP) particle formation from droplets emitted by pressurised metered dose inhalers (pMDIs). The hypothesis that differences in inhaler solutions result in different solid particle physical chemistry was tested using a suite of complementary calorimetric techniques. The atomisation of BDP-ethanol solutions from commercial HFA-pMDI produced aerodynamically-equivalent solid particle aerosols. However, differences in particle physico-chemistry (morphology and solvate/clathrate formation) were detected by differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and supported by hot stage microscopy (HSM). Increasing the ethanol content of the formulation from 8 to 12% (w/w), which retards the evaporation of propellant and slows the increase in droplet surface viscosity, enhanced the likelihood of particles drying with a smooth surface. The dissolution rate of BDP from the 12% (w/w) ethanol formulation-derived particles (63% dissolved over 120 min) was reduced compared to the 8% (w/w) ethanol formulation-derived particles (86% dissolved over 120 min). The addition of 0.01% (w/w) formoterol fumarate or 1.3% (w/w) glycerol to the inhaler solution modified the particles and reduced the BDP dissolution rate further to 34% and 16% dissolved in 120 min, respectively. These data provide evidence that therapeutic aerosols from apparently similar inhaler products, including those with similar aerodynamic performance, may behave non-equivalently after deposition in the lungs.

  19. 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....

  20. 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).

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

    Science.gov (United States)

    Rajput, Nav Nidhi; Qu, Xiaohui; 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 (Mg(2+) → 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.

  2. Computational chemistry

    OpenAIRE

    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 ...

  3. 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.

  4. 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...

  5. Chemistry Technology

    Data.gov (United States)

    Federal Laboratory Consortium — Chemistry technology experts at NCATS engage in a variety of innovative translational research activities, including:Design of bioactive small molecules.Development...

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

    CERN Document Server

    Andreussi, Oliviero; Marzari, Nicola

    2011-01-01

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

  7. 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.

  8. Reaction Rate Theory in Coordination Number Space: An Application to Ion Solvation

    Energy Technology Data Exchange (ETDEWEB)

    Roy, Santanu; Baer, Marcel D.; Mundy, Christopher J.; Schenter, Gregory K.

    2016-04-14

    Understanding reaction mechanisms in many chemical and biological processes require application of rare event theories. In these theories, an effective choice of a reaction coordinate to describe a reaction pathway is essential. To this end, we study ion solvation in water using molecular dynamics simulations and explore the utility of coordination number (n = number of water molecules in the first solvation shell) as the reaction coordinate. Here we compute the potential of mean force (W(n)) using umbrella sampling, predicting multiple metastable n-states for both cations and anions. We find with increasing ionic size, these states become more stable and structured for cations when compared to anions. We have extended transition state theory (TST) to calculate transition rates between n-states. TST overestimates the rate constant due to solvent-induced barrier recrossings that are not accounted for. We correct the TST rates by calculating transmission coefficients using the reactive flux method. This approach enables a new way of understanding rare events involving coordination complexes. We gratefully acknowledge Liem Dang and Panos Stinis for useful discussion. 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. SR, CJM, and GKS were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative, a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy.

  9. The effect of breaking gravity waves on the dynamics and chemistry of the mesosphere and lower thermosphere (invited review)

    Science.gov (United States)

    Garcia, R. R.

    1986-01-01

    The influence of breaking gravity waves on the dynamics and chemical composition of the 60 to 110 km region is investigated with a two dimensional model that includes a parameterization of gravity wave momentum deposition and diffusion. The dynamical model is described by Garcia and Solomon (1983) and Solomon and Garcia (1983) and includes a complete chemical scheme for the mesosphere and lower thermosphere. The parameterization of Lindzen (1981) is used to calculate the momentum deposited and the turbulent diffusion produced by the gravity waves. It is found that wave momentum deposition drives a very vigorous mean meridional circulation, produces a very cold summer mesopause and reverse the zonal wind jets above about 85 km. The seasonal variation of the turbulent diffusion coefficient is consistent with the behavior of mesospheric turbulences inferred from MST radar echoes. The large degree of consistency between model results and various types of dynamical and chemical data supports very strongly the hypothesis that breaking gravity waves play a major role in determining the zonally-averaged dynamical and chemical structure of the 60 to 110 km region of the atmosphere.

  10. Influence of Dynamics and Chemistry on the Diurnal Variation of VOCs in the Planetary Boundary Layer above a Mixed Forest Canopy in the Southeastern United States

    Science.gov (United States)

    Guenther, A. B.; Su, L.; Patton, E. G.; Vila-Guerau Arellano, J.; Mak, J. E.

    2014-12-01

    The planetary boundary layer (PBL) is a region of inherent interest because reactive VOCs emitted from the forest canopy are mixed with the residual and free tropospheric air masses, oxidized, and/or otherwise removed in this region. The characterization of diurnal variation of VOCs in the PBL is limited due to the lack of appropriate sampling platforms that are able to probe all the regions of interest: from the surface to the entrainment zone. Here we present the application of the Whole Air Sample Profiler (WASP) system during the 2013 Southeast Atmosphere Study (SAS) campaign. A total of 41 research flights (RFs) were carried out during the 2013 SAS campaign between June 1 and June 14 over the Alabama Aquatic Biodiversity Center (AABC) site and the SEARCH site. During each RF, ambient air sampling started from 50-100 m above the canopy top and stopped at ~1200 m above the mean sea level (a.m.s.l). The air samples were subsequently analyzed by using a proton-transfer-reaction time-of-flight mass spectrometry (PTR-TOF-MS). Here we analyze the vertical profiles and averaged diurnal variation of the mixing ratios of several reactive VOC species, including isoprene, the sum of monoterpenes, and first generation oxidation products of isoprene: methyl vinyl ketone and methacrolein (MVK+MACR). A MiXed Layer Chemistry (MXLCH) model, guided by the meteorological and chemical observations during the SAS campaign, is used to study the influence of boundary layer dynamics and new isoprene oxidation mechanism on the diurnal variation of major biogenic VOCs emitted from the forest canopy. The new scheme includes OH recycling through two pathways under low-NOx regime: (1) hydroxyl peroxy radicals (HOC5H8OO•; ISOPO2) unimolecular isomerization, and (2) ISOPO2+HO2. The model is able to reproduce the evolution of the boundary layer dynamics (including potential temperature, and boundary layer height) during the selected simulation dates. Based on the model results, budget

  11. 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

  12. Solvation of Na+, K+, and Their Dimers in Helium

    OpenAIRE

    An der Lan, Lukas; Bartl, Peter; Leidlmair, Christian; Jochum, Roland; Denifl, Stephan; Echt, Olof; Scheier, Paul

    2012-01-01

    Helium atoms bind strongly to alkali cations which, when embedded in liquid helium, form so-called snowballs. Calculations suggest that helium atoms in the first solvation layer of these snowballs form rigid structures and that their number (n) is well defined, especially for the lighter alkalis. However, experiments have so far failed to accurately determine values of n. We present high-resolution mass spectra of Na+He n , K+He n , Na2 +He n and K2 +He n , formed by electron ionization of do...

  13. 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.

  14. 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

  15. 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...

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

    Science.gov (United States)

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

    2017-03-06

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

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

    CERN Document Server

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

    2011-01-01

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

  18. Size-specific interaction of alkali metal ions in the solvation of M+-benzene clusters by Ar atoms.

    Science.gov (United States)

    Huarte-Larrañaga, F; Aguilar, A; Lucas, J M; Albertí, M

    2007-08-23

    The size-specific influence of the M+ alkali ion (M = Li, Na, K, Rb, and Cs) in the solvation process of the M+-benzene clusters by Ar atoms is investigated by means of molecular dynamic simulations. To fully understand the behavior observed in M+-bz-Ar(n) clusters, solvation is also studied in clusters containing either M+ or benzene only. The potential energy surfaces employed are based on a semiempirical bond-atom decomposition, which has been developed previously by some of the authors. The outcome of the dynamics is analyzed by employing radial distribution functions, studying the evolution of the distances between the Ar atoms and the alkali ion M+ or the benzene molecule for all M+-bz-Ar(n) clusters. For all members, in the M+-bz series, the benzene molecule (bz) is found to remain strongly bound to M+ even in the presence of solvent atoms. The radial distribution functions for the heavier clusters (K+-bz, Rb+-bz, and Cs+-bz), are found to be different than for the lighter (Na+-bz and Li+-bz) ones.

  19. Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach.

    Science.gov (United States)

    Pagliai, Marco; Mancini, Giordano; Carnimeo, Ivan; De Mitri, Nicola; Barone, Vincenzo

    2017-03-05

    The electronic absorption spectra of pyridine and nicotine in aqueous solution have been computed using a multistep approach. The computational protocol consists in studying the solute solvation with accurate molecular dynamics simulations, characterizing the hydrogen bond interactions, and calculating electronic transitions for a series of configurations extracted from the molecular dynamics trajectories with a polarizable QM/MM scheme based on the fluctuating charge model. Molecular dynamics simulations and electronic transition calculations have been performed on both pyridine and nicotine. Furthermore, the contributions of solute vibrational effect on electronic absorption spectra have been taken into account in the so called vertical gradient approximation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  20. Extreme events in total ozone over Arosa – Part 2: Fingerprints of atmospheric dynamics and chemistry and effects on mean values and long-term changes

    Directory of Open Access Journals (Sweden)

    H. E. Rieder

    2010-05-01

    Full Text Available In this study the frequency of days with extreme low (termed ELOs and extreme high (termed EHOs total ozone values and their influence on mean values and trends are analyzed for the world's longest total ozone record (Arosa, Switzerland. The results show (a an increase in ELOs and (b a decrease in EHOs during the last decades and (c that the overall trend during the 1970s and 1980s in total ozone is strongly dominated by changes in these extreme events. After removing the extremes, the time series shows a strongly reduced trend (reduction by a factor of 2.5 for trend in annual mean. Excursions in the frequency of extreme events reveal "fingerprints" of dynamical factors such as ENSO or NAO, and chemical factors, such as cold Arctic vortex ozone losses, as well as major volcanic eruptions of the 20th century (Gunung Agung, El Chichón, Mt. Pinatubo. Furthermore, atmospheric loading of ozone depleting substances leads to a continuous modification of column ozone in the Northern Hemisphere also with respect to extreme values (partly again in connection with polar vortex contributions. Application of extreme value theory allows the identification of many more such "fingerprints" than conventional time series analysis of annual and seasonal mean values. The analysis shows in particular the strong influence of dynamics, revealing that even moderate ENSO and NAO events have a discernible effect on total ozone. Overall the approach to extremal modelling provides new information on time series properties, variability, trends and the influence of dynamics and chemistry, complementing earlier analyses focusing only on monthly (or annual mean values.

  1. Extreme events in total ozone over Arosa – Part 2: Fingerprints of atmospheric dynamics and chemistry and effects on mean values and long-term changes

    Directory of Open Access Journals (Sweden)

    H. E. Rieder

    2010-10-01

    Full Text Available In this study the frequency of days with extreme low (termed ELOs and extreme high (termed EHOs total ozone values and their influence on mean values and trends are analyzed for the world's longest total ozone record (Arosa, Switzerland. The results show (i an increase in ELOs and (ii a decrease in EHOs during the last decades and (iii that the overall trend during the 1970s and 1980s in total ozone is strongly dominated by changes in these extreme events. After removing the extremes, the time series shows a strongly reduced trend (reduction by a factor of 2.5 for trend in annual mean. Excursions in the frequency of extreme events reveal "fingerprints" of dynamical factors such as ENSO or NAO, and chemical factors, such as cold Arctic vortex ozone losses, as well as major volcanic eruptions of the 20th century (Gunung Agung, El Chichón, Mt. Pinatubo. Furthermore, atmospheric loading of ozone depleting substances leads to a continuous modification of column ozone in the Northern Hemisphere also with respect to extreme values (partly again in connection with polar vortex contributions. Application of extreme value theory allows the identification of many more such "fingerprints" than conventional time series analysis of annual and seasonal mean values. The analysis shows in particular the strong influence of dynamics, revealing that even moderate ENSO and NAO events have a discernible effect on total ozone. Overall the approach to extremal modelling provides new information on time series properties, variability, trends and the influence of dynamics and chemistry, complementing earlier analyses focusing only on monthly (or annual mean values.

  2. 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,

  3. Molecular Thermodynamics of Methane Solvation in tert-Butanol-Water Mixtures.

    Science.gov (United States)

    Lee, Maeng-Eun; Van der Vegt, Nico F A

    2007-01-01

    We studied solvation structure and thermodynamics of methane in mixtures of tert-butanol and water using computer simulations. We show that for alcohol mole fractions below 20%, methane is preferentially solvated by hydrated alcohol clusters. Because methane expels water molecules from these clusters, a large endothermic solvent reorganization enthalpy occurs. This process is responsible for the experimentally observed maximum of the heat of methane solvation close to 5% alcohol in the mixture and contributes to a positive entropy change relative to solvation in pure water. Because the structural solvent reorganization enthalpy is enthalpy-entropy compensating, the methane solvation free energy is a smoothly varying function of the alcohol/water solution composition.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-11-13

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

  5. 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.

  6. Extending students' practice of metacognitive regulation strategies in the undergraduate chemistry laboratory and investigation of Pb2+ binding to calmodulin with circular dichroism and molecular dynamics modeling

    Science.gov (United States)

    Valencia Navarro, Laura N.

    The following dissertation was composed of two projects in chemistry education and benchwork/computational biochemistry. The chemistry education research explored students' practice of metacognitive strategies while solving open-ended laboratory problems when engaged in an instructional environment, the Science Writing Heuristic (SWH), that was characterized as supporting metacognitive regulation strategy use. Through in-depth interviews with students, results demonstrated that students in the SWH environment, compared to non-SWH students, used metacognitive strategies to a greater degree and to a greater depth when solving open-ended laboratory problems. As students engaged in higher levels of metacognitive regulation, their elective use of peers became a prominent path for supporting the practice of metacognitive strategies. Students claimed that the structure of the SWH weekly laboratory experiments improved their ability to solve open-ended lab problems. This research not only provided a lens into students' descriptions of their regulation strategy practices in the laboratory, but it also supported that the way that a laboratory environment is arranged can affect these regulation strategy practices and their transfer to new situations. In the biochemical study on the binding of Pb2+ to calmodulin (CaM), data was acquired via circular dichroism (CD) and molecular dynamics modeling. CD signal data indicated a unique signal from Pb-CaM and a significantly smaller ratio theta208/theta222 for Pb-CaM than Ca-CaM. An analysis of secondary structure content indicated that alpha-helical structure decreased and random coil structure increased when CaM was saturated with Pb2+ compared to Ca2+ saturated CaM. A molecular dynamics simulation of Pb2+ binding to CaM showed that Pb2+ ions bound to sites outside of the known canonical binding sites including the linker region, and indicated change in secondary structure. These results support the theory of opportunistic binding

  7. 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.

  8. Nuclear Chemistry.

    Science.gov (United States)

    Chemical and Engineering News, 1979

    1979-01-01

    Provides a brief review of the latest developments in nuclear chemistry. Nuclear research today is directed toward increased activity in radiopharmaceuticals and formation of new isotopes by high-energy, heavy-ion collisions. (Author/BB)

  9. 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...

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. Accurate calculation of conformational free energy differences in explicit water: the confinement-solvation free energy approach.

    Science.gov (United States)

    Esque, Jeremy; Cecchini, Marco

    2015-04-23

    The calculation of the free energy of conformation is key to understanding the function of biomolecules and has attracted significant interest in recent years. Here, we present an improvement of the confinement method that was designed for use in the context of explicit solvent MD simulations. The development involves an additional step in which the solvation free energy of the harmonically restrained conformers is accurately determined by multistage free energy perturbation simulations. As a test-case application, the newly introduced confinement/solvation free energy (CSF) approach was used to compute differences in free energy between conformers of the alanine dipeptide in explicit water. The results are in excellent agreement with reference calculations based on both converged molecular dynamics and umbrella sampling. To illustrate the general applicability of the method, conformational equilibria of met-enkephalin (5 aa) and deca-alanine (10 aa) in solution were also analyzed. In both cases, smoothly converged free-energy results were obtained in agreement with equilibrium sampling or literature calculations. These results demonstrate that the CSF method may provide conformational free-energy differences of biomolecules with small statistical errors (below 0.5 kcal/mol) and at a moderate computational cost even with a full representation of the solvent.

  16. 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

  17. 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.

  18. Solvation of graphite oxide in water-methanol binary polar solvents

    Energy Technology Data Exchange (ETDEWEB)

    You, Shujie; Yu, Junchun; Sundqvist, Bertil; Talyzin, Alexandr V. [Department of Physics, Umeaa University, SE-901 87 Umeaa (Sweden)

    2012-12-15

    The phase transition between two solvated phases was studied by DSC for graphite oxide (GO) powders immersed in water-methanol mixtures of various compositions. GO forms solid solvates with two different compositions when immersed in methanol. Reversible phase transition between two solvate states due to insertion/desertion of methanol monolayer occurs upon temperature variations. The temperature point and the enthalpy ({Delta}H) of the phase transition are maximal for pure methanol and decrease linearly with increase of water fraction up to 30%. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  19. 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...... by the solvation models do not significantly alter the conclusions made based solely on simple gas phase calculations. Abstraction of the amine hydrogens H61 and H62 and addition onto C8 are still the most likely reaction pathways....

  20. 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.

  1. 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

  2. Carbonate chemistry dynamics and biological processes along a river-sea gradient (Gulf of Trieste, northern Adriatic Sea)

    Science.gov (United States)

    Ingrosso, Gianmarco; Giani, Michele; Cibic, Tamara; Karuza, Ana; Kralj, Martina; Del Negro, Paola

    2016-03-01

    In this paper we investigated, for two years and with a bi-monthly frequency, how physical, chemical, and biological processes affect the marine carbonate system in a coastal area characterized by high alkalinity riverine discharge (Gulf of Trieste, northern Adriatic Sea, Mediterranean Sea). By combining synoptic measurements of the carbonate system with in situ determinations of the primary production (14C incorporation technique) and secondary prokaryotic carbon production (3H-leucine incorporation) along a river-sea gradient, we showed that the conservative mixing between river endmember and off-shore waters was the main driver of the dissolved inorganic carbon (DIC) distribution and seasonal variation. However, during spring and summer seasons also the influence of biological uptake and release of DIC was significant. In the surface water of June 2012, the spreading and persistence of nutrient-rich freshwater stimulated the primary production (3.21 μg C L- 1 h- 1) and net biological DIC decrease (- 100 μmol kg- 1), reducing the dissolved CO2 concentration and increasing the pHT. Below the pycnocline of August 2012, instead, an elevated bacterial carbon production rate (0.92 μg C L- 1 h- 1) was related with net DIC increase (92 μmol kg- 1), low dissolved oxygen concentration, and strong pHT reduction, suggesting the predominance of bacterial heterotrophic respiration over primary production. The flux of carbon dioxide estimated at the air-sea interface exerted a low influence on the seasonal variation of the carbonate system. A complex temporal and spatial dynamic of the air-sea CO2 exchange was also detected, due to the combined effects of seawater temperature, river discharge, and water circulation. On annual scale the system was a sink of atmospheric CO2. However, in summer and during elevated riverine discharges, the area close to the river's mouth acted as a source of carbon dioxide. Also the wind speed was crucial in controlling the air-sea CO2

  3. 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.

  4. 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.

  5. Solvation Reaction Field at the Interface Measured by Vibrational Sum Frequency Generation Spectroscopy.

    Science.gov (United States)

    Sorenson, Shayne A; Patrow, Joel G; Dawlaty, Jahan M

    2017-02-15

    Interfacial electric fields are important in several areas of chemistry, materials sciences, and device physics. However, they are poorly understood, partly because they are difficult to measure directly and model accurately. We present both a spectroscopic experimental investigation and a theoretical model for the interfacial field at the junction of a conductor and a dielectric. First, we present vibrational sum frequency generation (VSFG) results of the nitrile (CN) stretch of 4-mercaptobenzonitrile (4-MBN) covalently attached to a gold surface and in contact with a variety of liquid dielectrics. It is found that the CN stretch frequency red-shifts with increasing dielectric constant. Second, we build a model in direct analogy to the well-known Onsager reaction field theory, which has been successful in predicting vibrational frequency shifts in bulk dielectric media. Clearly, due to the asymmetric environment, with metal on one side and a dielectric on the other, the bulk Onsager model is not applicable at the interface. To address this, we apply the Onsager model to the interface accounting for the asymmetry. The model successfully explains the red-shift of the CN stretch as a function of the dielectric constant and is used to estimate the reaction field near the interface. We show the similarities and differences between the conventional bulk Onsager model and the interfacial reaction field model. In particular, the model emphasizes the importance of the metal as part of the solvation environment of the tethered molecules. We anticipate that our work will be of fundamental value to understand the crucial and often elusive electric fields at interfaces.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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...

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

    Science.gov (United States)

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

    2014-02-01

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

  12. 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.

  13. Weighted-density functionals for cavity formation and dispersion energies in continuum solvation models

    CERN Document Server

    Sundararaman, Ravishankar; Arias, T A

    2014-01-01

    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 ($n_c$), and a single solvent-dependent parameter: the dispersion scale factor ($s_6$), reproduces solvation energies of organic molecules in water, chloroform and carbon tetrachloride with RMS errors of 1.1, 0.6 and 0....

  14. Path-integral molecular dynamics simulations of BeO embedded in helium clusters: Formation of the stable HeBeO complex

    Science.gov (United States)

    Motegi, Haruki; Kakizaki, Akira; Takayanagi, Toshiyuki; Taketsugu, Yuriko; Taketsugu, Tetsuya; Shiga, Motoyuki

    2008-12-01

    Path-integral molecular dynamics simulations have been performed to understand the quantum helium solvation structures in the He nBeO cluster up to n = 100. Our simulations show that one helium atom is strongly bound to BeO to form HeBeO and that the first solvation shell around the HeBeO complex includes roughly 12-14 helium atoms. The second solvation structure was also observed for n > 20. Both the first and second solvation shells show an anisotropic behavior but the anisotropy for the second solvation shell was found to be much weaker than that for the first solvation shell, as expected. The present simulations suggest that the HeBeO complex may be formed in large helium clusters.

  15. Path-integral molecular dynamics simulations of BeO embedded in helium clusters: Formation of the stable HeBeO complex

    Energy Technology Data Exchange (ETDEWEB)

    Motegi, Haruki; Kakizaki, Akira [Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570 (Japan); Takayanagi, Toshiyuki [Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570 (Japan)], E-mail: tako@mail.saitama-u.ac.jp; Taketsugu, Yuriko; Taketsugu, Tetsuya [Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810 (Japan); Shiga, Motoyuki [Center for Computational Science and E-systems, Japan Atomic Energy Agency, Higashi-Ueno 6-9-3, Taito-ku, Tokyo 110-0015 (Japan)

    2008-12-10

    Path-integral molecular dynamics simulations have been performed to understand the quantum helium solvation structures in the He{sub n}BeO cluster up to n = 100. Our simulations show that one helium atom is strongly bound to BeO to form HeBeO and that the first solvation shell around the HeBeO complex includes roughly 12-14 helium atoms. The second solvation structure was also observed for n > 20. Both the first and second solvation shells show an anisotropic behavior but the anisotropy for the second solvation shell was found to be much weaker than that for the first solvation shell, as expected. The present simulations suggest that the HeBeO complex may be formed in large helium clusters.

  16. Density functional theory/molecular mechanics approach for electronic g-tensors of solvated molecules.

    Science.gov (United States)

    Rinkevicius, Zilvinas; Murugan, N Arul; Kongsted, Jacob; Aidas, Kestutis; Steindal, Arnfinn Hykkerud; Agren, Hans

    2011-04-21

    A general density functional theory/molecular mechanics approach for computation of electronic g-tensors of solvated molecules is presented. We apply the theory to the commonly studied di-tert-butyl nitroxide molecule, the simplest model compound for nitroxide spin labels, and explore the role of an aqueous environment and of various approximations for its treatment. It is found that successive improvements of the solvent shift of the g-tensor are obtained by going from the polarizable continuum model to discrete solvent models of various levels of sophistication. The study shows that an accurate parametrization of the electrostatic potential and polarizability of the solvent molecules in terms of distributed multipole expansions and anisotropic polarizabilities to a large degree relieves the need to explicitly include water molecules in the quantum region, which is the common case in density functional/continuum model approaches. It is also shown that the local dynamics of the solvent around the solute significantly influences the electronic g-tensor and should be included in benchmarking of exchange-correlation functionals for evaluation of solvent shifts of g-tensors. These findings can have important ramifications for the use of advanced hybrid density functional theory/molecular mechanics approaches for modeling spin labels in solvents, proteins, and membrane environments.

  17. 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.

  18. 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...

  19. 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...

  20. 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.

  1. Niclosamide methanol solvate and niclosamide hydrate: structure, solvent inclusion mode and implications for properties.

    Science.gov (United States)

    Harriss, Bethany I; Wilson, Claire; Radosavljevic Evans, Ivana

    2014-08-01

    Structural studies have been carried out of two solid forms of niclosamide [5-chloro-N-(2-chloro-4-nitrophenyl)-2-hydroxybenzamide, NCL], a widely used anthelmintic drug, namely niclosamide methanol monosolvate, C13H8Cl2N2O4·CH3OH or NCL·MeOH, and niclosamide monohydrate, denoted HA. The structure of the methanol solvate obtained from single-crystal X-ray diffraction is reported for the first time, elucidating the key host-guest hydrogen-bonding interactions which lead to solvate formation. The essentially planar NCL host molecules interact via π-stacking and pack in a herringbone-type arrangement, giving rise to channels along the crystallographic a axis in which the methanol guest molecules are located. The methanol and NCL molecules interact via short O-H...O hydrogen bonds. Laboratory powder X-ray diffraction (PXRD) measurements reveal that the initially phase-pure NCL·MeOH solvate readily transforms into NCL monohydrate within hours under ambient conditions. PXRD further suggests that the NCL monohydrate, HA, is isostructural with the NCL·MeOH solvate. This is consistent with the facile transformation of the methanol solvate into the hydrate when stored in air. The crystal packing and the topology of guest-molecule inclusion are compared with those of other NCL solvates for which the crystal structures are known, giving a consistent picture which correlates well with known experimentally observed desolvation properties.

  2. 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.

  3. Spicing up continuum solvation models with SaLSA: The spherically averaged liquid susceptibility ansatz

    Energy Technology Data Exchange (ETDEWEB)

    Sundararaman, Ravishankar; Schwarz, Kathleen A.; Letchworth-Weaver, Kendra; Arias, T. A. [Department of Physics, Cornell University, Ithaca, New York 14853 (United States)

    2015-02-07

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

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

    Science.gov (United States)

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

    2015-02-10

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

  5. Molecular Dynamics and Theoretical Chemistry

    Science.gov (United States)

    2013-03-08

    Ionic Liquids AFRL, AFOSR – XPAL, etc. AFRL – ultrafast methods, diode laser spect (ICOS) AFRL, PSI, SSI - Codes AFOSR - Simulation methods... Graphenes greatly lower IL viscosity as internal ‘lubricant’ & increase reactivity • Ionic liquids with metal nanoparticles - Passivating B and Al metal...TAILORABLE PROPERTIES Heaven, Michael EMORY UNIVERSITY DIODE LASER PUMPED ALKALI VAPOR LASERS WITH EXCIPLEX-ASSISTED ABSORPTION Hernandez

  6. 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.

  7. 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.

  8. Solvation of Na+, K+, and their dimers in helium.

    Science.gov (United States)

    An der Lan, Lukas; Bartl, Peter; Leidlmair, Christian; Jochum, Roland; Denifl, Stephan; Echt, Olof; Scheier, Paul

    2012-04-02

    Helium atoms bind strongly to alkali cations which, when embedded in liquid helium, form so-called snowballs. Calculations suggest that helium atoms in the first solvation layer of these snowballs form rigid structures and that their number (n) is well defined, especially for the lighter alkalis. However, experiments have so far failed to accurately determine values of n. We present high-resolution mass spectra of Na(+)He(n), K(+)He(n), Na(2)(+)He(n) and K(2)(+)He(n), formed by electron ionization of doped helium droplets; the data allow for a critical comparison with several theoretical studies. For sodium and potassium monomers the spectra indicate that the value of n is slightly smaller than calculated. Na(2)(+)He(n) displays two distinct anomalies at n=2 and n=6, in agreement with theory; dissociation energies derived from experiment closely track theoretical values. K(2)(+)He(n) distributions are fairly featureless, which also agrees with predictions.

  9. 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.

  10. 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

  11. Understanding and controlling laser-matter interactions: From solvated dye molecules to polyatomic molecules in gas phase

    Science.gov (United States)

    Konar, Arkaprabha

    The goal of my research is to obtain a better understanding of the various processes that occur during and following laser-matter interactions from both the physical and chemical point of view. In particular I focused my research on understanding two very important aspects of laser-matter interaction; 1) Intense laser-matter interactions for polyatomic molecules in the gas phase in order to determine to what extent processes like excitation, ionization and fragmentation can be controlled by modifying the phase and amplitude of the laser field according to the timescales for electronic, vibrational and rotational energy transfer. 2) Developing pulse shaping based single beam methods aimed at studying solvated molecules in order to elucidate processes like inhomogeneous broadening, solvatochromic shift and to determine the electronic coherence lifetimes of solvated molecules. The effect of the chirped femtosecond pulses on fluorescence and stimulated emission from solvated dye molecules was studied and it was observed that the overall effect depends quadratically on pulse energy, even where excitation probabilities range from 0.02 to 5%, in the so-called "linear excitation regime". The shape of the chirp dependence is found to be independent of the energy of the pulse. It was found that the chirp dependence reveals dynamics related to solvent rearrangement following excitation and also depends on electronic relaxation of the chromophore. Furthermore, the chirped pulses were found to be extremely sensitive to solvent environment and that the complementary phases having the opposite sign provide information about the electronic coherence lifetimes. Similar to chirped pulses, the effects of a phase step on the excitation spectrum and the corresponding changes to the stimulated emission spectrum were also studied and it was found that the coherent feature on the spectrum is sensitive to the dephasing time of the system. Therefore a single phase scanning method can

  12. Preferential solvation and solvation shell composition of free base and protonated 5, 10, 15, 20-tetrakis(4-sulfonatophenyl)porphyrin in aqueous organic mixed solvents.

    Science.gov (United States)

    Farajtabar, Ali; Jaberi, Fatemeh; Gharib, Farrokh

    2011-12-01

    The solvatochromic properties of the free base and the protonated 5, 10, 15, 20-tetrakis(4-sulfonatophenyl)porphyrin (TPPS) were studied in pure water, methanol, ethanol (protic solvents), dimethylsulfoxide, DMSO, (non-protic solvent), and their corresponding aqueous-organic binary mixed solvents. The correlation of the empirical solvent polarity scale (E(T)) values of TPPS with composition of the solvents was analyzed by the solvent exchange model of Bosch and Roses to clarify the preferential solvation of the probe dyes in the binary mixed solvents. The solvation shell composition and the synergistic effects in preferential solvation of the solute dyes were investigated in terms of both solvent-solvent and solute-solvent interactions and also, the local mole fraction of each solvent composition was calculated in cybotactic region of the probe. The effective mole fraction variation may provide significant physico-chemical insights in the microscopic and molecular level of interactions between TPPS species and the solvent components and therefore, can be used to interpret the solvent effect on kinetics and thermodynamics of TPPS. The obtained results from the preferential solvation and solvent-solvent interactions have been successfully applied to explain the variation of equilibrium behavior of protonation of TPPS occurring in aqueous organic mixed solvents of methanol, ethanol and DMSO.

  13. Preferential solvation and solvation shell composition of free base and protonated 5, 10, 15, 20-tetrakis(4-sulfonatophenyl)porphyrin in aqueous organic mixed solvents

    Science.gov (United States)

    Farajtabar, Ali; Jaberi, Fatemeh; Gharib, Farrokh

    2011-12-01

    The solvatochromic properties of the free base and the protonated 5, 10, 15, 20-tetrakis(4-sulfonatophenyl)porphyrin (TPPS) were studied in pure water, methanol, ethanol (protic solvents), dimethylsulfoxide, DMSO, (non-protic solvent), and their corresponding aqueous-organic binary mixed solvents. The correlation of the empirical solvent polarity scale ( ET) values of TPPS with composition of the solvents was analyzed by the solvent exchange model of Bosch and Roses to clarify the preferential solvation of the probe dyes in the binary mixed solvents. The solvation shell composition and the synergistic effects in preferential solvation of the solute dyes were investigated in terms of both solvent-solvent and solute-solvent interactions and also, the local mole fraction of each solvent composition was calculated in cybotactic region of the probe. The effective mole fraction variation may provide significant physico-chemical insights in the microscopic and molecular level of interactions between TPPS species and the solvent components and therefore, can be used to interpret the solvent effect on kinetics and thermodynamics of TPPS. The obtained results from the preferential solvation and solvent-solvent interactions have been successfully applied to explain the variation of equilibrium behavior of protonation of TPPS occurring in aqueous organic mixed solvents of methanol, ethanol and DMSO.

  14. 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...

  15. The impact of surface area, volume, curvature, and Lennard-Jones potential to solvation modeling.

    Science.gov (United States)

    Nguyen, Duc D; Wei, Guo-Wei

    2017-01-05

    This article explores the impact of surface area, volume, curvature, and Lennard-Jones (LJ) potential on solvation free energy predictions. Rigidity surfaces are utilized to generate robust analytical expressions for maximum, minimum, mean, and Gaussian curvatures of solvent-solute interfaces, and define a generalized Poisson-Boltzmann (GPB) equation with a smooth dielectric profile. Extensive correlation analysis is performed to examine the linear dependence of surface area, surface enclosed volume, maximum curvature, minimum curvature, mean curvature, and Gaussian curvature for solvation modeling. It is found that surface area and surfaces enclosed volumes are highly correlated to each other's, and poorly correlated to various curvatures for six test sets of molecules. Different curvatures are weakly correlated to each other for six test sets of molecules, but are strongly correlated to each other within each test set of molecules. Based on correlation analysis, we construct twenty six nontrivial nonpolar solvation models. Our numerical results reveal that the LJ potential plays a vital role in nonpolar solvation modeling, especially for molecules involving strong van der Waals interactions. It is found that curvatures are at least as important as surface area or surface enclosed volume in nonpolar solvation modeling. In conjugation with the GPB model, various curvature-based nonpolar solvation models are shown to offer some of the best solvation free energy predictions for a wide range of test sets. For example, root mean square errors from a model constituting surface area, volume, mean curvature, and LJ potential are less than 0.42 kcal/mol for all test sets. © 2016 Wiley Periodicals, Inc.

  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. Estudo da estrutura e da solvatação do HNP-3, um antibiótico natural, por dinâmica molecular Study of the structure and solvation of the HNP-3, a natural antibiotic, by molecular dynamics

    Directory of Open Access Journals (Sweden)

    Adriana M. Namba

    2004-02-01

    Full Text Available The structure and hydration of the HNP-3 have been derived from molecular dynamics data using root mean square deviation, radial and energy distributions. Three antiparallel beta sheets were found to be preserved. 15 intramolecular hydrogen bonds were identified together with 36 hydrogen bonds on the backbone and 35 on the side chain atoms. From the point of view of the hydration dynamics, the analysis shows a high solvent accessibility of the monomer and attractive interactions with water molecules.

  18. 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.

  19. Free energy of solvation of carbon nanotubes in pyridinium-based ionic liquids.

    Science.gov (United States)

    Chaban, Vitaly V; Fileti, Eudes Eterno

    2016-07-27

    Numerous prospective applications require the availability of individual carbon nanotubes (CNTs). Pristine CNTs, strongly hydrophobic in nature, are known to be either totally insoluble or poorly dispersible. While it is unlikely to be possible to prepare a real solution of CNTs in any solvent, the ability of certain solvents to maintain dispersions of CNTs for macroscopic times constitutes great research interest. In the present work, we characterize two pyridinium-based ionic liquids (ILs), N-butylpyridinium chloride [BPY][Cl] and N-butylpyridinium bis(trifluoromethanesulfonyl)imide [BPY][TFSI], with respect to their potential to solvate CNTs of different diameters, from the CNT (10,10) to the CNT (25,25). Using a universal methodology, we found that both ILs exhibit essentially the same solvation performance. Solvation of CNTs is strongly prohibited entropically, whereas the energy penalty increases monotonically with the CNT diameter. Weak van der Waals interactions, which guide enthalpy alteration upon the CNT solvation, are unable to compensate for the large entropic penalty from the destruction of the IL-IL electrostatic interactions. The structure of ILs inside and outside CNTs is also discussed. The reported results are necessary for gaining a fundamental understanding of the CNT solvation problems, thereby inspiring the search for more suitable solvents.

  20. 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.

  1. 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.

  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. 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.

  4. Science Update: Inorganic Chemistry

    Science.gov (United States)

    Rawls, Rebecca

    1978-01-01

    This first in a series of articles describing the state of the art of various branches of chemistry reviews inorganic chemistry, including bioinorganic, photochemistry, organometallic, and solid state chemistries. (SL)

  5. 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.

  6. Astronomical chemistry.

    Science.gov (United States)

    Klemperer, William

    2011-01-01

    The discovery of polar polyatomic molecules in higher-density regions of the interstellar medium by means of their rotational emission detected by radioastronomy has changed our conception of the universe from essentially atomic to highly molecular. We discuss models for molecule formation, emphasizing the general lack of thermodynamic equilibrium. Detailed chemical kinetics is needed to understand molecule formation as well as destruction. Ion molecule reactions appear to be an important class for the generally low temperatures of the interstellar medium. The need for the intrinsically high-quality factor of rotational transitions to definitively pin down molecular emitters has been well established by radioastronomy. The observation of abundant molecular ions both positive and, as recently observed, negative provides benchmarks for chemical kinetic schemes. Of considerable importance in guiding our understanding of astronomical chemistry is the fact that the larger molecules (with more than five atoms) are all organic.

  7. Environmental chemistry. Seventh edition

    Energy Technology Data Exchange (ETDEWEB)

    Manahan, S.E. [Univ. of Missouri, Columbia, MO (United States)

    1999-11-01

    This book presents a basic understanding of environmental chemistry and its applications. In addition to providing updated materials in this field, the book emphasizes the major concepts essential to the practice of environmental chemistry. Topics of discussion include the following: toxicological chemistry; toxicological chemistry of chemical substances; chemical analysis of water and wastewater; chemical analysis of wastes and solids; air and gas analysis; chemical analysis of biological materials and xenobiotics; fundamentals of chemistry; and fundamentals of organic chemistry.

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

    Science.gov (United States)

    Sakuraba, Shun; Matubayasi, Nobuyuki

    2014-08-05

    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.

  9. 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...

  10. 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.

  11. 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)

  12. 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.

  13. Advanced Chemistry Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Description/History: Chemistry laboratory The Advanced Chemistry Laboratory (ACL) is a unique facility designed for working with the most super toxic compounds known...

  14. 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)

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

    Science.gov (United States)

    Rane, Kaustubh; van der Vegt, Nico F A

    2016-03-21

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

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

    Science.gov (United States)

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

    2011-02-01

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

  17. A high-performance theory for thermodynamic study of solvation in mixed solvents

    Energy Technology Data Exchange (ETDEWEB)

    Rezaei Behbehani, G. [Department of Chemistry, Imam Khomeini International University Qazvin Iran, Imam Khomeini Street, Qazvin (Iran, Islamic Republic of)], E-mail: grb402003@yahoo.com; Waghorne, W.E. [School of Chemistry and Chemical Biology, UCD, Dublin 4 (Ireland)

    2008-11-20

    The enthalpies of transfer, {delta}H{sub t}{sup {theta}}, of the solutes from pure solvent A to mixtures of A and a second solvent B were studied by isothermal titration calorimetry and analysed in terms of the new extended solvation theory. These data are considered in terms of the new developed solvation theory including variable ({alpha}n + {beta}N), the net effect of the solute on the solvent-solvent bonding and is positive if there is a net breaking or weakening of solvent-solvent bonds.

  18. Application of Raman multivariate curve resolution to solvation-shell spectroscopy.

    Science.gov (United States)

    Fega, Kathryn Rebecca; Wilcox, David Scott; Ben-Amotz, Dor

    2012-03-01

    Raman spectroscopy and multivariate curve resolution (Raman-MCR) are combined to yield a powerful spectroscopic method for identifying solute-induced perturbations of solvent molecules. The principles and applications of the resulting solvation-shell spectroscopy are described and illustrated using both numerical model spectra and experimental Raman spectra, including water in acetone and aqueous OH(-), as well as of both neutral and ionic acetic acid solutions. The results illustrate the quantitative capabilities of Raman-MCR as a solvation-shell spectroscopy, including fundamental limitations arising from "intensity" and "rotational" ambiguities.

  19. 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.

  20. Systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions

    Energy Technology Data Exchange (ETDEWEB)

    Cooks, Robert Graham; Li, Anyin; Luo, Qingjie

    2017-01-24

    The invention generally relates to systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions. In certain aspects, the invention provides methods that involve providing a metal and a solvent. The methods additionally involve applying voltage to the solvated metal to thereby produce solvent droplets including ions of the metal containing compound, and directing the solvent droplets including the metal ions to a target. In certain embodiments, once at the target, the metal ions can react directly or catalyze reactions.

  1. 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.

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

    Science.gov (United States)

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

    2009-03-28

    Most aqueous biological and technological systems contain solvated ions. Atomistic explicit-water simulations of ionic solutions rely crucially on accurate ionic force fields, which contain most commonly two adjustable parameters: the Lennard-Jones diameter and the interaction strength. Assuming these parameters to be properly optimized, the plethora of parameters one finds in the literature for one and the same ion is surprising. In principle, the two parameters should be uniquely determined by matching two ionic properties obtained for a particular water model and within a given simulation protocol with the corresponding experimental observables. Traditionally, ion parameters were chosen in a somewhat unsystematic way to reproduce the solvation free energy and to give the correct ion size when compared with scattering results. Which experimental observable one chooses to reproduce should in principle depend on the context within which the ionic force field is going to be used. In the present work we suggest to use the solvation free energy in conjunction with the solvation entropy to construct thermodynamically sound force fields for the alkali and halide ions for the simulation of ion-specific effects in aqueous environment. To that end we determine the solvation free energy and entropy of both cations and anions in the entire relevant parameter space. As an independent check on the quality of the resulting force fields we also determine the effective ionic radius from the first peak of the radial ion-water distribution function. Several difficulties during parameter optimization are discussed in detail. (i) Single-ion solvation depends decisively on water-air surface properties, which experimentally becomes relevant when introducing extrathermodynamic assumptions on the hydronium (H(3)O(+)) solvation energy. Fitting ion pairs circumvents this problem but leaves the parameters of one reference ion (here we choose chloride) undetermined. (ii) For the halides the

  3. 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.

  4. 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

    2010-11-07

    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.

  5. 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)

  6. 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.

  7. IR SPECTRA BY DFT FOR GLUCOSE AND ITS EPIMERS: A COMPARISON BETWEEN VACUUM AND SOLVATED SPECTRA

    Science.gov (United States)

    Infrared spectra were calculated for the low energy geometry optimized structures of glucose and all of its epimers, at B3LYP/6-311++G** level of theory. Calculations were performed both in vacuo and using the COSMO solvation method. Frequencies, zero point energies, enthalpies, entropies, and rel...

  8. 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

    2016-02-09

    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.

  9. Role of Local Response in Ion Solvation: Born Theory and Beyond.

    Science.gov (United States)

    Remsing, Richard C; Weeks, John D

    2016-07-07

    The nature of ion solvation has drawn the interest of scientists for over a century, yet a thorough theoretical understanding is still lacking. In this work, we focus on the microscopic origins underlying ionic charge asymmetric and nonlinear response contributions to ion solvation free energies. We first derive an exact expression for the charging component of the ionic free energy, the free energy change when the Coulomb interactions between a fixed ion and the solvent are gradually "turned on". We then introduce the concept of a Gaussian test charge distribution, a generalization of the classical electrostatic point test charge that can be used to probe dielectric response in atomically detailed models. This enables the study of a thermodynamic cycle that isolates a linear and charge-symmetric contribution to the free energy that is well-described by Born-model-like dielectric continuum theories. We give a simple physical derivation of the classic Born model that locally relates the induced charge density in a linear dielectric model to the applied ionic charge distribution. The nonlinear response and charge asymmetric contributions to the ion solvation free energy are then examined in the remaining steps of the cycle and compared to classic thermodynamic cycles for this process using computer simulations. The insights provided by this work will aid the development of quantitative theories for the solvation of charged solutes.

  10. Solvation phenomena in association theories with applications to oil & gas and chemical industries

    DEFF Research Database (Denmark)

    Kontogeorgis, Georgios; Folas, Georgios; Muro Sunè, Nuria

    2008-01-01

    Association theories e.g. those belonging to the SAFT family account explicitly for self- and cross-association (solvation) phenomena. Such phenomena are of great practical importance as they affect, often dramatically, the phase behaviour of many mixtures of industrial relevance. From the scient...

  11. 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

  12. 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

  13. 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

  14. 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.

  15. Synchrotron radiation x-ray photoelectron spectroscopy study on the interface chemistry of high-k PrxAl2-xO3 (x=0-2) dielectrics on TiN for dynamic random access memory applications

    Science.gov (United States)

    Schroeder, T.; Lupina, G.; Sohal, R.; Lippert, G.; Wenger, Ch.; Seifarth, O.; Tallarida, M.; Schmeisser, D.

    2007-07-01

    Engineered dielectrics combined with compatible metal electrodes are important materials science approaches to scale three-dimensional trench dynamic random access memory (DRAM) cells. Highly insulating dielectrics with high dielectric constants were engineered in this study on TiN metal electrodes by partly substituting Al in the wide band gap insulator Al2O3 by Pr cations. High quality PrAlO3 metal-insulator-metal capacitors were processed with a dielectric constant of 19, three times higher than in the case of Al2O3 reference cells. As a parasitic low dielectric constant interface layer between PrAlO3 and TiN limits the total performance gain, a systematic nondestructive synchrotron x-ray photoelectron spectroscopy study on the interface chemistry of PrxAl2-xO3 (x =0-2) dielectrics on TiN layers was applied to unveil its chemical origin. The interface layer results from the decreasing chemical reactivity of PrxAl2-xO3 dielectrics with increasing Pr content x to reduce native Ti oxide compounds present on unprotected TiN films. Accordingly, PrAlO3 based DRAM capacitors require strict control of the surface chemistry of the TiN electrode, a parameter furthermore of importance to engineer the band offsets of PrxAl2-xO3/TiN heterojunctions.

  16. 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.

  17. 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.

  18. 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...

  19. 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...

  20. 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

  1. 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.

  2. Selected new developments in computational chemistry.

    Science.gov (United States)

    Darden, T A; Bartolotti, L; Pedersen, L G

    1996-01-01

    Molecular dynamics is a general technique for simulating the time-dependent properties of molecules and their environments. Quantum mechanics, as applied to molecules or clusters of molecules, provides a prescription for predicting properties exactly (in principle). It is reasonable to expect that both will have a profound effect on our understanding of environmental chemistry in the future. In this review, we consider several recent advances and applications in computational chemistry. Images Figure 1. PMID:8722111

  3. 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

  4. 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.

  5. 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.

  6. Advanced Chemistry Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Description/History: Chemistry laboratoryThe Advanced Chemistry Laboratory (ACL) is a unique facility designed for working with the most super toxic compounds known...

  7. Organometallic Chemistry of Molybdenum.

    Science.gov (United States)

    Lucas, C. Robert; Walsh, Kelly A.

    1987-01-01

    Suggests ways to avoid some of the problems students have learning the principles of organometallic chemistry. Provides a description of an experiment used in a third-year college chemistry laboratory on molybdenum. (TW)

  8. Chemistry for Potters.

    Science.gov (United States)

    Denio, Allen A.

    1980-01-01

    Relates pottery making to chemistry by providing chemical information about clay, its origin, composition, properties, and changes that occur during firing; also describes glaze compositions, examples of redox chemistry, salt glazing, crystalline glazes, and problems in toxicity. (CS)

  9. 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.

  10. Formation of solvated ions in the atmospheric interface of an electrospray ionization triple-quadrupole mass spectrometer.

    Science.gov (United States)

    Schlosser, Gitta; Takáts, Zoltán; Vékey, Károly

    2003-12-01

    A simple method capable of generating and investigating various solvent clusters and solvated ions was developed. The technique opens a door to studying these complexes on commercially available instruments. Formation of the desired solvated ion in the gas phase was achieved by introducing the appropriate volatile solvent vapour into the curtain gas stream. Capabilities of the technique are illustrated by generating alkali, alkaline earth and transition metal cations solvated by various volatile compounds such as water, methanol and acetonitrile. Depending on the ligands and on the experimental conditions, clusters of 2-100 molecules may be observed. Isotope labelling suggests that these are formed by a re-solvation process in the curtain gas region.

  11. 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.

  12. Invited article: The fast readout low noise camera as a versatile x-ray detector for time resolved dispersive extended x-ray absorption fine structure and diffraction studies of dynamic problems in materials science, chemistry, and catalysis

    Science.gov (United States)

    Labiche, Jean-Claude; Mathon, Olivier; Pascarelli, Sakura; Newton, Mark A.; Ferre, Gemma Guilera; Curfs, Caroline; Vaughan, Gavin; Homs, Alejandro; Carreiras, David Fernandez

    2007-09-01

    Originally conceived and developed at the European Synchrotron Radiation Facility (ESRF) as an "area" detector for rapid x-ray imaging studies, the fast readout low noise (FReLoN) detector of the ESRF [J.-C. Labiche, ESRF Newsletter 25, 41 (1996)] has been demonstrated to be a highly versatile and unique detector. Charge coupled device (CCD) cameras at present available on the public market offer either a high dynamic range or a high readout speed. A compromise between signal dynamic range and readout speed is always sought. The parameters of the commercial cameras can sometimes be tuned, in order to better fulfill the needs of specific experiments, but in general these cameras have a poor duty cycle (i.e., the signal integration time is much smaller than the readout time). In order to address scientific problems such as time resolved experiments at the ESRF, a FReLoN camera has been developed by the Instrument Support Group at ESRF. This camera is a low noise CCD camera that combines high dynamic range, high readout speed, accuracy, and improved duty cycle in a single image. In this paper, we show its application in a quasi-one-dimensional sense to dynamic problems in materials science, catalysis, and chemistry that require data acquisition on a time scale of milliseconds or a few tens of milliseconds. It is demonstrated that in this mode the FReLoN can be applied equally to the investigation of rapid changes in long range order (via diffraction) and local order (via energy dispersive extended x-ray absorption fine structure) and in situations of x-ray hardness and flux beyond the capacity of other detectors.

  13. 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.

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

    Science.gov (United States)

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

    2008-01-17

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

  15. 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.

  16. On-line preferential solvation studies of polymers by coupled chromatographic-Fourier transform infrared spectroscopic flow-cell technique.

    Science.gov (United States)

    Malanin, M; Eichhorn, K-J; Lederer, A; Treppe, P; Adam, G; Fischer, D; Voigt, D

    2009-12-18

    Qualitative and quantitative comparison between liquid chromatography (LC) and LC coupled with Fourier transform infrared spectroscopy (LC-FTIR) to evaluate preferential solvation phenomenon of polymers in a mixed solvent has been performed. These studies show that LC-FTIR technique leads to detailed structural information without the requirement for determination of additional parameters for quantitative analysis except calibration. Appropriate experimental conditions for preferential solvation study have been established by variation of polymer concentration, molar mass and eluent content.

  17. 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)

  18. Probing - and - Molecular Interactions via Irmpd Experiments and Computational Chemistry

    Science.gov (United States)

    Hopkins, Scott; McMahon, Terry

    2015-06-01

    Experiments carried out at the CLIO Free Electron Facility have been used to probe a range of novel bonding motifs and dissociation dynamics in a variety of chemical systems. Among these are species which exhibit anion-pi interactions in complexes of halide ions with aromatic ring systems with electron withdrawing substituents; charge solvated and zwitterionic clusters of protonated methylamines with phenylalanines; hydrogen bonded dimers of nucleic acid analogues and Pd complexes potentially involving agnostic hydrogen bond interactions. Accompanying DFT computational work is used to assist in identifying the most probable structure(s) present in the IRMPD experiments.

  19. 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).

  20. 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. .....

  1. 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 ...

  2. 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.

  3. 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.

  4. A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects.

    Science.gov (United States)

    Zgarbová, Marie; Luque, F Javier; Šponer, Jiří; Otyepka, Michal; Jurečka, Petr

    2012-09-11

    A procedure for deriving force field torsion parameters including certain previously neglected solvation effects is suggested. In contrast to the conventional in vacuo approaches, the dihedral parameters are obtained from the difference between the quantum-mechanical self-consistent reaction field and Poisson-Boltzmann continuum solvation models. An analysis of the solvation contributions shows that two major effects neglected when torsion parameters are derived in vacuo are (i) conformation-dependent solute polarization and (ii) solvation of conformation-dependent charge distribution. Using the glycosidic torsion as an example, we demonstrate that the corresponding correction for the torsion potential is substantial and important. Our approach avoids double counting of solvation effects and provides parameters that may be used in combination with any of the widely used nonpolarizable discrete solvent models, such as TIPnP or SPC/E, or with continuum solvent models. Differences between our model and the previously suggested solvation models are discussed. Improvements were demonstrated for the latest AMBER RNA χOL3 parameters derived with inclusion of solvent effects in a previous publication (Zgarbova et al. J. Chem. Theory Comput.2011, 7, 2886). The described procedure may help to provide consistently better force field parameters than the currently used parametrization approaches.

  5. Crystallization of toxic glycol solvates of rifampin from glycerin and propylene glycol contaminated with ethylene glycol or diethylene glycol.

    Science.gov (United States)

    de Villiers, Melgardt M; Caira, Mino R; Li, Jinjing; Strydom, Schalk J; Bourne, Susan A; Liebenberg, Wilna

    2011-06-06

    This study was initiated when it was suspected that syringe blockage experienced upon administration of a compounded rifampin suspension was caused by the recrystallization of toxic glycol solvates of the drug. Single crystal X-ray structure analysis, powder X-ray diffraction, thermal analysis and gas chromatography were used to identify the ethylene glycol in the solvate crystals recovered from the suspension. Controlled crystallization and solubility studies were used to determine the ease with which toxic glycol solvates crystallized from glycerin and propylene glycol contaminated with either ethylene or diethylene glycol. The single crystal structures of two distinct ethylene glycol solvates of rifampin were solved while thermal analysis, GC analysis and solubility studies confirmed that diethylene glycol solvates of the drug also crystallized. Controlled crystallization studies showed that crystallization of the rifampin solvates from glycerin and propylene glycol depended on the level of contamination and changes in the solubility of the drug in the contaminated solvents. Although the exact source of the ethylene glycol found in the compounded rifampin suspension is not known, the results of this study show how important it is to ensure that the drug and excipients comply with pharmacopeial or FDA standards.

  6. The Structure and Dynamics of An Active Galactic Nucleus Torus : CO Line Predictions for ALMA from Three-dimensional Hydrodynamical Simulations with X-ray-driven Chemistry

    NARCIS (Netherlands)

    Perez Beaupuits, J.P.; Wada, K.; Spaans, M.

    2011-01-01

    Several attempts 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 (3D) hydrodynamic simulations. The X-ray radiation from the AGN can drive the g

  7. The Structure and Dynamics of An Active Galactic Nucleus Torus: CO Line Predictions for ALMA from Three-dimensional Hydrodynamical Simulations with X-ray-driven Chemistry

    NARCIS (Netherlands)

    Pérez-Beaupuits, J. P.; Wada, K.; Spaans, M.

    2011-01-01

    Several attempts 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 (3D) hydrodynamic simulations. The X-ray radiation from the AGN can drive the g

  8. Integrating canopy and large-scale atmospheric effects in the convective boundary-layer dynamics and chemistry during the CHATS experiment

    NARCIS (Netherlands)

    Shapkalijevski, M.; Ouwersloot, Huug; Moene, A.F.; Vilà-Guerau De Arellano, J.

    2017-01-01

    By characterizing the dynamics of a convective boundary layer above a relatively sparse and uniform orchard canopy, we investigated the impact of the roughness-sublayer (RSL) representation on the predicted diurnal variability of surface fluxes and state variables. Our approach combined numerical ex

  9. Hybrid Perovskite Thin-Film Photovoltaics: In Situ Diagnostics and Importance of the Precursor Solvate Phases

    KAUST Repository

    Munir, Rahim

    2016-11-07

    Solution-processed hybrid perovskite semiconductors attract a great deal of attention, but little is known about their formation process. The one-step spin-coating process of perovskites is investigated in situ, revealing that thin-film formation is mediated by solid-state precursor solvates and their nature. The stability of these intermediate phases directly impacts the quality and reproducibility of thermally converted perovskite films and their photovoltaic performance.

  10. Using the theoretical linear energy solvation energy relationship to correlate and predict nasal pungency thresholds.

    Science.gov (United States)

    Famini, George R; Aguiar, Denise; Payne, Marvin A; Rodriquez, Ryan; Wilson, Leland Y

    2002-01-01

    The theoretical linear solvation energy relationship (TLSER) has been used to correlate and characterize 44 nasal pungency threshold (NPT) values in man with parameters derived from semi-empirical molecular orbital theory. The resulting relationship provides good correlative (R2 > 0.92) and predictive (R2cy > 0.88) capability. In addition, the TLSER parameters are used as a molecular probe to attempt to understand the fundamental properties influencing nasal pungency.

  11. Solvation behavior of carbonate-based electrolytes in sodium ion batteries.

    Science.gov (United States)

    Cresce, Arthur V; Russell, Selena M; Borodin, Oleg; Allen, Joshua A; Schroeder, Marshall A; Dai, Michael; Peng, Jing; Gobet, Mallory P; Greenbaum, Steven G; Rogers, Reginald E; Xu, Kang

    2016-12-21

    Sodium ion batteries are on the cusp of being a commercially available technology. Compared to lithium ion batteries, sodium ion batteries can potentially offer an attractive dollar-per-kilowatt-hour value, though at the penalty of reduced energy density. As a materials system, sodium ion batteries present a unique opportunity to apply lessons learned in the study of electrolytes for lithium ion batteries; specifically, the behavior of the sodium ion in an organic carbonate solution and the relationship of ion solvation with electrode surface passivation. In this work the Li(+) and Na(+)-based solvates were characterized using electrospray mass spectrometry, infrared and Raman spectroscopy, (17)O, (23)Na and pulse field gradient double-stimulated-echo pulse sequence nuclear magnetic resonance (NMR), and conductivity measurements. Spectroscopic evidence demonstrate that the Li(+) and Na(+) cations share a number of similar ion-solvent interaction trends, such as a preference in the gas and liquid phase for a solvation shell rich in cyclic carbonates over linear carbonates and fluorinated carbonates. However, quite different IR spectra due to the PF6(-) anion interactions with the Na(+) and Li(+) cations were observed and were rationalized with the help of density functional theory (DFT) calculations that were also used to examine the relative free energies of solvates using cluster - continuum models. Ion-solvent distances for Na(+) were longer than Li(+), and Na(+) had a greater tendency towards forming contact pairs compared to Li(+) in linear carbonate solvents. In tests of hard carbon Na-ion batteries, performance was not well correlated to Na(+) solvent preference, leading to the possibility that Na(+) solvent preference may play a reduced role in the passivation of anode surfaces and overall Na-ion battery performance.

  12. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Guowei; Baker, Nathan A.

    2016-11-11

    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, electrostatic potential, ion density, electron density, etc. Recently, differential geometry theory has been used to define the surfaces that separate the microscopic (solute) domains for biomolecules from the macroscopic (solvent) domains. In these approaches, the microscopic domains are modeled with atomistic or quantum mechanical descriptions, while continuum mechanics models (including fluid mechanics, elastic mechanics, and continuum electrostatics) are applied to the macroscopic domains. This multiphysics description is integrated through an energy functional formalism and the resulting Euler-Lagrange equation is employed to derive a variety of governing partial differential equations for different solvation and transport processes; e.g., the Laplace-Beltrami equation for the solvent-solute interface, Poisson or Poisson-Boltzmann equations for electrostatic potentials, the Nernst-Planck equation for ion densities, and the Kohn-Sham equation for solute electron density. Extensive validation of these models has been carried out over hundreds of molecules, including proteins and ion channels, and the experimental data have been compared in terms of solvation energies, voltage-current curves, and density distributions. We also propose a new quantum model for electrolyte transport.

  14. Influence of solvent polarity on preferential solvation of molecular recognition probes in solvent mixtures.

    Science.gov (United States)

    Amenta, Valeria; Cook, Joanne L; Hunter, Christopher A; Low, Caroline M R; Vinter, Jeremy G

    2012-12-13

    The association constants for formation of 1:1 complexes between a H-bond acceptor, tri-n-butylphosphine oxide, and a H-bond donor, 4-phenylazophenol, have been measured in a range of different solvent mixtures. Binary mixtures of n-octane and a more polar solvent (ether, ester, ketone, nitrile, sulfoxide, tertiary amide, and halogenated and aromatic solvents) have been investigated. Similar behavior was observed in all cases. When the concentration of the more polar solvent is low, the association constant is identical to that observed in pure n-octane. Once a threshold concentration of the more polar solvent in reached, the logarithm of the association constant decreases in direct proportion to the logarithm of the concentration of the more polar solvent. This indicates that one of the two solutes is preferentially solvated by the more polar solvent, and it is competition with this solvation equilibrium that determines the observed association constant. The concentration of the more polar solvent at which the onset of preferential solvation takes place depends on solvent polarity: 700 mM for toluene, 60 mM for 1,1,2,2-tetrachloroethane, 20 mM for the ether, ester, ketone, and nitrile, 0.2 mM for the tertiary amide, and 0.1 mM for the sulfoxide solvents. The results can be explained by a simple model that considers only pairwise interactions between specific sites on the surfaces of the solutes and solvents, which implies that the bulk properties of the solvent have little impact on solvation thermodynamics.

  15. Hybrid Perovskite Thin-Film Photovoltaics: In Situ Diagnostics and Importance of the Precursor Solvate Phases.

    Science.gov (United States)

    Munir, Rahim; Sheikh, Arif D; Abdelsamie, Maged; Hu, Hanlin; Yu, Liyang; Zhao, Kui; Kim, Taesoo; Tall, Omar El; Li, Ruipeng; Smilgies, Detlef-M; Amassian, Aram

    2017-01-01

    Solution-processed hybrid perovskite semiconductors attract a great deal of attention, but little is known about their formation process. The one-step spin-coating process of perovskites is investigated in situ, revealing that thin-film formation is mediated by solid-state precursor solvates and their nature. The stability of these intermediate phases directly impacts the quality and reproducibility of thermally converted perovskite films and their photovoltaic performance.

  16. Peptide adsorption on a hydrophobic surface results from an interplay of solvation, surface, and intrapeptide forces

    OpenAIRE

    Horinek, D.; Serr, A; Geisler, M.; Pirzer, T.; Slotta, U.; Lud, S. Q.; Garrido, J. A.; Scheibel, T.; Hugel, T; Netz, R. R.

    2008-01-01

    The hydrophobic effect, i.e., the poor solvation of nonpolar parts of molecules, plays a key role in protein folding and more generally for molecular self-assembly and aggregation in aqueous media. The perturbation of the water structure accounts for many aspects of protein hydrophobicity. However, to what extent the dispersion interaction between molecular entities themselves contributes has remained unclear. This is so because in peptide folding interactions and structural changes occur on ...

  17. Polymorph of dimethylacetamide-solvated crystals of 2,9-dichlorodithioketoquinacridone and their hydrogen bonding effect

    OpenAIRE

    Mizuguchi, Jin; Hoki, T.; Senju, T.

    2006-01-01

    2,9-Dichlorodithioketoquinacridone (DTQ-Cl) is a thionated derivative of industrially important 2,9-dichloroquinacridone used as colorants in painting and imaging industries. Crystallographic and electronic characterizations have been carried out on single crystals of DTQ-Cl recrystallized from solution in dimethylacetamide (DMA). Two kinds of DMA-solvated single crystals were isolated in the form of DTQ-Ci/(DMA)(2): modifications I and II. In both crystals, two DMA molecules are hydrogen-bon...

  18. 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.

  19. Phase diagrams and solvate structures of binary mixtures of glymes and Na salts.

    Science.gov (United States)

    Mandai, Toshihiko; Nozawa, Risa; Tsuzuki, Seiji; Yoshida, Kazuki; Ueno, Kazuhide; Dokko, Kaoru; Watanabe, Masayoshi

    2013-12-05

    We prepared a series of binary mixtures composed of selected Na salts and glymes (tetraglyme, G4, and pentaglyme, G5) with different salt concentrations and anionic species ([X](-): [N(SO2CF3)2](-) = [TFSA](-), [N(SO2F)2](-) = [FSA](-), ClO4(-), PF6(-)) and studied the effects of concentration, anionic structure, and glyme chain length on their phase diagrams and solvate structures. The phase diagrams clearly illustrate that all the mixtures form 1:1 complexes, [Na(G4 or G5)1][X]. The thermal stability of the equimolar mixtures was drastically improved in comparison with those of diluted systems, indicating that all the glyme molecules coordinate to Na(+) cations to form equimolar complexes. Single-crystal X-ray crystallography revealed that [Na(G5)1][X] forms characteristic solvate structures in the crystalline state irrespective of the paired anion species. A comparison of the solvate structures of the glyme-Na complexes with those of the glyme-Li complexes suggests that the ionic radii of the coordinated alkali-metal cations have substantial effects on the resulting solvate structures. The Raman bands of the complex cations were assigned by quantum chemical calculations. Concentration dependencies of cationic and anionic Raman spectra show good agreement with the corresponding phase diagrams. In addition, the Raman spectra of the 1:1 complexes strongly suggest that the glymes coordinate to Na(+) cation in the same way in both liquid and crystalline states. However, the aggregated structure in the crystalline state is broken by melting, which is accompanied by a change in the anion coordination.

  20. Surface chemistry essentials

    CERN Document Server

    Birdi, K S

    2013-01-01

    Surface chemistry plays an important role in everyday life, as the basis for many phenomena as well as technological applications. Common examples range from soap bubbles, foam, and raindrops to cosmetics, paint, adhesives, and pharmaceuticals. Additional areas that rely on surface chemistry include modern nanotechnology, medical diagnostics, and drug delivery. There is extensive literature on this subject, but most chemistry books only devote one or two chapters to it. Surface Chemistry Essentials fills a need for a reference that brings together the fundamental aspects of surface chemistry w

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

    Science.gov (United States)

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

    2016-10-05

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

  2. Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas

    Science.gov (United States)

    Santos-Martins, Diogo; Fernandes, Pedro Alexandrino; Ramos, Maria João

    2016-11-01

    In the context of SAMPL5, we submitted blind predictions of the cyclohexane/water distribution coefficient (D) for a series of 53 drug-like molecules. Our method is purely empirical and based on the additive contribution of each solute atom to the free energy of solvation in water and in cyclohexane. The contribution of each atom depends on the atom type and on the exposed surface area. Comparatively to similar methods in the literature, we used a very small set of atomic parameters: only 10 for solvation in water and 1 for solvation in cyclohexane. As a result, the method is protected from overfitting and the error in the blind predictions could be reasonably estimated. Moreover, this approach is fast: it takes only 0.5 s to predict the distribution coefficient for all 53 SAMPL5 compounds, allowing its application in virtual screening campaigns. The performance of our approach (submission 49) is modest but satisfactory in view of its efficiency: the root mean square error (RMSE) was 3.3 log D units for the 53 compounds, while the RMSE of the best performing method (using COSMO-RS) was 2.1 (submission 16). Our method is implemented as a Python script available at https://github.com/diogomart/SAMPL5-DC-surface-empirical.

  3. 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.

  4. 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.

  5. 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.

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

    Science.gov (United States)

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

    2015-02-01

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

  7. 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.

  8. 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.

  9. UV resonance Raman investigation of the aqueous solvation dependence of primary amide vibrations.

    Science.gov (United States)

    Punihaole, David; Jakubek, Ryan S; Dahlburg, Elizabeth M; Hong, Zhenmin; Myshakina, Nataliya S; Geib, Steven; Asher, Sanford A

    2015-03-12

    We investigated the normal mode composition and the aqueous solvation dependence of the primary amide vibrations of propanamide. Infrared, normal Raman, and UV resonance Raman (UVRR) spectroscopy were applied in conjunction with density functional theory (DFT) to assign the vibrations of crystalline propanamide. We examined the aqueous solvation dependence of the primary amide UVRR bands by measuring spectra in different acetonitrile/water mixtures. As previously observed in the UVRR spectra of N-methylacetamide, all of the resonance enhanced primary amide bands, except for the Amide I (AmI), show increased UVRR cross sections as the solvent becomes water-rich. These spectral trends are rationalized by a model wherein the hydrogen bonding and the high dielectric constant of water stabilizes the ground state dipolar (-)O-C═NH2(+) resonance structure over the neutral O═C-NH2 resonance structure. Thus, vibrations with large C-N stretching show increased UVRR cross sections because the C-N displacement between the electronic ground and excited state increases along the C-N bond. In contrast, vibrations dominated by C═O stretching, such as the AmI, show a decreased displacement between the electronic ground and excited state, which result in a decreased UVRR cross section upon aqueous solvation. The UVRR primary amide vibrations can be used as sensitive spectroscopic markers to study the local dielectric constant and hydrogen bonding environments of the primary amide side chains of glutamine (Gln) and asparagine (Asn).

  10. Significance of solvated electrons (e(aq)-) as promoters of life on earth.

    Science.gov (United States)

    Getoff, Nikola

    2014-01-01

    Based on the present state of knowledge a new hypothesis concerning the origin of life on Earth is presented, and emphasizes the particular significance of solvated electrons (e(aq)(-)). Solvated electrons are produced in seawater, mainly by (40)K radiation and in atmospheric moisture by VUV light, electrical discharges and cosmic ray. Solvated electrons are involved in primary chemical processes and in biological processes. The conversion of aqueous CO2 and CO into simple organic substances, the generation of ammonia from N2 and water, the formation of amines, amino acids and simple proteins under the action of e(aq)(-) has been experimentally proven. Furthermore, it is supposed that the generation of the primitive cell and equilibria of primitive enzymes are also realized due to the strong reducing property of e(aq)(-). The presented hypothesis is mainly founded on recently obtained experimental results. The involvement of e(aq)(-) in such mechanisms, as well as their action as an initiator of life is also briefly discussed.

  11. The New Color of Chemistry: Green Chemistry

    Directory of Open Access Journals (Sweden)

    Zuhal GERÇEK

    2012-01-01

    Full Text Available Green chemistry which is the new application of chemistry rules provides solutions to problems that mankind is faced with climate changes, sustainable agriculture, energy, toxics, depletion of natural sources e.g. designing new chemicals and processes that production and utilization of hazardous matters. So, it is the indispensible tool for sustainable development. Current and future chemists should consider the human health and ecological issues in their professional life. In order to provide a solution for this requirement, green chemistry rules and under standings should be primarily taken in the university curriculum and at all educational levels.

  12. 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.

  13. Exploring visuospatial thinking in chemistry learning

    Science.gov (United States)

    Wu, Hsin-Kai; Shah, Priti

    2004-05-01

    In this article, we examine the role of visuospatial cognition in chemistry learning. We review three related kinds of literature: correlational studies of spatial abilities and chemistry learning, students' conceptual errors and difficulties understanding visual representations, and visualization tools that have been designed to help overcome these limitations. On the basis of our review, we conclude that visuospatial abilities and more general reasoning skills are relevant to chemistry learning, some of students' conceptual errors in chemistry are due to difficulties in operating on the internal and external visuospatial representations, and some visualization tools have been effective in helping students overcome the kinds of conceptual errors that may arise through difficulties in using visuospatial representations. To help students understand chemistry concepts and develop representational skills through supporting their visuospatial thinking, we suggest five principles for designing chemistry visualization tools: (1) providing multiple representations and descriptions, (2) making linked referential connections visible, (3) presenting the dynamic and interactive nature of chemistry, (4) promoting the transformation between 2D and 3D, and (5) reducing cognitive load by making information explicit and integrating information for students.

  14. Contributions of radiation chemistry to research

    Energy Technology Data Exchange (ETDEWEB)

    Sangster, D. F. [University of Sydney, NSW (Australia). Chemistry School

    1998-12-31

    Many chemical processes involve free radical species. Radiolysis of water produces three very reactive free radicals, the solvated electron, the hydroxyl radical and the hydrogen atom. These undergo interesting reactions and have been the subject of many studies. However, in the presence of selected solutes, they will react to give a range of free radicals which may be used to investigate a series of free radical reactions. Research fostered by AINSE over the last 40 years, using the gamma sources, the pond, GATRI and the shielded cells, and the steady beam and the pulse radiolysis facilities associated with the 1.3 MeV electron accelerator and with the 0.5 MeV Febetron at Lucas Heights, has enabled insights to be gained which would not have been possible otherwise. Answers can be given to the two questions what is the reaction and how fast is it. Particularly valuable has been the determination of reaction rate constants and one finds these quoted extensively in the chemical literature. Although most of the work has been carried out on aqueous systems, there have been some studies on solutions in non-aqueous solvents and in the gas phase. Examples will be given from the fields of metal/organic, excited state, biological and polymer chemistry

  15. Solvent Effects upon Electrochemical Kinetics: Influences of Interfacial Solvation and Solvent Relaxation Dynamics.

    Science.gov (United States)

    1984-09-01

    by block number) incganic and organometallic complexes ; inner-shell barrier; electrochemical kinetics Z-. ASS-ACT (Continue on reverse aid* If...valuable class of model systems is provided by one- electron couples involving substitutionally inert inorganic and organometallic complexes . Important...specific ligand- solventOs interactions, perhaps with accompanying decreases in Kel (6). This explanation is consisterwith the observation that ksb decreases

  16. Going clean: structure and dynamics of peptides in the gas phase and paths to solvation

    Science.gov (United States)

    Baldauf, Carsten; Rossi, Mariana

    2015-12-01

    The gas phase is an artificial environment for biomolecules that has gained much attention both experimentally and theoretically due to its unique characteristic of providing a clean room environment for the comparison between theory and experiment. In this review we give an overview mainly on first-principles simulations of isolated peptides and the initial steps of their interactions with ions and solvent molecules: a bottom up approach to the complexity of biological environments. We focus on the accuracy of different methods to explore the conformational space, the connections between theory and experiment regarding collision cross section evaluations and (anharmonic) vibrational spectra, and the challenges faced in this field.

  17. Collision Dynamics and Solvation of Water Molecules in a Liquid Methanol Film

    CERN Document Server

    Thomson, Erik S; Andersson, Patrik U; Marković, Nikola; Pettersson, Jan B C; 10.1021/jz200929y

    2011-01-01

    Environmental molecular beam experiments are used to examine water interactions with liquid methanol films at temperatures from 170 K to 190 K. We find that water molecules with 0.32 eV incident kinetic energy are efficiently trapped by the liquid methanol. The scattering process is characterized by an efficient loss of energy to surface modes with a minor component of the incident beam that is inelastically scattered. Thermal desorption of water molecules has a well characterized Arrhenius form with an activation energy of 0.47{\\pm}0.11 eV and pre-exponential factor of 4.6 {\\times} 10^(15{\\pm}3) s^(-1). We also observe a temperature dependent incorporation of incident water into the methanol layer. The implication for fundamental studies and environmental applications is that even an alcohol as simple as methanol can exhibit complex and temperature dependent surfactant behavior.

  18. Metal-ion solvation and abundance in atmospheric media before strong earthquakes

    Science.gov (United States)

    Lemke, K.; Aitchison, J.

    2009-12-01

    Gas phase metal-ions form hydrated complexes, which have characteristic solvation enthalpies ranging from around -150kJ/mol for monohydrates to around -40kJ/mol for larger water clusters. Previous reports on seismo-ionospheric coupling have suggested that select metal-ions M+, such as sodium and iron, are dragged by anomalous electric fields up to E-layer altitudes before earthquakes and are responsible for sporadic ionospheric metal-ion layers [Pulinets,1997 Adv.SpaceRes.,20,2173]. This report applies quantum chemical methods to calculate the geometries, energetics, thermochemistry and ionospheric abundances of a suite of solvated alkali and ionic transition metal clusters with up to six water molecules. Structural and energetic properties of ion-water clusters are calculated using Møller-Plesset perturbation theory (MP2) with a large number of different basis sets. Calculated solvation enthalpies for Na+, K+, Fe+ and Cu+ reported here are in excellent agreement with experimental mass spectrometric data. For instance, the calculated solvation enthalpy for groundstate 6D Fe+(H2O) is -108.9 kJ/mol and is in good agreement with the experimental value of -120±12 kJ/mol [Magnera,JACS,111,4100]. The subsequent hydration step toward Fe+(H2O)2, which is accompanied by a spin change to a 4A1 ground state, is exothermic by -198.0 kJ/mol. The experimental enthalpy ΔH1,2 for water attachment onto Fe+(H2O) is -170.7 [Marinelli, 1998,JACS,111,4101]. Interestingly, results from both this ab initio study and mass spectrometry demonstrate that Fe+ binds a second water molecule somewhat more strongly than the first one. The subsequent solvation steps asymptotically approach values of around -44 kJ/mol, showing a trend toward the bulk water limit. An analysis of calculated clustering equilibria K indicates that ionospheric metal ion-water cluster abundances are governed by the shifting balance between the temperature induced changes of K and water monomer abundances. Results from

  19. The New Color of Chemistry: Green Chemistry

    OpenAIRE

    Zuhal GERÇEK

    2012-01-01

    Green chemistry which is the new application of chemistry rules provides solutions to problems that mankind is faced with climate changes, sustainable agriculture, energy, toxics, depletion of natural sources e.g. designing new chemicals and processes that production and utilization of hazardous matters. So, it is the indispensible tool for sustainable development. Current and future chemists should consider the human health and ecological issues in their professional life. In order to provid...

  20. Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport

    Directory of Open Access Journals (Sweden)

    Pavel V. Komarov

    2013-09-01

    Full Text Available Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic and minority (hydrophilic subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25–50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping mechanism as a significant contributor to the proton conductivity.